User:Kazkaskazkasako/Work

Category:Biology

Category:Health sciences

Structure-function

Resolution (electron density): measure of the resolvability in the electron density map of a molecule. X-ray vs (cryo-)EM definition. X-ray crystallography: >4.0 Å - Individual coordinates meaningless.

Fourier shell correlation (FSC [Harauz & van Heel (1986)]; AKA: spatial frequency correlation function [Saxton & Baumeister (1982)]): measures the normalised cross-correlation coefficient between two 3D volumes over corresponding shells in Fourier space (i.e., as a function of spatial frequency); extension of the two-dimensional Fourier ring correlation (FRC) [van Heel (1982)].

Topology and structure, symmetry in (bio)molecules

{q.v.

User:Kazkaskazkasako/Books/Mathematics#Geometry Topology; Symmetry
- Linking number: e.g. DNA linking number in plasmids
User:Kazkaskazkasako/Books/Mathematics#Discrete mathematics
- Kissing number: e.g. materials science, chemistry and physics - dense packing of atoms: only two possibilities in 3D: FCC (face-centered cubic) and HCP (hexagonal close-packed) [or a hybrid of both]
User:Kazkaskazkasako/Books/Mathematics#Group theory
- Coxeter group, Coxeter–Dynkin diagram

}

Mathematical 2D and 3D group/symmetry notations

Symmetries in 2D: tiling; crystallographic projections, molecule projections

Question: how is the symmetry number (IUPAC) calculated?

(bio)(chem)(phys): single molecules/particles, crystals & co

{q.v. User:Kazkaskazkasako/Books/Physical sciences#Theoretical chemistry}

Materials science, nanotechnology (bionanotech, nanobiotechnology)

{q.v.:

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Two-dimensional nuclear magnetic resonance spectroscopy (2D NMR): set of NMR methods which give data plotted in a space defined by two frequency axes rather than one. Types of 2D NMR include correlation spectroscopy (COSY), J-spectroscopy, exchange spectroscopy (EXSY), and nuclear Overhauser effect spectroscopy (NOESY). Two-dimensional NMR spectra provide more information about a molecule than one-dimensional NMR spectra and are especially useful in determining the structure of a molecule, particularly for molecules that are too complicated to work with using one-dimensional NMR. Homonuclear through-bond correlation methods: COSY, ECOSY, TOCSY, INADEQUATE. Heteronuclear through-bond correlation methods: HSQC, HMBC. Through-space correlation methods: NOESY, HOESY, ROESY. Resolved-spectrum methods. Higher-dimensional methods: HNCA, HNCOCA.

Heteronuclear single quantum coherence spectroscopy (heteronuclear single quantum correlation, HSQC): used frequently in NMR spectroscopy of organic molecules and is of particular significance in the field of protein NMR. The experiment was first described by Geoffrey Bodenhausen and D. J. Ruben in 1980. The resulting spectrum is two-dimensional (2D) with one axis for proton (¹H) and the other for a heteronucleus (an atomic nucleus other than a proton), which is usually ¹³C or ¹⁵N. The spectrum contains a peak for each unique proton attached to the heteronucleus being considered. The 2D HSQC can also be combined with other experiments in higher-dimensional NMR experiments, such as NOESY-HSQC or TOCSY-HSQC.

J-couplings (also called spin-spin coupling or indirect dipole–dipole coupling): mediated through chemical bonds connecting two spins. It is an indirect interaction between two nuclear spins that arises from hyperfine interactions between the nuclei and local electrons. In NMR spectroscopy, J-coupling contains information about relative bond distances and angles. Most importantly, J-coupling provides information on the connectivity of chemical bonds. It is responsible for the often complex splitting of resonance lines in the NMR spectra of fairly simple molecules. J-coupling is a frequency difference that is not affected by the strength of the magnetic field, so is always stated in Hz. Vector model and manifestations for chemical structure assignments: Multiplicity; Magnitude of J-coupling; Sign of J-coupling

Karplus equation: correlation between ³J-coupling constants and dihedral torsion angles in NMR spectroscopy.

J(\phi )=A\cos ^{2}\phi +B\cos \,\phi +C

, where J is the ³J coupling constant,

\phi

is the dihedral angle, and A, B, and C are empirically derived parameters whose values depend on the atoms and substituents involved.

Electron paramagnetic resonance

Electron paramagnetic resonance (EPR; electron spin resonance (ESR))

Tomography

Tomography: Types of tomography

Electron tomography

Cryo-electron tomography (de:Kryoelektronentomographie)

Ultramicrotomy & Microtome:

Diamond knife: conventional hardest material used in microtomes

Nanoknife: a new development; carbon nanotube (like a wire) is used to cut materials

Photoacoustic tomography (PAT, or photoacoustic computed tomography (PACT)): reconstruction of an internal photoacoustic source distribution from measurements acquired by scanning ultrasound detectors over a surface that encloses the source under study. The PA source is the thermal expansion that results from a small temperature rise, which is caused by the absorption of externally applied radiation of pulsed electromagnetic (EM) waves.

Photoacoustic imaging in biomedicine, Photoacoustic spectroscopy

X-ray computed tomography (X-ray CT): computed tomography; computed axial tomography (CAT scan); computer-aided/assisted tomography.

Magnetic resonance imaging (MRI): Neuroimaging; Cardiovascular; Musculoskeletal; Liver and gastrointestinal MRI; fMRI; Oncology.

Functional magnetic resonance imaging (fMRI): functional neuroimaging procedure using MRI technology that measures brain activity by detecting associated changes in blood flow.

Positron emission tomography (PET): nuclear medicine, functional imaging technique that produces a three-dimensional image of functional processes in the body. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule.

PET-CT

PET-MRI

Radioactive tracer (radioactive label): used in PET: ¹¹C, ¹³N, ¹⁸F, ¹²³I

Ultrasound

many others

Signal processing, image processing, data analysis

{q.v.:

}

Chemistry, chemical physics

{q.v.

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Biology

Category:Biology

Category:Biological rules

Category:Biotechnology

Category:Branches of biology

Category:Biophysics

Category:Cell biology

Category:Molecular biology

Category:Neuroscience

Category:Structural biology

{q.v.

}

Bibliography of biology: list of notable works, organized by subdiscipline, on the subject of biology. Anatomy; Biophysics; Botany; Cell biology; Ecology; Evolutionary biology; Genetics; Microbiology; Molecular biology; Physiology; Taxonomy; Zoology.

Biological rules (biological laws): generalized law, principle, or rule of thumb formulated to describe patterns observed in living organisms. Biological rules and laws are often developed as succinct, broadly applicable ways to explain complex phenomena or salient observations about the ecology and biogeographical distributions of plant and animal species around the world, though they have been proposed for or extended to all types of organisms. Many of these regularities of ecology and biogeography are named after the biologists who first described them. List of biological rules:

Bergmann's rule (1847) states that within a broadly distributed taxonomic clade, populations and species of larger size are found in colder environments, and species of smaller size are found in warmer regions. It applies with exceptions to many mammals and birds.
Deep-sea gigantism, noted in 1880 by Henry Nottidge Moseley, states that deep-sea animals are larger than their shallow-water counterparts. In the case of marine crustaceans, it has been proposed that the increase in size with depth occurs for the same reason as the increase in size with latitude (Bergmann's rule): both trends involve increasing size with decreasing temperature.
Foster's rule, the island rule, or the island effect states that members of a species get smaller or bigger depending on the resources available in the environment. The rule was first stated by J. Bristol Foster in 1964 in the journal Nature, in an article titled "The evolution of mammals on islands".
Haldane's rule states that if in a species hybrid only one sex is sterile, that sex is usually the heterogametic sex.
Harrison's rule states that parasite body sizes co-vary with those of their hosts. He proposed the rule for lice, but later authors have shown that it works equally well for many other groups of parasite including barnacles, nematodes, fleas, flies, mites, and ticks, and for the analogous case of small herbivores on large plants.
Hennig's progression rule states that when considering a group of species in cladistics, the species with the most primitive characters are found within the earliest part of the area, which will be the center of origin of that group.
Jordan's rule states that there is an inverse relationship between water temperature and meristic characteristics such as the number of fin rays, vertebrae, or scale numbers, which are seen to increase with decreasing temperature.
Lack's principle, proposed by David Lack, states that "the clutch size of each species of bird has been adapted by natural selection to correspond with the largest number of young for which the parents can, on average, provide enough food".
Rensch's rule (1950) states that, across animal species within a lineage, sexual size dimorphism increases with body size when the male is the larger sex, and decreases as body size increases when the female is the larger sex. The rule applies in primates, pinnipeds (seals), and even-toed ungulates (such as cattle and deer).
Schmalhausen's law, named after Ivan Schmalhausen, states that a population at the extreme limit of its tolerance in any one aspect is more vulnerable to small differences in any other aspect. Therefore, the variance of data is not simply noise interfering with the detection of so-called "main effects", but also an indicator of stressful conditions leading to greater vulnerability.
Thorson's rule (1971 by S. A. Mileikovsky) states that benthic marine invertebrates at low latitudes tend to produce large numbers of eggs developing to pelagic (often planktotrophic [plankton-feeding]) and widely dispersing larvae, whereas at high latitudes such organisms tend to produce fewer and larger lecithotrophic (yolk-feeding) eggs and larger offspring, often by viviparity or ovoviviparity, which are often brooded.
Van Valen's law states that the probability of extinction for species and higher taxa (such as families and orders) is constant for each group over time; groups grow neither more resistant nor more vulnerable to extinction, however old their lineage is.
Williston's law states that parts in an organism tend to become reduced in number and greatly specialized in function. He had studied the dentition of vertebrates, and noted that where ancient animals had mouths with differing kinds of teeth, modern carnivores had incisors and canines specialized for tearing and cutting flesh, while modern herbivores had large molars specialized for grinding tough plant materials.

Rosa's rule: observes the tendency to go from character variation in more primitive representatives of a taxonomic group or clade to a fixed character state in more advanced members. An example of Rosa's rule is that the number of thoracic segments in adults (or holaspids) may vary in Cambrian trilobite species, while from the Ordovician the number of thoracic segments is constant in entire genera, families, and even suborders. Thus, a trend of decreasing trait variation between individuals of a taxon as the taxon develops across evolutionary time can be observed.

Jarman-Bell principle (1968 P.J Jarman & 1971 R.H.V Bell): concept in ecology offering a link between a herbivore's diet and their overall size. It operates by observing the allometric (non- linear scaling) properties of herbivores. According to the Jarman-Bell principle, the food quality of a herbivore's intake decreases as the size of the herbivore increases, but the amount of such food increases to counteract the low quality foods. Large herbivores can subsist on low quality food. Their gut size is larger than smaller herbivores. The increased size allows for better digestive efficiency, and thus allow viable consumption of low quality food. Small herbivores require more energy per unit of body mass compared to large herbivores. A smaller size, thus smaller gut size and lower efficiency, imply that these animals need to select high quality food to function. Their small gut limits the amount of space for food, so they eat low quantities of high quality diet. Some animals practice coprophagy, where they ingest fecal matter to recycle untapped/ undigested nutrients.

Biosafety level: all survival horror fans' beloved facilities in truth

Brain-computer interfacing

Biomimicry

Biological organisation (hierarchy of life, ecological organization): hierarchy of complex biological structures and systems that define life using a reductionistic approach; each level in the hierarchy represents an increase in organizational complexity, with each "object" being primarily composed of the previous level's basic unit; basic principle behind the organization is the concept of emergence—the properties and functions found at a hierarchical level are not present and irrelevant at the lower levels. A-cellular level and Pre-cellular level {atom/molecule} → (macro)molecular assemblies {structural and machines} → Sub-cellular level {organelle} → Cellular level {cell} → Super-cellular level (Multicellular level) {tissue} → {organ → organ system → organism → population → biocoenosis/community → ecosystem → biosphere → [ecosphere (magnetosphere + atmosphere + biosphere + hydrosphere + pedosphere + geosphere)]}

Molecular Biology (Biochemistry) + Cellular Biology:

Wikipedia:WikiProject Molecular and Cell Biology: aims to better organize information in articles related to molecular and cell biology on Wikipedia. {q.v. Gene Wiki; Portal:Gene Wiki}

Wikipedia:WikiProject Molecular and Cell Biology/Style guide (gene and protein articles): scope of a gene/protein article is the human gene/protein (included all splice variants derived from that gene) as well as orthologs (as listed in HomoloGene) that exist in other species. If there are paralogs in humans (and by extension other species), then a gene family article in addition to the gene specific articles (see for example dopamine receptor) would be appropriate. Article name: if short, recommended UniProt protein name should be used as the article name; if verbose, either a widely used protein acronym or the official HUGO gene symbol, followed by "(gene)" if necessary to disambiguate. Abbreviations of genes are according to HUGO Gene Nomenclature Committee and written in italic font style, human gene names are written in capitals {q.v. #Genetics: Gene nomenclature}

Quantum mechanics and biology

Quantum biology: study of applications of quantum mechanics and theoretical chemistry to aspects of biology that cannot be accurately described by the classical laws of physics. An understanding of fundamental quantum interactions is important because they determine the properties of the next level of organization in biological systems. Processes involve chemical reactions, light absorption, formation of excited electronic states, transfer of excitation energy, and the transfer of electrons and protons (hydrogen ions) in chemical processes, such as photosynthesis, olfaction and cellular respiration. Applications: Photosynthesis; DNA mutation; Vibration theory of olfaction; Visual phototransduction: Quantum vision implications; Enzymatic activity (quantum biochemistry): Mitochondria; Molecular solitons in proteins; Magnetoreception.

Vibration theory of olfaction: proposes that a molecule's smell character is due to its vibrational frequency in the infrared range. This controversial theory is an alternative to the more widely accepted docking theory of olfaction (formerly termed the shape theory of olfaction), which proposes that a molecule's smell character is due to a range of weak non-covalent interactions between its protein odorant receptor (found in the nasal epithelium), such as electrostatic and Van der Waals interactions as well as H-bonding, dipole attraction, pi-stacking, metal ion, Cation–pi interaction, and hydrophobic effects, in addition to the molecule's conformation.

Quantum Aspects of Life, R

Biochemistry and Molecular Biology

Category:Molecular biology

Category:Biomolecules

Category:Biomolecules by type

Category:Biomolecules by physiological function

Category:Hormones

Hypothetical types of biochemistry

Transcription Translation

Trans-acting (trans-regulatory, trans-regulation; la: "across from"): "acting from a different molecule" (i.e., intermolecular). In the context of transcription regulation, a trans-acting element is usually a DNA sequence that contains a gene. This gene codes for a protein (or microRNA or other diffusible molecule) that will be used in the regulation of another target gene.

Cis-regulatory element (cis-element; la: "on the same side as"): region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA (often a chromosome). A cis-element may be located upstream of the coding sequence of the gene it controls (in the promoter region or even further upstream), in an intron, or downstream of the gene's coding sequence, either in the translated or untranscribed region.

Genetic code: set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells. Translation is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time.

Aminoacyl tRNA synthetase (aaRS): enzyme that attaches the appropriate amino acid onto its tRNA. It does so by catalyzing the esterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. In humans, the 21 different types of aa-tRNA are made by the 21 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code.

Sense (molecular biology): of nucleic acid molecules (often DNA or RNA) is the nature of their roles and their complementary molecules' nucleic acid units' roles in specifying amino acids.

Golden Gate Cloning (Golden Gate assembly): molecular cloning method that allows a researcher to simultaneously and directionally assemble multiple DNA fragments into a single piece using Type IIS restriction enzymes and T4 DNA ligase. This assembly is performed in vitro. Most commonly used Type IIS enzymes include BsaI, BsmBI, and BbsI. Unlike standard Type II restriction enzymes like EcoRI and BamHI, these enzymes cut DNA outside of their recognition sites and, therefore, can create non-palindromic overhangs.

Gateway Technology: invented and commercialized by Invitrogen since the late 1990s, is a molecular biology method that enables researchers to efficiently transfer DNA-fragments between plasmids using a proprietary set of recombination sequences, the "Gateway att" sites, and two proprietary enzyme mixes, called "LR Clonase", and "BP Clonase". Gateway Cloning Technique allows transfer of DNA fragments between different cloning vectors while maintaining the reading frame. Using Gateway, one can clone subclone DNA segments for functional analysis.

Biomolecules, Biochemical substances, pharmacy, pharmacology

Category:Biomolecules

Category:Biomolecules by type

Category:Biomolecules by chemical classification

Category:Amino acids

Category:Proteinogenic amino acids

{q.v. #Pharmaceutics, Pharmacology }

Proteinogenic amino acid: amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms. Both eukaryotes and prokaryotes can incorporate selenocysteine into their proteins via a nucleotide sequence known as a SECIS element, which directs the cell to translate a nearby UGA codon as selenocysteine (UGA is normally a stop codon). In some methanogenic prokaryotes, the UAG codon (normally a stop codon) can also be translated to pyrrolysine.

Homocysteine: non-proteinogenic α-amino acid. It is a homologue of the amino acid cysteine, differing by an additional methylene bridge (-CH₂-); biosynthesized from methionine by the removal of its terminal C^ε methyl group. In the body, homocysteine can be recycled into methionine or converted into cysteine with the aid of certain B-vitamins. High levels of homocysteine in the blood (hyperhomocysteinemia) is regarded as a marker of cardiovascular disease, likely working through atherogenesis, which can result in ischemic injury. Therefore, hyperhomocysteinemia is a possible risk factor for coronary artery disease.

Template:Phytochemical

Saponin=Sapogenin (key organic feature: steroid or other triterpene frameworks) +. :

Quinoa saponins are classified as a mild eye and respiratory irritant and a low gastrointestinal irritant
medicinal uses: e.g. digoxin (from Digitalis sp., cardiac glycoside: treat heart diseases), eleutheroside A (from Eleutherococcus senticosus, aka Siberian Ginseng), ginsenoside (Panax sp., aka ginseng; Rb1 group: Rb1, Rb2, Rc, Rd; Rg1 group: Rg1, Re, Rf, Rg2)

Physiologically based pharmacokinetic modelling (PBPK): mathematical modeling technique for predicting the absorption, distribution, metabolism and excretion (ADME) of synthetic or natural chemical substances in humans and other animal species. PBPK modeling is used in pharmaceutical research and drug development, and in health risk assessment for cosmetics or general chemicals.

Proteins, enzymes

Category:Proteins

Category:Protein families

Category:Protein structure

Category:Protein domains

{q.v. #Structural biology; #Protein complexes, macromolecular assemblies}

Template:Posttranslational modification: the enzymes and proteins involved: chaperons (heat shock or chaperonins); protein targeting - signal peptide; ubiquitin: E1, E2, E3, deubiquitinating enzymes; SUMO.

Template:Protein primary structure (Protein primary structure and posttranslational modifications): PTM modified amino acids: S/T, Y, C, D, E, N, Q, K, R, P, H, W. Disulfide bond (C-C), ...

Proteinogenic amino acid: 22 standard amino acids, but only 21 are found in eukaryotes. 21st and 22nd: selenocysteine and pyrrolysine are incorporated into proteins by distinctive biosynthetic mechanisms; other 20 are directly encoded by the universal genetic code.

PYLIS downstream sequence (PYLIS: pyrrolysine insertion sequence): stem-loop mRNA structure; causes the UAG (amber) stop codon to be translated to the amino acid pyrrolysine instead of ending the protein translation. In archaea the PYLIS downstream sequence is positioned straight after the UAG codon which is translated as pyrrolysine.

SECIS element (SECIS: selenocysteine insertion sequence): stem-loop mRNA structure of around 60 nts; translate UGA codons as selenocysteines. In bacteria the SECIS element appears soon after the UGA codon it affects. In archaea and eukaryotes, it occurs in the 3' UTR of an mRNA, and can cause multiple UGA codons within the mRNA to code for selenocysteine. In Methanococcus (archeon) it is located in the 5' UTR.

Posttranslational modification (PTM): chemical modification of a protein after its translation.

Protein phosphorylation: reversible PTM of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or modifying its function. Approximately 13000 human proteins have sites that are phosphorylated. The reverse reaction of phosphorylation is called dephosphorylation, and is catalyzed by protein phosphatases. Protein kinases and phosphatases work independently and in a balance to regulate the function of proteins. The amino acids most commonly phosphorylated are S, T, Y in eukaryotes, and also H in prokaryotes and plants (though it is now known to be common in humans). These phosphorylations play important and well-characterized roles in signaling pathways and metabolism. However, other amino acids can also be phosphorylated post-translationally, including R, K, D, E and C, and these phosphorylated amino acids have recently been identified to be present in human cell extracts and fixed human cells using a combination of antibody-based analysis (for pHis) and mass spectrometry (for all other amino acids).

Kinase: enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates (phosphorylation). Kinases are part of the larger family of phosphotransferases. Kinases should not be confused with phosphorylases, nor with phosphatases. The phosphorylation state of a molecule, whether it be a protein, lipid or carbohydrate, can affect its activity, reactivity and its ability to bind other molecules. Therefore, kinases are critical in metabolism, cell signalling, protein regulation, cellular transport, secretory processes and many other cellular pathways, which makes them very important to human physiology.

Phosphatase: enzyme that removes a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group. This action is directly opposite to that of phosphorylases and kinases, which attach phosphate groups to their substrates by using energetic molecules like ATP. Protein phosphatases (PPs) can be grouped into three main classes based on sequence, structure and catalytic function: phosphoprotein phosphatase (PPP) family (contains also protein phosphatase Mg²⁺- or Mn²⁺-dependent (PPM) family); protein Tyr phosphatase (PTP) super-family; aspartate-based protein phosphatase group.

Phosphorylase: enzymes that catalyze the addition of a phosphate group from an inorganic phosphate (phosphate+hydrogen) to an acceptor.

Metallothionein: family of cysteine-rich, 0.5 to 14 kDa proteins; localized to the membrane of the Golgi apparatus; bind both physiological (such as zinc, copper, selenium) and xenobiotic (such as cadmium, mercury, silver, arsenic) heavy metals through the thiol group of its cysteine residues, which represents nearly the 30% of its amino acidic residues

Fragment antigen-binding (Fab): region on an antibody that binds to antigens. Composed of one constant and one variable domain of each of the heavy and the light chain.

Single-chain variable fragment (scFv): fusion protein of the variable regions of the heavy (V_H) and light chains (V_L) of immunoglobulins, connected with a short linker peptide of ten to about 25 amino acids.

Short linear motifs (SLiMs): short stretches of protein sequence that mediate protein protein interaction. SLiMs are generally situated in intrinsically disordered regions (over 80% of known SLiMs), however, upon interaction with a structured partner secondary structure is often induced.

Protein families

Category:Protein families

Category:Protein structure

Category:Protein domains

DExD/H box proteins: refer to the DEAD box, DEAH, and the Ski families of proteins; quite distinct from one another and there is not one protein that belongs to more than one of these families; each family has a specific role in RNA metabolism

DEAD/DEAH box helicase: family of proteins whose purpose is to unwind nucleic acids. "DEAD box and DEAH box proteins NTPase activities become stimulated by RNA, but DEAD box proteins use ATP and DEAH does not" {from "DExD/H box proteins"}.

DEAD box: involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids; highly conserved in nine motifs and can be found in both prokaryotes and eukaryotes. "Involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression" {from "DEAD/DEAH box helicase"}.

Receptors

Circadian rhythms

Cryptochrome (Greek κρυπτός χρώμα "hidden colour"): class of flavoproteins that are sensitive to blue light; found in plants and animals. Cryptochromes are involved in the circadian rhythms of plants and animals, and in the sensing of magnetic fields in a number of species. The two genes Cry1 and Cry2 code for the two cryptochrome proteins CRY1 and CRY2. In insects and plants, CRY1 regulates the circadian clock in a light-dependent fashion, whereas, in mammals, CRY1 and CRY2 act as light-independent inhibitors of CLOCK-BMAL1 components of the circadian clock. In plants, blue-light photoreception can be used to cue developmental signals. Besides chlorophylls, cryptochromes are the only proteins known to form photoinduced radical-pairs in vivo. Cryptochromes (CRY1, CRY2) are evolutionarily old and highly conserved proteins that belong to the flavoproteins superfamily that exists in all kingdoms of life. Circadian rhythm: In Drosophila, In mammals; Magnetoception.

CLOCK (Circadian Locomotor Output Cycles Kaput): gene encoding a basic helix-loop-helix-PAS transcription factor (CLOCK) that affects both the persistence and period of circadian rhythms. CLOCK functions as an essential activator of downstream elements in the pathway critical to the generation of circadian rhythms. CYCLE (CYC) (also known as dBMAL for the BMAL1 ortholog in mammals) dimerizes with CLK via their respective PAS domains. This dimer then recruits co-activator CREB-binding protein (CBP) and is further phosphorylated. Once phosphorylated, this CLK-CYC complex binds to the E-box elements of the promoters of period (per) and timeless (tim) via its bHLH domain, causing the stimulation of gene expression of per and tim.

ARNTL (Aryl hydrocarbon receptor nuclear translocator-like protein 1): in humans is encoded by the ARNTL gene also known as Bmal, Mop3, TIC, JAP3, PASD3, Bmal1c, bHLHe5. ARNTL encodes for a transcription factor with a basic helix-loop-helix (bHLH) and a PAS domain; plays a key role as one of the positive elements in the mammalian autoregulatory transcription translation negative feedback loop (TTFL), which is responsible for generating molecular circadian rhythms.

Period (gene): gene located on the X chromosome of Drosophila melanogaster. Oscillations in levels of both per transcript and its corresponding protein PER have a period of approximately 24 h and together play a central role in the molecular mechanism of the Drosophila biological clock driving circadian rhythms in eclosion and locomotor activity. In mammals, there are three known PER family genes: PER1, PER2, and PER3.

Peptides

Category:Opioid peptides

Opioid peptides: bind to opioid receptors in the brain; opiates and opioids mimic the effect of these peptides. Such peptides may be produced by the body itself, for example endorphins. The effects of these peptides vary, but they all resemble those of opiates. Brain opioid peptide systems are known to play an important role in motivation, emotion, attachment behaviour, the response to stress and pain, and the control of food intake. Opioid-like peptides may also be absorbed from partially digested food (casomorphins, exorphins, and rubiscolins). The opioid food peptides have lengths of typically 4–8 amino acids.

Enkephalin: pentapeptide involved in regulating nociception in the body. The enkephalins are termed endogenous ligands, as they are internally derived and bind to the body's opioid receptors. Met-enkephalin is Tyr-Gly-Gly-Phe-Met; Leu-enkephalin has Tyr-Gly-Gly-Phe-Leu.

Enzymes for recycling

PETase: esterase class of enzymes that catalyze the hydrolysis of polyethylene terephthalate (PET) plastic to monomeric mono-2-hydroxyethyl terephthalate (MHET). Trace amount of the PET breaks down to bis(2-hydroxyethyl) terephthalate (BHET). PETases can also break down PEF-plastic (polyethylene-2,5-furandicarboxylate), which is a bioderived PET replacement, into the analogous MHEF. PETases can't catalyze the hydrolysis of aliphatic polyesters like polybutylene succinate or polylactic acid. PETases can degrade PET in matter of days.

Polyethylene terephthalate (PET)

Bis(2-Hydroxyethyl) terephthalate

Terephthalic acid

2-Hydroxyethyl terephthalic acid

MHETase: hydrolase, which was discovered in 2016. It cleaves Mono-(2-hydroxyethyl)terephthalic acid, the PET degradation product by PETase, to ethylene glycol and terephthalic acid. This pair of enzymes, PETase and MHETase, enable the bacterium Ideonella sakaiensis to live on the plastic PET as sole carbon source.

Protein biosynthesis, post-translational modification

Category:Protein biosynthesis

Category:Post-translational modification

Glycosylation: reaction in which a carbohydrate (or 'glycan'), i.e. a glycosyl donor, is attached to a functional group of another molecule (a glycosyl acceptor) in order to form a glycoconjugate. In biology (but not always in chemistry), glycosylation usually refers to an enzyme-catalysed reaction, whereas glycation (also 'non-enzymatic glycation' and 'non-enzymatic glycosylation') may refer to a non-enzymatic reaction. Glycosylation is a form of co-translational and post-translational modification. Glycans serve a variety of structural and functional roles in membrane and secreted proteins. The majority of proteins synthesized in the rough endoplasmic reticulum undergo glycosylation. Glycosylation is also present in the cytoplasm and nucleus as the O-GlcNAc modification. Five classes of glycans are produced:

N-linked glycans attached to a nitrogen of asparagine or arginine side-chains. N-linked glycosylation requires participation of a special lipid called dolichol phosphate.
O-linked glycans attached to the hydroxyl oxygen of serine, threonine, tyrosine, hydroxylysine, or hydroxyproline side-chains, or to oxygens on lipids such as ceramide.
Phosphoglycans linked through the phosphate of a phosphoserine.
C-linked glycans, a rare form of glycosylation where a sugar is added to a carbon on a tryptophan side-chain. Aloin is one of the few naturally occurring substances.
Glypiation, which is the addition of a GPI anchor that links proteins to lipids through glycan linkages.

N-linked glycosylation: attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine (Asn) residue of a protein), in a process called N-glycosylation, studied in biochemistry. The resulting protein is called an N-linked glycan, or simply an N-glycan. The N-linked glycosylation process occurs in eukaryotes and widely in archaea, but very rarely in bacteria. Different species synthesize different types of N-linked glycan.

Addictive substances (narcotics, ethanol, drugs), addiction

Category:Psychedelic drugs

Overall weighted scores for each of the drugs in the 2010 Drug Harms study. The colored bars indicate the part scores for each of the criteria. The legend shows the normalized weight for each criterion. A higher weight indicates a larger difference between the most harmful drug on the criterion and no harm.

Rat Park: study into drug addiction conducted in the late 1970s (and published in 1980) by Canadian psychologist Bruce K. Alexander and his colleagues at Simon Fraser University in British Columbia, Canada. Alexander's hypothesis was that drugs do not cause addiction, and that the apparent addiction to opiate drugs commonly observed in laboratory rats exposed to it is attributable to their living conditions, and not to any addictive property of the drug itself. He told the Canadian Senate in 2001 that prior experiments in which laboratory rats were kept isolated in cramped metal cages, tethered to a self-injection apparatus, show only that "severely distressed animals, like severely distressed people, will relieve their distress pharmacologically if they can."

Empathogen-entactogen: used to describe a class of psychoactive drugs that produce distinctive emotional and social effects similar to those of MDMA (ecstasy). Putative members of this class include 2C-B, 2C-I(at 2-14mg), MDMA, MDA, MDEA, MBDB, 6-APB and mephedrone among others. The chemical structure of many entactogens contains a substituted amphetamine core, and most belong to the phenethylamine class of psychoactive drugs, although several (AET and AMT) are tryptamines. When referring to MDMA and its counterparts, the term 'MDxx' is often used with the exception of MDPV.

Substituted amphetamine

MDMA (3,4-Methylenedioxymethamphetamine; ecstasy): psychoactive drug used primarily as a recreational drug. Desired effects of MDMA include increased empathy, pleasure, and heightened sensations. When taken by mouth, effects begin after 30–45 minutes and last 3–6 hours. Adverse effects of MDMA use include addiction, memory problems, paranoia, difficulty sleeping, teeth grinding, blurred vision, sweating, and a rapid heartbeat. Use may also lead to depression and fatigue. Deaths have been reported due to increased body temperature and dehydration.

Methamphetamine: strong CNS stimulant that is mainly used as a recreational drug and less commonly as a treatment for attention deficit hyperactivity disorder and obesity. Methamphetamine was discovered in 1893 and exists as two enantiomers: dextromethamphetamine and levomethamphetamine. Methamphetamine properly refers to a specific chemical, the racemic free base, which is an equal mixture of levomethamphetamine and dextromethamphetamine in their pure amine forms. Dextromethamphetamine is a much stronger central stimulant than levomethamphetamine. Both enantiomers are neurotoxic and addictive.

Rick Strassman (1952.02.08-): USA clinical associate professor of psychiatry at the University of New Mexico School of Medicine. He has held a fellowship in clinical psychopharmacology research at the University of California San Diego and was Professor of Psychiatry for eleven years at the University of New Mexico. After 20 years of intermission, Strassman was the first person in the United States to undertake human research with psychedelic, hallucinogenic, or entheogenic substances with his research on N,N-dimethyltryptamine, also known as DMT. Melatonin research. Research into DMT: Religious models for integrating DMT experiences.

DMT: The Spirit Molecule: 2010 documentary film based on a book of the same name by Dr. Rick Strassman. Directed by Mitch Schultz and starring Joe Rogan as narrator, the documentary deals primarily with the psychedelic and entheogenic drug DMT through the lens of interviews with those who have used the drug, either as part of Strassman's scientific studies, or in combination with MAOIs (as ayahuasca).

Psilocybin: naturally occurring psychedelic prodrug compound produced by more than 200 species of fungi. Psilocybin is itself biologically inactive but is quickly converted by the body to psilocin, which has mind-altering effects similar, in some aspects, to those of LSD, mescaline, and DMT. In general, the effects include euphoria, visual and mental hallucinations, changes in perception, a distorted sense of time, and perceived spiritual experiences. It can also include possible adverse reactions such as nausea and panic attacks.

Psilocin (4-HO-DMT, 4-hydroxy DMT, psilocine, psilocyn, or psilotsin): substituted tryptamine alkaloid and a serotonergic psychedelic substance. It is present in most psychedelic mushrooms together with its phosphorylated counterpart psilocybin. Psilocin is a Schedule I drug under the Convention on Psychotropic Substances. The mind-altering effects of psilocin are highly variable and subjective and resemble those of LSD and DMT.

Nora Volkow: addiction science

Behavioral addiction

Compulsive buying disorder (CBD): found in 5.8% of the United States population, approximately 80% of those affected are female

Overeating & Binge eating

Problem gambling

Self-harm (SH) (deliberate self-harm (DSH), self-poisoning, self-mutilation): self-harm is found in 40–60% of suicides; generalising self-harmers to be suicidal is, in the majority of cases, inaccurate.

Sexual addiction

Workaholic: Workaholism is not the same as working hard. Despite logging in an extraordinary amount of hours and sacrificing their health and loved ones for their jobs, workaholics are frequently ineffective employees.

Computer & Internet:

Computer addiction

Internet addiction disorder (IAD)

Information addiction

Video game addiction

Delirium tremens (latin: "shaking frenzy"; "the horrors" or "the shakes"): acute episode of delirium that is usually caused by withdrawal from alcohol (or other sedative-hypnotics, such as benzodiazepines, or barbiturates), first described in 1813; can result in death. Withdrawal from other drugs which are not sedative-hypnotics such as caffeine, cocaine, etc. does not have major medical complications, and is not life-threatening.

Benzodiazepine withdrawal syndrome (benzo withdrawal, BZD withdrawal): cluster of signs and symptoms that emerge when a person who has been taking benzodiazepines, either medically or recreationally, and has developed a physical dependence, undergoes dosage reduction or discontinuation. Development of physical dependence and the resulting withdrawal symptoms, some of which may last for years, may result from taking the medication as prescribed. Benzodiazepine withdrawal is characterized by sleep disturbance, irritability, increased tension and anxiety, panic attacks, hand tremor, shaking, sweating, difficulty with concentration, confusion and cognitive difficulty, memory problems, dry retching and nausea, weight loss, palpitations, headache, muscular pain and stiffness, a host of perceptual changes, hallucinations, seizures, psychosis, and increased risk of suicide. Further, these symptoms are notable for the manner in which they wax and wane and vary in severity from day to day or week by week instead of steadily decreasing in a straightforward monotonic manner. This phenomenon is often referred to as "waves" and "windows". Benzodiazepine withdrawal can be severe and can provoke life-threatening withdrawal symptoms, such as seizures, particularly with abrupt or overly rapid dosage reduction from high doses or long-time use. A severe withdrawal response can nevertheless occur despite gradual dose reduction, or from relatively low doses in short-time users; even after a single large dose in animal models. A minority of individuals will experience a protracted withdrawal syndrome, whose symptoms may persist at a sub-acute level for months or years after cessation of benzodiazepines. The likelihood of developing a protracted withdrawal syndrome can be minimized by a slow, gradual reduction in dosage.

The Natural History of Alcoholism Revisited (1955): book by psychiatrist George E. Vaillant that describes two multi-decade studies of the lives of 600 American males, non-alcoholics at the outset, focusing on their lifelong drinking behaviours. By following the men from youth to old age it was possible to chart their drinking patterns and what factors may have contributed to alcoholism. Another study followed 100 severe alcoholics from a clinic eight years after their detoxification. Some of the main conclusions of Vaillant’s book are:

That alcoholism is as much a social as a medical condition. "Alcoholism can simultaneously reflect both a conditioned habit and a disease."
Factors predicting alcoholism were related to ethnic culture, alcoholism in relatives, and a personality that is antisocial and extroverted. An unhappy childhood predicted mental illness but not alcoholism—unless the family problems were due to alcoholism.
That alcoholism was generally the cause of co-occurring depression, anxiety, and sociopathic (delinquent) behaviour, not the result.
That even though alcoholism is not solely a medical condition, it is therapeutically effective to explain it as a disease to patients. The disease concept encourages patients to take responsibility for their drinking, without debilitating guilt.
That for most alcoholics, attempts at controlled drinking in the long term end in either abstinence or a return to alcoholism.
That there is as yet no cure for alcoholism, and that medical treatment can only provide short-term crisis intervention.
Achieving long-term sobriety usually involves (1) a less harmful, substitute dependency; (2) new relationships; (3) sources of inspiration and hope; and (4) experiencing negative consequences of drinking.

Time Well Spent: nonprofit organization which seeks to reverse what they call the "digital attention crisis", caused by technology companies designing mobile devices and social media features in order to capture as much attention as possible, regardless of their impact on users' quality of life. Former Google employee Tristan Harris founded the project to raise awareness about the intentional design to make consumer technology addictive. James Williams co-founded the movement, and also dedicates his time to focusing on the ethics of technology design. The two men founded the organization to spread awareness and talk about the aspects of technology that are often ignored, such as attention and distraction and their effects on the user. In a 2018 post, Facebook CEO Mark Zuckerberg described feeling a "responsibility to make sure our services aren’t just fun to use, but also good for people's well-being", announcing "a major change to how we build Facebook" so that time spent on the site is "time well spent." It has been suggested that this is an allusion to the organization.

Opioid epidemic: rapid increase in the use of prescription and non-prescription opioid drugs in USA and Canada beginning in the late 1990s and continuing throughout the next two decades. Opioids are a diverse class of moderately strong painkillers, including oxycodone (commonly sold under the trade names OxyContin and Percocet), hydrocodone (Vicodin, Norco), and a very strong painkiller, fentanyl, which is synthesized to resemble other opiates such as opium-derived morphine and heroin. The potency and availability of these substances, despite their high risk of addiction and overdose, have made them popular both as medical treatments and as recreational drugs. Due to their sedative effects on the part of the brain which regulates breathing, the respiratory center of the medulla oblongata, opioids in high doses present the potential for respiratory depression, and may cause respiratory failure and death.

Fentanyl: opioid used as a pain medication and together with other medications for anesthesia. Fentanyl is also made illegally and used as a recreational drug, often mixed with heroin or cocaine. It has a rapid onset and effects generally last less than an hour or two. Medically, fentanyl is used by injection, as a patch on the skin, as a nasal spray, or in the mouth. Fentanyl works primarily by activating μ-opioid receptors; is around 100 times stronger than morphine, and some analogues such as carfentanil are around 10,000 times stronger.

Drug policy

Category:Drug policy

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Drug policy of Portugal: put in place in 2000, and was legally effective from July 2001. The new law maintained the status of illegality for using or possessing any drug for personal use without authorization. However, the offense was changed from a criminal one, with prison a possible punishment, to an administrative one if the amount possessed was no more than ten days' supply of that substance. After-care and social re-integration of drug users in Portugal is organised through three major programmes targeting different regions in Portugal (Programa Vida Emprego, Programa Quadro Reinserir and the PIDDAC incentives for re-integration). All three programmes finance different initiatives and projects supporting drug users through training opportunities, employment support, and/or housing.

Germany:

Drug policy of Nazi Germany: Civilian-sector drug policy in Nazi Germany; Drug policy and use within the Wehrmacht: In an effort to make its front-line soldiers and fighter pilots fight longer, harder, and with less concern for individual safety, the German army ordered them to take military-issue pills made from methamphetamine and a primarily cocaine-based stimulant. After Pervitin, a methamphetamine drug newly developed by the Berlin-based Temmler pharmaceutical company, first entered the civilian market in 1938, it quickly became a top seller among the German population. Cocaine, whose effects substantially overlap with those of amphetamine but feature greater euphoria, was later added to the formulation to increase its potency through the multiplicative effects of drug interaction and to reinforce its use by individuals.; Drug use inside the Nazi Party.

Anti-tobacco movement in Nazi Germany: After German doctors became the first to identify the link between smoking and lung cancer, Germany initiated a strong anti-tobacco movement and led the first public anti-smoking campaign in modern history. Anti-tobacco movements grew in many nations from the beginning of the 20th century, but these had little success, except in Germany, where the campaign was supported by the government after the Nazis came to power. It was the most powerful anti-smoking movement in the world during the 1930s and early 1940s. The National Socialist leadership condemned smoking and several of them openly criticized tobacco consumption. Research on smoking and its effects on health thrived under Nazi rule and was the most important of its type at that time. Adolf Hitler's personal distaste for tobacco and the Nazi reproductive policies were among the motivating factors behind their campaign against smoking. The Nazi anti-tobacco campaign included banning smoking in trams, buses and city trains, promoting health education, limiting cigarette rations in the Wehrmacht, organizing medical lectures for soldiers, and raising the tobacco tax.

Biochemistry methods

Category:Laboratory techniques

Category:Instrumental analysis

Category:Biochemistry methods

Category:Polymerase chain reaction

Category:Chromatography

Category:Separation processes

Category:Chromatography

Cross-link: cross-links in synthetic polymer chemistry; crosslinks in the biological sciences: protein-protein interaction, photo-reactive aa analogs (mass spectrometry); uses for crosslinked polymers: polyacrylamide gels for gel electrophoresis, rubber.

Real-time polymerase chain reaction: The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines propose that the abbreviation qPCR be used for quantitative real-time PCR and that RT-qPCR be used for reverse transcription–qPCR. The acronym "RT-PCR" commonly denotes reverse transcription polymerase chain reaction and not real-time PCR, but not all authors adhere to this convention.

TaqMan: probes are hydrolysis probes that are designed to increase the specificity of quantitative PCR. TaqMan probe principle relies on the 5´–3´ exonuclease activity of Taq polymerase to cleave a dual-labeled probe during hybridization to the complementary target sequence and fluorophore-based detection.

Taq polymerase: thermostable DNA polymerase named after the thermophilic bacterium Thermus aquaticus from which it was originally isolated by Chien et al. in 1976.

Φ29 DNA polymerase: enzyme from the bacteriophage Φ29. It is being increasingly used in molecular biology for multiple displacement DNA amplification procedures, and has a number of features that make it particularly suitable for this application.

Multiple displacement amplification: non-PCR based DNA amplification technique. This method can rapidly amplify minute amounts of DNA samples to a reasonable quantity for genomic analysis. The reaction starts by annealing random hexamer primers to the template: DNA synthesis is carried out by a high fidelity enzyme, preferentially Φ29 DNA polymerase, at a constant temperature. Compared with conventional PCR amplification techniques, MDA generates larger sized products with a lower error frequency. This method has been actively used in whole genome amplification and is a promising method for application to single cell genome sequencing and sequencing-based genetic studies.

Dynamic light scattering (DLS): technique in physics that can be used to determine the size distribution profile of small particles in suspension or polymers in solution. In the scope of DLS, temporal fluctuations are usually analyzed by means of the intensity or photon auto-correlation function (also known as photon correlation spectroscopy or quasi-elastic light scattering).

Proteinase K: broad-spectrum serine protease. The enzyme was discovered in 1974 in extracts of the fungus Engyodontium album. Proteinase K is able to digest hair (keratin), hence, the name "Proteinase K". The predominant site of cleavage is the peptide bond adjacent to the carboxyl group of aliphatic and aromatic amino acids with blocked alpha amino groups. It is commonly used for its broad specificity. M_r = 28,900 daltons (28.9 kDa). Activated by calcium, the enzyme digests proteins preferentially after hydrophobic amino acids (aliphatic, aromatic and other hydrophobic amino acids). Although calcium ions do not affect the enzyme activity, they do contribute to its stability. Proteins will be completely digested if the incubation time is long and the protease concentration high enough.

Dialysis (biochemistry): process of separating molecules in solution by the difference in their rates of diffusion through a semipermeable membrane, such as dialysis tubing. Dialysis membranes are produced and characterized according to MWCO limits. While membranes with MWCOs ranging from 1-1,000,000 kDa are commercially available, membranes with MWCOs near 10 kDa are most commonly used.

Molecular weight cut-off (MWCO): lowest molecular weight solute (in daltons) in which 90% of the solute is retained by the membrane, or the molecular weight of the molecule (e.g. globular protein) that is 90% retained by the membrane.

Spin column-based nucleic acid purification: solid phase extraction method to quickly purify nucleic acids. This method relies on the fact that nucleic acid will bind to the solid phase of silica under certain conditions.

Salting out

Ammonium sulfate precipitation: purify proteins by altering their solubility. Ammonium sulfate is commonly used as its solubility is so high that salt solutions with high ionic strength are allowed. Useful to quickly remove large amounts of contaminant proteins, as a first step in many purification schemes.

Hofmeister series (lyotropic series): classification of ions in order of their ability to salt out or salt in proteins.

High-performance liquid chromatography (HPLC; formerly referred to as high-pressure liquid chromatography): technique in analytical chemistry used to separate, identify, and quantify each component in a mixture. It relies on pumps to pass a pressurized liquid solvent containing the sample mixture through a column filled with a solid adsorbent material. Each component in the sample interacts slightly differently with the adsorbent material, causing different flow rates for the different components and leading to the separation of the components as they flow out the column. The active component of the column, the adsorbent, is typically a granular material made of solid particles (e.g. silica, polymers, ...), 2–50 μm in size. The components of the sample mixture are separated from each other due to their different degrees of interaction with the adsorbent particles. The pressurized liquid is typically a mixture of solvents (e.g. water, acetonitrile and/or methanol) and is referred to as a "mobile phase". Its composition and temperature play a major role in the separation process by influencing the interactions taking place between sample components and adsorbent. These interactions are physical in nature, such as hydrophobic (dispersive), dipole–dipole and ionic, most often a combination. The schematic of an HPLC instrument typically includes a degasser, sampler, pumps, and a detector. Types: Partition chromatography, Normal–phase chromatography, Displacement chromatography, Reversed-phase chromatography (RPC), Size-exclusion chromatography, Ion-exchange chromatography, Bioaffinity chromatography, Aqueous normal-phase chromatography. Parameters: Theoretical, Internal diameter, Particle size, Pore size, Pump pressure, Detectors, Autosamplers.

Biophysics, physical chemistry

{q.v. User:Kazkaskazkasako/Books/Physical sciences#Biophysics, physical chemistry}

Structural biology

Category:Structural biology

{q.v. #Structure-function}

Template:Biomolecular structure & Biomolecular structure

Template:Protein structural analysis

Nucleic acid structure determination: Physical methods (X-ray, NMR, EM...); RNA sequencing; Chemical methods (Hydroxyl radical probing, DMS, CMCT, Kethoxal, Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE)); In-line probing; Nucleotide analog interference mapping

Nucleic acid design

RNA containing complexes

{q.v. #Cell nucleus}

Template:Post transcriptional modification

Ribonucleoprotein (RNP): nucleoprotein that contains RNA, i.e. protein + RNA.

Ribonucleoprotein particle: complex formed between RNA and RBPs. 'RNP foci' is used to denote an intracellular compartment involved in processing of RNA transcripts. RNP granules: stress granules, processing bodies, and exosomes in somatic cells; cell type and/or species specific.

Exosome complex (PM/Scl complex): multi-protein intracellular complex capable of degrading various types of RNA molecules. Exosome complexes are found in both eukaryotic cells and archaea, while in bacteria a simpler complex called the degradosome carries out similar functions.

Degradosome: multiprotein complex present in most bacteria that is involved in the processing of ribosomal RNA and the degradation of messenger RNA and is regulated by Non-coding RNA. It contains the proteins RNA helicase B, RNase E and Polynucleotide phosphorylase.

RNAs:

Small nucleolar RNA (snoRNAs): primarily guide chemical modifications of other RNAs, mainly: rRNAs, tRNAs, snRNAs. Two main classes of snoRNA: the C/D box snoRNAs which are associated with methylation, and the H/ACA box snoRNAs which are associated with pseudouridylation. Commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes.

Template:Small nucleolar RNA: J; MB; Me; psi; R, SNORA; SNORD; snR; TBR; U (e.g. U3; U2-19; U8); Z; other.

Small Cajal body-specific RNA (scaRNAs): specifically localise to the Cajal body, a nuclear organelle involved in the biogenesis snRNPs; guide the modification (methylation and pseudouridylation) of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12.

RNA processing

transcriptosome:

Capping enzyme: addition of the cap occurs co-transcriptionally, after the growing RNA molecule contains about 30 nucleotides. The enzyme can only catalyze its reaction when bound to the phosphorylated carboxyl-terminal domain of RNA polymerase II; therefore it is specific to RNAs synthesized by this polymerase rather than those synthesized by RNA polymerase I or RNA polymerase III.

RNA polymerase (esp. RNA polymerase II)

transcription factors

splicing {q.v. #Spliceosome, splicing}

Five-prime cap (5′ cap): specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is highly regulated and vital in the creation of stable and mature messenger RNA able to undergo translation during protein synthesis. Mitochondrial mRNA and chloroplastic mRNA are not capped.

Eukaryotic initiation factor 4F: heterotrimeric protein complex that binds the 5' cap of messenger RNAs (mRNAs) to promote eukaryotic translation initiation. The eIF4F complex is composed of three non-identical subunits: the DEAD-box RNA helicase eIF4A, the cap-binding protein eIF4E, and the large "scaffold" protein eIF4G.

EIF4E (Eukaryotic translation initiation factor 4E): most eukaryotic cellular mRNAs are blocked at their 5'-ends with the 7-methyl-guanosine five-prime cap structure, m7GpppX (where X is any nucleotide). eIF4E is a eukaryotic translation initiation factor involved in directing ribosomes to the cap structure of mRNAs. It is a 24-kD polypeptide that exists as both a free form and as part of the eIF4F pre-initiation complex. Almost all cellular mRNA require eIF4E in order to be translated into protein. The eIF4E polypeptide is the rate-limiting component of the eukaryotic translation apparatus and is involved in the mRNA-ribosome binding step of eukaryotic protein synthesis.

RNA polymerase (RNAP, RANpol; DNA-dependent RNA polymerase)

RNA polymerase I (Pol I): in higher eukaryotes, the enzyme that only transcribes 18S, 5.8S, 28S rRNA (but not 5S rRNA, which is synthesized by RNA Polymerase III), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell. rDNA transcription is confined to the nucleolus where several hundreds of copies of rRNA genes are present, arranged as tandem head-to-tail repeats. Pol I transcribes one large transcript, encoding an rDNA gene over and over again; fastest-acting polymerase.

RNA polymerase II (RNAP II, Pol II): transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA; 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. Carboxy-terminal domain (CTD) of Pol II typically consists of up to 52 repeats of the sequence YSPTSPS.

RNA polymerase II holoenzyme: form of eukaryotic Pol II that is recruited to the promoters of protein-coding genes in living cells; consists of Pol II, a subset of general transcription factors, and regulatory proteins known as SRB proteins. CTD phosphorylation.

Mediator (coactivator) (Vitamin D Receptor Interacting Protein (DRIP) coactivator complex and the Thyroid Hormone Receptor-associated Proteins (TRAP)): multiprotein complex that functions as a transcriptional coactivator in all eukaryotes; required for the successful transcription of nearly all class II gene promoters in yeast. Human mediator complex: 26+ subunits, 1.2 MDa.

RNA polymerase III (Pol III): transcribes DNA to synthesize 5S rRNA, tRNA and other small RNAs

RNA polymerase IV: specific to plants genomes and is required for the synthesis of over 90% of 24-nt heterochromatic siRNA

RNA polymerase V: synthesizes RNAs involved in siRNA-directed heterochromatin formation in plants.

Post-transcriptional modification (co-transcriptional modification)

Non-coding RNA (ncRNA; sometimes: non-protein-coding RNA (npcRNA), non-messenger RNA (nmRNA), functional RNA (fRNA)): functional RNA molecule that is not translated into a protein; DNA sequence from which a non-coding RNA is transcribed is often called an RNA gene. tRNA, rRNA, snoRNA, microRNA, siRNA, snRNA, exRNA, piRNA, long ncRNA...

Long non-coding RNA (lncRNA {pronounced: lincRNA}): non-protein coding transcripts longer than 200 nucleotides:: somewhat arbitrary limit distinguishes lncRNAs from small regulatory RNAs: miRNAs, siRNAs, piRNAs, snoRNAs, and other short RNAs. Many well-described long ncRNAs, such as Air and Xist, are poorly conserved, suggesting that ncRNAs may be subject to different selection pressures; selection may conserve only short regions of long ncRNAs that are constrained by structure or sequence-specific interactions; selection act only over small regions of the long ncRNA transcript. Those conserved regions of the human genome that are subject to recent evolutionary change relative to the chimpanzee genome occurs mainly in non-coding regions, many of which are transcribed

Piwi-interacting RNAs (piRNAs)

Bacterial small RNA

Small hairpin RNA (short hairpin RNA (shRNA)): makes a tight hairpin turn that can be used to silence target gene expression via RNAi

Polyadenylation (addition of poly(A) tail): to RNA. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation. Nuclear polyadenylation: Function, Mechanism.Cytoplasmic polyadenylation: germ line, early embryogenesis, post-synaptic sites of neurons. Tagging for degradation in eukaryotes. Evolution: polyadenylation is seen in almost all organisms, it is not universal.

RNA-binding protein (RBP): bind to the ds or ss RNA; contain RRMs.

Spliceosome, splicing

RNA splicing (splicing)

alternative splicing (differential splicing): regulated process during gene expression that results in a single gene coding for multiple proteins.

LSm several duplications: SmD1/LSm10 paralog pair and the SmD2/LSm11 paralog pair exist only in animals, fungi, and the amoebozoa; the SmB/SmN (neural tissue Sm) paralog pair is seen only in the placental mammals. SmB has alternatively spliced variant SmB'; very similar protein, SmN replaces SmB'/B in certain (mostly neural) tissues. LSm's are found in U1, U2, U4, U5, U6 as a ring around Sm motif in U1, U2, U4, U5, U6 RNAs.

Sm ring: SmG, SmD3, SmB/SmB'/SmN, SmD1, SmD2, SmF. + U1, U2, U4, U5, U11, U12, U4atac snRNAs.

Lsm2-8 ring: (Theorized order: LSm5, LSm7, LSm4, LSm8, LSm2, LSm3, LSm6.) ~20 times less abundant than the Sm rings. + U6, U6atac, snRNAs; + U8 snoRNA (for rRNA, tRNA processing in nucleolus).

Sm10/Sm11 ring: LSM10 replace SmD1 and LSm11 replaces SmD2. + U7 snRNA.

Lsm1-7 ring: same as Lsm2-8 except LSm1 replaces LSm8. Localizes in the cytoplasm where it assists in degrading messenger RNA in ribonucleoprotein complexes.

SMN complex: SMN + Gemins 2-8. Gemin 6 and Gemin7 have been discovered to have the LSm structure, and to form a heterodimer. PRMT5 complex stabilizes SmB+SmD3 dimer, SmD1+SmD2 dimer, and SmD1+SmD2+SmF+SmE+SmG pentamer by attaching pICln to these. The pentamer and SmB+SmD3 dimer are loaded onto the SMN complex, which in turn loads the Sm ring onto snRNAs. SnRNP#Assembly of core snRNPs in the SMN complex: involved in the assembly of snRNPs.

GEMINs 2-8: GEMIN8 (Gem-associated protein 8) + GEMIN7 + GEMIN6 + GEMIN5 + GEMIN4 + DDX20 (Probable ATP-dependent RNA helicase DDX20; aka GEMIN3) + Survival of motor neuron protein-interacting protein 1 (SIP1 gene; aka GEMIN2)

Survival of motor neuron (SMN1 gene): due to SMN1 deletion, (incomplete SMN complex?) results in widespread splicing defects, especially in spinal motor neurons, and is one cause of spinal muscular atrophy (SMA)

PRMT5 complex = Protein arginine methyltransferase 5 + CLNS1A (pICln) + WD repeat-containing protein 77 (Mep50)

LSm12-16 and other multi-domain LSm proteins: ataxin-2 is large protein and has N-terminal LSm domain.

Archaeal Sm rings: Sm1 (SmAP1) and Sm2 (SmAP2) form homoheptamer or homohexamer rings; reported to associate with RNase P RNA. Crenarchaeotes have Sm3.

Bacterial LSm rings: Hfq - homohexamer rings; YlxS (sometimes also called YhbC) - two-domain protein with a N-terminal LSm domain. MscS

SnRNPs (pronounced "snurps"; small nuclear ribonucleoproteins): U1, U2, U5, U5, U6 (in addition, in metazoans: U11 snRNA, U12 snRNA, U4atac snRNA, U6atac snRNA). Also: U7 snRNP, which processes 3′ loop of histone pre-mRNA. Biogenesis.

Small nuclear RNA (snRNA; U-RNA): found within the nucleus of eukaryotic cells; length of an average snRNA is approximately 150 nt

U7 snRNP = U7 small nuclear RNA + Sm10/Sm11 ring + ZPF100 + (HBP (aka SLBP) + Histone 3' UTR stem-loop). For histone 3' UTR stem-loop processing.

Histone 3' UTR stem-loop: involved in nucleocytoplasmic transport of the histone mRNAs, and in the regulation of stability and of translation efficiency in the cytoplasm; mRNAs of metazoan histone genes lack polyadenylation and a poly-A tail, instead 3' end processing occurs at a site between this highly conserved stem-loop and a purine rich region around 20 nucleotides downstream (the histone downstream element, or HDE).

SLBP (histone RNA hairpin-binding protein (HBP) or stem-loop binding protein):

Minor spliceosome: splices atypical class of spliceosomal introns (U12-type) from eukaryotic messenger RNAs in plant, insects, vertebrates and some fungi. U12-type introns represent less than 1% of all introns in human cells. However they are found in genes performing essential cellular functions.

Spliceosome and spliceosomal "subunits" and complexes (U1, U2 (SF3a + SF3b), U4/6&U5 (tri-snRNP) → U1+U2+U4/6&U5 (B) → U2/6&U5 (B^act, B*, C))

Introns + Exons = pre-mRNA; pre-mRNA-(Spliceosome)→mRNA

U1 snRNP = U1 spliceosomal RNA + SnRNP70 (aka, U1 small nuclear ribonucleoprotein 70 kDa) + Sm ring + U1-A

U2 snRNP = U2 spliceosomal RNA + PRPF8 {2335 AA} (YPrp8)

U4 snRNP = U4 spliceosomal RNA + (+ PRPF3)

U5 snRNP = U5 spliceosomal RNA + WDR57 (Y????)

U6 snRNP = U6 spliceosomal RNA + Lsm2-8 ring + (+ PRPF3)

U4/U6-U5 tri-snRNP = U4 + U6 + U5 + PRPF31

Splicing factor: protein involved in the removal of introns from pre-mRNA.

U2AF2 (U2 small nuclear RNA auxiliary factor 1): required for binding of U2 snRNP to pre-mRNA; PAP1 (RP9) interacts with U2AF

ASF/SF2 (SFRS1)

EFTUD2 (interacts with WDR57 and PRPF8)

SR protein: conserved family of proteins involved in RNA splicing; protein domain with long repeats of S and R aa; length of SR proteins: 50-300 aa; RS domain and at least one RRM domain; more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm. Metazoans appear to have SR proteins and unicellular organisms lack SR proteins. Important in constitutive and alternative pre-mRNA splicing, mRNA export, genome stabilization, NMD, and translation. 9 human genes: SFRS1, SFRS2, SFRS3, SFRS4, SFRS5, SFRS6, SFRS7, SFRS9, SFRS11. mRNA export; Genomic stabilization; NMD; Translation. Diseases: Cancer; HIV-1; Spinal muscular atrophy.

RNA recognition motif (RRM, RNP-1): putative RNA-binding domain of about 90 aa that are known to bind single-stranded RNAs; found in many eukaryotic proteins

Kinases: Serine/threonine-protein kinases: SRPK1, SRPK2; CLK1

Heterogeneous ribonucleoprotein particle (hnRNP): present in the cell nucleus during gene transcription and subsequent post-transcriptional modification of pre-mRNA. Proteins involved in the hnRNP complexes are collectively known as heterogeneous ribonucleoproteins

Polypyrimidine tract-binding protein (PTB): plays a regulatory role in alternative splicing.

Protein K (gene expression); K-homology or KH domains

pre-mRNA structures:

Polypyrimidine tract: region of mRNA that promotes the assembly of the spliceosome. PTB and U2AF associate with polypyrimidine tract.

Exonic splicing enhancer (ESE): DNA sequence motif consisting of 6 bases within an exon that directs, or enhances, accurate splicing of hnRNA or pre-mRNA into mRNA.

Exonic splicing silencer (ESS): small region of an exon that inhibits or silences splicing of pre-mRNA.

Precursor mRNA (pre-mRNA is the major part of heterogeneous nuclear RNA (hnRNA)): immature single strand of mRNA. Processed pre-mRNA is called "mature mRNA" or simply "mRNA".

Splicing-associated genetic diseases:

Retinitis pigmentosa (RP): a group of genetic eye conditions that lead to incurable blindness. RPs linked to splicing: RP13=PRPF8, RP11=PRPF31, RP18=PRPF3, RP9=PAP1.

Exon junction complex (EJC): has major influences on translation, surveillance and localization of the spliced mRNA

Nonsense-mediated decay (NMD): surveillance pathway that exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons.

mRNA surveillance: mechanisms are pathways utilized by organisms to ensure fidelity and quality of mRNA; function at various steps of the mRNA biogenesis pathway to detect and degrade transcripts that have not properly been processed.

Trans-splicing & de:Transspleißen: special form of pre-mRNA processing in eukaryotes where exons from two different primary RNA transcripts are joined end to end and ligated.

Ribozymes

Ribosome

Processome: the "-some" which processes at least 16S rRNA of ribosome and assembles the small subunit of ribosome; made of U3 snoRNP, tUTP, bUTP, BMS1/RCL1.

Ribosomal RNA (rRNA): RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rRNA and 40% protein by weight. Ribosomes contain two major rRNAs and 50 or more proteins. rRNA is one of only a few gene products present in all cells; therefore, genes that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic group, calculate related groups, and estimate rates of species divergence.

Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are typically organized as a co-transcribed operon.
Eukaryotes generally have many copies of the rRNA genes organized in tandem repeats; in humans approximately 300–400 repeats are present in five clusters (on chromosomes 13, 14, 15, 21 and 22).

Ribosomal DNA (rDNA): DNA sequence that codes for ribosomal RNA. rDNA of eukaryotes consists of a tandem repeat of a unit segment, an operon, composed of NTS, ETS, 18S, ITS1, 5.8S, ITS2, and 28S tracts. rDNA has another gene, coding for 5S rRNA, located in the genome in most eukaryotes. In the nucleus, the rDNA region of the chromosome is visualized as a nucleolus which forms expanded chromosomal loops with rDNA

5S ribosomal RNA (5S rRNA): ~120 nt ribosomal RNA molecule with a mass of 40 kDa. It is a structural and functional component of the large subunit of the ribosome in all domains of life (bacteria, archaea, and eukaryotes), with the exception of mitochondrial ribosomes of fungi and animals. Current evidence indicates that mitochondrial DNA of only a few groups, notably animals, fungi, alveolates and euglenozoans lacks the gene. The central protuberance, otherwise occupied by 5S rRNA and its associated proteins, L5 and L18 (see Figure 2), was remodeled in various ways. In the fungal mitochondrial ribosomes, 5S rRNA is replaced by LSU rRNA expansion sequences. In kinetoplastids (euglenozoans), the central protuberance is made entirely of evolutionarily novel mitochondrial ribosomal proteins. Lastly, animal mitochondrial ribosomes have coopted a specific mitochondrial tRNA to substitute the missing 5S rRNA.

Prokaryotic ribosome (70S):

23S ribosomal RNA (in E. coli 2904 nt): component of the large subunit (50S) of the bacterial ribosome.

16S ribosomal RNA: component of the small subunit (30S) of prokaryotic ribosomes. The genes coding for it are referred to as 16S rDNA and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. Multiple sequences of 16S rRNA can exist within a single bacterium. Universal primers: 16S rRNA gene is used for phylogenetic studies as it is highly conserved between different species of bacteria and archaea. Some (hyper)thermophilic archaea (i.e. order Thermoproteales) contain 16S rRNA gene introns that are located in highly conserved regions and can impact the annealing of "universal" primers. Mitochondrial and chloroplastic rRNA are also amplified. PCR applications: 16S rRNA gene sequences contain hypervariable regions that can provide species-specific signature sequences useful for identification of bacteria. As a result, 16S rRNA gene sequencing has become prevalent in medical microbiology as a rapid and cheap alternative to phenotypic methods of bacterial identification.

Eukaryotic ribosome (80S): are much larger than prokaryotic (bacterial and archaeal) ribosomes and subject to more complex regulation and biogenesis pathways; small subunit (40S) and large subunit (60S). Architecture:

General features: In the characteristic "crown view" of the large subunit, structural landmarks include the central protuberance, the L1-stalk and the P-stalk. The majority of the eukaryote-specific RNA and protein elements are found on the solvent-exposed sides of the 40S and 60S subunits. The subunit interface, as well as important functional regions such as the peptidyl transferase center and the decoding site are mostly conserved (across kingdoms), with some differences observed in the surrounding regions. In stark contrast to prokaryotic ribosomal proteins, which interact primarily with RNA, the eukaryote-specific protein segments engage in a multitude of protein-protein interactions. Long distance interactions are mediated by eukaryote-specific helical extensions of ribosomal proteins, and several eukaryotic ribosomal proteins jointly to form inter-protein beta-sheets.
Co-evolution of rRNA and proteins: eukaryote-specific proteins (rpS7, rpS10, rpS12 and RACK1), as well as numerous eukaryote-specific extensions of proteins, are located on the solvent-exposed side of the small subunit. Here, they participate in the stabilization of rRNA expansion segments. Beak of the 40S subunit is remodeled, as rRNA has been replaced by proteins rpS10 and rpS12. As observed for the 40S subunit, all eukaryote-specific proteins of the 60S subunit (RPL6, RPL22, RPL27, RPL28, RPL29 and RPL36) and many extensions are located at the solvent-exposed side, forming an intricate network of interactions with eukaryotic-specific RNA expansion segments. RPL6, RPL27 and RPL29 mediate contacts between the ES sets ES7–ES39, ES31–ES20–ES26 and ES9–ES12, respectively and RPL28 stabilized expansion segment ES7A.
Ubiquitin fusion proteins: small subunit protein RPS27A (or eS31) and the large subunit protein RPL40 (or eL40) are processed polypeptides, which are translated as fusion proteins carrying N-terminal ubiquitin domains. These positions suggest that proteolytic cleavage is an essential step in the production of functional ribosomes.
Active site: Comparisons between bacterial, archaeal and eukaryotic ribosome structures reveal a very high degree of conservation in the active site—the peptidyl transferase center (PTC) -- region. None of the eukaryote-specific protein elements is close enough to directly participate in catalysis.

5.8S ribosomal RNA (5.8S rRNA): non-coding RNA component of the large subunit (60S) of the eukaryotic ribosome and so plays an important role in protein translation.

28S ribosomal RNA: component of the large subunit (LSU, 60S) of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. It is the eukaryotic nuclear homologue of the prokaryotic 23S and mitochondrial 16S ribosomal (MT-RNR2) RNAs.

18S ribosomal RNA: component of the small eukaryotic ribosomal subunit (40S). The genes coding for 18S rRNA are referred to as 18S rDNA. It is the eukaryotic citosolic homologue of 16S ribosomal RNA in prokaryotes and mitochondria. Sequence data from these genes is widely used in molecular analysis to reconstruct the evolutionary history of organisms, especially in vertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences. 18S rRNA is eukaryotic nuclear homologue of 16S ribosomal RNA in Prokaryotes and mitochondria.

MT-RNR1 (Mitochondrially encoded 12S RNA): component of the small subunit (SSU) of the mitochondrial ribosome. In humans, 12S is encoded by the MT-RNR1 gene and is 959 nt long. MT-RNR1 is one of the 37 genes contained in animal mitochondria genomes.

MT-RNR2 (Mitochondrially encoded 16S RNA): mitochondrial rRNA that in humans is encoded by the MT-RNR2 gene. The MT-RNR2 gene also encodes the Humanin polypeptide that has been the target of Alzheimer's disease research.

Release factor: protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence. They are named so because they release new peptides from the ribosome. Bacterial release factors include RF1, RF2, and RF3 (or PrfA, PrfB, PrfC in the "peptide release factor" gene nomenclature). RF1 and RF2 are class 1 RFs: RF1 recognizes UAA and UAG while RF2 recognizes UAA and UGA. RF3 is the class 2 release factor. Eukaryotic and archaeal release factors are similar, with the naming changed to "eRF" for "eukaryotic release factor" and vice versa. a/eRF1 can recognize all three stop codons, while eRF3 (archaea use EF-1α instead) works just like RF3.

Ribosome-binding site (RBS): sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation. Mostly, RBS refers to bacterial sequences, although internal ribosome entry sites (IRES) have been described in mRNAs of eukaryotic cells or viruses that infect eukaryotes. Ribosome recruitment in eukaryotes is generally mediated by the 5' cap present on eukaryotic mRNAs.

RNase P: cleave off an extra, or precursor, sequence of RNA on tRNA molecules. Bacterial RNase P has two components: an RNA chain, called M1 RNA, and a polypeptide chain, or protein, called C5 protein (class A and B). Archaeal RNase P ribonucleoproteins consist of 4-5 protein subunits that are associated with RNA.

Nuclear RNase P: eukaryotic RNase P.

Intron

Spliceosomal introns: in nuclear protein-coding genes that are removed by spliceosomes

Introns in nuclear and archaeal transfer RNA genes that are removed by proteins (tRNA splicing enzymes)

Group I catalytic intron: large self-splicing ribozymes; catalyze their own excision from mRNA, tRNA and rRNA precursors in Eukaryota, Bacteria, Viruses.

Group II intron: large class of self-catalytic ribozymes as well as mobile genetic element found within the genes of all three domains of life. Self-splicing can occur under high-salt conditions in vitro; however, assistance from proteins is required for in vivo splicing.

Group III intron: found in mRNA genes of chloroplasts in euglenoid protists; have a conventional group II-type dVI with a bulged adenosine, a streamlined dI, no dII-dV, and a relaxed splice site consensus. Much shorter than other self-splicing intron classes, ranging from 95 to 110 nucleotides amongst those known to Christopher and Hallick, and identified in chloroplasts; conserved sequences proximal to the splicing sites have similarities to those of group II introns, but have fewer conserved positions; very A+T rich.

Protein complexes, macromolecular assemblies

Category:Protein complexes

Macromolecular assemblies are studied in bio, chem, phys, maths, CS/IT(dynamics(molecular, modeling,...)); sometimes (NOT always) called "-somes", from Greek soma->body.

Protein quaternary structure: fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. Structure Prediction: One such development is AlphaFold-Multimer built upon the AlphaFold model for predicting protein tertiary structure. Protein–protein interactions. Intragenic complementation. Assembly: Direct interaction of two nascent proteins emerging from nearby ribosomes appears to be a general mechanism for oligomer formation. Hundreds of protein oligomers were identified that assemble in human cells by such an interaction. The most prevalent form of interaction was between the N-terminal regions of the interacting proteins. Dimer formation appears to be able to occur independently of dedicated assembly machines.

Macromolecular assembly (MA): massive chemical structures such as viruses and non-biologic nanoparticles, cellular organelles and membranes and ribosomes, etc. that are complex mixtures of polypeptide, polynucleotide, polysaccharide or other polymeric macromolecules. They are generally of more than one of these types, and the mixtures are defined spatially (i.e., with regard to their chemical shape), and with regard to their underlying chemical composition and structure. Macromolecules are found in living and nonliving things, and are composed of many hundreds or thousands of atoms held together by covalent bonds; they are often characterized by repeating units (i.e., they are polymers). Assemblies of these can likewise be biologic or non-biologic, though the MA term is more commonly applied in biology, and the term supramolecular assembly is more often applied in non-biologic contexts (e.g., in supramolecular chemistry and nanotechnology). MAs of macromolecules are held in their defined forms by non-covalent intermolecular interactions (rather than covalent bonds), and can be in either non-repeating structures (e.g., as in the ribosome and cell membrane architectures), or in repeating linear, circular, spiral, or other patterns (e.g., as in actin filaments and the flagellar motor). The process by which MAs are formed has been termed molecular self-assembly, a term especially applied in non-biologic contexts. Biomolecular complex, also called a biomacromolecular complex, is any biological complex made of more than one biopolymer (protein, RNA, DNA, carbohydrate) or large non-polymeric biomolecules (lipid). The interactions between these biomolecules are non-covalent.

Protein complex (multiprotein complex): group of two or more associated polypeptide chains; distinct from a multienzyme polypeptide, in which multiple catalytic domains are found in a single polypeptide chain. Many of the techniques used to enter cells and isolate proteins are inherently disruptive to such large complexes, complicating the task of determining the components of a complex. Obligate vs non-obligate protein complex; Transient vs permanent/stable protein complex; Fuzzy complex.

Protein dimer: macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers. A protein homodimer is formed by two identical proteins. A protein heterodimer is formed by two different proteins.

Tetrameric protein: protein with a quaternary structure of four subunits (tetrameric). Homotetramers have four identical subunits (such as glutathione S-transferase), and heterotetramers are complexes of different subunits. A tetramer can be assembled as dimer of dimers with two homodimer subunits (such as sorbitol dehydrogenase), or two heterodimer subunits (such as hemoglobin).

Protein trimer: macromolecular complex formed by three, usually non-covalently bound, macromolecules like proteins or nucleic acids. A homotrimer would be formed by three identical molecules. A heterotrimer would be formed by three different macromolecules. Type II Collagen is an example of homotrimeric protein.

Protein–protein interaction (PPI): two or more proteins bind together, often to carry out their biological function

Proteasome: the center for protein and peptide degradation:

20S: core of proteasome; lids: 19S (10-protein base and 9-protein lid); 11S

19S+20S=26S

11S+20S=PA28/REG (11S is induced by interferon gamma; responsible for the generation of peptides for MHC)

Anaphase-promoting complex (cyclosome; APC/C): E3 ubiquitin ligase that marks target cell cycle proteins for degradation by the 26S proteasome.

Nuclear pore complex (NPC)

Rhodopsin = Opsin + retinal

Cap binding complex (CBC): DE version has structures [12/02/09]

Origin recognition complex (ORC): multi-subunit DNA binding complex (6 subunits: ORC1-ORC6); binds in all eukaryotes to origins of replication in ATP-dependent manner. Serves as foundation for assembly of pre-replication complex (pre-RC; complex of Cdc6, Tah11 (aka Cdt1), Mcm2-Mcm7).

Cdc6 (Cell Division Cycle 6, in S. cerevisiae): essential regulator of DNA replication and plays important roles in the activation and maintenance of the checkpoint mechanisms in the cell cycle that coordinate S phase and mitosis. In humans: CDC6 (cell division control protein 6 homolog).

Segrosome: ensure accurate segregation (partitioning) of plasmids or chromosomes during bacterial cell division; "minimalist spindles".

SMC protein (Structural Maintenance of Chromosomes): large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics. Any relation between SMCs and segrosome?

Oxidative phosphorylation#Organization of complexes: "respirasomes"

Template:Hemeproteins

Globins: related family of proteins, which are thought to share a common ancestor.

Myoglobin: iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals.

Hemoglobin (Hb): iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates as well as the tissues of some invertebrates.

Hemocyanins: respiratory proteins in the form of metalloproteins containing two copper atoms that reversibly bind a single oxygen molecule.

Inositol trisphosphate receptor (InsP3R; IP₃R; type = 1,2,3): membrane glycoprotein complex acting as a Ca²⁺ channel activated by IP₃; very diverse among organisms, and is necessary for the control of cellular and physiological processes including cell division, cell proliferation, apoptosis, fertilization, development, behavior, learning and memory; strong evidence suggesting that IP₃R plays an important role in the conversion of external stimuli to intracellular Ca²⁺ signals characterized by complex patterns relative to both space and time; (e.g. Ca²⁺ waves and oscillations). Rat cerebellum IP₃R is type 1 (IP₃R1).

Ryanodine receptors (RyRs): form a class of intracellular calcium channels in various forms of excitable animal tissue like muscles and neurons; major cellular mediator of calcium-induced calcium release (CICR) in animal cells. In the muscle cells RyRs are in the membrane of sarcoplasmic reticulum. Similar to IP₃R. Small amount of Ca²⁺ in the cytosol near RyR will cause it to release even more Ca²⁺ (CICR).

Calcium-induced calcium release (CICR)

Calcium (Ca²⁺) sparks

Template:ATPase & ATPase (EC 3.6.1.3; adenylpyrophosphatase, ATP monophosphatase, triphosphatase..., ATP hydrolase...): cation(s) pump vs ATP. Cations: H⁺; Na⁺/K⁺; H⁺/K⁺; Ca⁺⁺; Mg⁺⁺; Cu⁺⁺.

ATP synthase (EC 3.6.3.14; TCDB 3.A.2 (F-type, V-type and A-type ATPase (sometimes just F-ATPase) superfamily))

F-ATPase: bacterial plasma membranes, in mitochondrial inner membranes, and in chloroplast thylakoid membranes. F₀ + F₁

V-ATPase: vacuoles and other intracellular organelles of eukaryotes and in bacteria. V₀ + V₁

A-ATPase: found in archaea.

E-ATPase: cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.

Inflammasome: cytosolic multiprotein oligomers of the innate immune system responsible for the activation of inflammatory responses. Activation and assembly of the inflammasome promotes proteolytic cleavage, maturation and secretion of pro-inflammatory cytokines interleukin 1β (IL-1β) and interleukin 18 (IL-18), as well as cleavage of gasdermin D. The N-terminal fragment resulting from this cleavage induces a pro-inflammatory form of programmed cell death distinct from apoptosis, referred to as pyroptosis, and is responsible for secretion of the mature cytokines, presumably through the formation of pores in the plasma membrane. Additionally, inflammasomes can be incorporated into larger cell death-inducing complexes called PANoptosomes, which drive another distinct form of pro-inflammatory cell death called PANoptosis.

Genetics

Category:Genetics

Category:Chromosomes

Category:Classical genetics

Category:Cytogenetics

Category:Genes

Category:Pseudogenes

Category:Genetic engineering

Category:Genetics techniques

Category:Gene delivery

Category:Genomics

Polycistronic operon

Regulatory sequence

Enhancer

/silencer

Operator

Promoter

5'UTR

ORF

UTR

3'UTR

Start

Stop

Terminator

Transcription

DNA

RBS

Protein coding region

mRNA

Translation

Protein

The structure of a prokaryotic operon of protein-coding genes. Regulatory sequence controls when expression occurs for the multiple protein coding regions (red). Promoter, operator and enhancer regions (yellow) regulate the transcription of the gene into an mRNA. The mRNA untranslated regions (blue) regulate translation into the final protein products.^[1]

Regulatory sequence

Enhancer

/silencer

Promoter

5'UTR

Open reading frame

3'UTR

Enhancer

/silencer

Proximal

Core

Start

Stop

Terminator

Transcription

DNA

Exon

Intron

Post-transcriptional
modification

Pre-
mRNA

Protein coding region

Translation

The structure of a eukaryotic protein-coding gene. Regulatory sequence controls when and where expression occurs for the protein coding region (red). Promoter and enhancer regions (yellow) regulate the transcription of the gene into a pre-mRNA which is modified to remove introns (light grey) and add a 5' cap and poly-A tail (dark grey). The mRNA 5' and 3' untranslated regions (blue) regulate translation into the final protein product.^[1]

Centromere: part of a chromosome that links sister chromatids or a dyad. During mitosis, spindle fibers attach to the centromere via the kinetochore. There are, broadly speaking, two types of centromeres. "Point centromeres" bind to specific proteins that recognise particular DNA sequences with high efficiency. Any piece of DNA with the point centromere DNA sequence on it will typically form a centromere if present in the appropriate species. The best characterised point centromeres are those of the budding yeast, Saccharomyces cerevisiae. "Regional centromeres" is the term coined to describe most centromeres, which typically form on regions of preferred DNA sequence, but which can form on other DNA (Deoxyribonucleic acid ) sequences as well. The signal for formation of a regional centromere appears to be epigenetic. Most organisms, ranging from the fission yeast Schizosaccharomyces pombe to humans, have regional centromeres. Positions: Metacentric; Submetacentric; Acrocentric; Telocentric.

Giemsa stain: named after German chemist and bacteriologist Gustav Giemsa, is used in cytogenetics and for the histopathological diagnosis of malaria and other parasites. Stain is specific for the phosphate groups of DNA.

G banding (G-banding, Giemsa banding): technique used in cytogenetics to produce a visible karyotype by staining condensed chromosomes. It is useful for identifying genetic diseases through the photographic representation of the entire chromosome complement. The metaphase chromosomes are treated with trypsin (to partially digest the chromosome) and stained with Giemsa stain. Heterochromatic regions, which tend to be rich with adenine and thymine (AT-rich) DNA and relatively gene-poor, stain more darkly in G-banding. In contrast, less condensed chromatin—which tends to be rich with guanine and cytosine (GC-rich) and more transcriptionally active—incorporates less Giemsa stain, and these regions appear as light bands in G-banding. The pattern of bands are numbered on each arm of the chromosome from the centromere to the telomere.This numbering system allows any band on the chromosome to be identified and described precisely. The less condensed the chromosomes are, the more bands that appear when G-banding. This means that the different chromosomes are more distinct in prophase than they are in metaphase.

Cytogenetics: branch of genetics that is concerned with how the chromosomes relate to cell behaviour, particularly to their behaviour during mitosis and meiosis. Techniques used include karyotyping, analysis of G-banded chromosomes, other cytogenetic banding techniques, as well as molecular cytogenetics such as FISH and CGH.

Nucleolus organizer region (NOR): chromosomal regions crucial for the formation of the nucleolus. In humans, the NORs are located on the short arms of the acrocentric chromosomes 13, 14, 15, 21 and 22, the genes RNR1, RNR2, RNR3, RNR4, and RNR5 respectively. The exact sequence of these regions is not included in the human reference genome as of 2016 or the GRCh38.p10 released 2017.01.06. However, it is known that NORs contain tandem copies of ribosomal DNA (rDNA) genes.

Gene Wiki: project that facilitates transferring information on human genes to Wikipedia article stubs with the goal of promoting collaboration and expansion of the articles.

Portal:Gene Wiki: dedicated to the goal of applying community intelligence to the annotation of gene and protein function. {http://genewikiplus.org/wiki/Main_Page} mirror of the Gene Wiki project on Wikipedia, running on top of the Semantic Mediawiki framework.

Wikipedia:WikiProject Molecular Biology/Genetics/Gene Wiki/Other Wikis

Zygosity: degree of similarity of the alleles for a trait in an organism. Most eukaryotes have two matching sets of chromosomes; that is, they are diploid. Diploid organisms have the same loci on each of their two sets of homologous chromosomes except that the sequences at these loci may differ between the two chromosomes in a matching pair and that a few chromosomes may be mismatched as part of a chromosomal sex-determination system. If both alleles of a diploid organism are the same, the organism is homozygous at that locus. If they are different, the organism is heterozygous at that locus. If one allele is missing, it is hemizygous, and, if both alleles are missing, it is nullizygous. Heterozygosity in population genetics.

Compound heterozygosity: condition of having two heterogeneous recessive alleles at a particular locus that can cause genetic disease in a heterozygous state. That is, an organism is a compound heterozygote when it has two recessive alleles for the same gene, but with those two alleles being different from each other (for example, both alleles might be mutated but at different locations). Compound heterozygosity reflects the diversity of the mutation base for many autosomal recessive genetic disorders; mutations in most disease-causing genes have arisen many times. This means that many cases of disease arise in individuals who have two unrelated alleles, who technically are heterozygotes, but both the alleles are defective. In its compound heterozygous forms, the disease may have lower penetrance, because the mutations involved are often less deleterious in combination than for a homozygous individual with the classic symptoms of the disease. As a result, compound heterozygotes often become ill later in life, with less severe symptoms.

Genome

Genome size: 1 pg = 978 Mb; 1991 Drake proposed a rule: that the mutation rate within a genome and its size were inversely correlated.

C-value: amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism; in polyploids the C-value may represent two or more genomes contained within the same nucleus.

C-value enigma (C-value paradox): observation that genome size does not correlate with organismal complexity.

List of sequenced eukaryotic genomes: all the eukaryotes known to have publicly available complete nuclear and organelle genome sequences that have been assembled, annotated and published; draft genomes are not included, nor are organelle-only sequences.

Whole genome sequencing (full genome sequencing, complete genome sequencing, entire genome sequencing): entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. Almost all truly complete genomes are of microbes; the term "full genome" is thus sometimes used loosely to mean "greater than 95%". The remainder of this article focuses on nearly complete human genomes. Cells used for sequencing: single cell genome sequencing

Synteny: in classical genetics, synteny describes the physical co-localization of genetic loci on the same chromosome within an individual or species. In current biology, synteny more commonly refers to colinearity, i.e. conservation of blocks of order within two sets of chromosomes that are being compared with each other. These blocks are referred to as syntenic blocks.

Repeated sequence (DNA) (repetitive elements, repeating units or repeats): patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. Repetitive DNA was first detected because of its rapid re-association kinetics. In many organisms, a significant fraction of the genomic DNA is highly repetitive, with over two-thirds of the sequence consisting of repetitive elements in humans. Main types: Tandem repeats: are copies which lie adjacent to each other, either directly or inverted (Satellite DNA - centromeres, heterochromatin; minisatellite); Interspersed repeats (aka. interspersed nuclear elements: transposable element, retrotransposons, SINEs, LINEs)

Satellite DNA: consists of very large arrays of tandemly repeating, non-coding DNA. Satellite DNA is the main component of functional centromeres, and form the main structural constituent of heterochromatin. The name "satellite DNA" refers to the phenomenon that repetitions of a short DNA sequence tend to produce a different frequency of the bases adenine, cytosine, guanine and thymine, and thus have a different density from bulk DNA such that they form a second or 'satellite' band when genomic DNA is separated on a density gradient.

Human satellite II: exceptionally high-copy but unexplored sequence of the human genome thought of as junk DNA has a surprising ability to impact master regulators of our genome, and it goes awry in 50 percent of tumors. Because HSAT-II DNA is normally methylated (a form of gene regulation), it remains dormant in healthy cells.

Phylogenetic tree shows the relationship between the best-documented instances of paleopolyploidy in eukaryotes.

Polyploid: containing more than two paired (homologous) sets of chromosomes; most eukaryotic species are diploid, meaning they have two sets of chromosomes — one set inherited from each parent, however polyploidy is found in some organisms and is especially common in plants.

Paleopolyploidy: result of genome duplications which occurred at least several mya; most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are currently considered diploids.

Gene–environment interaction (genotype–environment interaction, G×E)

Genomic imprinting: certain genes are expressed in a parent-of-origin-specific manner; inheritance process independent of the classical Mendelian inheritance. Forms of genomic imprinting have been demonstrated in insects, mammals and flowering plants. Epigenetic process that involves DNA methylation and histone methylation in order to achieve monoallelic gene expression without altering the genetic sequence; epigenetic marks are established in the germline and are maintained throughout all somatic cells of an organism. At least 80 imprinted genes in humans and mice, many of which are involved in embryonic and placental growth and development [~2005-2006]. Mouse: ~80% of imprinted genes are found in clusters such as these, called imprinted domains, suggesting a level of co-ordinated control [2001]. In the developing sperm (during spermatogenesis), a paternal imprint is established, whereas in developing oocytes (oogenesis), a maternal imprint is established. Majority of imprinted genes in mammals have been found to have roles in the control of embryonic growth and development, including development of the placenta. Beckwith–Wiedemann syndrome (BWS); Silver–Russell syndrome (SRS; Silver–Russell dwarfism; Russell–Silver syndrome (RSS)); Angelman syndrome (AS); Prader–Willi syndrome (P.W.S)

Experiments on Plant Hybridization (1865; de: Versuche über Pflanzen-Hybriden): by Mendel; result after years spent studying genetic traits in pea plants; Mendel discovered that one inheritable trait would invariably be dominant to its recessive alternative.

Gene nomenclature: scientific naming of genes, the units of heredity in living organisms; international committee published recommendations for genetic symbols and nomenclature in 1957. For many genes and their corresponding proteins, an assortment of alternate names is in use across the scientific literature and public biological databases, posing a challenge to effective organization and exchange of biological information.

Bacterial genetic nomenclature: standards were proposed in 1966 by Demerec et al. Each bacterial gene is denoted by a mnemonic of three lower case letters which indicate the pathway or process in which the gene-product is involved, followed by a capital letter signifying the actual gene; in some cases, the gene letter may be followed by an allele number; all letters and numbers are underlined or italicised.
Vertebrate gene and protein symbol conventions: HGNC is responsible for providing human gene naming guidelines and approving new, unique human gene names and symbols (short form abbreviations); research communities of vertebrate model organisms have adopted guidelines whereby genes in these species are given, whenever possible, the same names as their human orthologs. Human: italicised, with all letters in uppercase (e.g. SHH); proteins not italicised, first letter uppercase and the rest lowercase (e.g. Shh/SHH). Mouse and rat: similar to human (Shh and SHH). Chicken (Gallus sp.): the same as humans (SHH and SHH). Frog (Xenopus sp.): shh and Shh. Zebrafish: shh and Shh.

Genetic recombination: process by which two DNA molecules exchange genetic information, resulting in the production of a new combination of alleles

Homologous recombination: ype of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks.

Holliday junction: mobile junction between four strands of DNA; highly conserved structures, from prokaryotes to mammals.

Branch migration: ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous.

Homologous chromosome: set of one maternal chromosome and one paternal chromosome that pair up with each other inside a cell during meiosis; copies have the same genes in the same locations, or loci. Genetic recombination occurs during meiosis in cells containing these parental chromosomes, producing genotypes in the offspring that are new and different combinations of the parental alleles.

E. coli:

RecBCD: initiates recombinational repair from potentially lethal double strand breaks in DNA; both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA.

RecA (38 kDa): essential for the repair and maintenance of DNA; RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homologous DNA repair proteins.

Chi site: short stretch of DNA in the genome of a bacterium near which homologous recombination is more likely than expected to occur; Chi sequence serves as a signal to the RecBCD helicase-exonuclease that triggers a major change in the activities of this enzyme.

RuvABC: complex of three proteins that mediate branch migration and resolve the Holliday junction created during homologous recombination in bacteria; critical to bacterial DNA repair.

Pseudogene (shadow gene): segments of DNA that are related to real genes. Pseudogenes have lost at least some functionality, relative to the complete gene, in cellular gene expression or protein-coding ability. Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism, but can also be caused by genomic CNV where segments of 1+ kb are duplicated or deleted. Although not fully functional, pseudogenes may be functional, similar to other kinds of noncoding DNA, which can perform regulatory functions. The "pseudo" in "pseudogene" implies a variation in sequence relative to the parent coding gene, but does not necessarily indicate pseudo-function. Despite being non-coding, many pseudogenes have important roles in normal physiology and abnormal pathology.

Origin of replication: particular sequence in a genome at which replication is initiated.

ori (genetics): DNA sequence that signals for the origin of replication, sometimes referred to simply as origin. In E. coli, ori is some 250 nucleotides in length for the chromosomal origin (oriC). The plasmid ori sequences are similar to oriC, and are called oriV (origin of vegetative replication).

Fertility factor (bacteria): allows genes to be transferred from one bacterium carrying the factor to another bacterium lacking the factor by conjugation. Unlike other plasmids, F factor is constitutive for transfer proteins due to the gene traJ. The F plasmid belongs to a class of conjugative plasmids that control sexual functions of bacteria with a fertility inhibition (Fin) system.

Hfr cell (high-frequency recombination cell): bacterium with a conjugative plasmid (for example, the F-factor) integrated into its chromosomal DNA. The integration of the plasmid into the cell's chromosome is through homologous recombination. A conjugative plasmid capable of chromosome integration is also called an episome (a segment of DNA that can exist as a plasmid or become integrated into the chromosome). When conjugation occurs, Hfr cells are very efficient in delivering chromosomal genes of the cell into recipient F⁻ cells, which lack the episome.

Insertion sequence: short DNA sequence that acts as a simple transposable element. Insertion sequences have two major characteristics: they are small relative to other transposable elements (generally around 700 to 2500 bp in length) and only code for proteins implicated in the transposition activity (they are thus different from other transposons, which also carry accessory genes such as antibiotic resistance genes).

Mosaic (genetics) (mosaicism): presence of two or more populations of cells with different genotypes in one individual, who has developed from a single fertilized egg. Mosaicism has been reported to be present in as high as 70% of cleavage stage embryos and 90% of blastocyst-stage embryos derived from in vitro fertilization.

46, XX/46,XY: chimeric genetic disorder caused by having two distinct cell populations within the body. The chimerism arises in utero from the combination of an XX zygote and an XY zygote (which otherwise would have developed into twins) into a single embryo.

Trisomic rescue (trisomy zygote rescue): genetic phenomenon in which a fertilized ovum containing three copies of a chromosome loses one of these chromosomes to form a normal, diploid chromosome complement. If both of the retained chromosomes come from the same parent, then uniparental disomy results. The mechanism of trisomic rescue has been well confirmed in vivo, and alternative mechanisms that occur in trisomies are rare in comparison.

Chimera (genetics) (chimaera): single organism composed of cells with distinct genotypes. In animals, this means an individual derived from two or more zygotes, which can include possessing blood cells of different blood types, subtle variations in form (phenotype) and, if the zygotes were of differing sexes, then even the possession of both female and male sex organs (this is just one of many different ways that may result in intersexuality). Animal chimeras are produced by the merger of multiple fertilized eggs. Animals: Tetragametic chimerism; Microchimerism; Symbiotic chimerism in anglerfish; Germline chimerism (discovered that marmosets can carry the reproductive cells of their (fraternal) twin siblings, because of placental fusion during development. (Marmosets almost always give birth to fraternal twins)); Research; Mice: Underlying biology, Methods of production. Plants: Graft chimeras; Chromosomal chimeras; Nuclear gene-differential chimeras; Plastid gene-differential chimeras. Ethics and legislation.

Lydia Fairchild: USA woman who exhibits chimerism, in having two distinct populations of DNA among the cells of her body. She was pregnant with her third child when she and the father of her children, Jamie Townsend, separated. When Fairchild applied for enforcement of child support in 2002, providing DNA evidence of Townsend's paternity was a routine requirement. While the results showed Townsend to be certainly their father, they seemed to rule out her being their mother. Fairchild's case might also be caused by chimerism. As in Keegan's case, DNA samples were taken from members of the extended family. The DNA of Fairchild's children matched that of Fairchild's mother to the extent expected of a grandmother. They also found that, although the DNA in Fairchild's skin and hair did not match her children's, the DNA from a cervical smear test did match. Fairchild was carrying two different sets of DNA, the defining characteristic of chimerism.

Mobilome: entire set of mobile genetic elements in a genome. Mobilomes are found in eukaryotes, prokaryotes, and viruses. The compositions of mobilomes differ among lineages of life, with transposable elements being the major mobile elements in eukaryotes, and plasmids and prophages being the major types in prokaryotes. Virophages contribute to the viral mobilome.

Gene transfer agent (GTA): DNA-containing virus-like particles that are produced by some bacteria and archaea and mediate horizontal gene transfer. Different GTA types have originated independently from viruses in several bacterial and archaeal lineages. These cells produce GTA particles containing short segments of the DNA present in the cell. After the particles are released from the producer cell, they can attach to related cells and inject their DNA into the cytoplasm. The DNA can then become part of the recipient cells' genome.

Microchromosome: type of very small chromosome which is a typical component of the karyotype of birds, some reptiles, fish, and amphibians; they tend to] be absent in mammals. They are less than 20 Mb in size; chromosomes which are greater than 40 Mb in size are known as macrochromosomes, while those between 20 and 40 Mb are classified as intermediate chromosomes. Microchromosomes are characteristically very small and often cytogenetically indistinguishable in a karyotype. While originally thought to be insignificant fragments of chromosomes, in species where they have been studied they have been found to be rich in genes. In chickens, microchromosomes have been estimated to contain between 50 and 75% of all genes. The presence of microchromosomes makes ordering and identifying chromosomes into a coherent karyotype particularly difficult. During metaphase, they appear merely as 0.5-1.5 μm long specks. Their small size and poor condensation into heterochromatin means they generally lack the diagnostic banding patterns and distinct centromere locations used for chromosome identification.

Epistasis: phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dependent on the genetic background in which it appears. The concept of epistasis originated in genetics in 1907 but is now used in biochemistry, computational biology and evolutionary biology. It arises due to interactions, either between genes (such as mutations also being needed in regulators of gene expression) or within them (multiple mutations being needed before the gene loses function), leading to non-linear effects. Epistasis has a great influence on the shape of evolutionary landscapes, which leads to profound consequences for evolution and for the evolvability of phenotypic traits.

Gene delivery: process of introducing foreign genetic material, such as DNA or RNA, into host cells. Gene delivery must reach the genome of the host cell to induce gene expression. Successful gene delivery requires the foreign gene delivery to remain stable within the host cell and can either integrate into the genome or replicate independently of it. Methods: When genes are delivered to bacteria or plants the process is called transformation and when it is used to deliver genes to animals it is called transfection. This is because transformation has a different meaning in relation to animals, indicating progression to a cancerous state. Chemical: Heat shock; Calcium phosphate; Liposomes and polymers; Nanoparticles. Physical: Electroporation; Biolistics; Microinjection; Sonoporation; Photoporation (laser pulses are used to create pores in a cell membrane); Magnetofection; Hydroporation. Agrobacterium (plants). Viral delivery: RNA-based viral vectors; DNA-based viral vectors.

Transfection: process of deliberately introducing naked or purified nucleic acids into eukaryotic cells. It may also refer to other methods and cell types, although other terms are often preferred: "transformation" is typically used to describe non-viral DNA transfer in bacteria and non-animal eukaryotic cells, including plant cells. In animal cells, transfection is the preferred term as transformation is also used to refer to progression to a cancerous state (carcinogenesis) in these cells. Transduction is often used to describe virus-mediated gene transfer into eukaryotic cells. he word transfection is a portmanteau of trans- and infection. Methods: Physical methods; Chemical methods: calcium phosphate, cationic polymers, Lipofection, Fugene, Dendrimer; Viral methods. Stable and transient transfection. RNA transfection: Endogenous vs. exogenous long RNA; Repeated long-RNA transfection.

Transduction (genetics): process by which foreign DNA is introduced into a cell by a virus or viral vector. An example is the viral transfer of DNA from one bacterium to another and hence an example of horizontal gene transfer.

Statistical genetics

Category:Statistical genetics

Genetic linkage: tendency of alleles that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked. This distance is expressed in terms of a genetic map unit (m.u.), or a centimorgan and is defined as the distance between genes for which one product of meiosis in 100 is recombinant. A recombinant frequency (RF) of 1% is equivalent to 1 m.u.

Imputation (genetics): statistical inference of unobserved genotypes. It is achieved by using known haplotypes in a population, for instance from the HapMap or the 1000 Genomes Project in humans, thereby allowing to test initially-untyped genetic variants for association with a trait of interest.

Gametic phase: represents the original allelic combinations that an individual received from its parents.

Identity by descent: DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is 'identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment.

Genetic architecture: underlying genetic basis of a phenotypic trait and its variational properties. Phenotypic variation for quantitative traits is, at the most basic level, the result of the segregation of alleles at QTLs; broad term that can be described for any given individual based on information regarding gene and allele number, the distribution of allelic and mutational effects, and patterns of pleiotropy, dominance, and epistasis.

Quantitative trait locus (QTL) is a section of DNA (the locus) that correlates with variation in a phenotype (the quantitative trait); linked to, or contains, the genes that control that phenotype. QTLs are mapped by identifying which molecular markers (such as SNPs or AFLPs) correlate with an observed trait. This is often an early step in identifying and sequencing the actual genes that cause the trait variation. QTLs are often found on different chromosomes. Knowing the number of QTLs that explains variation in the phenotypic trait tells us about the genetic architecture of a trait.

Expression quantitative trait loci (eQTL): genomic loci that contribute to variation in expression levels of mRNAs.

Genome-wide association study (GWAS): examination of many common genetic variants in different individuals to see if any variant is associated with a trait; this approach is known as phenotype-first, in which the participants are classified first by their clinical manifestation(s), as opposed to genotype-first. If one type of the variant (one allele) is more frequent in people with the disease, the variant is said to be associated with the disease. In contrast to methods that specifically test one or a few genetic regions, the GWA studies investigate the entire genome. After odds ratios and P-values have been calculated for all SNPs, a common approach is to create a Manhattan plot. In the context of GWA studies, this plot shows the negative logarithm of the P-value as a function of genomic location. Thus the SNPs with the most significant association stands out on the plot, usually as stacks of points because of haploblock structure. Rapidly decreasing price of complete genome sequencing have also provided a realistic alternative to genotyping array-based GWA studies; it can be discussed if the use of this new technique is still referred to as a GWA study, but high-throughput sequencing does have potential to side-step some of the shortcomings of non-sequencing GWA.

Epigenetics

Category:Epigenetics

Transgenerational epigenetic inheritance: transmission of information from one generation of an organism to the next (i.e., parent–child transmission) that affects the traits of offspring without alteration of the primary structure of DNA (i.e., the sequence of nucleotides)—in other words, epigenetically.

Dutch famine of 1944: children of pregnant women exposed to famine were more susceptible to diabetes, obesity, cardiovascular disease, microalbuminuria...; children of the women who were pregnant during the famine were smaller, as expected. However, surprisingly, when these children grew up and had children those children were also smaller than average. These data suggested that the famine experienced by the mothers caused some kind of epigenetic changes that were passed down to the next generation.

Överkalix study: study conducted on the physiological effects of various environmental factors on transgenerational epigenetic inheritance. The study was conducted utilizing historical records, including harvests and food prices, in Överkalix, a small isolated municipality in northeast Sweden. The study was of 303 probands, 164 men and 139 women, born in 1890, 1905, or 1920, and their 1,818 children and grandchildren. 44 were still alive in 1995 when mortality follow-up stopped. Mortality risk ratios (RR) on children and grandchildren were determined based on available food supply, as indicated by historical data. The paternal grandfather's food supply was only linked to the mortality RR of grandsons and not granddaughters. The paternal grandmother's food supply was only associated with the granddaughters' mortality risk ratio.

CpG site: regions of DNA where a cytosine nucleotide occurs next to a guanine nucleotide in the linear sequence of bases along its length. "CpG" is shorthand for "—C—phosphate—G—", that is, cytosine and guanine separated by only one phosphate; phosphate links any two nucleosides together in DNA. The "CpG" notation is used to distinguish this linear sequence from the CG base-pairing of cytosine and guanine. CpG islands (or CG islands) are regions with a high frequency of CpG sites, though objective definitions for CpG islands are limited. The usual formal definition of a CpG island is a region with at least 200 bp, and a GC percentage that is greater than 50 %, and with an observed-to-expected CpG ratio that is greater than 60 %.

Epigenetic clock: biochemical test that can be used to measure age. The test is based on DNA methylation levels, measuring the accumulation of methyl groups to one's DNA molecules. Lifestyle factors: In general, lifestyle factors have only weak associations with epigenetic age acceleration in blood. Cerebellum ages slowly: It has been difficult to identify tissues that seem to evade aging due to the lack of biomarkers of tissue age that allow one to contrast compare the ages of different tissues. An application of epigenetic clock to 30 anatomic sites from six centenarians and younger subjects revealed that the cerebellum ages slowly: it is about 15 years younger than expected in a centenarian. Centenarians age slowly: The offspring of semi-supercentenarians (subjects who reached an age of 105–109 years) have a lower epigenetic age than age-matched controls (age difference = 5.1 years in blood) and centenarians are younger (8.6 years) than expected based on their chronological age. HIV infection: Infection with HIV-1 is associated with clinical symptoms of accelerated aging, as evidenced by increased incidence and diversity of age-related illnesses at relatively young ages. Menopause accelerates epigenetic aging: First, early menopause has been found to be associated with an increased epigenetic age acceleration of blood. Second, surgical menopause (due to bilateral oophorectomy) is associated with epigenetic age acceleration in blood and saliva. Progeria: associated with epigenetic age acceleration in blood.

Transcription factors

Category:Transcription factors

Category:Forkhead transcription factors

FOX proteins (Forkhead box): family of transcription factors that play important roles in regulating the expression of genes involved in cell growth, proliferation, differentiation, and longevity. Many FOX proteins are important to embryonic development. Founding member and namesake of the FOX family is the fork head transcription factor in Drosophila, discovered by Detlef Weigel and Herbert Jäckle.

Fork head domain: 80-100 aa; binds DNA; "winged helix".

FOXP1

FOXP2 (Forkhead box protein P2, encoded by FOXP2 gene): FOXP2 is found in many vertebrates, where it plays an important role in mimicry in birds (such as birdsong) and echolocation in bats. FOXP2 is also required for the proper development of speech and language in humans. In humans, mutations in FOXP2 cause the severe speech and language disorder developmental verbal dyspraxia. Studies of the gene in mice and songbirds indicate that it is necessary for vocal imitation and the related motor learning. Outside the brain, FOXP2 has also been implicated in development of other tissues such as the lung and digestive system. Evolution: FOXP2 gene is highly conserved in mammals. Human gene differs from non-human primates by the substitution of two amino acids: T303N, N325S. In mice it differs from that of humans by three substitutions, and in zebra finch by seven amino acids. One of the two amino acid difference between human and chimps also arose independently in carnivores and bats. Similar FOXP2 proteins can be found in songbirds, fish, and reptiles such as alligators. Insertion of both human mutations into mice, whose version of FOXP2 otherwise differs from the human and chimpanzee versions in only one additional base pair, causes changes in vocalizations as well as other behavioral changes, such as a reduction in exploratory tendencies. A reduction in dopamine levels and changes in the morphology of certain nerve cells are also observed. However, FOXP2 is extremely diverse in echolocating bats. Twenty-two sequences of non-bat eutherian mammals revealed a total number of 20 nonsynonymous mutations in contrast to half that number of bat sequences, which showed 44 nonsynonymous mutations. Interestingly, all cetaceans share three amino acid substitutions, but there are not differences between echolocating and non-echolocating baleen cetaceans.

Population genetics

Category:Population genetics

Topics in population genetics (Template:Popgen):

Founder effect

Genetic history of Europe: since the Upper Paleolithic is inseparable from that of wider Western Eurasia. By about 50 ka a basal West Eurasian lineage had emerged (alongside a separate East Asian lineage) out of the undifferentiated "non-African" lineage of 70 ka. The basal Western Eurasians were early exposed to significant Neanderthal admixture. Introgression of Neanderthal traits persisted in European populations into the present, affecting traits such as skin tone and hair color, height, sleeping patterns and mood. European early modern humans; West European Hunter-Gatherer; Early European Farmers; Ancient North Eurasian.

Human genetics

Category:Human genetics

Category:Genome projects

Category:Human genome projects

Category:Medical genetics

Category:Genetic epidemiology

{q.v.:

#Human evolution, extinct and extant "cousins"

}

Human chromosomes (Template:Chromosomes)

Pseudoautosomal region (PAR1, PAR2): homologous sequences of nucleotides on the X and Y chromosomes. The pseudoautosomal regions get their name because any genes within them (so far at least 29 have been found) are inherited just like any autosomal genes. PAR1 comprises 2.6 Mbp of the short-arm tips of both X and Y chromosomes in humans and great apes (X and Y are 155 Mbp and 59 Mbp in total). PAR2 is at the tips of the long arms, spanning 320 kbp. Normal male mammals have two copies of these genes: one in the pseudoautosomal region of their Y chromosome, the other in the corresponding portion of their X chromosome. Normal females also possess two copies of pseudoautosomal genes, as each of their two X chromosomes contains a pseudoautosomal region. Crossing over between the X and Y chromosomes is normally restricted to the pseudoautosomal regions; thus, pseudoautosomal genes exhibit an autosomal, rather than sex-linked, pattern of inheritance. So, females can inherit an allele originally present on the Y chromosome of their father.

Chromosome 2 (human) (8% of total DNA): all members of Hominidae except humans, Neanderthals, and Denisovans have 24 pairs of chromosomes. Humans have only 23 pairs of chromosomes. Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes.

Human genome: complete set of nucleic acid sequence for humans (Homo sapiens), encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization creates a zygote) consist of three billion DNA base pairs, while diploid genomes (found in somatic cells) have twice the DNA content. While there are significant differences among the genomes of human individuals (on the order of 0.1%), these are considerably smaller than the differences between humans and their closest living relatives, the chimpanzees (approximately 4%) and bonobos. There are an estimated 20,000-25,000 human protein-coding genes (about 1.5% of whole genome), the rest is associated with non-coding RNA, regulatory DNA sequences, LINEs, SINEs, introns, and noncoding DNA (no function yet found). Size of protein-coding genes: median size of an exon is 122 bp (mean = 145 bp), the median number of exons is 7 (mean = 8.8), and the median coding sequence encodes 367 amino acids (mean = 447 amino acids). Human reference genome (HRG).

HRG is haploid sequence. Each chromosome is represented once.
The HRG is composite sequence, and does not correspond to any actual human individual.
The HRG is periodically updated to correct errors and ambiguities.
The HRG in no way represents an "ideal" or "perfect" human individual. HRG is simply a standardized representation or model that is used for comparative purposes.

Reference genome: digital nucleic acid sequence database, assembled by scientists as a representative example of a species' set of genes. As they are often assembled from the sequencing of DNA from a number of donors, reference genomes do not accurately represent the set of genes of any single person. Instead a reference provides a haploid mosaic of different DNA sequences from each donor.

DNA annotation (genome annotation): process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. An annotation (irrespective of the context) is a note added by way of explanation or commentary. Once a genome is sequenced, it needs to be annotated to make sense of it. For DNA annotation, a previously unknown sequence representation of genetic material is enriched with information relating genomic position to intron-exon boundaries, regulatory sequences, repeats, gene names and protein products. This annotation is stored in genomic databases such as Mouse Genome Informatics, FlyBase, and WormBase. {q.v. Ensembl, Vega, ENCODE, Gene Ontology}

Human evolutionary genetics: Speciation of humans and the African apes. Genetic differences between humans and other great apes: Gene loss (80 genes were lost in the human lineage after separation from the last common ancestor with the chimpanzee. 36 of those were for olfactory receptors. Genes involved in chemoreception and immune response are overrepresented.); Hair keratin gene KRTHAP1 (loss of that particular gene may have caused the thinning of human body hair); Myosin gene MYH16 (mutation that led to the inactivation (a two base pair deletion) occurred 2.4 mya → marked by a strong increase in cranial capacity). Genetic differences between modern humans and Neanderthals. Sequence divergence between humans and apes.

Human accelerated regions (HARs): set of 49 segments of the human genome that are conserved throughout vertebrate evolution but are strikingly different in humans; named according to their degree of difference between humans and chimpanzees (HAR1 showing the largest degree of human-chimpanzee differences). Several of the HARs encompass genes known to produce proteins important in neurodevelopment. HAR1 sequence is found (and conserved) in chickens and chimpanzees but is not present in fish or frogs that have been studied. HAR2 includes HACNS1 a gene enhancer "that may have contributed to the evolution of the uniquely opposable human thumb, and possibly also modifications in the ankle or foot that allow humans to walk on two legs"; of the 110,000 gene enhancer sequences identified in the human genome, HACNS1 has undergone the most change during the evolution of humans following the split with the ancestors of chimpanzees.

Ultra-conserved element (UCE): region of DNA that is identical in at least two different species

UCbase: 100% identity among human, mouse and rat = 481 UCEs have been identified in the human genome longer than 200 nt

Template:Human genetics:

Race and genetics: relationship between race and genetics is relevant to the controversy concerning race classification. In everyday life, many societies classify populations into groups based on phenotypical traits and impressions of probable geographic ancestry and cultural identity—these are the groups usually called "races" in countries like USA, Brazil, and South Africa. Patterns of variation of human genetic traits are generally clinal, with more abrupt shifts at places where steady gene flow is interrupted.

Human genetic enhancement

Wikipedia:Articles for deletion/Human genetic clustering (Human genetic clustering): del?{~85% of genetic variation is found within groups, ~6–10% between groups within the same continent and ~6–10% is found between continental groups (e.g. Human Genome Project states: "two random individuals from any one group are almost as different [genetically] as any two random individuals from the entire world.", 85% vs 15%). The more markers are used the better one can cluster the individuals into "subgroups", but these "subgroups" depend a bit on the classification/clustering methods used. Heavy statistics and models.}

Human Genetic Diversity: Lewontin's Fallacy

Human genetic variation: genetic differences both within and among populations. There may be multiple variants of any given gene in the human population (genes), leading to polymorphism. Many genes are not polymorphic, meaning that only a single allele is present in the population: the gene is then said to be fixed. On average, in terms of DNA sequence all humans are 99.5% similar to any other humans. SNPs, Structural variation, Copy number variation, ...

Human geneology:

Human Y-chromosome DNA haplogroup: male line (father to son), so the longer ago in history, the smaller the portion of contribution (besides Y chromosome, which has its own doubts), i.e. 1/2 for father, 1/4 for paternal grandfather, for 10 generations back,

({\frac {1}{2}})^{10}

Template:Y-chromosome haplogroups by populations:

Y-DNA haplogroups in European populations

Category:Genetic genealogy projects

Human Genome Diversity Project (HGDP): was started by Stanford University's Morrison Institute and a collaboration of scientists around the world; many years of work by Luigi Cavalli-Sforza. Some NGOs, human rights organizations, indigenious communities objected to the project; concern about misuse of the gathered data (also: insurance and genetic sequencing).

Genographic Project: Indigenous Peoples Council on Biocolonialism (IPCB) protested against the project because of the connections with HGDP

List of haplogroups of historical and famous figures

Template:Human group differences

HCONDELs: regions of deletions within the human genome containing sequences that are highly conserved among closely related relatives. Almost all of these deletions fall within regions that perform non-coding functions. These represent a new class of regulatory sequences and may have played an important role in the development of specific traits and behavior that distinguish closely related organisms from each other. Nomenclature: The group of CONDELs of a specific organism is specified by prefixing the CONDELs with the first letter of the organism. For instance, hCONDELs refer to the group of CONDELs found in humans whereas mCONDELs and cCONDELs refer to mouse and chimpanzee CONDELs respectively. Impact in humans: Sialic acid loss (92 bp); Loss of whiskers and penile spine (60.7kb); Expansion of brain size (3,181 bp).

Copy-number variation (CNV): phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals in the human population. Copy number variation is a type of structural variation: specifically, it is a type of duplication or deletion event that affects a considerable number of base pairs. Recent research indicates that approximately two thirds of the entire human genome is composed of repeats and 4.8-9.5% of the human genome can be classified as copy number variations. In mammals, copy number variations play an important role in generating necessary variation in the population as well as disease phenotype.

Genetic studies on Jews

HERC2: mutation in the HERC2 gene adjacent to OCA2, affecting OCA2's expression in the human iris, is found common to nearly all people with blue eyes. It has been hypothesized that all blue eyed humans share a single common ancestor with whom the mutation originated.

Sequencing and interpretation, genomes, human genomes

Category:DNA sequencing

Category:Repetitive DNA sequences

Gene mapping: describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. Genetic maps' distances are based on the genetic linkage information, while physical maps use actual physical distances usually measured in number of base pairs. Genetic distance to physical distance ratio varies greatly at different genomic regions which reflects different recombination rates, and such rate is often indicative of euchromatic (usually gene-rich) vs heterochromatic (usually gene poor) regions of the genome. Genome sequencing: while the scope, purpose and process are totally different, a genome assembly can be viewed as the "ultimate" form of physical map, in that it provides in a much better way all the information that a traditional physical map can offer.

Shotgun sequencing: method used for sequencing long DNA strands. It is named by analogy with the rapidly expanding, quasi-random firing pattern of a shotgun. "Sanger sequencing" can only be used for fairly short strands of 100 to 1000 base pairs. In shotgun sequencing, DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method to obtain reads. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Broader application benefited from pairwise end sequencing, known colloquially as double-barrel shotgun sequencing. As sequencing projects began to take on longer and more complicated DNA sequences, multiple groups began to realize that useful information could be obtained by sequencing both ends of a fragment of DNA. Although sequencing both ends of the same fragment and keeping track of the paired data was more cumbersome than sequencing a single end of two distinct fragments, the knowledge that the two sequences were oriented in opposite directions and were about the length of a fragment apart from each other was valuable in reconstructing the sequence of the original target fragment. The classical shotgun sequencing was based on the Sanger sequencing method: this was the most advanced technique for sequencing genomes from about 1995–2005. The shotgun strategy is still applied today, however using NGS. These technologies produce shorter reads (anywhere from 25–500bp) but many hundreds of thousands or millions of reads in a relatively short time (on the order of a day). This results in high coverage, but the assembly process is much more computationally intensive. These technologies are vastly superior to Sanger sequencing due to the high volume of data and the relatively short time it takes to sequence a whole genome.

Human Genome Organisation (HUGO): Human Genome Project (HGP); HGNC is the hugest subgroup of HUGO (bio nomenclature).

Knome: sells human whole genome and exome (exons) analysis and sequencing services to researchers and consumers.

1000 Genomes Project (launched 2008.01): international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists plan to sequence the genomes of at least 1000 anonymous participants from a number of different ethnic groups till 2012[???], using newly developed technologies which are faster and less expensive. In 2015, two papers in Nature reported results and the completion of the project and opportunities for future research. Many rare variations, restricted to closely related groups, were identified, and eight structural-variation classes were analyzed. UK (Wellcome Trust Sanger Institute), PRC (Beijing Genomics Institute, Shenzhen), USA (NHGRI).

Personal Genome Project: long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personalized medicine.

Single cell sequencing: examines the sequence information from individual cells with optimized next generation sequencing (NGS) technologies, providing a higher resolution of cellular differences and a better understanding of the function of an individual cell in the context of its microenvironment. Typical human cell consists of about 6 billion base pairs of DNA, 600 million bases of mRNA and ?? non-coding RNA. The minimal amount of starting materials from a single cell make degradation, sample loss and contamination exert pronounced effects on quality of sequencing data. In addition, due to the picogram level of the amount of nucleic acids used, heavy amplification is often needed during sample preparation of single cell sequencing, resulting in the uneven coverage, noise and inaccurate quantification of sequencing data. Single cell genome (DNA) sequencing. Single cell DNA methylome sequencing. Single-cell RNA sequencing (scRNA-seq).

Hendrikje van Andel-Schipper#Genome: senility research; old-age disease research (cardiovascular; various dementias)

Beijing Genomics Institute (BGI): one of the world’s premier genome sequencing centers

ENCODE (Encyclopedia of DNA Elements): public research project launched by the US National Human Genome Research Institute (NHGRI) in September 2003. Intended as a follow-up to the Human Genome Project, the ENCODE project aims to identify all functional elements in the human genome. For use in the ENCODE pilot project, defined regions of the human genome - corresponding to 30Mb, roughly 1% of the total human genome - were selected. These regions served as the foundation on which to test and evaluate the effectiveness and efficiency of a diverse set of methods and technologies for finding various functional elements in human DNA. Prior to embarking upon the target selection, it was decided that 50% of the 30Mb of sequence would be selected manually while the remaining sequence would be selected randomly. The two main criteria for manually selected regions were: 1) the presence of well-studied genes or other known sequence elements, and 2) the existence of a substantial amount of comparative sequence data. A total of 14.82Mb of sequence was manually selected using this approach, consisting of 14 targets that range in size from 500kb to 2Mb.

SNPedia: wiki-based bioinformatics web site that serves as a database of SNPs. Each article on a SNP provides a short description, links to scientific articles and personal genomics web sites, as well as microarray information about that SNP. Thus SNPedia may support the interpretation of results of personal genotyping from, e.g., 23andMe and similar companies. An associated computer program called Promethease, also developed by the SNPedia team, allows users to compare personal genetics results against the SNPedia database, generating a report with information about a person's attributes, such as propensity to diseases, based on the presence of specific SNPs within their genome. In May 2008 Cariaso, using Promethease, won an online contest sponsored by 23andMe to determine as much information as possible about an anonymous woman based only on her genome. Cariaso won in all three categories of "accuracy, creativity and cleverness". In 2009, the anonymous woman ("Lilly Mendel") was revealed to be 23andMe co-founder Linda Avey, allowing a direct comparison between her actual traits and those predicted by Promethease a year earlier.

DbSNP (Single Nucleotide Polymorphism Database): free public archive for genetic variation within and across different species developed and hosted by NCBI in collaboration with the National Human Genome Research Institute (NHGRI). Although the name of the database implies a collection of one class of polymorphisms only (i.e., single nucleotide polymorphisms (SNPs)), it in fact contains a range of molecular variation: (1) SNPs, (2) short deletion and insertion polymorphisms (indels/DIPs), (3) microsatellite markers or short tandem repeats (STRs), (4) multinucleotide polymorphisms (MNPs), (5) heterozygous sequences, and (6) named variants.

Retrotransposon: (transposons via RNA intermediates): genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are one of the two subclasses of transposon, where the other is DNA transposon, which does not involve an RNA intermediate. They are particularly abundant in plants, where they are often a principal component of nuclear DNA. In maize, 49–78% of the genome is made up of retrotransposons. In wheat, about 90% of the genome consists of repeated sequences and 68% of transposable elements. In mammals, almost half the genome (45% to 48%) is transposons or remnants of transposons. Around 42% of the human genome is made up of retrotransposons, while DNA transposons account for about 2–3%.

LTR retrotransposons:

Long terminal repeat (LTR): dentical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA.

Non-LTR retrotransposons:

Long interspersed nuclear element (LINE): group of non-LTR retrotransposons which are widespread in the genome of many eukaryotes. They make up around 20% of the human genome. LINEs make up a family of transposons, where each LINE is about 7000 bp long.

SINEs: Short Interspersed Nuclear Elements are short DNA sequences (<500 bases) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into transfer RNA, 5S ribosomal RNA, and other small nuclear RNAs. The mechanism of retrotransposition of these elements is more complicated than LINEs, and less dependent solely on the actual elements that they encode. SINEs do not encode a functional reverse transcriptase protein and rely on other mobile elements for transposition. In some cases they may have their own endonuclease that will allow them to cleave their way into the genome, but the majority of SINEs integrate at chromosomal breaks by using random DNA breaks to prime reverse transcriptase. With about 1,500,000 copies, SINEs make up about 11% of the human genome.

Alu element: short stretch of DNA originally characterized by the action of the Alu (Arthrobacter luteus) restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant transposable elements in the human genome. They are derived from the small cytoplasmic 7SL RNA, a component of the signal recognition particle. The event, when a copy of the 7SL RNA became a precursor of the Alu elements, took place in the genome of an ancestor of Supraprimates. There are over one million Alu elements interspersed throughout the human genome, and it is estimated that about 10.7% of the human genome consists of Alu sequences.

Variable number tandem repeat (VNTR): location in a genome where a short nucleotide sequence is organized as a tandem repeat. These can be found on many chromosomes, and often show variations in length between individuals.

Minisatellite: tract of repetitive DNA in which certain DNA motifs (ranging in length from 10–60 base pairs) are typically repeated 5-50 times.

Microsatellite: tract of repetitive DNA in which certain DNA motifs (ranging in length from 2–5 base pairs) are repeated, typically 5–50 times.

Geneology, kinship

Category:Kinship and descent

Category:Genealogy

Category:Incest

Coefficient of relationship: measure of the degree of consanguinity (or biological relationship) between two individuals. The term coefficient of relationship was defined by Sewall Wright in 1922, and was derived from his definition of the coefficient of inbreeding of 1921. The measure is most commonly used in genetics and genealogy. A coefficient of inbreeding can be calculated for an individual, and is typically one-half the coefficient of relationship between the parents.

Consanguinity: property of being from the same kinship as another person. In that aspect, consanguinity is the quality of being descended from the same ancestor as another person. The laws of many jurisdictions set out degrees of consanguinity in relation to prohibited sexual relations and marriage parties. Such rules are also used to determine heirs of an estate according to statutes that govern intestate succession, which vary from jurisdiction to jurisdiction. In some places and times, cousin marriage is approved and expected; in others, it is as taboo as incest.

Sequencing DNA, RNA

DNA sequencing:

gel (microfluidic: :Sanger method and its comparison to other methods in 2009 Feb.)

Polony sequencing

454 pyrosequencing

Illumina (Solexa) sequencing

Combinatorial probe anchor synthesis (cPAS)

SOLiD sequencing

Ion Torrent semiconductor sequencing: detection of hydrogen ions that are released during the polymerization of DNA. Released Feb., 2010.

DNA nanoball sequencing

Heliscope single molecule sequencing

Single molecule real time (SMRT) sequencing

Nanopore DNA sequencing

DNA fragmentation: separation or breaking of DNA strands into pieces. Men with sperm motility defects often have high levels of sperm DNA fragmentation. Intentional: Restriction digest; Acoustic shearing; Nebulization forces DNA through a small hole in a nebulizer unit, which results in the formation of a fine mist that is collected; Sonication; Point-sink shearing, a type of hydrodynamic shearing, uses a syringe pump to create hydrodynamic shear forces by pushing a DNA library through a small abrupt contraction; Needle shearing creates shearing forces by passing DNA libraries through small gauge needle; French pressure cells pass DNA through a narrow valve under high pressure to create high shearing forces; Transposome mediated fragmentation (tagmentation). Spontaneous: Apoptotic DNA fragmentation

RNA

{q.v. #Bioinformatics}

Wikipedia:WikiProject RNA

Wikipedia:Wikiproject RNA/external links: number of good databases for RNA that might be consulted for further information: Rfam, The noncoding RNA database, RNAdb: mammalian noncoding RNA database, fRNAdb: functional RNA database, miRBase: microRNA database, methylation guide snoRNA database, snoRNAbase: human H/ACA and C/D box snoRNA database, tRNA database, tmRDB: database of tmRNA sequences, ...

{q.v.

#RNA containing complexes
#RNA processing

}

Circular RNA (circRNA): type of single-stranded RNA which, unlike linear RNA, forms a covalently closed continuous loop. In circular RNA, the 3' and 5' ends normally present in an RNA molecule have been joined together. Many types of circular RNA arise from otherwise protein-coding genes. Some circular RNA have been shown to code for proteins. Some types of circular RNA have also recently shown potential as gene regulators. The biological function of most circular RNA is unclear. Because circular RNA do not have 5' or 3' ends, they are resistant to exonuclease-mediated degradation and are presumably more stable than most linear RNA in cells. Circular RNA has been linked to some diseases such as cancer. RNA splicing. Alternative splicing. Non-canonical splicing: Exon scrambling: exons are spliced in a "non-canonical" (atypical) order: 1. Tandem exon duplication; 2. Trans-splicing, in which two RNA transcripts fuse; 3. A splice donor site being joined to a splice acceptor site further upstream in the primary transcript, yielding a circular transcript. Alu elements impact circRNA splicing. Impact of RNA editing on circRNA formation. Characteristics of circular RNA: Early discoveries of circular RNAs led to the belief that they lacked significance due to their rarity; Genome-wide identification of circRNAs: Scrambled isoforms and circRNAs, Discovery of a higher abundance of circRNAs, CircRNAs tissue specificity and antagonist activity, CircRNAs and ENCODE Ribozero RNA-seq data, Genome-wide calling of circRNA in Alzheimer disease cases; Classes of CircRNA; Length of circRNAs: human circRNAs revealed that these molecules are usually composed of 1–5 exons; Location of circRNAs in the cell: predominantly found in the cytoplasm, where the number of circular RNA transcripts derived from a gene can be up to ten times greater than the number of associated linear RNAs generated from that locus; CircRNAs are more stable than linear RNAs. Plausible functions of circular RNA: Evolutionary conservation of circularization mechanisms and signals; CDR1as/CiRS-7 as a miR-7 sponge; Circular intronic long non-coding RNAs (ciRNAs). Circular RNA and disease: Circular RNAs play a role in Alzheimer disease pathogenesis. Viroids as circular RNAs.

Gender, sex, reproductive biology

Category:Sex

Category:Sex-determination systems

Category:Reproduction

Category:Sexual reproduction

Category:Mating

Category:Sexual selection

Category:Fertility

{q.v. #Human reproduction and reproductive organs}

Sex-determination system: biological system that determines the development of sexual characteristics in an organism. Most organisms that create their offspring using sexual reproduction have two sexes. In some species there are hermaphrodites. There are also some species that are only one sex due to parthenogenesis, the act of a female reproducing without fertilization. In many species, sex determination is genetic: males and females have different alleles or even different genes that specify their sexual morphology. In animals this is often accompanied by chromosomal differences, generally through combinations of XY, ZW, XO, ZO chromosomes, or haplodiploidy. The sexual differentiation is generally triggered by a main gene (a "sex locus"), with a multitude of other genes following in a domino effect. In other cases, sex of a fetus is determined by environmental variables (such as temperature). The details of some sex-determination systems are not yet fully understood. Some species such as various plants and fish do not have a fixed sex, and instead go through life cycles and change sex based on genetic cues during corresponding life stages of their type. This could be due to environmental factors such as seasons and temperature. In some gonochoric species, a few individuals may have sex characteristics of both sexes, a condition called intersex. Evolution: Origin of sex chromosomes: The accepted hypothesis of XY and ZW sex chromosome evolution is that they evolved at the same time, in two different branches.

XY sex-determination system: used to classify many mammals, including humans, some insects (Drosophila), some snakes, some fish (guppies), and some plants (Ginkgo tree). In this system, the sex of an individual is determined by a pair of sex chromosomes. Females have two of the same kind of sex chromosome (XX), and are called the homogametic sex. Males have two different kinds of sex chromosomes (XY), and are called the heterogametic sex. In humans, the presence of the Y chromosome is responsible for triggering male development; in the absence of the Y chromosome, the fetus will undergo female development. More specifically, it is the SRY gene located on the Y chromosome that is of importance to male differentiation. In most species with XY sex determination, an organism must have at least one X chromosome in order to survive.

X0 sex-determination system: determines the sex of offspring among: most arachnids with the exception of mites where a small majority are haplodiploid; almost all apterygote and Paleopteran insects; most exopterygote insects; some nematodes, crustaceans, gastropod molluscs and bony fish, notably in the genus Ancistrus; Several mammals (A few species of bat, including the hammer-headed bat, Buettikofer's epauletted fruit bat, Franquet's epauletted fruit bat, Peters's epauletted fruit bat, and Gambian epauletted fruit bat. The Ryukyu spiny rat). There is only one sex chromosome, referred to as X. Males only have one X chromosome (X0), while females have two (XX). The zero (sometimes, the letter O) signifies the lack of a second X. Maternal gametes always contain an X chromosome, so the sex of the animals’ offspring depends on whether a sex chromosome is present in the male gamete. Its sperm normally contain either one X chromosome or no sex chromosomes at all.

ZW sex-determination system: chromosomal system that determines the sex of offspring in birds, some fish and crustaceans such as the giant river prawn, some insects (including butterflies and moths), the schistosome family of flatworms, and some reptiles, e.g. majority of snakes, lacertid lizards and monitors including Komodo dragons. It is also used in some plants where it has probably evolved independently on several occasions. The letters Z and W are used to distinguish this system from the XY sex-determination system. In this system, females have a pair of dissimilar ZW chromosomes, and males have two similar ZZ chromosomes. In the ZW system, the ovum determines the sex of the offspring.

Significance of the ZW and XY systems: No genes are shared between the avian ZW and mammalian XY chromosomes, and, from a comparison between chicken and human, the Z chromosome appeared similar to the autosomal chromosome 9 in humans, rather than X or Y, leading researchers to believe that the ZW and XY sex determination systems do not share an origin, but that the sex chromosomes are derived from autosomal chromosomes of the common ancestor. These autosomes are thought to have evolved sex-determining loci that eventually developed into the respective sex chromosomes once the recombination between the chromosomes (X and Y or Z and W) was suppressed. The platypus, a monotreme mammal, has a system of five pairs of XY chromosomes. They form a multiple chain due to homologous regions in male meiosis and finally segregates into XXXXX-sperm and YYYYY-sperm. The bird Z-like pair shows up on opposite ends of the chain. Areas homologous to the bird Z chromosome are scattered throughout X3 and X5. Although the sex-determination system is not necessarily linked to that of birds and definitely not to that of therian mammals, the similarity at least allowed for the conclusion that mammals evolved sex chromosomes twice. The previous report that platypus has X chromosomes similar to that of therian mammals is now considered a mistake. Bird and snake ZW are unrelated, having evolved from different autosomes. However, the bird-like chromosomes of platypus may indicate that ancestors of snakes had a bird-like ZW system.

Z0 sex-determination system: determines the sex of offspring in several moths. In those species, there is one sex chromosome, Z. Males have two Z chromosomes, whereas females have one Z. Males are ZZ, while females are Z0.

Haplodiploidy: sex-determination system in which males develop from unfertilized eggs and are haploid, and females develop from fertilized eggs and are diploid. Haplodiploidy determines the sex in all members of the insect orders Hymenoptera (bees, ants, and wasps) and Thysanoptera ('thrips'). The system also occurs sporadically in some spider mites, Hemiptera, Coleoptera (bark beetles), and rotifers.

Heterogametic sex (digametic sex): sex of a species in which the sex chromosomes are not the same, e.g. human and Drosophila males have an X and a Y sex chromosome, while birds' and some reptiles' females have one Z and one W chromomose. The opposite is referred to as the homogametic sex (females for humans and Drosophila, while males for birds and some reptiles).

Sequential hermaphroditism (dichogamy in botany): type of hermaphroditism that occurs in many fish, gastropods, and plants. Sequential hermaphroditism occurs when the individual changes its sex at some point in its life. In particular, a sequential hermaphrodite produces eggs (female gametes) and sperm (male gametes) at different stages in life. Species that can undergo these changes from one sex to another do so as a normal event within their reproductive cycle that is usually cued by either social structure or the achievement of a certain age or size. In animals, the different types of change are male to female (protandry), female to male (protogyny), female to hermaphrodite (protogynous hermaphroditism), and male to hermaphrodite (protandrous hermaphroditism).

Sex-chromosome dosage compensation: process by which organisms equalize the expression of genes between members of different biological sexes. Across species, different sexes are often characterized by different types and numbers of sex chromosomes. Replicating the actual gene is impossible; thus organisms instead equalize the expression from each gene. For example, in humans, females (XX) silence the transcription of one X chromosome of each pair, and transcribe all information from the other, expressed X chromosome. Thus, human females have the same number of expressed X-linked genes as do human males (XY), both sexes having essentially one X chromosome per cell, from which to transcribe and express genes. Random inactivation of one ♀ X. Two-fold increased transcription of a single ♂ X. Decreased transcription of both hermaphroditic Xs by half. Other species-specific methods: Birds; Monotremes; Reptiles; Plants. X chromosome inactivation and embryonic stem cells. Xist, Xite, and Tsix and their roles in X-inactivation.

Reproductive isolation (mechanisms of reproductive isolation; hybridization barriers): collection of mechanisms, behaviors and physiological processes that prevent the members of two different species that cross or mate from producing offspring, or which ensure that any offspring that may be produced is not fertile; maintain the integrity of a species over time, reducing or directly impeding gene flow between individuals of different species, allowing the conservation of each species’ characteristics.

Spermatozoon (plural spermatozoa): motile sperm cell, or moving form of the haploid cell that is the male gamete. A spermatozoon joins an ovum to form a zygote. The spermatozoon is characterized by a minimum of cytoplasm and the most densely packed DNA known in eukaryotes. Compared to mitotic chromosomes in somatic cells, sperm DNA is at least sixfold more highly condensed. DNA damages present in spermatozoa in the period after meiosis but before fertilization may be repaired in the fertilized egg, but if not repaired, can have serious deleterious effects on fertility and the developing embryo. Human spermatozoa are particularly vulnerable to free radical attack and the generation of oxidative DNA damage.

Protamines: small, arginine-rich, nuclear proteins that replace histones late in the haploid phase of spermatogenesis and are believed essential for sperm head condensation and DNA stabilization. They may allow for denser packaging of DNA in the spermatozoon than histones, but they must be decompressed before the genetic data can be used for protein synthesis. However, in humans and maybe other primates, 10-15% of the sperm's genome is packaged by histones thought to bind genes that are essential for early embryonic development. Protamine and protamine-like (PL) proteins are among the sperm specific nuclear basic proteins (SNBPs). The PL proteins are intermediate in structure between protamine and Histone H1, the C-terminal of which being the precursor of vertebrate protamine.

Assortative mating: mating pattern and form of sexual selection in which individuals with similar phenotypes mate with one another more frequently than would be expected under a random mating pattern.

Human mating strategies: set of behaviors used by individuals to select, attract, and retain mates. Mating strategies overlap with reproductive strategies, which encompass a broader set of behaviors involving the timing of reproduction and the trade-off between quantity and quality of offspring. human mating strategies are unique in their relationship with cultural variables such as the institution of marriage. Humans may seek out individuals with the intention of forming a long-term intimate relationship, marriage, casual relationship, or friendship. The human desire for companionship is one of the strongest human drives. It is an innate feature of human nature and may be related to the sex drive. Sex similarities: Assortative mating, Dating, Flirting, Matchmaking. Sex differences: Short-term and long-term mating, Mate value, Sexual desire, Mate retention

Major histocompatibility complex and sexual selection: how MHC molecules allow for immune system surveillance of the population of protein molecules in a host's cells. In 1976, Yamazaki et al. demonstrated a sexual selection mate choice by male mice for females of a different MHC. MHC genes, which control the immune response and effective resistance against pathogens, have been able to maintain an extremely high level of allelic diversity throughout time and throughout different populations. Studies suggest that the MHC is involved in mate choice for many vertebrates through olfactory cues.

The relationship between olfaction and MHC: MHC-based sexual selection is known to involve olfactory mechanisms in such vertebrate taxa as fish, mice, humans, primates, birds, and reptiles. At its simplest level, humans have long been acquainted with the sense of olfaction for its use in determining the pleasantness or the unpleasantness of one's resources, food, etc. At a deeper level, it has been predicted that olfaction serves to personally identify individuals based upon the genes of the MHC. Although it is not known exactly how MHC-specific odors are recognized, it is currently believed that proteins bound to the peptide-binding groove of the MHC may produce the odorant. Each MHC protein binds to a specific peptide sequence, yielding a set of uniquely bound peptide-MHC complexes for each individual. During cellular turnover, the MHC-peptide complex is shed from the cell surface and the fragments are dispensed in bodily fluids such as blood serum, saliva, and urine.

https://wiki.riteme.site/wiki/Fermi%E2%80%93Dirac_statistics

Bioengineering

Category:Biological engineering

Category:Biochemical engineering {q.v. User:Kazkaskazkasako/Books/Physical sciences#Chemical engineering}

Category:Biomedical engineering

Category:Synthetic biology

Category:Tissue engineering

Category:Stem cell research

Biological engineering (bioengineering)

BioBrick standard biological parts: DNA sequences of defined structure and function; they share a common interface and are designed to be composed and incorporated into living cells such as E. coli to construct new biological systems.

International Genetically Engineered Machine (iGEM) competition: worldwide synthetic biology competition that was initially aimed at undergraduate university students, but has since expanded to include divisions for high school students, entrepreneurs, and community laboratories, as well as 'overgraduates'.

Biological systems engineering (biosystems engineering)

Synthetic biology

Category:Synthetic biology

{q.v. #Scientific modeling, artificial life}

Synthetic biology (SynBio): seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature. Encompasses a broad range of methodologies from various disciplines, such as biotechnology, biomaterials, material science/engineering,genetic engineering, molecular biology, molecular engineering, systems biology, membrane science, biophysics, chemical and biological engineering, electrical and computer engineering, control engineering and evolutionary biology. Due to more powerful genetic engineering capabilities and decreased DNA synthesis and sequencing costs, the field of synthetic biology is rapidly growing. Enabling technologies: DNA and gene synthesis; Sequencing; Modularity; Modeling; Microfluidics; Synthetic transcription factors. Applications: Biosensors; Food and drink (Cellular agriculture); Materials (spider silk); Biological computers; Cell transformation; Designed proteins; Designed nucleic acid systems; Space exploration; Synthetic life; Drug delivery platforms (Engineered bacteria-based platform, Cell-based platform); Organoids; Bioprinted organs; Other transplants and induced regeneration; Nanoparticles, artificial cells and micro-droplets.

Synthetic biological circuits: an application of synthetic biology where biological parts inside a cell are designed to perform logical functions mimicking those observed in electronic circuits. The applications range from simply inducing production to adding a measurable element, like GFP, to an existing natural biological circuit, to implementing completely new systems of many parts.

Mycoplasma genitalium: small pathogenic bacterium that lives on the ciliated epithelial cells of the urinary and genital tracts in humans. Its existence was first reported in 1981, and was eventually identified as a new species of Mycoplasma in 1983.

Mycoplasma laboratorium: designed, partially synthetic species of bacterium derived from the genome of Mycoplasma genitalium. This effort in synthetic biology is being undertaken at the J. Craig Venter Institute by a team of approximately 20 scientists headed by Nobel laureate Hamilton Smith, and including DNA researcher Craig Venter and microbiologist Clyde A. Hutchison III. Synthetic genome: JCVI-syn1.0. JCVI-syn3.0: in 2016, the Venter Institute used genes from JCVI-syn1.0 to synthesize an even smaller genome they call JCVI-syn3.0, that contains 531,560 base pairs and 473 genes, 149 of which whose functions are completely unknown.

BioBrick: parts are DNA sequences which conform to a restriction-enzyme assembly standard.

Biomedical engineering

Category:Biomedical engineering

Biomedical engineering: application of engineering principles and design concepts to medicine and biology for healthcare purposes; to close the gap between engineering and medicine, combining the design and problem solving skills of engineering with medical and biological sciences to advance health care treatment, including diagnosis, monitoring, and therapy. Regulatory issues: medical device engineering area is among the most heavily regulated fields of engineering, and practicing biomedical engineers must routinely consult and cooperate with regulatory law attorneys and other experts.

Organ-on-a-chip: multi-channel 3-D microfluidic cell culture chip that simulates the activities, mechanics and physiological response of entire organs and organ systems, a type of artificial organ. Organs that have been simulated by microfluidic devices include the heart, the lung, kidney, artery, bone, cartilage, skin and more. Replacing animal testing with organs-on-chips.

Lung on a chip: complex, 3D model of a living, breathing human lung on a microchip. The device is made using human lung and blood vessel cells and it can predict absorption of airborne nanoparticles and mimic the inflammatory response triggered by microbial pathogens.

Rare diseases

Category:Rare diseases

Category:Genetic disorders

Progeroid syndromes: group of rare genetic disorders that mimic physiological aging, making affected individuals appear to be older than they are.

Progeria (Hutchinson–Gilford progeria syndrome): extremely rare genetic disorder wherein symptoms resembling aspects of aging are manifested at a very early age. Farnesyl group remains attached to prelamin A, which is named progerin. Progerin is anchored to the nuclear rim, results in abnormally shaped nucleus.

Genetic diseases

Rare disease (orphan disease): a window to human mutations (mainly) and some extremely rare pathogens (seldom); lots of discoveries into human biology and genetics.

Finnish disease heritage

Organizations:

European Organization for Rare Diseases (EURORDIS, non-governmental patient-driven alliance of patient organizations and individuals active in the field of rare diseases)

National Organization for Rare Disorders (NORD, American non-profit organization aiming to provide support individuals with rare diseases)

Orphan drug: politics and economics of rare disease treatment

Applied genetics, gene therapy

Category:Applied genetics

Category:Breeding

Category:Eugenics

Category:Gene therapy

Category:Genetic engineering

Category:Genetically modified organisms

Gene therapy: therapeutic delivery of nucleic acid polymers into a patient's cells as a drug to treat disease. The first attempt at modifying human DNA was performed in 1980 by Martin Cline, but the first successful nuclear gene transfer in humans, approved by NIH, was performed in 1989.05. The first therapeutic use of gene transfer as well as the first direct insertion of human DNA into the nuclear genome was performed by French Anderson in a trial starting in September 1990.

Alipogene tiparvovec (Glybera): gene therapy treatment, developed and marketed by uniQure N.V., that compensates for lipoprotein lipase deficiency (LPLD), a rare inherited disorder which can cause severe pancreatitis. 2012.07 the European Medicines Agency recommended it for approval, the first recommendation for a gene therapy treatment in either Europe or USA. The recommendation was endorsed by the European Commission in November 2012.

Jesse Gelsinger (1981.06.18-1999.09.17): first person publicly identified as having died in a clinical trial for gene therapy. 1999.09.13 he was injected with adenoviral vector carrying corrected gene to test the safety of the procedure; died 4d. later apparently having suffered a massive immune response.

Template:Genetic engineering

Pharming (genetics) (portmanteau of "farming" and "pharmaceutical"): refers to the use of genetic engineering to insert genes that code for useful pharmaceuticals into host animals or plants that would otherwise not express those genes, thus creating a GMO. Pharming is also known as molecular farming, molecular pharming or biopharming.

Politics

The Race Question: UNESCO statement issued on 18 July 1950 following World War II. No "race", only "ethnic groups". In the current scientific light: "ethnic groups" as everything non-hereditary (culture, language, religion...) while human genetic groups (in the older times called "races") as everything hereditary (genes and from genotypes coming phenotypes).

Cell biology

Category:Cell biology

Category:Cell anatomy

Category:Cell imaging

Category:Staining

Category:Cellular processes

Category:Protein targeting

Category:Histology

Subcellular localization: eukaryotes vs prokaryotes

Protein subcellular localization prediction

Pseudo amino acid composition

{Low-frequency collective motion in proteins and DNA: solitons} (Kuo-Chen Chou#Editorial misconduct and citation abuse)

Anatomical terms of microanatomy: anatomical terminology is used to describe microanatomical (or histological) structures; internationally accepted lexicon is Terminologia Histologica.

Hayflick limit: number of times a normal human cell population will divide until cell division stops. Empirical evidence shows that the telomeres associated with each cell's DNA will get slightly shorter with each new cell division until they shorten to a critical length.

Endomembrane system: composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cell. These membranes divide the cell into functional and structural compartments, or organelles. In eukaryotes the organelles of the endomembrane system include: the nuclear membrane, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, endosomes, and plasma (cell) membrane among others. The system is defined more accurately as the set of membranes that form a single functional and developmental unit, either being connected directly, or exchanging material through vesicle transport.

Endosome: collection of intracellular sorting organelles in eukaryotic cells. They are part of endocytic membrane transport pathway originating from the trans Golgi network. Molecules or ligands internalized from the plasma membrane can follow this pathway all the way to lysosomes for degradation or can be recycled back to the cell membrane in the endocytic cycle. Molecules are also transported to endosomes from the trans Golgi network and either continue to lysosomes or recycle back to the Golgi apparatus. Endosomes can be classified as early, sorting, or late depending on their stage post internalization.

Protein targeting (protein sorting): biological mechanism by which proteins are transported to their appropriate destinations in the cell or outside it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to the exterior of the cell via secretion. This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases. Targeting signals: Target peptide. Protein translocation: translocon; Co-translational translocation; Post-translational translocation. Sorting of proteins: Mitochondria (TOM70, TOM20, TOM22); Chloroplasts; Both chloroplasts and mitochondria; Peroxisomes. In bacteria and archaea: Gram-negative bacteria; Gram-positive bacteria.

Signal peptide (signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence, leader peptide): short peptide (usually 16-30 amino acids long) present at the N-terminus of the majority of newly synthesized proteins that are destined toward the secretory pathway. These proteins include those that reside either inside certain organelles (the endoplasmic reticulum, Golgi or endosomes), secreted from the cell, or inserted into most cellular membranes.

Exosome (vesicle): membrane-bound extracellular vesicles (EVs) that are produced in the endosomal compartment of most eukaryotic cells. The multivesicular body (MVB) is an endosome defined by intraluminal vesicles (ILVs) that bud inward into the endosomal lumen. If the MVB fuses with the cell surface (the plasma membrane), these ILVs are released as exosomes.

Cellular membranes, plasma membrane

Category:Membrane biology

Category:Phospholipids

{q.v. User:Kazkaskazkasako/Books/Physical sciences#Lipids, waxes, fatty acids, oils}

Template:Phospholipids

Membrane lipid: group of compounds (structurally similar to fats and oils) which form the double-layered surface of all cells (lipid bilayer). The three major classes of membrane lipids are phospholipids, glycolipids, and cholesterol.

Glycerophospholipid (phosphoglyceride)

Phosphatidylcholine (PC): class of phospholipids that incorporate choline as a headgroup; major component of biological membranes; member of the lecithin group of yellow-brownish fatty substances occurring in animal and plant tissues. While phosphatidylcholines are found in all plant and animal cells, they are absent in the membranes of most bacteria.

Phosphatidylethanolamine (PE)

Phosphatidylserine (PS)

Phosphatidylinositol (PI)

Phosphatidylglycerol (PG): consists of a L-glycerol 3-phosphate backbone ester-bonded to either saturated or unsaturated fatty acids on carbons 1 and 2. The head group substituent glycerol is bonded through a phosphomonoester.

Phosphatidic acid (PA): consists of a glycerol backbone, with, in general, a saturated fatty acid bonded to carbon-1, an unsaturated fatty acid bonded to carbon-2, and a phosphate group bonded to carbon-3. Anionic phospholipids important to cell signaling and direct activation of lipid-gated ion channels. PA is a unique phospholipid in that it has a small highly charged head group that is very close to the glycerol backbone. PA is known to play roles in both vesicle fission and fusion, and these roles may relate to the biophysical properties of PA. PA is kept low in the bulk of the membrane in order to transiently burst and signal locally in high concentration.

Cardiolipin (1,3-bis(sn-3'-phosphatidyl)-sn-glycerol): important component of the inner mitochondrial membrane, where it constitutes about 20% of the total lipid composition. It can also be found in the membranes of most bacteria.

Sphingolipids: class of lipids containing a backbone of sphingoid bases, a set of aliphatic amino alcohols that includes sphingosine; play important roles in signal transduction and cell recognition. A sphingolipid with an R group consisting of a hydrogen atom only is a ceramide. Other common R groups include phosphocholine, yielding a sphingomyelin, and various sugar monomers or dimers, yielding cerebrosides and globosides, respectively. Cerebrosides and globosides are collectively known as glycosphingolipids.

Sphingomyelin (SPH): type of sphingolipid found in animal cell membranes, especially in the membranous myelin sheath that surrounds some nerve cell axons. It usually consists of phosphocholine and ceramide, or a phosphoethanolamine head group; therefore, sphingomyelins can also be classified as sphingophospholipids. In humans, SPH represents ~85% of all sphingolipids, and typically make up 10–20 mol % of plasma membrane lipids.

Cholesterol: Cholesterol composes about 30% of all animal cell membranes. It is required to build and maintain membranes and modulates membrane fluidity over the range of physiological temperatures. The hydroxyl group of each cholesterol molecule interacts with water molecules surrounding the membrane, as do the polar heads of the membrane phospholipids and sphingolipids, while the bulky steroid and the hydrocarbon chain are embedded in the membrane, alongside the nonpolar fatty-acid chain of the other lipids. Through the interaction with the phospholipid fatty-acid chains, cholesterol increases membrane packing, which both alters membrane fluidity and maintains membrane integrity so that animal cells do not need to build cell walls (like plants and most bacteria). The membrane remains stable and durable without being rigid, allowing animal cells to change shape and animals to move.

Plasmalogens: subclass of ether phospholipids that are commonly found in cell membranes in the nervous, immune and cardiovascular systems. There are two types of ether phospholipids, plasmanyl and plasmenyl. Plasmenyl-phospholipids, which include plasmalogen, and have an ether bond in position sn1 to an alkenyl group. Plasmanyl-phospholipids, in distinction, have an ether bond in position sn1 to an alkyl group.

Cell culture

Category:Cell culture

Category:Cell culture media

Category:Microbiological media

Trypticase soy agar (TSA; Tryptone Soya Agar): growth media for the culturing of bacteria. They are general-purpose, non-selective media providing enough nutrients to allow for a wide variety of microorganisms to grow. They are used for a wide range of applications, including culture storage, enumeration (counting), isolation of pure cultures, or simply general culture. TSA contains enzymatic digests of casein and soybean meal, which provides amino acids and other nitrogenous substances, making it a nutritious medium for a variety of organisms. Glucose is the energy source. Sodium chloride maintains the osmotic equilibrium, while dipotassium phosphate acts as buffer to maintain pH. Agar extracted from any number of organisms is used as a gelling agent.

Tryptone: assortment of peptides formed by the digestion of casein by the protease trypsin.

Casein: name for a family of related phosphoproteins (αS1, αS2, β, κ). These proteins are commonly found in mammalian milk, making up 80% of the proteins in cow's milk and between 20% and 45% of the proteins in human milk. Casein has a wide variety of uses, from being a major component of cheese, to use as a food additive, to a binder for safety matches. As a food source, casein supplies amino acids, carbohydrates, and the two inorganic elements calcium and phosphorus.

Cell bank: facility that stores cells of specific genome for the purpose of future use in a product or medicinal needs. They often contain expansive amounts of base cell material that can be utilized for various projects. The advantages of cell banks is that the facilities will include a "detailed characterization of the cell line" and will have a "decrease in the likelihood and an increase in the detection" of cross-contamination of a cell line.

Vero cell: 'Vero' lineage was isolated from kidney epithelial cells extracted from an African green monkey (Chlorocebus sp.; formerly called Cercopithecus aethiops, this group of monkeys has been split into several different species). The lineage was developed in 1962.03.27, by Yasumura and Kawakita at the Chiba University in Chiba, Japan.

Chinese hamster ovary cell (CHO)

Cell nucleus

Category:Nuclear organization

{q.v. #RNA processing; #Spliceosome, splicing}

Template:Nucleus

Cell nucleus: membrane-enclosed organelle found in eukaryotic cells; contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. Nuclear envelope; Nuclear pores; Nuclear lamina; Chromosomes; subnuclear bodies: Nucleolus; Cajal bodies and gems; RAFA and PTF domains; PML bodies; Paraspeckles; Splicing speckles (At the fluorescence-microscope level they appear as irregular, punctate structures, which vary in size and shape, and when examined by electron microscopy they are seen as clusters of interchromatin granules). Nuclear transport; Assembly and disassembly. Anucleated and multinucleated cells.

Cajal body (CB): spherical sub-organelles of 0.3-1.0 µm in diameter found in the nucleus of proliferative cells like embryonic cells and tumor cells, or metabolically active cells like neurons (hence the finding by Santiago Ramón y Cajal in 1903: nucleolar accessory bodies); largely consisting of proteins and RNA. Rediscovered by electron microscopists and named coiled bodies, according to their appearance as coiled threads on EM images, and later renamed after their discoverer. Marker protein: p80/coilin. Implicated in RNA-related metabolic processes such as snRNP biogenesis, maturation and recycling, histone mRNA processing and telomere maintenance

Nuclear dots ("Nuclear bodies", "nuclear domains", "PML bodies")

Paraspeckle: irregularly shaped, 0.2-1 μm in size, found in the nucleus' interchromatin space; "para" is short for parallel and the "speckle" refers to the splicing speckles to which they are always in close proximity; function not known [2013], but they may localize proteins in the nucleus; in the absence of RNA polymerase II transcription the paraspeckle disappears

Heterochromatin: tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a role in the expression of genes. Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed, however according to Volpe et al. (2002), and many other papers since, much of this DNA is in fact transcribed, but it is continuously turned over via RNA-induced transcriptional silencing (RITS). Recent studies with electron microscopy and OsO4 staining reveal that the dense packing is not due to the chromatin.

Constitutive heterochromatin domains: regions of DNA found throughout the chromosomes of eukaryotes. The majority of constitutive heterochromatin is found at the pericentromeric regions of chromosomes, but is also found at the telomeres and throughout the chromosomes. In humans there is significantly more constitutive heterochromatin found on chromosomes 1, 9, 16, 19 and Y. Constitutive heterochromatin is composed mainly of high copy number tandem repeats known as satellite repeats, minisatellite and microsatellite repeats, and transposon repeats. In humans these regions account for about 200Mb or 6.5% of the total human genome, but their repeat composition makes them difficult to sequence, so only small regions have been sequenced.

Histone code: hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends. Together with similar modifications such as DNA methylation it is part of the epigenetic code.

Euchromatin: lightly packed form of chromatin that is enriched in genes, and is often (but not always) under active transcription. Euchromatin comprises the most active portion of the genome within the cell nucleus. 92% of the human genome is euchromatic.

Cell anatomy

Category:Cell anatomy

Cytosol (cytoplasmic matrix): liquid found inside cells. It constitutes most of the intracellular fluid (ICF). It is separated into compartments by membranes. In the eukaryotic cell, the cytosol is within the cell membrane and is part of the cytoplasm, which also comprises the mitochondria, plastids, and other organelles (but not their internal fluids and structures); the cell nucleus is separate. The cytosol is thus a liquid matrix around the organelles. In prokaryotes, most of the chemical reactions of metabolism take place in the cytosol, while a few take place in membranes or in the periplasmic space. In eukaryotes, while many metabolic pathways still occur in the cytosol, others are contained within organelles. Although it was once thought to be a simple solution of molecules, the cytosol has multiple levels of organization. These include concentration gradients of small molecules such as calcium, large complexes of enzymes that act together to carry out metabolic pathways, and protein complexes such as proteasomes and carboxysomes that enclose and separate parts of the cytosol. Most of the cytosol is water, which makes up about 70% of the total volume of a typical cell. The viscosity of cytoplasm is roughly the same as pure water, although diffusion of small molecules through this liquid is about fourfold slower than in pure water, due mostly to collisions with the large numbers of macromolecules in the cytosol. Studies in the brine shrimp have examined how water affects cell functions; these saw that a 20% reduction in the amount of water in a cell inhibits metabolism, with metabolism decreasing progressively as the cell dries out and all metabolic activity halting when the water level reaches 70% below normal. In contrast to extracellular fluid, cytosol has a high concentration of potassium ions and a low concentration of sodium ions. This difference in ion concentrations is critical for osmoregulation, since if the ion levels were the same inside a cell as outside, water would enter constantly by osmosis - since the levels of macromolecules inside cells are higher than their levels outside. Instead, sodium ions are expelled and potassium ions taken up by the Na⁺/K⁺-ATPase, potassium ions then flow down their concentration gradient through potassium-selection ion channels, this loss of positive charge creates a negative membrane potential. To balance this potential difference, negative chloride ions also exit the cell, through selective chloride channels. The loss of sodium and chloride ions compensates for the osmotic effect of the higher concentration of organic molecules inside the cell.

Cytoskeleton: complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is composed of similar proteins in the various organisms. It is composed of three main components: microfilaments, intermediate filaments, and microtubules, and these are all capable of rapid growth or disassembly depending on the cell's requirements. To give the cell its shape and mechanical resistance to deformation, and through association with extracellular connective tissue and other cells it stabilizes entire tissues. The cytoskeleton can also contract, thereby deforming the cell and the cell's environment and allowing cells to migrate. Involved in many cell signaling pathways and in the uptake of extracellular material (endocytosis), the segregation of chromosomes during cellular division, the cytokinesis stage of cell division, as scaffolding to organize the contents of the cell in space and in intracellular transport (for example, the movement of vesicles and organelles within the cell) and can be a template for the construction of a cell wall. Can form specialized structures, such as flagella, cilia, lamellipodia and podosomes.

Microfilaments (actin filaments): primarily composed of polymers of actin, but are modified by and interact with numerous other proteins in the cell. Microfilaments are usually about 7 nm in diameter and made up of two strands of actin. Microfilament functions include cytokinesis, amoeboid movement, cell motility, changes in cell shape, endocytosis and exocytosis, cell contractility, and mechanical stability. Microfilaments are flexible and relatively strong, resisting buckling by multi-pN compressive forces and filament fracture by nN tensile forces. In inducing cell motility, one end of the actin filament elongates while the other end contracts, presumably by myosin II molecular motors. Additionally, they function as part of actomyosin-driven contractile molecular motors, wherein the thin filaments serve as tensile platforms for myosin's ATP-dependent pulling action in muscle contraction and pseudopod advancement.

Intermediate filaments (IFs): cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Intermediate filaments are composed of a family of related proteins sharing common structural and sequence features. Initially designated 'intermediate' because their average diameter (10 nm) is between those of narrower microfilaments (actin) and wider myosin filaments found in muscle cells, the diameter of intermediate filaments is now commonly compared to actin microfilaments (7 nm) and microtubules (25 nm). Animal intermediate filaments are subcategorized into six types based on similarities in amino acid sequence and protein structure. Structure: all IF proteins appear to have a central alpha-helical rod domain that is composed of four alpha-helical segments (named as 1A, 1B, 2A and 2B) separated by three linker regions. Types:

Types I and II – acidic and basic keratins:
- epithelial keratins (about 20) in epithelial cells
- trichocytic keratins (about 13) (hair keratins), which make up hair, nails, horns and reptilian scales
Type III:
- Desmin IFs are structural components of the sarcomeres in muscle cells and connect different cell organells like the desmosomes with the cytoskeleton.
- Glial fibrillary acidic protein (GFAP) is found in astrocytes and other glia.
- Peripherin found in peripheral neurons.
- Vimentin, the most widely distributed of all IF proteins, can be found in fibroblasts, leukocytes, and blood vessel endothelial cells. They support the cellular membranes, keep some organelles in a fixed place within the cytoplasm, and transmit membrane receptor signals to the nucleus.
- Syncoilin is an atypical type III IF protein
Type IV
- Alpha-internexin
- Neurofilaments – the type IV family of intermediate filaments that is found in high concentrations along the axons of vertebrate neurons
- Synemin
- Syncoilin
Type V – nuclear lamins: Lamins - fibrous proteins having structural function in the cell nucleus

Microtubule organizing center (MTOC): structure found in eukaryotic cells from which microtubules emerge; two main functions: the organization of eukaryotic flagella and cilia and the organization of the mitotic and meiotic spindle apparatus, which separate the chromosomes during cell division.

Centriole: usually 9*3 MTs; absent in higher plants and fungi. D. melanogaster embryos: 9*2; C. elegans sperm cells and early eambryos: 9*1; crabs maybe 9*2.

Centrosome: organelle that serves as the main MTOC of the animal cell as well as a regulator of cell-cycle progression; composed of two orthogonally arranged centrioles surrounded by an amorphous mass of protein termed PCM.

Pericentriolar material (PCM): amorphous mass of protein which makes up the part of the animal centrosome that surrounds the two centrioles.

Basal body (basal granule, kinetosome): organelle formed from a centriole, and a short cylindrical array of microtubules. Found at the base of a eukaryotic undulipodium and serves as a nucleation site for the growth of the axoneme microtubules; 9*3 helicoidal configuration forms a hollow cylinder.

Undulipodium (9+2 organelle): eukaryotic flagella and cilia; extension of the cell membrane containing both cytoplasm and a regular arrangement of microtubules known as an axoneme.

Axoneme: inner core of the undulipodium. Motile cilia/flagela: 9*2+2 axoneme; non-motile/primary cilia: no dynein arms are found, 9*2+0 (sometimes 9*2+1), (sensory functions?).

Tubulin: most common members of the tubulin family are α-tubulin and β-tubulin (αβ dimers make up microtubules). FtsZ is a prokaryotic homolog of eukaryotic tubulins. γ-tubulin important in the nucleation and polar orientation of microtubules, found in centrosomes. Tubulin/FtsZ family, GTPase domain - evolutionary conserved protein domain.

Microtubule nucleation (γ-tubulin ring complex (γ-TuRC)): cap of the (−) end while microtubule growth continues towards the (+) direction; found typically in MTOC.

Microtubules (MTs): component of the cytoskeleton; outer diameter of microtubule is ~25 nm. Kinesins are motor proteins binding MTs; katanin severs MTs & co.

Cell cycle, cell division

Category:Cell cycle

Image of the mitotic spindle in a human cell: microtubules - green, chromosomes - blue, kinetochores - red.

Cell cycle checkpoint: control mechanisms in eukaryotic cells which ensure proper division of the cell. Three known checkpoints: the G1 checkpoint, also known as the restriction or start checkpoint; the G2/M checkpoint; and the metaphase checkpoint, also known as the spindle checkpoint.

Spindle checkpoint: prevents separation of the duplicated chromosomes until each chromosome is properly attached to the spindle apparatus. Spindle assembly checkpoint (SAC).

Aurora kinases: serine/threonine kinases that are essential for cell proliferation. The enzyme helps the dividing cell dispense its genetic materials to its daughter cells. More specifically, Aurora kinases play a crucial role in cellular division by controlling chromatid segregation. Defects in this segregation can cause genetic instability, a condition which is highly associated with tumorigenesis. Elevated expression profiles in many human cancers.

Aurora A kinase (serine/threonine-protein kinase 6; AURKA): activity peaks during the G2 phase to M phase transition in the cell cycle. Aurora A is critical for proper formation of mitotic spindle; required for the recruitment of several different proteins important to the spindle formation.

Aurora B kinase: attachment of the mitotic spindle to the centromere. Aurora B localizes to the chromosomes in prophase, the centromere in prometaphase and metaphase, and the central mitotic spindle in anaphase. Inhibition of Aurora B function by RNA interference or microinjection of blocking antibodies impairs the alignment of chromosomes at the equator of the mitotic spindle.

Aurora C (AURKC)

Aurora inhibitor

Developmental biology

X-inactivation: random in placental mammals, inactivation in marsupials applies exclusively to the paternally derived X chromosome

Barr body: inactive X chromosome in a female somatic cell, rendered inactive in a process called lyonization, in those species in which sex is determined by the presence of the Y (including humans) or W chromosome rather than the diploidy of the X. The Lyon hypothesis states that in cells with multiple X chromosomes, all but one are inactivated during mammalian embryogenesis. This happens early in embryonic development at random in mammals, except in marsupials and in some extra-embryonic tissues of some placental mammals, in which the father's X chromosome is always deactivated.

Anencephaly: cephalic disorder that results from a neural tube defect that occurs when the rostral (head) end of the neural tube fails to close, usually between the 23rd and 26th day of conception, resulting in the absence of a major portion of the brain, skull, and scalp. With very few exceptions, most babies with this disorder do not survive.

Baby K (1992-1995): was an anencephalic baby who became the center of a major U.S. court case and a debate among bioethicists; kept alive much longer than most anencephalic babies.

Evolution

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*Ice Ages

Evolution as a process during which the fidelity of replication increased several folds of magnitude (RNA world, RNP world / DNA world, protein (the machines, hardware) & DNA (the code, software) world; next step (non-bio): human literature → computer programs & digital storage (copying errors are extremely small compared to human genome replication in digital world))

Speed of reactions catalyzed by these molecules (from the slowest to the fastest): RNA (RNA world) → RNP (early protein + RNA world) → protein (current world of proteins as machines, DNA as storage, mRNA as intermediate remaining as relic & more from the previous "ages"). Human technological evolution: stone → bronze → iron → steel, plastic, silicon, periodic table, all of organic chemistry and biochemistry → speed of light machines running on electricity: computers (→ AI ? )

evo-devo:

Evolutionary developmental biology (informally: evo-devo): compares the developmental processes of different organisms to determine the ancestral relationship between them, and to discover how developmental processes evolved. History: Recapitulation theory, Evolutionary morphology, The modern synthesis of the early 20th century.

Modern synthesis (20th century): early 20th-century synthesis reconciling Charles Darwin's theory of evolution and Gregor Mendel's ideas on heredity in a joint mathematical framework. Julian Huxley coined the term in his 1942 book, Evolution: The Modern Synthesis. Different syntheses followed, accompanying the gradual breakup of the early 20th century synthesis, including with social behaviour in E. O. Wilson's sociobiology in 1975, evolutionary developmental biology's integration of embryology with genetics and evolution, starting in 1977, and Massimo Pigliucci's proposed extended evolutionary synthesis of 2007. In the view of the evolutionary biologist Eugene Koonin in 2009, the modern synthesis will be replaced by a 'post-modern' synthesis that will include revolutionary changes in molecular biology, the study of prokaryotes and the resulting tree of life, and genomics. Developments leading up to the synthesis: Darwin's evolution by natural selection, 1859; The eclipse of Darwinism, 1880s onwards; Weismann's germ plasm, 1892. Disputed beginnings: Genetics, mutationism and biometrics, 1900–1918; Castle's hooded rats, 1911; Morgan's fruit flies, 1912. An obstruction: Woodger's positivism, 1929. Events in the synthesis: Fisher and Haldane's mathematical population genetics, 1918–1930; De Beer's embryology, 1930; Wright's adaptive landscape, 1932; Dobzhansky's evolutionary genetics, 1937; Ford's ecological genetics, 1940; Schmalhausen's stabilizing selection, 1941; Huxley's popularising synthesis, 1942; Mayr's allopatric speciation, 1942; Simpson's palaeontology, 1944; The Society for the Study of Evolution, 1946; Stebbins's botany, 1950. After the synthesis: Hamilton's inclusive fitness, 1964; Williams's gene-centred evolution, 1966; Wilson's sociobiology, 1975; Lewis's homeotic genes, 1978. Later syntheses: Pigliucci's extended evolutionary synthesis, 2007; Koonin's 'post-modern' evolutionary synthesis, 2009; Towards a replacement synthesis.

eco-evo:

Eco-evolutionary Dynamics: reciprocal effects that ecology and evolution have on each other. The effects of ecology on evolutionary processes are commonly observed in studies, but the realization that evolutionary changes can be rapid led to the emergence of eco-evolutionary dynamics. The idea that evolutionary processes can occur quickly and on one timescale with ecological processes led scientists to begin studying the influence evolution has on ecology along with the affects ecology has on evolution. Recent studies have documented eco-evolutionary dynamics and feedback, which is the cyclic interaction between evolution and ecology, in natural and laboratory systems at different levels of biological organization, such as populations, communities, and ecosystems.

1860 Oxford evolution debate took place at the Oxford University Museum in Oxford, England, 1860.06.30, seven months after the publication of Charles Darwin's On the Origin of Species. Several prominent British scientists and philosophers participated, including Thomas Henry Huxley, Bishop Samuel Wilberforce, Benjamin Brodie, Joseph Dalton Hooker and Robert FitzRoy. The debate is best remembered today for a heated exchange in which Wilberforce supposedly asked Huxley whether it was through his grandfather or his grandmother that he claimed his descent from a monkey. Huxley is said to have replied that he would not be ashamed to have a monkey for his ancestor, but he would be ashamed to be connected with a man who used his great gifts to obscure the truth. There is considerable uncertainty regarding what Huxley and Wilberforce actually said, and subsequent accounts were subject to distortion. Legacy: The debate has been called "one of the great stories of the history of science" and it is often regarded as a key moment in the acceptance of evolution. However, at the time it received only a few passing references in newspapers, and Brooke argues that "the event almost completely disappeared from public awareness until it was resurrected in the 1890s as an appropriate tribute to a recently deceased hero of scientific education". The debate marked the beginning of a bitter three-year dispute between Owen and Huxley over human origins, satirised by Charles Kingsley as the "Great Hippocampus Question", which concluded with the defeat of Owen and his backers.

Modern evolutionary synthesis: 20th c. union of ideas from several biological specialties which provides a widely accepted account of evolution

Evolution: The Modern Synthesis (1942): book by Julian Huxley, one of the most important books of the modern evolutionary synthesis.

Evolution as theory and fact

Punctuated equilibrium: is it a tiny part of the modern evolution synthesis or a huge one? What could tiny/huge mean in terms of genetics and evo-devo?

Arsenic-based life

GFAJ-1: isolated from the shore of Mono Lake, California, USA {highest natural concentrations of arsenic in the world (200 μM)}. Molecular analysis based on 16S rRNA sequences shows GFAJ-1 to be closely related to other moderate halophile ("salt-loving") bacteria of the family Halomonadaceae. Many bacteria are known to be able to tolerate high levels of arsenic, and to have a proclivity to take it up into their cells. However, GFAJ-1 was controversially proposed to go a step further; when starved of phosphorus, it was proposed to instead incorporate arsenic into its metabolites and macromolecules and continue growing. Immediately after publication, other microbiologists and biochemists expressed doubt about this claim which was robustly criticized in the scientific community. Subsequent independent studies published in 2012 found no detectable arsenate in the DNA of GFAJ-1, refuted the claim, and demonstrated that GFAJ-1 is simply an arsenate-resistant, phosphate-dependent organism.

Human evolution, extinct and extant "cousins"

Category:Human evolution

Category:Evolution of language

Category:Paleoanthropology

{q.v.:

}

Hominin timeline

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Pleistocene

Hominini

Nakalipithecus

Samburupithecus

Ouranopithecus
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Chororapithecus

Oreopithecus

Sivapithecus

Sahelanthropus

Graecopithecus

Orrorin

(O. praegens)
(O. tugenensis)

Ardipithecus

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(Ar. ramidus)

Australopithecus
(Au. africanus)
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H. habilis
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H. erectus
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(H. ergaster)
(Au. sediba)

H. heidelbergensis

Homo sapiens

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H o m i n i d s

P a r a n t h r o p u s

(million years ago)

Discovery of human antiquity: major achievement of science in the middle of the 19th century, and the foundation of scientific paleoanthropology. The antiquity of man, human antiquity, or in simpler language the age of the human race, are names given to the series of scientific debates it involved, which with modifications continue in the 21st century. These debates have clarified and given scientific evidence, from a number of disciplines, towards solving the basic question of dating the first human being. Historical debates: Theological debates: Human origins and the "universal deluge" debated, La Peyrère and the completeness of the Biblical account, Debate on race, Incompatible views of chronology, Creation of man in a world not ready; Archaeological context; Debate on uniformity and change; Glacial conditions; Acceptance of human association with extinct animal species. List of key sites for the 19th century debate

Monogenism: theory of human origins which posits a common descent for all human races. The negation of monogenism is polygenism. This issue was hotly debated in the Western world in 19th c., as the assumptions of scientific racism came under scrutiny both from religious groups and in the light of developments in the life sciences and human science. It was integral to the early conceptions of ethnology. Mid-century contention in the United Kingdom: In the face of advocates of polygenism, monogenism received a second wind after the recognition of the antiquity of man, and the almost simultaneous publication of Darwin's theory of evolution. Once the biblical timescale of 6000 years was dropped, the objections to environmentalist monogenism were weakened, since the "unity and migration" hypothesis of the origins of human diversity could operate over tens of thousands of years. Since polygenists such as Hunt and Crawfurd were opponents of Darwin, monogenism became part of a larger debate on evolution. Augustus Henry Keane in 1896 wrote of: "[...] two assumptions, both strenuously denied by many ethnologists, firstly, that the Hominidæ descend from a single precursor, secondly, that their differences are comparatively slight, or not sufficiently pronounced to be regarded as specific."

Human evolution: primates diverged from other mammals about 85 mya, in the Late Cretaceous period, and the earliest fossils appear in the Paleocene, around 55 Mya. Within the Hominoidea (apes) superfamily, the Hominidae family diverged from the Hylobatidae (gibbon) family some 15–20 Mya; African great apes (subfamily Homininae) diverged from orangutans (Ponginae) about 14 Mya; the Hominini tribe (humans, Australopithecines and other extinct biped genera, and chimpanzees) parted from the Gorillini tribe (gorillas) between 9 Mya and 8 Mya; and, in turn, the subtribes Hominina (humans and biped ancestors) and Panina (chimps) separated about 7.5 Mya to 5.6 Mya. The basic adaptation of the hominin line is bipedalism. Humans and bonobos are the only apes in which the female is fertile year round and in which no special signals of fertility are produced by the body (such as genital swelling during estrus).

Human: only extant members of Hominina tribe (or human tribe), a branch of the tribe Hominini belonging to the family of great apes. They are characterized by erect posture and bipedal locomotion; manual dexterity and increased tool use, compared to other animals; and a general trend toward larger, more complex brains and societies. Hominins began to exhibit evidence of behavioral modernity around 50,000 years ago. In several waves of migration, anatomically modern humans ventured out of Africa and populated most of the world. Humans use tools to a much higher degree than any other animal, are the only extant species known to build fires and cook their food, and are the only extant species to clothe themselves and create and use numerous other technologies and arts. Most significant adaptions after split between the last common ancestor of humans and chimpanzees: 1. bipedalism, 2. increased brain size, 3. lengthened ontogeny (gestation and infancy), 4. decreased sexual dimorphism (neoteny). Chimpanzee babies are cognitively more developed than human babies until the age of six months, when the rapid development of human brains surpasses chimpanzees. Women go through the menopause and become unfertile decades before the end of their lives; all species of non-human apes are capable of giving birth until death. Average human has more hair follicles on his or her body than the average chimpanzee. Males have higher circulating clotting factors (vitamin K, prothrombin and platelets). These differences lead to faster healing of wounds and higher peripheral pain tolerance. Females typically have more white blood cells (stored and circulating), more granulocytes and B and T lymphocytes. Additionally, they produce more antibodies at a faster rate than males. Hence they develop fewer infectious diseases and these continue for shorter periods. Ethologists argue that females, interacting with other females and multiple offspring in social groups, have experienced such traits as a selective advantage. According to Daly and Wilson, "The sexes differ more in human beings than in monogamous mammals, but much less than in extremely polygamous mammals." There is more human genetic diversity in Africa than anywhere else on Earth.

Homo sapiens: binomial nomenclature for the only extant human species. Homo is the human genus, which also includes Neanderthals and many other extinct species of hominid; H. sapiens is the only surviving species of the genus Homo. Since 2010, genetic research has led to the emergence of an intermediate position, characterised by mostly recent African origin plus limited admixture with archaic humans.

Early human migrations: began 2 mya with the migration out of Africa of Homo erectus. This was followed by the migrations of other pre-modern humans including H. heidelbergensis, the likely ancestor of both modern humans and Neanderthals. Finally, Homo sapiens ventured out of Africa around 100,000 years ago, spread across Asia around 60,000 years ago and arrived on new continents and islands since then.

List of human evolution fossils: following tables give a brief overview of several notable hominin fossil finds relating to human evolution beginning with the formation of the Hominini tribe in the late Miocene (roughly 6 mya). As there are thousands of fossils, mostly fragmentary, often consisting of single bones or isolated teeth with complete skulls and skeletons rare, this overview is not complete, but does show some of the most important finds. The fossils are arranged by approximate age as determined by radiometric dating and/or incremental dating and the species name represents current consensus; if there is no clear scientific consensus the other possible classifications are indicated. Most of the fossils shown are not considered direct ancestors to Homo sapiens but are closely related to direct ancestors and are therefore important to the study of the lineage.

Jebel Irhoud: archaeological site located just north of the locality known as Tlet Ighoud, about 50 km (30 mi) south-east of the city of Safi in Morocco. It is noted for the Hominin fossils that have been found there since the site's discovery in 1960. Originally thought to be Neanderthals, the specimens have since been assigned to Homo sapiens and have been dated to over 300,000 years old. If correct, this would make them by far the oldest known fossil remains of Homo sapiens.

Template:Apes:

Neanderthal Genome Project

Chimpanzee genome project

Genes of humans vs non-human apes:

SRGAP2: protein twice duplicated in human genome as compared to chimps and other extant apes. First duplication 3.4 mya, next 2.4 mya (this duplication allows neurons to migrate faster in the human brain).

Chimpanzee–human last common ancestor: last common ancestor shared by the extant Homo (human) and Pan (chimpanzee and bonobo) genera of Hominini. Due to complex hybrid speciation, it is not possible to give a precise estimate on the age of this ancestral individual. While "original divergence" between populations may have occurred as early as 13 Mya (Miocene), hybridization may have been ongoing until as recent as 4 Mya.

Graecopithecus: hominid originally identified by a single mandible found in 1944. Since then analysis of tooth specimens has led to suggestions that Graecopithecus may be the oldest known direct ancestor of modern man, though the claim is contested.

Baculum: penis bone; absent in humans but present in nearest extant relative the chimpanzee

Population bottleneck: Humans (Toba; 'long bottleneck')

Recent African origin of modern humans: supposition - archaic Homo sapiens evolved to anatomically modern humans solely in Africa, between 200 ka and 150 ka, that members of one branch of Homo sapiens left Africa by between 125 ka and 60 ka, and that over time these humans replaced earlier human populations such as Neanderthals and Homo erectus without interbreeding with them.

Toba catastrophe theory: between 69 ka and 77 ka at Lake Toba (Sumatra, Indonesia); supposed bottleneck in human evolution

Multiregional origin of modern humans: less probable explanation (esp. considering Toba), but maybe the synthesis of both (with majority of modern humans coming from Africa 125 ka - 60 ka, while very small amount survived Toba from the migrations as far back as 2Ma?) is also possible

Template:Human Evolution

Anatomically modern humans vs Archaic humans (includes Homo heidelbergensis, Homo rhodesiensis, Homo neanderthalensis and sometimes Homo antecessor):

Omo remains: 198 ± 14 ka (geologic layer below the fossil), 104 ± 7 ka (geologic layer above the fossil)

Homo sapiens idaltu: ~160 ka

Skhul and Qafzeh hominids: 80 - 120 ka; a few Neanderthal features, but huge resemblance to modern humans

Denisova hominin: ~41 ka mtDNA and genome sequenced; between 4% and 6% of the genome of Melanesians derives from a Denisovan population; mtDNA of the Denisova hominin is distinct from the mtDNAs of Neanderthals and modern humans

Homo erectus soloensis, aka Solo Man: While most subspecies of Homo erectus disappeared from the fossil record roughly 400,000 years ago, H. e. soloensis persisted up until 50,000 years ago in regions of Java and was possibly absorbed by a local Homo sapiens population at the time of its decline.

Researchers: Svante Pääbo

Interbreeding between archaic and modern humans: during the Middle Paleolithic and early Upper Paleolithic. The interbreeding happened in several independent events that included Neanderthals, Denisovans, as well as several unidentified hominins respectively. In Eurasia, interbreeding between Neanderthals and Denisovans (both assumed to be derived from Eurasian Homo heidelbergensis) with modern humans took place several times between about 100,000 and 40,000 years ago, both before and after the recent out-of-Africa migration 70,000 years ago. Neanderthal-derived DNA was found in the genome of contemporary populations in Europe and Asia, estimated as accounting for between 1% and 6% of modern genomes. The highest rates of archaic admixture overall have been found in indigenous Oceanian and Southeast Asian populations, with an estimated 4–6% of the genome of modern Melanesians being derived from Denisovans. Neanderthal-derived and Denisovan-derived ancestry is significantly absent from most modern populations in Sub-Saharan Africa. However, archaic alleles consistent with several independent admixture events in the subcontinent have been found.

Neanderthals: These results suggest that a majority of the admixture into modern humans came from Neanderthal populations that had diverged (about 80–100kya) from the Vindija and Mezmaiskaya Neanderthal lineages before the latter two diverged from each other. Analyzing chromosome 21 of the Altai (Siberia), El Sidrón (Spain), and Vindija (Croatia) Neanderthals, it is determined that—of these three lineages—only the El Sidrón and Vindija Neanderthals display significant rates of gene flow (0.3–2.6%) into modern humans, suggesting that the El Sidrón and Vindija Neanderthals are more closely related than the Altai Neanderthal to the Neanderthals that interbred with modern humans about 47,000–65,000 years ago. About 20% of the Neanderthal genome has been found introgressed in the modern human population (by analyzing East Asians and Europeans), but the figure has also been estimated at one-third. A higher Neanderthal admixture was found in East Asians than in Europeans, which is estimated to be about 20% more introgression into East Asians. It has also been observed that there's a small but significant variation of Neanderthal admixture rates within European populations, but no significant variation within East Asian populations. No evidence of Neanderthal mitochondrial DNA has been found in modern humans. This would suggest that successful admixture with Neanderthals happened paternally rather than maternally on the side of Neanderthals. Possible hypotheses are that Neanderthal mitochondrial DNA had detrimental mutations that led to the extinction of carriers, that the hybrid offspring of Neanderthal mothers were raised in Neanderthal groups and became extinct with them, or that female Neanderthals and male Sapiens did not produce fertile offspring. It has been found that there is a presence of large genomic regions with strongly reduced Neanderthal contribution in modern humans due to negative selection, partly caused by hybrid male infertility. These large regions of low Neanderthal contribution were most-pronounced on the X chromosome—with fivefold lower Neanderthal ancestry compared to autosomes—and contained relatively high numbers of genes specific to testes. This means that modern humans have relatively few Neanderthal genes that are located on the X chromosome or expressed in the testes, consistent with the fact that male infertility is affected by a disproportionately large amount of genes on X chromosomes. Looking at heterozygous individuals (carrying both Neanderthal and modern human versions of a gene), the allele-specific expression of introgressed Neanderthal alleles was found to be significantly lower in the brain and testes relative to other tissues. In the brain, this was most pronounced at the cerebellum and basal ganglia. This downregulation suggests that modern humans and Neanderthals possibly experienced a relative higher rate of divergence in these specific tissues.
Denisovans: Denisovan DNA has been found in modern humans, and it has been estimated that 90% of the Denisovan genome is still present. It has been shown that Melanesians (e.g. Papua New Guinean and Bougainville Islander) share relatively more alleles with Denisovans when compared to other Eurasians and Africans. It estimated that 4% to 6% of the genome in Melanesians derives from Denisovans, while no other Eurasians or Africans displayed contributions of the Denisovan genes. In addition, Aboriginal Australians also show a relative increased allele sharing with Denisovans, compared to other Eurasians and African populations, consistent with the hypothesis of increased admixture between Denisovans and Melanesians. The Denisovan-derived EPAS1 gene variant is common in Tibetans and was positively selected in their ancestors after they colonized the Tibetan plateau.
Archaic African hominins: Rapid decay of fossils in Sub-Saharan African environments makes it currently unfeasible to compare modern human admixture with reference samples of archaic Sub-Saharan African hominins. From three candidate regions with introgression found by searching for unusual patterns of variations (showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size) in 61 non-coding regions from two hunter-gatherer groups (Biaka Pygmies and San who have significant admixture) and one West African agricultural group (Mandinka who don't have significant admixture), it is concluded that roughly 2% of the genetic material found in these Sub-Saharan African populations was inserted into the human genome approximately 35,000 years ago from archaic hominins that broke away from the modern human lineage around 700,000 years ago. A survey for the introgressive haplotypes across many Sub-Saharan populations suggest that this admixture event happened with archaic hominins who once inhabited Central Africa.

Man's Place in Nature (1863): book by Thomas Henry Huxley, in which he gives evidence for the evolution of man and apes from a common ancestor. It was the first book devoted to the topic of human evolution, and discussed much of the anatomical and other evidence. Backed by this evidence, the book proposed to a wide readership that evolution applied as fully to man as to all other life.

The Descent of Man, and Selection in Relation to Sex (1871): book on evolutionary theory by English naturalist Charles Darwin. The book discusses many related issues, including evolutionary psychology, evolutionary ethics, differences between human races, differences between sexes, the dominant role of women in choosing mating partners, and the relevance of the evolutionary theory to society.

Recent human evolution: evolutionary adaptation and selection and genetic drift within anatomically modern human populations, since their separation and dispersal in the Middle Paleolithic. Following the peopling of Africa some 130,000 years ago, and the recent Out-of-Africa expansion some 70,000 to 50,000 years ago, some sub-populations of H. sapiens have been essentially isolated for tens of thousands of years prior to the early modern Age of Discovery. Combined with archaic admixture this has resulted in significant genetic variation, which in some instances has been shown to be the result of directional selection taking place over the past 15,000 years, i.e. significantly later than possible archaic admixture events. Selection pressures were especially severe for populations affected by the Last Glacial Maximum in Eurasia, and for sedentary farming populations since the Neolithic. Adaptations have also been found in modern populations living in extreme climatic conditions such as the Arctic and the Tibetan Plateau, as well as immunological adaptations such as resistance against brain disease in populations practicing mortuary cannibalism. Recent divergence of Eurasian lineages was sped up significantly during the Last Glacial Maximum, the Mesolithic and the Neolithic, due to increased selection pressures and due to founder effects associated with migration. Alleles predictive of light skin have been found in Neanderthals, but the alleles for light skin in Europeans and East Asians, associated with, KITLG and ASIP, are (as of 2012) thought to have not been acquired by archaic admixture but recent mutations since the LGM. Phenotypes associated with the "white" or "Caucasian" populations of Western Eurasian stock emerge during the LGM, from about 19,000 years ago. The light skin pigmentation characteristic of modern Europeans is estimated to have spread across Europe in a "selective sweep" during the Mesolithic (19 to 11 ka). The associated TYRP1 SLC24A5 and SLC45A2 alleles emerge around 19 ka, still during the LGM, most likely in the Caucasus. The HERC2 variation for blue eyes first appears around 14 ka in Italy and the Caucasus. Both Neanderthal and EEMH had somewhat larger cranial volumes on average than modern Europeans, suggesting the relaxation of selection pressures for larger brain volume after the end of the LGM. In modern historical times, since industrialization, some trends have been observed: for instance, menopause is evolving to occur later.

High-altitude adaptation in humans:

Tibetans: have been living in this region for 3,000 years, do not exhibit the elevated haemoglobin concentrations to cope with oxygen deficiency as observed in other populations who have moved temporarily or permanently at high altitudes. Instead, the Tibetans inhale more air with each breath and breathe more rapidly than either sea-level populations or Andeans. Tibetans have better oxygenation at birth, enlarged lung volumes throughout life, and a higher capacity for exercise. They show a sustained increase in cerebral blood flow, lower haemoglobin concentration, and less susceptibility to chronic mountain sickness than other populations, due to their longer history of high-altitude habitation. Tibetans have high levels (mostly double) of nitric oxide in their blood, when compared to lowlanders, and this probably helps their blood vessels dilate for enhanced blood circulation. Further, their haemoglobin level is not significantly different (average 15.6 g/dl in males and 14.2 g/dl in females), from those of people living at low altitude. (Normally, mountaineers experience >2 g/dl increase in Hb level at Mt. Everest base camp in two weeks.) In this way they are able to evade both the effects of hypoxia and mountain sickness throughout life. Even when they climbed the highest summits like Mt. Everest, they showed regular oxygen uptake, greater ventilation, more brisk hypoxic ventilatory responses, larger lung volumes, greater diffusing capacities, constant body weight and a better quality of sleep, compared to people from the lowland.
Andeans: Andean haemoglobin concentration is higher compared to those of lowlander population, which also happens to lowlanders moving to high altitude. When they spend some weeks in the lowland their haemoglobin drops to average of other people. This shows only temporary and reversible acclimatisation. However, in contrast to lowland people, they do have increased oxygen level in their haemoglobin, that is, more oxygen per blood volume than other people. This confers an ability to carry more oxygen in each red blood cell, making a more effective transport of oxygen in their body, while their breathing is essentially at the same rate. Andeans have developmentally acquired enlarged residual lung volume and its associated increase in alveolar area, which are supplemented with increased tissue thickness and moderate increase in red blood cells. Though the physical growth in body size is delayed, growth in lung volumes is accelerated. An incomplete adaptation such as elevated haemoglobin levels still leaves them at risk for mountain sickness with old age. Among the Quechua people of the Altiplano, there is a significant variation in NOS3 (the gene encoding endothelial nitric oxide synthase, eNOS), which is associated with higher levels of nitric oxide in high altitude. Among the Bolivian Aymara people, the resting ventilation and hypoxic ventilatory response were quite low (roughly 1.5 times lower), in contrast to those of the Tibetans. The intrapopulation genetic variation was relatively less among the Aymara people. Moreover, unlike the Tibetans, the blood haemoglobin level is quite normal among Aymarans, with an average of 19.2 g/dl for males and 17.8 g/dl for females.
Ethiopians: among healthy individuals, the average haemoglobin concentrations are 15.9 and 15.0 g/dl for males and females respectively (which is lower than normal, almost similar to the Tibetans), and an average oxygen saturation of haemoglobin is 95.3% (which is higher than average, like the Andeans). Additionally, Ethiopian highlanders do not exhibit any significant change in blood circulation of the brain, which has been observed among the Peruvian highlanders (and attributed to their frequent altitude-related illnesses). Yet, similar to the Andeans and Tibetans, the Ethiopian highlanders are immune to the extreme dangers posed by high-altitude environment, and their pattern of adaptation is definitely unique from that of other highland peoples.

Evolutionary biology, chemistry

Category:Biological evolution

Category:Evolutionary biology {also q.v. Category:Phylogenetics}

Category:Evolutionary processes

Category:Molecular evolution

{q.v. User:Kazkaskazkasako/Books/Physical sciences#Origin of life, abiogenesis}

Homology (biology): relationship between a pair of structures, or genes, due to having shared ancestry. Anatomical homology. Sequence homology: Orthology - homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous (orthologs, or orthologous genes); Paralogy - homologous sequences are paralogous if they were created by a duplication event within the genome. Homology between sexes and forms.

Deep homology: growth and differentiation processes are governed by genetic mechanisms that are homologous and deeply conserved across a wide range of species.

Abiogenesis (biopoesis): "how biological life arises from inorganic matter through natural processes, and the method by which life on Earth arose". Early life on earth: at high temperature(?), at high pressure (?), at which concentrations of simple "bio-molecules"? "Primordial soup": Miller–Urey experiment (nowadays: reducing atmosphere, monomer formation); deep sea vent theory; Fox's experiments; Eigen's hypothesis: self-replicating hypercycle; iron–sulfur world theory; radioactive beach hypothesis; RNA world hypothesis...

Last universal ancestor (LUA; last universal common ancestor (LUCA), cenancestor): most recent organism from which all organisms now living on Earth descend; MRCA of all current life on Earth. LUA is estimated to have lived some 3.5-3.8 bya. LUA was a small, single-cell organism; had a cell wall and a ring-shaped coil of DNA floating freely within the cell, like modern bacteria; genetic code was based on DNA; genetic code was expressed via RNA intermediates, which were single-stranded; genetic code was expressed into proteins; proteins were assembled from free amino acids by translation of an mRNA by ribosomes, tRNA and a group of related proteins; ATP was used as an energy intermediate; several hundred protein enzymes which catalyzed chemical reactions that extract energy from fats, sugars, and amino acids, and that synthesize fats, sugars, amino acids, and nucleic acid bases using arbitrary chemical pathways; inside the cell, the concentration of sodium was lower, and potassium was higher, than outside; cell multiplied by duplicating all its contents followed by cellular division.

Evolutionary arms race: prey vs predator, parasite vs host, within the species.

Sexual conflict (sexual antagonism):

Penis fencing: flatworms

Traumatic insemination (hypodermic insemination): bed bugs

Sexual coercion

Sexual cannibalism: primarily by members of arachnid orders as well as several insect orders (mantis).

Love dart (gypsobelum)

Error threshold (evolution): limit on the number of base pairs a self-replicating molecule may have before mutation will destroy the information in subsequent generations of the molecule. The error threshold is crucial to understanding "Eigen's paradox". "mutation process places a limit on the number of digits a molecule may have. If a molecule exceeds this critical size, the effect of the mutations become overwhelming and a runaway mutation process will destroy the information in subsequent generations of the molecule." (Eigen, 1971)

E. coli long-term evolution experiment: ongoing study in experimental evolution led by Richard Lenski that has been tracking genetic changes in 12 initially identical populations of asexual Escherichia coli bacteria since 1988.02.24. Over the course of the experiment, Lenski and his colleagues have reported a wide array of phenotypic and genotypic changes in the evolving populations. These have included changes that have occurred in all 12 populations and others that have only appeared in one or a few populations. For example, all 12 populations showed a similar pattern of rapid improvement in fitness that decelerated over time, faster growth rates, and increased cell size. Half of the populations have evolved defects in DNA repair that have caused mutator phenotypes marked by elevated mutation rates. The most striking adaptation reported so far is the evolution of aerobic growth on citrate, which is unusual in E. coli, in one population at some point between generations 31,000 and 31,500.

Darwin–Wallace Medal: medal awarded by the Linnean Society of London for "major advances in evolutionary biology". Historically, the medals have been awarded every 50 years, beginning in 1908. That year marked 50 years after the joint presentation by Charles Darwin and Alfred Russel Wallace of two scientific papers—On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection—to the Linnean Society of London in 1858.07.01. Fittingly, Wallace was one of the first recipients of the medal, in his case it was, exceptionally, in gold, rather than the silver version presented in the six other initial awards. However, in 2008 the Linnean Society announced that due to the continuing importance of evolutionary research, the medal will be awarded on an annual basis beginning in 2010.

Parasitism, parasites

Category:Parasitism

Category:Parasites

Category:Parasites by host

Category:Parasites of animals

Category:Mind-altering parasitism

Behavior-altering parasite: parasites with two or more hosts, capable of causing changes in the behavior of one of their hosts to enhance their transmission, sometimes directly affecting the hosts' decision-making and behavior control mechanisms. They do this by making the intermediate host, where they may reproduce asexually, more likely to be eaten by a predator at a higher trophic level which becomes the definitive host where the parasite reproduces sexually - parasite increased trophic facilitation or parasite increased trophic transmission. Parasites may also alter the host behaviour to increase the protection to the parasites or their offspring - bodyguard manipulation.

Mass extinctions

Category:Evolutionarily significant biological phenomena

Category:Extinction

Category:Extinction events

Category:Endings

Category:Natural disasters

Category:Extinction events

{q.v.

User:Kazkaskazkasako/Books/Physical sciences#Volcanology, vulcanology

}

Extinction event (mass extinction, biotic crisis)

Permian–Triassic extinction event (P-Tr, P-T): occurred about 252 mya, forming the boundary between the Permian and Triassic geologic periods, as well as between the Paleozoic and Mesozoic eras. It is the Earth's most severe known extinction event, with up to 96% of all marine species and 70% of terrestrial vertebrate species becoming extinct. It is the only known mass extinction of insects. Some 57% of all biological families and 83% of all genera became extinct. Because so much biodiversity was lost, the recovery of land-dwelling life took significantly longer than after any other extinction event, possibly up to 10 Ma. U–Pb zircon dates from five volcanic ash beds from the Global Stratotype Section and Point for the Permian–Triassic boundary at Meishan, China - extinction occurred between 251.941 ± 0.037 and 251.880 ± 0.031 Ma ago, a duration of 60 ± 48 ka. Further evidence for environmental change around the P–Tr boundary suggests an 8 °C (14 °F) rise in temperature, and an increase in CO₂ levels by 2000 ppm (for comparison, the concentration immediately before the industrial revolution was 280 ppm, and the amount today is about 410 ppm). It has been suggested that the Permian–Triassic boundary is associated with a sharp increase in the abundance of marine and terrestrial fungi, caused by the sharp increase in the amount of dead plants and animals fed upon by the fungi. The groups with the highest survival rates generally had active control of circulation, elaborate gas exchange mechanisms, and light calcification; more heavily calcified organisms with simpler breathing apparatuses suffered the greatest loss of species diversity. In the case of the brachiopods, at least, surviving taxa were generally small, rare members of a formerly diverse community. No coal deposits are known from the Early Triassic, and those in the Middle Triassic are thin and low-grade. Coal-producing ecosystems, rather than disappearing, may have moved to areas where we have no sedimentary record for the Early Triassic. A study (δ¹⁸O) published in the journal Science found that during the Great Extinction, ocean surface temperatures reached 40 °C in some places. This explains why recovery took so long: it was too hot for life to survive. Anoxic waters may have also delayed the recovery. Evidence for widespread ocean anoxia (severe deficiency of oxygen) and euxinia (presence of hydrogen sulfide) is found from the Late Permian to the Early Triassic. Throughout most of the Tethys and Panthalassic Oceans, evidence for anoxia, including fine laminations in sediments, small pyrite framboids, high uranium/thorium ratios, and biomarkers for green sulfur bacteria, appear at the extinction event. However, in some sites, including Meishan, China, and eastern Greenland, evidence for anoxia precedes the extinction.

Ecological extinction: "the reduction of a species to such low abundance that, although it is still present in the community, it no longer interacts significantly with other species".

Empty forest: term coined by Kent H. Redford's article "The Empty Forest" (1992), which was published in BioScience. An "empty forest" refers to an ecosystem that is void of large mammals. Empty forests are characterized by an otherwise excellent habitat, and often have large, fully grown trees, although they lack large mammals as a result of human impact. Empty forests show that human impact can destroy an ecosystem from within as well as from without.

Cretaceous–Paleogene extinction event

Category:Cretaceous–Paleogene boundary

Cretaceous–Paleogene boundary: geological signature, usually a thin band of rock. The K–Pg boundary marks the end of the Cretaceous Period, the last period of the Mesozoic Era, and marks the beginning of the Paleogene Period, the first period of the Cenozoic Era. Its age is usually estimated at around 66 Ma (mya), with radioisotope dating yielding a more specific age of 66.043 ± 0.011 Ma.

Cretaceous–Paleogene extinction event (K–Pg, aka: Cretaceous–Tertiary (K–T) extinction): sudden mass extinction of three-quarters of the plant and animal species on Earth, approximately 66 mya. With the exception of some ectothermic species such as sea turtles and crocodilians, no tetrapods weighing more than 25 kilograms (55 pounds) survived. It marked the end of the Cretaceous Period, and with it the Mesozoic era, while heralding the beginning of the Cenozoic era, which continues to this day. As originally proposed in 1980 by a team of scientists led by Luis Alvarez and his son Walter, it is now generally thought that the K–Pg extinction was caused by the impact of a massive asteroid 10 to 15 km wide, 66 mya, which devastated the global environment, mainly through a lingering impact winter which halted photosynthesis in plants and plankton. The impact hypothesis, also known as the Alvarez hypothesis, was bolstered by the discovery of the 180 km Chicxulub crater in the Gulf of Mexico's Yucatán Peninsula in the early 1990s, which provided conclusive evidence that the K–Pg boundary clay represented debris from an asteroid impact. The fact that the extinctions occurred simultaneously provides strong evidence that they were caused by the asteroid. A 2016 drilling project into the Chicxulub peak ring confirmed that the peak ring comprised granite ejected within minutes from deep in the earth, but contained hardly any gypsum, the usual sulfate-containing sea floor rock in the region: the gypsum would have vaporized and dispersed as an aerosol into the atmosphere, causing longer-term effects on the climate and food chain. In October 2019, researchers reported that the event rapidly acidified the oceans, producing ecological collapse and, in this way as well, produced long-lasting effects on the climate, and accordingly was a key reason for the mass extinction at the end of the Cretaceous. A wide range of terrestrial species perished in the K–Pg extinction, the best-known being the non-avian dinosaurs, along with mammals, birds, lizards, insects, plants, and all the pterosaurs. In the oceans, the K–Pg extinction killed off plesiosaurs and mosasaurs and devastated teleost fish, sharks, mollusks (especially ammonites, which became extinct), and many species of plankton. It is estimated that 75% or more of all species on Earth vanished. Yet the extinction also provided evolutionary opportunities: in its wake, many groups underwent remarkable adaptive radiation—sudden and prolific divergence into new forms and species within the disrupted and emptied ecological niches. 22/12/25Mammals in particular diversified in the Paleogene, evolving new forms such as horses, whales, bats, and primates. The surviving group of dinosaurs were avians, a few species of ground and water fowl, which radiated into all modern species of birds. Among other groups, teleost fish and perhaps lizards also radiated.

Evidence for impact: In 1980, a team of researchers consisting of Nobel Prize-winning physicist Luis Alvarez, his son, geologist Walter Alvarez, and chemists Frank Asaro and Helen Michel discovered that sedimentary layers found all over the world at the Cretaceous–Paleogene boundary contain a concentration of iridium many times greater than normal (30, 160, and 20 times in three sections originally studied). Iridium is extremely rare in Earth's crust because it is a siderophile element which mostly sank along with iron into Earth's core during planetary differentiation. As iridium remains more abundant in most asteroids and comets, the Alvarez team suggested that an asteroid struck the Earth at the time of the K–Pg boundary.
Alternative hypotheses: Deccan Traps: Combining these theories, some geophysical models suggest that the impact contributed to the Deccan Traps. These models, combined with high-precision radiometric dating, suggest that the Chicxulub impact could have triggered some of the largest Deccan eruptions, as well as eruptions at active volcanoes anywhere on Earth.

Chicxulub crater: impact crater buried underneath the Yucatán Peninsula in Mexico. Its center is located near the town of Chicxulub, after which the crater is named. It was formed when a large asteroid or comet about 11 to 81 km in diameter, known as the Chicxulub impactor, struck the Earth. The date of the impact coincides precisely with the Cretaceous–Paleogene boundary (K–Pg boundary), slightly less than 66 Ma, and a widely accepted theory is that worldwide climate disruption from the event was the cause of the Cretaceous–Paleogene extinction event, a mass extinction in which 75% of plant and animal species on Earth became extinct, including all non-avian dinosaurs. The crater is estimated to be 150 km in diameter and 20 km in depth, well into the continental crust of the region of about 10–30 km depth. It is the second largest confirmed impact structure on Earth, and the only one whose peak ring is intact and directly accessible for scientific research.

Impact winter: hypothesized period of prolonged cold weather due to the impact of a large asteroid or comet on the Earth's surface. If an asteroid were to strike land or a shallow body of water, it would eject an enormous amount of dust, ash, and other material into the atmosphere, blocking the radiation from the Sun. This would cause the global temperature to decrease drastically. If an asteroid or comet with the diameter of about 5 km or more were to hit in a large deep body of water or explode before hitting the surface, there would still be an enormous amount of debris ejected into the atmosphere. It has been proposed that an impact winter could lead to mass extinction, wiping out many of the world's existing species. The Cretaceous–Paleogene extinction event probably involved an impact winter, and led to mass extinction of most tetrapods weighing more than 25 kg.

Ecology

{q.v. User:Kazkaskazkasako/Books/Physical sciences#Ecology}

Biogeography

{q.v. User:Kazkaskazkasako/Books/Physical sciences#Biogeography}

Zoology

Ethology: scientific and objective study of animal behaviour, and is a sub-topic of zoology; animal behaviour under natural conditions, as opposed to behaviourism, which focuses on behavioural response studies in a laboratory setting.

Animals

{q.v. #Human medicine and human biology}

Animal (Animalia, Metazoa)

Parazoa {subkingdom}: Sponge (phylum=Porifera) Placozoa (phylum; "flat animals")

Animal sexual behaviour:

Monogamy: social monogamy (90% of bird species are socially monogamous) vs sexual monogamy vs genetic monogamy (very few species show 100% genetic monogamy; out of 180 different species of socially monogamous songbirds, only 10% are sexually monogamous).

Polygamy: polygyny: when a new alpha male arrives, the current embryos and the young are killed/aborted in one of several ways: competitive infanticide (lions, hippopotamuses, some monkeys), harassment to miscarriage (horses, baboons), pheromone based spontaneous abortion (some rodents (e.g. mice): Bruce-Parkes effect).

Promiscuity: chimpanzees and bonobos.

Against Nature?

Diagram of homologous bones and analogous flying adaptions in the forelimbs of three groups of flying vertebrates both recent and fossilized: pterosaur (Pterosauria), bat (Chiroptera), bird (Aves).

Flying and gliding animals: a number of animals are capable of aerial locomotion, either by powered flight or by gliding. This trait has appeared by evolution many times, without any single common ancestor. Flight has evolved at least four times in separate animals: insects, pterosaurs, birds, and bats. Gliding has evolved on many more occasions. Usually the development is to aid canopy animals in getting from tree to tree, although there are other possibilities. Gliding, in particular, has evolved among rainforest animals, especially in the rainforests in Asia (most especially Borneo) where the trees are tall and widely spaced. Several species of aquatic animals, and a few amphibians and reptiles have also evolved this gliding flight ability, typically as a means of evading predators. Evolution and ecology: Gliding and parachuting, Powered flight evolution.

Limits and extremes:
- Flying and soaring: the largest known flying animal was formerly thought to be Pteranodon, a pterosaur with a wingspan of up to 7.5 m.
- Smallest: is no minimum size for getting airborne. Indeed, there are many bacteria floating in the atmosphere that constitute part of the aeroplankton.
- Fastest: peregrine falcon, which when diving travels at 300 km/h or faster.
- Slowest: Most flying animals need to travel forward to stay aloft. However, some creatures can stay in the same spot, known as hovering, either by rapidly flapping the wings, as do hummingbirds, hoverflies, dragonflies, and some others, or carefully using thermals, as do some birds of prey. The slowest flying non-hovering bird recorded is the American woodcock, at 8 km/h.
- Highest flying: records of a Rüppell's vulture Gyps rueppelli, a large vulture, being sucked into a jet engine 11,550 m above Côte d'Ivoire in West Africa. The animal that flies highest most regularly is the bar-headed goose Anser indicus, which migrates directly over the Himalayas between its nesting grounds in Tibet and its winter quarters in India. They are sometimes seen flying well above the peak of Mount Everest at 8,848 m.
Flying animals: Extant: Insects, Birds, Mammals (bats); Extinct: Reptiles (Pterosaurs), Non-avian dinosaurs
Gliding animals: Extant: Insects, Spiders, Molluscs (flying squid), Fish, Amphibians, Reptiles, Mammals (flying squirrels, anomalures, colugos, sifaka, flying phalangers, greater glider, feather-tailed possums); Extinct: Reptiles, Non-avian dinosaurs, Fish, Mammals.

Arthropod (Arthropoda)

Category:Arthropods

Category:Arthropods by classification

Category:Hexapoda

Category:Insects

Trilobites
Chelicerates
Myriapods
Crustaceans
Hexapods

Panarthropoda

Onychophora

Tardigrada

Euarthropoda

Chelicerata

Mandibulata

Myriapoda

Pancrustacea

Ostracoda, Branchiura, Pentastomida, Mystacocarida

Branchiopoda, Copepoda, Malacostraca, Thecostraca

	Remipedia, Cephalocarida

	Hexapoda

traditional Crustacea

Phylogenetic relationships of the major extant arthropod groups according to Regier et al. (2010); traditional subphyla in bold

Crustacea

Crustacean

Barnacle (subclass Cirripedia, Latin "curl-footed"): related to crabs and lobsters. Barnacles are exclusively marine, and tend to live in shallow and tidal waters, typically in erosive settings. They are sessile (nonmobile) and most are suspension feeders, but those in infraclass Rhizocephala are highly specialized parasites on crustaceans. They have four nektonic (active swimming) larval stages. Around 1,000 barnacle species are currently known. Barnacles were originally classified by Linnaeus and Cuvier as Mollusca, but in 1830 John Vaughan Thompson published observations showing the metamorphosis of the nauplius and cypris larvae into adult barnacles, and noted how these larvae were similar to those of crustaceans. In 1834 Hermann Burmeister published further information, reinterpreting these findings. The effect was to move barnacles from the phylum of Mollusca to Articulata, showing naturalists that detailed study was needed to reevaluate their taxonomy. Charles Darwin took up this challenge in 1846, and developed his initial interest into a major study published as a series of monographs in 1851 and 1854. Darwin undertook this study, at the suggestion of his friend Joseph Dalton Hooker, to thoroughly understand at least one species before making the generalisations needed for his theory of evolution by natural selection.

Hexanuplia

Copepod ("oar-feet"): group of small crustaceans found in nearly every freshwater and saltwater habitat. Some species are planktonic (inhabiting sea waters), some are benthic (living on the ocean floor), a number of species have parasitic phases, and some continental species may live in limnoterrestrial habitats and other wet terrestrial places, such as swamps, under leaf fall in wet forests, bogs, springs, ephemeral ponds, and puddles, damp moss, or water-filled recesses (phytotelmata) of plants such as bromeliads and pitcher plants. Many live underground in marine and freshwater caves, sinkholes, or stream beds. Copepods are sometimes used as biodiversity indicators.

Crustacean larva: may pass through a number of larval and immature stages between hatching from their eggs and reaching their adult form. Each of the stages is separated by a moult, in which the hard exoskeleton is shed to allow the animal to grow. The larvae of crustaceans often bear little resemblance to the adult, and there are still cases where it is not known what larvae will grow into what adults. This is especially true of crustaceans which live as benthic adults (on the sea bed), more-so than where the larvae are planktonic, and thereby easily caught.

Insects (Insecta), hexapods

Category:Insects

Category:Insects by classification

Orthoptera: order of insects includes the grasshoppers, crickets, cave crickets, Jerusalem crickets, katydids, weta, lubber, Acrida, and locusts.

Ensifera

Weta: although they are of an ancient lineage, the present species are quite young, which conflicts with those earlier ideas about dispersal of weta forebears around the Southern Hemisphere (Wallis et al. 2000). Giant, tree, ground, and tusked weta are all members of the family Anostostomatidae (formerly in the Stenopelmatidae, but recently separated (Johns, 1997)). Cave weta are better called tokoriro, and are members of the family Rhaphidophoridae called cave crickets or camel crickets elsewhere, in a different ensiferan superfamily.

Ants (family Formicidae): eusocial insects, along with the related wasps and bees, belong to the order Hymenoptera. Ants appear in the fossil record across the globe in considerable diversity during the latest Early Cretaceous and early Late Cretaceous, suggesting an earlier origin. Ants evolved from vespoid wasp ancestors in the Cretaceous period, and diversified after the rise of flowering plants. More than 13,800 of an estimated total of 22,000 species have been classified. They are easily identified by their elbowed antennae and the distinctive node-like structure that forms their slender waists. Ants form colonies that range in size from a few dozen predatory individuals living in small natural cavities to highly organised colonies that may occupy large territories and consist of millions of individuals. Larger colonies consist of various castes of sterile, wingless females, most of which are workers (ergates), as well as soldiers (dinergates) and other specialised groups. Nearly all ant colonies also have some fertile males called "drones" and one or more fertile females called "queens" (gynes). The colonies are described as superorganisms because the ants appear to operate as a unified entity, collectively working together to support the colony. Ants have colonised almost every landmass on Earth. The only places lacking indigenous ants are Antarctica and a few remote or inhospitable islands. Ants thrive in most ecosystems and may form 15–25% of the terrestrial animal biomass. Ant societies have division of labour, communication between individuals, and an ability to solve complex problems.

Weaver ants (green ants; genus Oecophylla): live in trees (they are obligately arboreal) and are known for their unique nest building behaviour where workers construct nests by weaving together leaves using larval silk. Colonies can be extremely large consisting of more than a hundred nests spanning numerous trees and containing more than half a million workers. Like many other ant species, weaver ants prey on small insects and supplement their diet with carbohydrate-rich honeydew excreted by small insects (Hemiptera). Weaver ant workers exhibit a clear bimodal size distribution, with almost no overlap between the size of the minor and major workers.

Army ants: applied to over 200 ant species in different lineages. Due to their aggressive predatory foraging groups, known as "raids", a huge number of ants forage simultaneously over a limited area. Unlike most ant species, army ants do not construct permanent nests; an army ant colony moves almost incessantly over the time it exists. All species are members of the true ant family, Formicidae, but several groups have independently evolved the same basic behavioural and ecological syndrome. This syndrome is often referred to as "legionary behaviour", and may be an example of convergent evolution.

Argentine ants (Linepithema humile): native to northern Argentina, Uruguay, Paraguay, Bolivia and southern Brazil. It is an invasive species that has been established in many Mediterranean climate areas, inadvertently introduced by humans to many places, including South Africa, New Zealand, Japan, Easter Island, Australia, Europe, Hawaii, and the continental USA.

Fire ants (genus Solenopsis): only a minority in the genus, which includes over 200 species of Solenopsis worldwide. Solenopsis are stinging ants, and most of their common names reflect this, for example, ginger ants and tropical fire ants. Many species also are called red ants because of their light brown color, though species of ants in many other genera are similarly named for similar reasons.

Necrophoresis: sanitation behavior found in social insects – such as ants, bees, wasps, and termites – in which they carry away the dead bodies of members of their colony from the nest or hive area. The term was introduced in 1958 by E.O. Wilson and his colleagues.

Worker policing: behavior seen in colonies of social hymenopterans (ants, bees, and wasps) whereby worker females eat or remove eggs that have been laid by other workers rather than those laid by a queen. Worker policing ensures that the offspring of the queen will predominate in the group. In certain species of bees, ants and wasps, workers or the queen may also act aggressively towards fertile workers. Worker policing has been suggested as a form of coercion to promote the evolution of altruistic behavior in eusocial insect societies.

Gamergate (ant) (/ˈɡæmərˌɡeɪt/ GAMM-ər-gayt): mated worker ant that can reproduce sexually, i.e., lay fertilized eggs that will develop as females. In the vast majority of ant species, workers are sterile and gamergates are restricted to taxa where the workers have a functional sperm reservoir ('spermatheca'). In some species, gamergates reproduce in addition to winged queens (usually upon the death of the original foundress), while in other species the queen caste has been completely replaced by gamergates. In gamergate species, all workers in a colony have similar reproductive potentials, but as a result of physical interactions, a dominance hierarchy is formed and only one or a few top-ranking workers can mate (usually with foreign males) and produce eggs. Subsequently however, aggression is no longer needed as gamergates secrete chemical signals that inform the other workers of their reproductive status in the colony. Depending on the species, there can be one gamergate per colony (monogyny) or several gamergates (polygyny). Most gamergate species have colonies with a few hundred or fewer workers. "Gamergate" derives from the Greek words γάμος (gámos) and ἐργάτης (ergátēs) and means "married worker".

From first amniotes to modern animals

Amniote

Synapsid: (Greek, 'fused arch'), synonymous with theropsids (Greek, 'beast-face'), are a group of animals that includes mammals and every animal more closely related to mammals than to other living amniotes.

Sauropsida: ("lizard faces") is a group of amniotes that includes all existing reptiles and birds and their fossil ancestors.

Evolution of mammals: has passed through many stages since the first appearance of their synapsid ancestors in the late Carboniferous period. The most ancestral forms in the class Mammalia are the egg-laying mammals in the subclass Prototheria. This class first started out as something close to the platypus and evolved to modern day mammals. After the Cretaceous–Paleogene extinction event wiped out the non-avian dinosaurs (birds being the only surviving dinosaurs) and several mammalian groups, placental and marsupial mammals diversified into many new forms and ecological niches throughout the Paleogene and Neogene, by the end of which all modern orders had appeared. Mammals are the only living synapsids. The synapsid lineage became distinct from the sauropsid lineage in the late Carboniferous period, between 320 and 315 mya. The sauropsids are today's reptiles and birds along with all the extinct animals more closely related to them than to mammals. Although mammary glands are a signature feature of modern mammals, little is known about the evolution of lactation as these soft tissues are not often preserved in the fossil record. Most research concerning the evolution of mammals centers on the shapes of the teeth, the hardest parts of the tetrapod body. Other important research characteristics include the evolution of the middle ear bones, erect limb posture, a bony secondary palate, fur, hair, and warm-bloodedness. Evolution of mammalian features: Jaws and middle ears; Lactation; Hair and fur; Erect limbs; Warm-bloodedness: Respiratory turbinates, Bony secondary palate, Diaphragm, Limb posture; Brain.

Nocturnal bottleneck: hypothesis to explain several mammal traits. The hypothesis states that mammals were mainly or even exclusively nocturnal through most of their evolutionary story, starting with their origin 225 mya, and only ending with the demise of the dinosaurs 65 millions years ago. While some mammal groups have later evolved to fill diurnal niches, the 160 Ma spent as nocturnal animals has left a lasting legacy on basal anatomy and physiology, and most mammals are still nocturnal.

Carrier's constraint: observation that air-breathing vertebrates which have two lungs and flex their bodies sideways during locomotion find it very difficult to move and breathe at the same time, because the sideways flexing expands one lung and compresses the other, shunting stale air from lung to lung instead of expelling it completely to make room for fresh air.

Cloaca: posterior orifice that serves as the only opening for the digestive, reproductive, and urinary tracts (if present) of certain animals, opening at the vent. All amphibians, birds, reptiles, and a few mammals (monotremes, tenrecs, golden moles, and marsupial moles) have this orifice, from which they excrete both urine and feces; this is in contrast to most placental mammals, which have two or three separate orifices for evacuation.

Amphibia

Sauropsida and Reptilia

Reptile (class Reptilia): paraphyletic grouping comprising all amniotes except synapsids (mammals and their extinct relatives) and Aves (birds). The class comprises turtles, crocodilians, snakes, amphisbaenians, lizards, tuatara, and their extinct relatives. In the traditional Linnaean classification system, birds are considered a separate class to reptiles. However, crocodilians are more closely related to birds than they are to other living reptiles, and so modern cladistic classification systems include birds within Reptilia, redefining the term as a clade. Other cladistic definitions abandon the term reptile altogether in favor of the clade Sauropsida, which refers to all animals more closely related to modern reptiles than to mammals. The earliest known proto-reptiles originated around 312 million years ago during the Carboniferous period, having evolved from advanced reptiliomorph tetrapods which became increasingly adapted to life on dry land. The earliest known eureptile ("true reptile") was Hylonomus, a small and superficially lizard-like animal. Genetic and fossil data argues that the two largest lineages of reptiles, Archosauromorpha (crocodilians, birds and kin) and Lepidosauromorpha (lizards and kin), diverged near the end of the Permian period. In addition to the living reptiles, there are many diverse groups that are now extinct, in some cases due to mass extinction events. In particular, the Cretaceous–Paleogene extinction event wiped out the pterosaurs, plesiosaurs, ornithischians, and sauropods, alongside many species of theropods, crocodyliforms, and squamates (e.g., mosasaurs).

Evolution of reptiles: Reptiles arose about 310–320 mya during the Carboniferous period. Reptiles, in the traditional sense of the term, are defined as animals that have scales or scutes, lay land-based hard-shelled eggs, and possess ectothermic metabolisms. So defined, the group is paraphyletic, excluding endothermic animals like birds and mammals that are descended from early reptiles. A definition in accordance with phylogenetic nomenclature, which rejects paraphyletic groups, includes birds while excluding mammals and their mammal-like reptile ancestors. So defined, Reptilia is identical to Sauropsida.

Squamata (Latin squamatus (“scaly, having scales”)): largest order of reptiles, comprising lizards, snakes, and amphisbaenians (worm lizards), which are collectively known as squamates or scaled reptiles. With over 10,900 species, it is also the second-largest order of extant (living) vertebrates, after the perciform fish. Members of the order are distinguished by their skins, which bear horny scales or shields. They also possess movable quadrate bones, making possible movement of the upper jaw relative to the neurocranium. This is particularly visible in snakes, which are able to open their mouths very wide to accommodate comparatively large prey. Squamata is the most variably sized order of reptiles, ranging from the 16 mm (0.63 in) dwarf gecko (Sphaerodactylus ariasae) to the 5.21 m (17.1 ft) green anaconda (Eunectes murinus) and the now-extinct mosasaurs, which reached lengths over 14 m (46 ft).

Hemipenis (plural hemipenes): one of a pair of intromittent organs of male squamates (snakes, lizards and worm lizards). Hemipenes are usually held inverted within the body, and are everted for reproduction via erectile tissue, much like that in the human penis. They come in a variety of shapes, depending on species, with ornamentation, such as spines or hooks. Other vertebrates: Among vertebrates, penises can be found in a variety of shapes, sizes and structures, such as the lymphatic erection mechanism of ratites and the single vascular erectile body of turtles. One of the most similar organs to the squamata hemipenes, however, is the four-headed penis of echidnas (@mammals).

Tuatara: reptiles endemic to New Zealand. Although resembling most lizards, they are part of a distinct lineage, the order Rhynchocephalia. Their name derives from the Māori language, and means "peaks on the back". The single species of tuatara is the only surviving member of its order, which flourished around 240 million years ago. Their most recent common ancestor with any other extant group is with the squamates (lizards and snakes). For this reason, tuatara are of interest in the study of the evolution of lizards and snakes, and for the reconstruction of the appearance and habits of the earliest diapsids, a group of amniote tetrapods that also includes dinosaurs, birds, and crocodilians. Tuatara are greenish brown and grey, and measure up to 80 cm from head to tail-tip and weigh up to 1.3 kg with a spiny crest along the back, especially pronounced in males. They have two rows of teeth in the upper jaw overlapping one row on the lower jaw, which is unique among living species. They are also unusual in having a pronounced photoreceptive eye, the third eye, which is thought to be involved in setting circadian and seasonal cycles. They are able to hear, although no external ear is present, and have unique features in their skeleton, some of them apparently evolutionarily retained from fish. Tuatara are sometimes referred to as "living fossils", which has generated significant scientific debate. While mapping its genome, researchers have discovered that the species has between 5 and 6 billion base pairs of DNA sequence, nearly twice that of humans. The tuatara (Sphenodon punctatus) has been protected by law since 1895. A second species, the Brothers Island tuatara (S. guntheri), was recognised in 1989, but since 2009 it has been reclassified as a subspecies (S. p. guntheri).

Ichthyosaur: large extinct marine reptiles. Ichthyosaurs belong to the order known as Ichthyosauria or Ichthyopterygia ('fish flippers' – a designation introduced by Sir Richard Owen in 1842, although the term is now used more for the parent clade of the Ichthyosauria). Ichthyosaurs thrived during much of the Mesozoic era; based on fossil evidence, they first appeared around 250 Ma and at least one species survived until about 90 Ma, into the Late Cretaceous. During the Early Triassic epoch, ichthyosaurs evolved from a group of unidentified land reptiles that returned to the sea, in a development similar to how the mammalian land-dwelling ancestors of modern-day dolphins and whales returned to the sea millions of years later, which they gradually came to resemble in a case of convergent evolution. Ichthyosaurs were particularly abundant in the Late Triassic and Early Jurassic periods, until they were replaced as the top aquatic predators by another marine reptilian group, the Plesiosauria, in the later Jurassic and Early Cretaceous, though previous views of ichthyosaur decline during this period are probably overstated. Ichthyosaurs diversity declined due to environmental volatility caused by climatic upheavals in the early Late Cretaceous, mostly becoming extinct at the Cenomanian-Turonian boundary. Less than 4 million years later, the last extant ichthyosaurs went extinct, probably due to increasing competition.

Lepidosauria: reptiles with overlapping scales. This subclass includes Squamata and Rhynchocephalia. It is a monophyletic group and therefore contains all descendents of a common ancestor. Squamata includes snakes, lizards, and amphisbaenia. Rhynchocephalia was a widespread and diverse group 220-100 mya; however, it is now represented only by the genus Sphenodon, which contains two species of tuatara, native to New Zealand.

Squamata: largest order of reptiles, comprising lizards, snakes and amphisbaenians (worm lizards), which are collectively known as squamates or scaled reptiles. With over 10,000 species, it is also the second-largest order of extant (living) vertebrates, after the perciform fish, and roughly equal in number to the Saurischia (one of the two major groups of dinosaurs). Members of the order are distinguished by their skins, which bear horny scales or shields. They also possess movable quadrate bones, making it possible to move the upper jaw relative to the neurocranium. This is particularly visible in snakes, which are able to open their mouths very wide to accommodate comparatively large prey.

Turtle (order: Testudines): characterised by a special bony or cartilaginous shell developed from their ribs and acting as a shield.

Archosaur (Archosauria): group of diapsid amniotes whose living representatives consist of birds and crocodilians. This group also includes all extinct dinosaurs, extinct crocodilian relatives, and pterosaurs. Archosauria, the archosaur clade, is a crown group that includes the most recent common ancestor of living birds and crocodilians.

Pseudosuchia ("false crocodiles"): one of two major divisions of Archosauria and includes living crocodilians and all archosaurs more closely related to crocodilians than to birds (what are often called "crocodilian-line archosaurs").

Avemetatarsalia (Ornithodira): clade name established by British palaeontologist Michael Benton in 1999 for all crown group archosaurs that are closer to birds than to crocodiles.

Crocodylomorpha

Crocodilia (Crocodylia): order of mostly large, predatory, semiaquatic reptiles, known as crocodilians. They first appeared 95 million years ago in the Late Cretaceous period (Cenomanian stage) and are the closest living relatives of birds, as the two groups are the only known survivors of the Archosauria. Members of the order's total group, the clade Pseudosuchia, appeared about 250 million years ago in the Early Triassic period, and diversified during the Mesozoic era. The order Crocodilia includes the true crocodiles (family Crocodylidae), the alligators and caimans (family Alligatoridae), and the gharial and false gharial (family Gavialidae).

Crocodylidae

Tomistominae

False gharial

Crocodile (Crocodylinae)

Alligatoridae

Alligatorinae (many extinct) → Alligator

Caiman (Caimaninae)

Saltwater crocodile: largest of all living reptiles, as well as the largest terrestrial and riparian predator in the world.

Nile crocodile: African crocodile and the second largest extant reptile in the world, after the saltwater crocodile. The Nile crocodile is quite widespread throughout Sub-Saharan Africa, occurring mostly in the central, eastern, and southern regions of the continent and lives in different types of aquatic environments such as lakes, rivers and marshlands. Although capable of living in saline environments, this species is rarely found in saltwater, but occasionally inhabits deltas and brackish lakes. The range of this species once stretched northward throughout the Nile, as far north as the Nile delta. Since a majority of fatal attacks are believed to be predatory in nature, the Nile crocodile can be considered the most prolific predator of humans among wild animals.

Avemetatarsalia: Dinosaurs and birds (aves)

Avemetatarsalia:

Dinosaur: diverse group of reptiles of the clade Dinosauria. They first appeared during the Triassic period, between 243 and 233.23 million years ago, although the exact origin and timing of the evolution of dinosaurs is the subject of active research. They became the dominant terrestrial vertebrates after the Triassic–Jurassic extinction event 201.3 million years ago; their dominance continued throughout the Jurassic and Cretaceous periods. The fossil record shows that birds are modern feathered dinosaurs, having evolved from earlier theropods during the Late Jurassic epoch, and are the only dinosaur lineage to survive the Cretaceous–Paleogene extinction event approximately 66 million years ago. Dinosaurs can therefore be divided into avian dinosaurs, or birds; and the extinct non-avian dinosaurs, which are all dinosaurs other than birds. Dinosaurs are a varied group of animals from taxonomic, morphological and ecological standpoints. Birds, at over 10,700 living species, are among the most diverse group of vertebrates.

Feathered dinosaur

Bird (Aves)

Evolution of dinosaurs: Dinosaurs evolved with single lineage of archosaurs 243-233 Ma (million years ago) from the Anisian to the Carnian ages, the latter part of the middle Triassic. Dinosauria is a well-supported clade, present in 98% of bootstraps. It is diagnosed by many features including loss of the postfrontal on the skull and an elongate deltopectoral crest on the humerus.

Dinosaur classification

Chicken (Gallus gallus domesticus), a subspecies of the red junglefowl, is a type of domesticated fowl. Rooster or cock is a term for an adult male bird. A younger male may be called a cockerel; a male that has been castrated is a capon.

Junglefowl: the only four living species of bird from the genus Gallus in the bird order Galliformes, and occur in India, Sri Lanka, and Southeast Asia. They diverged from their common ancestor about 4–6 mln years ago. As with many birds in the pheasant family, the male takes no part in the incubation of the egg or rearing of the precocial young. These duties are performed by the drab and well-camouflaged female. Females and males do not form pair bonds; instead, the species has a polygynandrous mating system in which each female will usually mate with several males. Aggressive social hierarchies exist among both females and males, from which the term "pecking order" originates. The junglefowl are omnivorous, eating a variety of leaves, plant matter, invertebrates such as slugs and insects, and occasionally small mice and frogs.

Peregrine falcon (Falco peregrinus): widespread bird of prey in the family Falconidae. A large, crow-sized falcon, it has a blue-grey back, barred white underparts, and a black head and "moustache". As is typical of bird-eating raptors, peregrine falcons are sexually dimorphic, females being considerably larger than males. The peregrine is renowned for its speed, reaching over 322 km/h during its characteristic hunting stoop (high speed dive), making it the fastest member of the animal kingdom.

=Birds (aves)=

Bird vision: most important sense for birds, since good eyesight is essential for safe flight, and this group has a number of adaptations which give visual acuity superior to that of other vertebrate groups; a pigeon has been described as "two eyes with wings". Avian eye resembles that of a reptile, with ciliary muscles that can change the shape of the lens rapidly and to a greater extent than in the mammals. Birds have the largest eyes relative to their size in the animal kingdom, and movement is consequently limited within the eye's bony socket.

Pecten oculi: In the vertebrate eye, blood vessels lie in front of the retina, partially obscuring the image. The pecten helps to solve this problem by greatly reducing the number of blood vessels in the retina and leading to the extremely sharp eyesight of birds such as hawks. The pigmentation of the pecten is believed to protect the blood vessels against damage from ultraviolet light. Birds of prey have a very high density of receptors and other adaptations that maximise visual acuity. The placement of their eyes gives them good binocular vision enabling accurate judgement of distances. Nocturnal species have tubular eyes, low numbers of colour detectors, but a high density of rod cells which function well in poor light. Terns, gulls and albatrosses are amongst the seabirds which have red or yellow oil droplets in the colour receptors to improve distance vision especially in hazy conditions.

Oil droplet: found in the eyes of some animals, being located in the photoreceptor cells. They are especially common in the eyes of diurnal (active during the day) reptiles (e.g. lizards, turtles) and birds (see bird vision), though are present in other taxa such as lungfish. They are found in cone cells far more often than in rods, suggesting a role in colour vision. Occurrence in rod cells may imply that they have been modified from a cone cell ancestor. They occasionally occur in double cones/double rods. Some oil droplets are coloured, while others appear colourless. They are located in the cone inner segment, where they intercept and filter light before it can pass through to the cone outer segment where the visual pigment is. The adaptive advantage of oil droplets is not firmly established.

Pecten oculi: comb-like structure of blood vessels belonging to the choroid in the eye of a bird. It is a non-sensory, pigmented structure that projects into the vitreous humor from the point where the optic nerve enters the eyeball. The pecten is believed to both nourish the retina and control the pH of the vitreous body. High level of enzyme alkaline phosphatase activity in pecten oculi has been linked to transport of nutrient molecules from highly vascularized pecten oculi into vitreous and then into retinal cells for nourishment. It is present in all birds and some reptiles. In the vertebrate eye, blood vessels lie in front of the retina, partially obscuring the image. The pecten helps to solve this problem by greatly reducing the number of blood vessels in the retina and leading to the extremely sharp eyesight of birds such as hawks. The pigmentation of the pecten is believed to protect the blood vessels against damage from ultraviolet light. Stray light absorption by melanin granules of pecten oculi is also considered to give rise to small increments in temperature of pecten and eye; this may offer increased metabolic rate to optimize eye physiology in low temperatures at high-altitude flights. The structure varies across bird species and is conical in the kiwi, vaned in the ostrich and pleated in most other birds.

List of birds by flight heights

Rüppell's vulture (Gyps rueppelli): large bird of prey, mainly native to the Sahel region and East Africa. The current population of 22,000 is decreasing due to loss of habitat, incidental poisoning, and other factors. Rüppell's vulture is considered to be the highest-flying bird, with confirmed evidence of a flight at an altitude of 11,300 m above sea level.

Common crane (Grus grus; Eurasian crane; Pilkoji gervė / gervė): During these migratory flights, common cranes have been known to fly at altitudes of up to 10,000 m, one of the highest of any species of bird, second only to the Ruppell's Griffin Vulture. A medium-sized species, it is the only crane commonly found in Europe besides the demoiselle crane (Grus virgo).

Mammals

Category:Mammaliaformes

Category:Mammals

Category:Milk

Category:Mammalogy

Mammal: any members of a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair [with a few exceptions, all of them cetaceans], three middle ear bones, mammary glands, and a neocortex (a region of the brain). The mammalian brain regulates body temperature and the circulatory system, including the four-chambered heart. The mammals include the largest animals on the planet, the rorquals and other large whales, as well as some of the most intelligent, such as elephants, some primates, including humans, and some of the cetaceans. The largest group of mammals, the placentals, have a placenta, which enables feeding the fetus during gestation. Mammals range in size from the 30–40 mm (1.2–1.6 in) bumblebee bat to the 33-meter (108 ft) blue whale.

Template:Mammals

Yinotheria → Australosphenida: Monotremata (Platypus and 4 echidnas)

Metatheria: Marsupial:

Ameridelphia

Paucituberculata (Shrew opossums)

Didelphimorphia (Opossums)

Australidelphia

Microbiotheria (Monito del monte)

Notoryctemorphia (Marsupial moles)

Dasyuromorphia (Quolls and dunnarts)

Peramelemorphia (Bilbies and bandicoots)

Diprotodontia (Kangaroos and relatives)

Eutheria

Atlantogenata

Afrotheria

Afrosoricida (Tenrecs and golden moles)

Macroscelidea (Elephant shrews)

Tubulidentata (Aardvark)

Hyracoidea (Hyraxes)

Proboscidea (Elephants)

Sirenia (Dugongs and manatees)

Xenarthra (Ancient Greek ξένος, xénos, "foreign, alien" + ἄρθρον, árthron, "joint")):

Cingulata (Armadillos)

Pilosa (Anteaters and sloths)

Boreoeutheria

Laurasiatheria

Eulipotyphla (Hedgehogs, shrews, moles and relatives)

Scrotifera

Chiroptera (Bats)

Yinpterochiroptera

Yangochiroptera

Ferungulata

Ferae

Pholidota (Pangolins)

Carnivora (Caniformia: Canidae: dogs, Ursida: bears, Pan-Pinnipedia: seals, Musteloidea; Feliformia: Nandinia binotata (two-spotted palm civet), Hyaenidae: hyenas, Herpestidae, Prionodontidae, Felidae: cats)

Euungulata

Odd-toed ungulate (Perissodactyla): horses (Equidae), tapirs (Tapiridae), rhinos (Rhinocerotidae), etc.

Even-toed ungulate (Artiodactyla/Cetartiodactyla): pigs, peccaries, hippopotamuses, antelopes, deer, giraffes, camels, llamas, alpacas, sheep, goats, and cattle; whales, dolphins, and porpoises

Euarchontoglires (synonymous with Supraprimates)

Glires

Lagomorpha (rabbits, hares and pikas)

Rodentia (rodents)

Euarchonta

Scandentia (treeshrews)

Primatomorpha

Dermoptera (colugos: Sunda flying lemur (Galeopterus variegatus), Philippine flying lemur (Cynocephalus volans))

Primates (†Plesiadapiformes, Strepsirrhini, Haplorrhini)

Marine mammal: aquatic mammals that rely on the ocean and other marine ecosystems for their existence. They include animals such as seals, whales, manatees, sea otters and polar bears. They do not represent a distinct taxon or systematic grouping, but rather have a polyphyletic relation due to convergent evolution, as in they do not have an immediate common ancestor.

Phylogeny of marine mammals

Tethytheria

Proboscidea

Elephantidae

Sirenia

Dugongidae (dugongs)

Trichechidae

	Trichechus manatus (West Indian manatee)

	Trichechus senegalensis (African manatee)

	Trichechus inunguis (Amazonian manatee; freshwater species)

Cetartiodactyla

Cetacea

	Mysticeti (baleen whales)

	Odontoceti (toothed whales, except river dolphins)

	Ursus maritimus (polar bear)

	all other ursids

Mustelidae

	Enhydra lutris (sea otter)

	Lontra felina (marine otter)

	†Neovison macrodon (sea mink)

	all other mustelids

Pinnipedia

	Otariidae (eared seals)

	Odobenidae (walruses)

	Phocidae (earless seals)

The taxa in bold are marine.^[2]

Milk allergy: adverse immune reaction to one or more proteins in cow's milk. Symptoms may take hours to days to manifest, with symptoms including atopic dermatitis, inflammation of the esophagus, enteropathy involving the small intestine and proctocolitis involving the rectum and colon. However, rapid anaphylaxis is possible, a potentially life-threatening condition that requires treatment with epinephrine, among other measures. In USA, 90% of allergic responses to foods are caused by eight foods, and cow's milk is the most common. Recognition that a small number of foods are responsible for the majority of food allergies has led to requirements to prominently list these common allergens, including dairy, on food labels. Heating milk proteins can cause them to become denatured, losing their three-dimensional configuration and allergenicity, so baked goods containing dairy products may be tolerated while fresh milk triggers an allergic reaction. Milk allergy affects between 2% and 3% of babies and young children. To reduce risk, recommendations are that babies should be exclusively breastfed for at least four months, preferably six months, before introducing cow's milk. The majority of children outgrow milk allergy, but for about 0.4% the condition persists into adulthood.

Beta-lactoglobulin (BLG): major whey protein of cow and sheep's milk (~3 g/L), and is also present in many other mammalian species; a notable exception being humans. BLG is considered to be a milk allergen. The major protein in whey is β-lactoglobulin, followed by α-lactalbumin (β-lactoglobulin ≈65%, α-lactalbumin ≈25%, serum albumin ≈8%, other ≈2%). β-lactoglobulin is a lipocalin protein, and can bind many hydrophobic molecules, suggesting a role in their transport.

Monotremata, monotremes

{q.v.

#Gender, sex, reproductive biology

}

Monotreme: one of the three main groups of living mammals, along with placentals (Eutheria) and marsupials (Metatheria). The monotremes are typified by laying eggs rather than bearing live young, and by structural differences in their brains, jaws, digestive and reproductive tracts, and other body parts compared to the more common mammalian types. However, like all mammals, the female monotremes nurse their young with milk. The only surviving examples of monotremes are all indigenous to Australia and New Guinea although there is evidence that they were once more widespread including some extinct species in South America. The existing monotreme species are the platypus and four species of echidnas.

Metatheria, marsupials

Metatheria: mammalian clade that includes all mammals more closely related to marsupials than to placentals (such as sparassodontans). First proposed by Thomas Henry Huxley in 1880, it is a slightly more inclusive group than the marsupials; it contains all marsupials as well as their more primitive ancestors and relatives. The relationships between the three extant divisions of mammals (monotremes, marsupials, and placental mammals) was long a matter of debate among taxonomists. Most morphological evidence comparing traits, such as the number and arrangement of teeth and the structure of the reproductive and waste elimination systems, favors a closer evolutionary relationship between marsupials and placental mammals than either has with the monotremes, as does most genetic and molecular evidence.

Marsupial: any members of the mammalian infraclass Marsupialia. All extant marsupials are endemic to Australasia and the Americas. A distinctive characteristic common to these species is that most of the young are carried in a pouch. Well-known marsupials include kangaroos, wallabies, koalas, possums, opossums, wombats, and Tasmanian devils. Some lesser known marsupials are the potoroo and the quokka. Marsupials represent the clade originating from the last common ancestor of extant metatherians. Like other mammals in the Metatheria, they give birth to relatively undeveloped young that often reside with the mother in a pouch, for a certain amount of time. Close to 70% of the 334 extant species occur on the Australian continent (the mainland, Tasmania, New Guinea and nearby islands). The remaining 100 are found in the Americas — primarily in South America, but thirteen in Central America, and one in North America, north of Mexico.

Virginia opossum (Didelphis virginiana, North American opossum): marsupial found in North America. It is the only marsupial found north of Mexico. In the United States, it is typically referred to simply as a possum. It is a solitary and nocturnal animal about the size of a domestic cat. It is a successful opportunist. It is familiar to many North Americans as it is often seen near towns, rummaging through garbage cans.

=Diprotodontia (Kangaroos and relatives)=

Diprotodontia: 155 species of marsupial mammals including the kangaroos, wallabies, possums, koala, wombats, and many others.

Xenarthra (Armadillos, Anteaters and sloths)

Afrotheria, Elephants, Soricomorpha (split up)

Afrotheria

	Chrysochloridae

	Tenrecidae

Paenungulata

Hyracoidea

Procaviidae

Tethytheria

Proboscidea

Elephantidae

Sirenia

	Dugongidae

	Trichechidae

Afrotheria: clade of mammals, the living members of which belong to groups that are either currently living in Africa or of African origin: golden moles, elephant shrews (also known as sengis), tenrecs, aardvarks, hyraxes, elephants, sea cows, and several extinct clades. They share few anatomical features but many are partly or entirely African in their distribution. This probably reflects the fact that Africa was an island continent through the early Cenozoic. Because the continent was isolated by water, Laurasian groups such as insectivores, rabbits, carnivorans and ungulates could not become established. Instead, the niches occupied by those groups were filled by tenrecs, hyraxes and elephants that evolved from the ancestral afrothere. This adaptive radiation may have occurred in response to the Cretaceous–Paleogene mass extinction.

Paenungulata

Tethytheria: clade of mammals that includes the sirenians and proboscideans, as well as the extinct order Embrithopoda. The tethytheres are united by several characters, including anteriorly facing orbits and more or less bilophodont cheek teeth (double transverse ridges on the crowns of the teeth). Proboscidea and Sirenia are linked together based on auditory characters in their petrosal bones, but this link may be a homoplasy.

Proboscidea: taxonomic order of afrotherian mammals containing one living family (Elephantidae) and several extinct families. This order, first described by J. Illiger in 1811, encompasses the trunked mammals. In addition to their enormous size, later proboscideans are distinguished by tusks and long, muscular trunks; these features were less developed or absent in the smaller early proboscideans. Beginning in the mid-Miocene, most members of this order were very large animals. The largest land mammal today is the African elephant weighing up to 10.4 t with a shoulder height of up to 4 m. Proboscideans evolved in Africa, where they increased in size and diversity during the Eocene and early Oligocene.

Musth (must; word from Indian languages meaning a state of enjoyment): periodic condition in bull (male) elephants characterized by highly aggressive behavior and accompanied by a large rise in reproductive hormones. Testosterone levels in an elephant in musth can be on average 60 times greater than in the same elephant at other times (in specific individuals these testosterone levels can even reach as much as 140 times the normal). However, whether this hormonal surge is the sole cause of musth, or merely a contributing factor, is unknown. Cases of rogue elephants randomly attacking native villages or goring and killing rhinoceroses without provocation in national parks in Africa have been documented and attributed to musth in young male elephants, especially those growing in the absence of older males. Studies show that reintroducing older males into the elephant population of the area seems to prevent younger males from entering musth, and therefore, stop this aggressive behavior.

Soricomorpha (order): taxon within the class of mammals. In previous years it formed a significant group within the former order Insectivora. However, that order was shown to be polyphyletic and various new orders were split off from it, including Afrosoricida (tenrecs and golden moles), Macroscelidea (elephant shrews), and Erinaceomorpha (hedgehogs and gymnures), leaving just four families as shown here, leaving Insectivora empty and disbanded.

Afrosoricida (order)

Elephant shrew (order: Macroscelididae)

Erinaceidae (order)

Golden mole: small, insectivorous burrowing mammals endemic to Southern Africa, where their Afrikaans names are gouemolle or kruipmolle (singular gouemol or kruipmol). They comprise the family Chrysochloridae and as such they are taxonomically distinct from the true moles, family Talpidae, and other mole-like families, all of which, to various degrees, they resemble as a result of convergence. Furthermore, like the tenrecs, they possess a cloaca, and males lack a scrotum. However, such points are no longer regarded as strongly suggestive that golden moles are undeveloped "reptilian mammals"; some are seen rather as adaptations to regional climatic conditions. Going into a torpor when resting or during cold weather, enables them to conserve energy and reduce urgent requirements for food. Similarly, they have developed particularly efficient kidneys and most species do not need to drink water at all; in fact they tend to drown easily if they fall into water.

Tenrec: any species of mammal within the family Tenrecidae, found on Madagascar and in parts of the African mainland. Tenrecs are widely diverse; as a result of convergent evolution they resemble hedgehogs, shrews, opossums, mice and even otters. They occupy aquatic, arboreal, terrestrial and fossorial environments. Some of these species, including the greater hedgehog tenrec, can be found in the Madagascar dry deciduous forests. Unusual among placental mammals, the anus and urogenital tracts of tenrecs share a common opening, or cloaca, a feature more commonly seen in birds, reptiles, and amphibians. They have a low body temperature, sufficiently so that they do not require a scrotum to cool their sperm as do most other mammals.

Insectivora: now-abandoned biological grouping within the class of mammals. Some species have now been moved out, leaving the remaining ones in the order Eulipotyphla, within the larger clade Laurasiatheria, which makes up one of the most basic clades of placental mammals.

Eulipotyphla: order of mammals suggested by molecular methods of phylogenetic reconstruction, and includes members of the now-invalid order Insectivora except for those in the order Afrosoricida (tenrecs and golden moles), i.e. comprising the solenodons (family Solenodontidae); the order Eulipotyphla includes hedgehogs and gymnures (family Erinaceidae) as well as desmans, moles, and shrew moles (family Talpidae) and the true shrews (family Soricidae). True shrews and talpids are sometimes included in the clade Soricomorpha, which however appears as paraphyletic in some analyses.

Laurasiatheria

=Eulipotyphla=

=Bats (Chiroptera)=

Bat: forelimbs form webbed wings, making them the only mammals naturally capable of true and sustained flight. Bats do not flap their entire forelimbs, as birds do, but instead flap their spread-out digits, which are very long and covered with a thin membrane or patagium. Bats are the second largest order of mammals (after the rodents), representing about 20% of all classified mammal species worldwide, with about 1,240 bat species divided into two suborders: the less specialized and largely fruit-eating megabats, or flying foxes, and the highly specialized and echolocating microbats. Most molecular biological evidence supports the view that bats form a single or monophyletic group.

Megabat: have well-developed visual cortices and show good visual acuity; eat fruit, nectar, or pollen (cf microbat).

Microbat: rely on echolocation for navigation and finding prey; use echolocation; lack the claw at the second finger of the forelimb; lack underfur; most microbats eat insects; others may feed on fruit, nectar, pollen, fish, frogs, small mammals, or the blood of animals (cf. megabat).

=Pangolins=

Pangolin (scaly anteaters, Order: Pholidota): one extant family, Manidae, has three genera: Manis (4 species), Phataginus (2 species) and Smutsia (2 species). Pangolins have large, protective keratin scales covering their skin; they are the only known mammals with this feature. They live in hollow trees or burrows, depending on the species. Pangolins are nocturnal, and their diet consists of mainly ants and termites, which they capture using their long tongues. They tend to be solitary animals, meeting only to mate and produce a litter of one to three offspring, which they raise for about two years.

=Carnivora=

Carnivora (carnivorans): includes over 280 species of placental mammals. Carnivorans are the most diverse in size of any mammalian order, ranging from the least weasel (Mustela nivalis), at as little as 25 g and 11 cm, to the polar bear (Ursus maritimus), which can weigh up to 1,000 kg, to the southern elephant seal (Mirounga leonina), whose adult males weigh up to 5,000 kg and measure up to 6.9 m in length. Some carnivorans, such as cats and pinnipeds, depend entirely on meat for their nutrition. Others, such as raccoons and bears, depending on the local habitat, are more omnivorous: the giant panda is almost exclusively a herbivore, but will take fish, eggs and insects, while the polar bear subsists mainly on seals. Carnivorans have teeth and claws adapted for catching and eating other animals. Many hunt in packs and are social animals.

Carnivoraformes

†Miacidae (paraphyletic family)

†Ceruttia

†Walshius

Carnivora

Feliformia

Aeluroidea

Viverroidea

Herpestoidea

Hyaenidae

	†Percrocutidae

	Hyaenidae (hyaenas)

	†Lophocyonidae

sensu lato

Herpestidae

	Herpestidae (mongoose)

	Eupleridae (Malagasy mongooses)

sensu lato

Viverridae (viverrids)

	†Shandgolictis

	†Asiavorator

	†Alagtsavbaatar

†Anictis

Feloidea

Prionodontidae

	Prionodontidae (Asiatic linsangs)

	†Palaeoprionodon

sensu lato

†Haplogale

†Stenoplesictis

?

†Pseudictis

Felidae

†Barbourofelidae

†Viretictis

	†Stenogale

	Felidae (cats)

sensu lato

Nandiniidae (African palm civet)

†Nimravidae (false saber-toothed cats)

†Palaeogalidae

Caniformia

†Amphicyonoidea	†Amphicyonidae ("bear-dogs")

†Lycophocyon

Canoidea

Cynoidea

Canidae (canids)

Arctoidea

Ursida

Ursoidea	Ursidae (bears)

	†Adracon

Musteloidea

	Procyonidae (raccoons)

	Mustelidae (mustelids)

Ailuridae

?

†Peignictis

Mephitidae (skunks)

†Plesiogale

Pinnipedimorpha

†Semantoridae

†Enaliarctidae

†Pinnarctidion

Pinnipediformes

	†Pacificotaria

	†Pteronarctos

Pinnipedia

Otarioidea

Otariidae
(eared seals)

Odobenidae
(walruses)

Phocoidea

†Desmatophocidae

Phocidae
(earless seals)

sensu stricto

(Pinnipedia sensu lato)

==Wolves (wolf), dogs, foxes, Canidae==

Canidae: domestic dogs, wolves, foxes, jackals, dingoes, and many other extant and extinct dog-like mammals. A member of this family is called a canid.

	Side-striped jackal

	Black-backed jackal

	Dog

	Gray wolf

Ethiopian wolf

	African wild dog

==Pinnipeds (seals)==

Pinniped (seals): widely distributed and diverse clade of carnivorous, fin-footed, semiaquatic marine mammals. They comprise the extant families Odobenidae (whose only living member is the walrus), Otariidae (the eared seals: sea lions and fur seals), and Phocidae (the earless seals, or true seals). There are 33 extant species of pinnipeds, and more than 50 extinct species have been described from fossils. While seals were historically thought to have descended from two ancestral lines, molecular evidence supports them as a monophyletic lineage (descended from one ancestral line). Pinnipeds belong to the order Carnivora and their closest living relatives are believed to be bears and the superfamily of musteloids (weasels, raccoons, skunks, and red pandas), having diverged about 50 mya. Seals range in size from the 1 m and 45 kg Baikal seal to the 5 m and 3,200 kg southern elephant seal, which is also the largest member of the order Carnivora. Several species exhibit sexual dimorphism. They have streamlined bodies and four limbs that are modified into flippers. Though not as fast in the water as dolphins, seals are more flexible and agile.

=Odd-toed ungulates=

=Even-toed ungulate (Artiodactyla, Cetartiodactyla)=

Even-toed ungulate (Artiodactyla, from Ancient Greek ἄρτιος (ártios), meaning 'even', and δάκτυλος (dáktylos), meaning 'finger / toe'): ungulates – hoofed animals – which bear weight equally on two (an even number) of the five toes: their third and fourth toes. The other three toes are either present, absent, vestigial, or pointing posteriorly. Even-toed ungulates digest plant cellulose in one or more stomach chambers rather than in their intestine as the odd-toed ungulates do. The aquatic cetaceans (whales, dolphins, and porpoises) evolved from even-toed ungulates, so modern taxonomic classification sometimes combines the Artiodactyla and Cetacea into the Cetartiodactyla (from Cetacea + Artiodactyla). Roughly 220 land-based even-toed ungulate species include pigs, peccaries, hippopotamuses, camels, llamas, alpacas, mouse deer, deer, giraffes, antelopes, sheep, goats, and cattle. Many of these are of great dietary, economic, and cultural importance to humans.

Wild boar (wild swine, common wild pig, simply wild pig): suid native to much of the Palearctic, as well as introduced numbers in the Americas and Southeast Asia. Human intervention has spread it further, making the species one of the widest-ranging mammals in the world, as well as the most widely spread suiform; become an invasive species in part of its introduced range. The animal probably originated in Southeast Asia during the Early Pleistocene, and outcompeted other suid species as it spread throughout the Old World. Boars are typically social animals, living in female-dominated sounders consisting of barren sows and mothers with young led by an old matriarch. Male boars leave their sounder at the age of 8–15 months, while females either remain with their mothers or establish new territories nearby. Subadult males may live in loosely knit groups, while adult and elderly males tend to be solitary outside the breeding season. Long history of association with humans, having been the ancestor of most domestic pig breeds and a big-game animal for millennia. Boars have also re-hybridized in recent decades with feral pigs. Relationships with humans: In culture: The wild boar features prominently in the cultures of Indo-European people, many of which saw the animal as embodying warrior virtues. Cultures throughout Europe and Asia Minor saw the killing of a boar as proof of one's valor and strength. Virtually all heroes in Greek mythology fight or kill a boar at one point. The boar as a warrior also appears in Scandinavian, Germanic and Anglo-Saxon culture, with its image having been frequently engraved on helmets, shields and swords. As a game animal and food source. Crop and garbage raiding. Attacks on humans.

Cattle (taurine cattle, Eurasian cattle, or European cattle; Bos taurus or Bos primigenius taurus): large domesticated cloven-hooved herbivores. They are a prominent modern member of the subfamily Bovinae and the most widespread species of the genus Bos. In taxonomy, adult females are referred to as cows and adult males are referred to as bulls. In colloquial speech however, cow is used as a common name for the species as a whole. Cattle are commonly raised as livestock for meat (beef or veal, see beef cattle), for milk (see dairy cattle), and for hides, which are used to make leather. They are used as riding animals and draft animals (oxen or bullocks, which pull carts, plows and other implements). Another product of cattle is their dung, which can be used to create manure or fuel. Around 10,500 years ago, taurine cattle were domesticated from as few as 80 progenitors in central Anatolia, the Levant and Western Iran. According to FAO, there are approximately 1.5 bln cattle in the world as of 2018. Cattle are the main source of greenhouse gas emissions from livestock, and are responsible for around 10% of global greenhouse gas emissions. In 2009, cattle became one of the first livestock animals to have a fully mapped genome.

Highland cattle (Scottish Gaelic: Bò Ghàidhealach; Scots: Hielan coo): Scottish breed of rustic cattle. It originated in the Scottish Highlands and the Outer Hebrides islands of Scotland and has long horns and a long shaggy coat. It is a hardy breed, bred to withstand the intemperate conditions in the region. The first herd-book dates from 1885; two types – a smaller island type, usually black, and a larger mainland type, usually dun – were registered as a single breed. It is reared primarily for beef, and has been exported to several other countries.

Bison: large, even-toed ungulates in the genus Bison within the subfamily Bovinae. Two extant and six extinct species are recognised. Of the six extinct species, five became extinct in the Quaternary extinction event. Of the two surviving species, the American bison, B. bison, found only in North America, is the more numerous. Although colloquially referred to as a buffalo in the United States and Canada, it is only distantly related to the true buffalo. The North American species is composed of two subspecies, the Plains bison, B. b. bison, and the wood bison, B. b. athabascae, which is the namesake of Wood Buffalo National Park in Canada. The European bison, B. bonasus, or wisent, or zubr, or colloquially European buffalo, is found in Europe and the Caucasus, reintroduced after being extinct in the wild.

Whippomorpha (Cetancodonta): group of animals that contains all living cetaceans (whales, dolphins, etc.) and hippopotamuses, as well as their extinct relatives, i.e. Entelodonts, Andrewsarchus. Whippomorpha is a suborder within the order Artiodactyla (even-toed ungulates). The placement of Whippomorpha within Artiodactyla is a matter of some contention, as hippopotamuses were previously considered to be more closely related to Suidae (pigs) and Tayassuidae (peccaries). Most contemporary scientific phylogenetic and morphological research studies link hippopotamuses with cetaceans, and genetic evidence has overwhelmingly supported an evolutionary relationship between Hippopotamidae and Cetacea. Modern Whippomorphs all share a number of behavioural and physiological traits; such as a dense layer of subcutaneous fat and largely hairless bodies. They exhibit amphibious and aquatic behaviors and possess similar auditory structures.

==Cetaceans==

Cetacea (Cetaceans): 89 living species, which are divided into two parvorders. The first is the Odontoceti, the toothed whales, which consist of around 70 species, including the dolphin (which includes killer whales), porpoise, beluga whale, narwhal, sperm whale, and beaked whale. The second is the Mysticeti, the baleen (from Latin: balæna, lit. 'whale') whales, which have a filter-feeder system, and consist of 15 species divided into 3 families, and include the right whale, bowhead whale, rorqual, pygmy right whale, and gray whale. They diverged from even-toed ungulates; their closest living relatives are hippopotamuses and others such as cows and pigs. They were semiaquatic and evolved in the shallow waters that separated India from Asia. Around 30 species adapted to a fully oceanic life. Baleen whales split from toothed whales around 34 mya. The smallest cetacean is Maui's dolphin, at 1 m and 50 kg; the largest is the blue whale, at 29.9 m and 173 t. Cetaceans have well-developed senses—their eyesight and hearing are adapted for both air and water. They have a layer of fat, or blubber, under the skin to maintain body heat in cold water. Several species exhibit sexual dimorphism. Two external forelimbs are modified into flippers; two internal hindlimbs are vestigial. Cetaceans have streamlined bodies: they can swim very quickly, with the killer whale able to travel at 56 km/h in short bursts, the fin whale able to cruise at 48 km/h, dolphins able to make very tight turns at high speeds, and some species diving to great depths. Although cetaceans are widespread, most species prefer the colder waters of the Northern and Southern Hemispheres. The male genitals and mammary glands of females are sunken into the body. Hind legs are not present in cetaceans, nor are any other external body attachments such as a pinna (external ear) and hair. Sperm whales have the largest brain mass of any animal on earth, averaging 8,000 cm³ and 7.8 kg in mature males. The number of vertebrae that make up the spine varies by species, ranging from forty to ninety-three. The cervical spine, found in all mammals, consists of seven vertebrae which, however, are reduced or fused. This fusion provides stability during swimming at the expense of mobility. Cetaceans have powerful hearts. An individual cetacean can last without a breath from a few minutes to over two hours depending on the species. Cetacea are deliberate breathers who must be awake to inhale and exhale. When stale air, warmed from the lungs, is exhaled, it condenses as it meets colder external air. As with a terrestrial mammal breathing out on a cold day, a small cloud of 'steam' appears. This is called the 'spout' and varies across species in shape, angle and height. Species can be identified at a distance using this characteristic. The kidneys are long and flattened. The salt concentration in cetacean blood is lower than that in seawater, requiring kidneys to excrete salt. This allows cetaceans to drink seawater. Among cetaceans, whales are distinguished by an unusual longevity compared to other higher mammals. Some species, such as the bowhead whale (Balaena mysticetus), can reach over 200 years.

Sperm whale (cachalot): only living member of genus Physeter, and one of three extant species in the sperm whale family, along with the pygmy sperm whale and dwarf sperm whale of the genus Kogia. Mature males average at 16 metres in length but some may reach 20.5 metres, with the head representing up to one-third of the animal's length. Plunging to 3 kilometres (9,800 ft) for prey, it is the deepest diving mammal. Its clicking vocalization, a form of echolocation and communication, may be as loud as 230 decibels (re 1 µPa at 1 m) underwater, making it the loudest sound produced by any animal; has the largest brain of any animal on Earth, more than five times heavier than a human's; can live for more than 60 years.

Euarchontoglires

=Rodents=

Rodent (Rodentia): mammals which are characterized by a single pair of unremittingly growing incisors in each of the upper and lower jaws. ~40% of all mammal species are rodents. Most rodents are small animals with robust bodies, short limbs and long tails. They use their sharp incisors to gnaw food, excavate burrows and defend themselves. Most eat seeds or other plant material, but some have more varied diets.

Muroidea

Rat (Rattus): Rats are typically distinguished from mice by their size. Generally, when someone discovers a large muroid rodent, its common name includes the term rat, while if it is smaller, the name includes the term mouse.

Brown rat (Rattus norvegicus: misnomer): thought to have originated in northern China, this rodent has now spread to all continents except Antarctica, and is the dominant rat in Europe and much of North America—making it by at least this particular definition the most successful mammal on the planet after humans. With rare exceptions, the brown rat lives wherever humans live, particularly in urban areas. Selective breeding of Rattus norvegicus has produced the laboratory rat, a model organism in biological research, as well as pet rats.

Black rat (Rattus rattus): species originated in tropical Asia and spread through the Near East in Roman times before reaching Europe by the 1st century and spreading with Europeans across the world; generalist omnivores.

Naked mole-rat: lives completely underground and can form colonies of up to eighty individuals. Only one female and up to three males in the colony reproduce, while the rest of the members are smaller, sterile and function as workers. Some individuals are of intermediate size. They help with the rearing of the young and can take the place of a reproductive if one dies.

Damaraland mole-rat: characterized by having a single reproductively active male and female in a colony where the remaining animals are not truly sterile, but only become fertile if they establish a colony of their own.

Rats in New York City

Behavioral sink: John B. Calhoun conducted over-population experiments on rats which culminated in 1962 with the publication of an article in the Scientific American of a study of behavior under conditions of overcrowding.

=Lagomorphs (rabbits and pikas)=

Lagomorpha (order Lagomorpha): two living families: the Leporidae (hares and rabbits) and the Ochotonidae (pikas). ~80 species of lagomorph: 30 species of pika, 20 species of rabbit and cottontail, and 30 species of hare.

=Primates=

Purgatorius: genus of seven extinct eutherian species typically believed to be the earliest example of a primate or a proto-primate, a primatomorph precursor to the Plesiadapiformes, dating to as old as 66 Mya. The first remains (P. unio and P. ceratops) were reported in 1965, from what is now eastern Montana's Tullock Formation (early Paleocene, Puercan), specifically at Purgatory Hill (hence the animal's name) in deposits believed to be about 63 million years old, and at Harbicht Hill in the late Cretaceous and lower Paleocene Hell Creek Formation.

Plesiadapiformes ("Adapid-like" or "near Adapiformes"): group of Primates, a sister of the Dermoptera. While none of the groups normally directly assigned to this group survived, the group appears actually not to be literally extinct (in the sense of having no living descendants) as the remaining primates (the crown primates or "Euprimates") appear to be derived Plesiadapiformes, as a sister of e.g. the Carpolestidae. The term Plesiadapiformes may still be used for all primates which are not crown primates, but this usage is paraphyletic. When the crown primates are cladistically granted, it becomes an obsolete junior synonym to primates. Plesiadapiformes first appear in the fossil record between 65 and 55 Mya, although many were extinct by the beginning of the Eocene. They may have been the first mammals to have finger nails in place of claws.

Primate (eutherian mammal, taxonomic order Primates): arose 85–55 million years ago first from small terrestrial mammals, which adapted to living in the trees of tropical forests: many primate characteristics represent adaptations to life in this challenging environment, including large brains, visual acuity, color vision, a shoulder girdle allowing a large degree of movement in the shoulder joint, and dextrous hands. Primates range in size from Madame Berthe's mouse lemur, which weighs 30 g, to the eastern gorilla, weighing over 200 kg. Primates are classified as the strepsirrhines (lit. 'twisted-nostriled') and the haplorhines (lit. 'simple-noses'). Strepsirrhines include the lemurs, galagos, and lorisids, while haplorhines include the tarsiers and the simians (apes and monkeys). Simians (lit. 'snub-noses') can be further reduced to the platyrrhines (lit. 'flat-noses'), or New World monkeys, and the catarrhines (lit. 'narrow-noses'), which are Old World monkeys and apes (including humans). 40 mya, simians from Africa migrated to South America presumably by drifting on debris, which gave rise to the five families of New World monkeys. The remaining simians diverged into apes (Hominoidea) and Old World monkeys (Cercopithecoidea) ~25 mya. Primates have large brains (relative to body size) compared to other mammals, as well as an increased reliance on visual acuity at the expense of the sense of smell, which is the dominant sensory system in most mammals. These features are more developed in monkeys and apes, and noticeably less so in lorises and lemurs. Some primates are trichromats, with three independent channels for conveying color information. Except for apes (including humans), primates have tails. Most primates also have opposable thumbs. Many species are sexually dimorphic; differences may include muscle mass, fat distribution, pelvic width, canine tooth size, hair distribution, and coloration. Primates have slower rates of development than other similarly sized mammals, reach maturity later, and have longer lifespans. Primates are among the most social of animals, forming pairs or family groups, uni-male harems, and multi-male/multi-female groups. Non-human primates have at least four types of social systems, many defined by the amount of movement by adolescent females between groups. Most primate species remain at least partly arboreal: the exceptions are humans, some other great apes, and baboons, all of which left the trees for the ground and now inhabit every continent. Thousands of non-human primates are used in research around the world because of their psychological and physiological similarity to humans. About 60% of primate species are threatened with extinction.

Haplorhini ("dry-nosed" primates): all lost the function of the terminal enzyme which manufactures vitamin C; haplorhine upper lip, which has replaced the ancestral rhinarium found in strepsirrhines, is not directly connected to their nose or gum, allowing a large range of facial expressions. Their brain to body ratio is significantly greater than the strepsirrhines, and their primary sense is vision.

Simian (infraorder Simiiformes, Anthropoidea): "higher primates"

Catarrhini: catarrhines (from Ancient Greek kata-, "down" and rhin-, "nose") have nostrils which face downwards; never have prehensile tails, and have flat fingernails and toenails, a tubular ectotympanic (ear bone), 2.1.2.32.1.2.3

Ape (Hominoidea; hominoids): branch of Old World tailless anthropoid primates native to Africa and Southeast Asia. They are distinguished from other primates by a wider degree of freedom of motion at the shoulder joint as evolved by the influence of brachiation. There are two extant branches of the superfamily Hominoidea: the gibbons, or lesser apes; and the hominids, or great apes. The largest primates and the orangutan, an ape, is the largest living arboreal animal. Except for gorillas and humans, hominoids are agile climbers of trees. Their diet is best described as vegetarian or omnivorous, consisting of leaves, nuts, seeds and fruits, including grass seeds, and in most cases other animals, either hunted or scavenged (or farmed in the case of humans), along with anything else available and easily digested. Great apes, including humans, go through a menstrual cycle. History of hominoid taxonomy: Changes in taxonomy and terminology ("hominid" v "hominin").

Hominidae (great apes): Physical description: large, tailless primates; degree of sexual dimorphism varies greatly among species; most species are omnivorous, but fruit is the preferred food among all but some human groups; human teeth and jaws are markedly smaller for their size than those of other apes, which may be an adaptation to eating cooked food for more than a Ma; gestation: 8-9 months. 4 genera:

Orangutan (Pongo): Bornean orangutan (P. pygmaeus) and the Sumatran orangutan (P. abelii); both species had their genomes sequenced and they appear to have diverged around 400,000 years ago. Orangutans diverged from the rest of the great apes 15.7 to 19.3 mya; most arboreal of the great apes and spend most of their time in trees. Most solitary of the great apes, with social bonds occurring primarily between mothers and their dependent offspring, who stay together for the first two years

Homininae (hominine, hominines): includes two tribes, with their extant as well as extinct species: the Hominini tribe (with the genus Homo including modern humans, and the genus Pan including chimpanzees and bonobos), and the Gorillini tribe (gorillas).

Gorilla: DNA of gorillas is highly similar to that of a human, from 95–99% depending on what is counted, and they are the next closest living relatives to humans after the bonobo and common chimpanzee.

Hominini: comprises three subtribes: Hominina, with its one genus Homo; Australopithecina, comprising at least three extinct genera; and Panina, with its one genus Pan, the chimpanzees (see the evolutionary tree below).

Chimpanzee (chimp; genus Pan): Common chimpanzee (Pan troglodytes; W. + C. Africa) + Bonobo (Pan paniscus; DR Congo)

Homo: genus is estimated to be about 2.3 to 2.4 mya.

Old World monkey (Superfamily: Cercopithecoidea; Family: Cercopithecidae): most have tails (the family name means "tailed ape"); tails are never prehensile; distinction of Old World monkeys from apes depends on dentition (the number of teeth is the same in both, but they are shaped differently)

Gibbon: apes in the family Hylobatidae /ˌhaɪlɵˈbeɪtɨdiː/. The family historically contained one genus, but now is split into four genera. Gibbons occur in tropical and subtropical rainforests from eastern Bangladesh and northeast India to southern China and Indonesia (including the islands of Sumatra, Borneo, and Java).

Strepsirrhini: suborder of primates that includes the lemuriform primates, which consist of the lemurs of Madagascar, galagos ("bushbabies") and pottos from Africa, and the lorises from India and southeast Asia.

Chimpanzees:

Common chimpanzee (Pan troglodytes)

Bonobo (Pan paniscus): Behavior: Social behavior: Most studies indicate that females have a higher social status in bonobo society; Sexual social behavior: Sexual activity generally plays a major role in bonobo society, being used as what some scientists perceive as a greeting, a means of forming social bonds, a means of conflict resolution, and postconflict reconciliation.

Gorillas:

Western gorilla (Gorilla gorilla)

Eastern gorilla (Gorilla beringei)

Mountain gorilla (Gorilla beringei beringei)

Eastern lowland gorilla (Gorilla beringei graueri)

Orangutans:

Bornean orangutan (Pongo pygmaeus)

Sumatran orangutan (Pongo abelii)

Australopithecus is not shown. Genetic distance below the diagram; temporal remoteness above the diagram (MYA).

=Scandentia (treeshrews)=

Treeshrew

Anatomy

Category:Anatomy

Category:Anatomical simulation

Category:Animal anatomy

Anatomography: interactive website which supports generating anatomical diagrams and animations of the human body.

Zygote Body (formerly: Google Body): web application by Zygote Media Group that rendered manipulable 3D anatomical models of the human body.

Long bones: longer than they are wide. Long bones, especially the femur and tibia, are subjected to most of the load during daily activities and they are crucial for skeletal mobility. They grow primarily by elongation of the diaphysis, with an epiphysis at each end of the growing bone. The ends of epiphyses are covered with hyaline cartilage ("articular cartilage").

Short bones: designated as those bones that are as wide as they are long. Their primary function is to provide support and stability with little to no movement.

Flat bones: principal function is either extensive protection or the provision of broad surfaces for muscular attachment. These bones are expanded into broad, flat plates, as in the cranium (skull), the ilium (pelvis), sternum and the rib cage. The flat bones are: the occipital, parietal, frontal, nasal, lacrimal, vomer, hip bone (coxal bone), sternum, ribs, and scapulae.

Sesamoid bone: embedded within a tendon or a muscle. It is derived from the Latin word "sesamum" (sesame seed), due to the small size of most sesamoids. Often, these bones form in response to strain, or can be present as a normal variant. The kneecap is the largest sesamoid bone in the body. Sesamoids act like pulleys, providing a smooth surface for tendons to slide over, increasing the tendon's ability to transmit muscular forces.

Irregular bones: cannot be grouped as long, short, flat or sesamoid bones. Irregular bones serve various purposes in the body, such as protection of nervous tissue (such as the vertebrae protect the spinal cord), affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. Irregular bones can also be used for joining all parts of the spinal column together. The spine is the place in the human body where the most irregular bones can be found.

Hyoid bone (lingual bone, tongue-bone): horseshoe-shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. At rest, it lies at the level of the base of the mandible in the front and the third cervical vertebra (C3) behind. Unlike other bones, the hyoid is only distantly articulated to other bones by muscles or ligaments. It is the only bone in the human body that is not connected to any other bones nearby. The hyoid is anchored by muscles from the anterior, posterior and inferior directions, and aids in tongue movement and swallowing. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. Clinical significance: The hyoid bone is important to a number of physiological functions, including breathing, swallowing and speech. It is also thought to play a key role in keeping the upper airway open during sleep, and as such, the development and treatment of obstructive sleep apnea (OSA; characterized by repetitive collapse of the upper airway during sleep). Other animals: The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle, and is often called the hyoid arch. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua.

Body fluids: blood

Category:Body fluids

Category:Blood

Category:Blood antigen systems

Category:Blood donation

Category:Blood proteins

Human blood group systems: International Society of Blood Transfusion (ISBT) as systems in the human species where cell-surface antigens—in particular, those on blood cells—are "controlled at a single gene locus or by two or more very closely linked homologous genes with little or no observable recombination between them".

Rh blood group system: human blood group system. It contains proteins on the surface of red blood cells. It is the second most important blood group system, after the ABO blood group system. The Rh blood group system consists of 49 defined blood group antigens, among which the five antigens D, C, c, E, and e are the most important. There is no d antigen. Rh(D) status of an individual is normally described with a positive or negative suffix after the ABO type (e.g., someone who is A Positive has the A antigen and the Rh(D) antigen, whereas someone who is A Negative lacks the Rh(D) antigen). The terms Rh factor, Rh positive, and Rh negative refer to the Rh(D) antigen only. Antibodies to Rh antigens can be involved in hemolytic transfusion reactions and antibodies to the Rh(D) and Rh antigens confer significant risk of hemolytic disease of the fetus and newborn. Rh_null phenotype. Other Rh group antigens: 50 antigens have been described in the Rh group system; among those described here, the D, C, c, E and e antigens are the most important.

Albumin: family of globular proteins, the most common of which are the serum albumins. All of the proteins of the albumin family are water-soluble, moderately soluble in concentrated salt solutions, and experience heat denaturation. Albumins are commonly found in blood plasma and differ from other blood proteins in that they are not glycosylated. Substances containing albumins are called albuminoids. Function: Human types include: Human serum albumin - makes up around 50% of human plasma proteins, binds water, cations (such as Ca²⁺, Na⁺ and K⁺), fatty acids, hormones, bilirubin, thyroxine (T4) and pharmaceuticals (including barbiturates); Alpha-fetoprotein is a fetal plasma protein that binds various cations, fatty acids and bilirubin; Vitamin D-binding protein; afamin; Extracellular matrix protein 1 - regulates bone mineralization. Other albumin types: Ovalbumin; Lactalbumin (whey protein); some plant seeds, including hemp, encode "2S albumins".

Serum albumin (blood albumin): found in vertebrate blood. Human serum albumin is encoded by the ALB gene. Other mammalian forms, such as bovine serum albumin, are chemically similar. Albumin is a globular, water-soluble, un-glycosylated serum protein of approximate molecular weight of 65 kDa.

Plant lipid transfer proteins (LTPs/PLTPs): group of highly-conserved proteins of about 7-9kDa found in higher plant tissues. As its name implies, lipid transfer proteins facilitate the shuttling of phospholipids and other fatty acid groups between cell membranes. The LTP domain is also found in seed storage proteins (including 2S albumin, gliadin, and glutelin) and bifunctional trypsin/alpha-amylase inhibitors.

Domesticated animals, feral animals

Category:Domesticated animals

Category:Beekeeping

Category:Domesticated birds

Category:Feral animals

Category:Feral parrots

Category:Ferrets

Category:Livestock

Opinion 2027: ruling of the International Commission on Zoological Nomenclature (ICZN) concerning the conservation of 17 species names of wild animals with domestic derivatives. If these wild animals and their domesticated derivatives are regarded as one species, then the scientific name of that species is the scientific name of the wild animal.

Origin of the domestic dog: includes the dog's evolutionary divergence from the wolf, its domestication, and its development into dog types and dog breeds. The dog is a member of the genus Canis, which forms part of the wolf-like canids, and was the first species and the only large carnivore to have been domesticated. The dog and the extant gray wolf are sister taxa, as modern wolves are not closely related to the population of wolves that was first domesticated.

Dog type: road categories of dogs based on form, function or style of work, lineage, or appearance. In contrast, modern dog breeds are particular breed standards, sharing a common set of heritable characteristics, determined by the kennel club that recognizes the breed. The genetic divergence between dogs and wolves occurred between 40,000–20,000 years ago, just before or during the Last Glacial Maximum. The ancestors of humans and dogs would ultimately meet in Eurasia. The domestication of animals commenced over 15,000 YBP, beginning with the grey wolf (Canis lupus) by nomadic hunter-gatherers. Genetic studies indicate that the gray wolf is the closest living relative of the dog, with no evidence of any other canine species having contributed. The phylogenetic analyses revealed that three of the four major mDNA clades of dogs relate most closely to the ancient canids from Europe rather than those from China or the Middle East, which supports a European origin of modern dogs. No modern wolf population related closer to dogs than the ancient canids from Europe, indicating that the wolf population that was the ancestor of the dog is extinct. Some ancient dog populations that once occupied Europe and the New World no longer exist. This implies that some ancient dog populations were entirely replaced and others admixed over a long period of time. European dog populations have undergone extensive turnover during the last 15,000 years which has erased the genomic signature of early European dogs, the genetic heritage of the modern breeds has become blurred due to admixture, and there was the possibility of past domestication events that had gone extinct or had been largely replaced by more modern dog populations. The study proposes that dogs may have been domesticated separately in both eastern and western Eurasia from two genetically distinct and now extinct wolf populations. East Eurasian dogs then made their way with migrating people to western Europe between 14,000-6,400 YBP where they partially replaced the dogs of Europe. Two domestication events in western Eurasia and eastern Eurasia has recently been found for the domestic pig. The study indicates that the western Eurasian wolf and dog populations genetically diverged 20,000-60,000 YBP. Immediately after this divergence, the dog population outnumbered the wolf population, and later the dog population underwent a population reduction to be much lower. The earlier association of dogs with humans may have allowed dogs to have a profound influence on the course of early human history and the development of civilization. Genetic studies support two population bottlenecks having occurred to the dog lineage, one due to the initial domestication and one due to the formation of dog breeds. Unlike other domestic species which were primarily selected for production-related traits, dogs were initially selected for their behaviors. In 2016, a study found that there were only 11 fixed genes that showed variation between wolves and dogs. These gene variations were unlikely to have been the result of natural evolution, and indicate selection on both morphology and behavior during dog domestication. Dogs have evolved specialized skills for reading human social and communicative behavior. These skills seem more flexible – and possibly more human-like – than those of other animals more closely related to humans phylogenetically, such as chimpanzees, bonobos and other great apes. This raises the possibility that convergent evolution has occurred: both Canis familiaris and Homo sapiens might have evolved some similar (although obviously not identical) social-communicative skills – in both cases adapted for certain kinds of social and communicative interactions with human beings. The pointing gesture is a human-specific signal, is referential in its nature, and is a foundation building-block of human communication. Human infants acquire it weeks before the first spoken word. In 2009, a study compared the responses to a range of pointing gestures by dogs and human infants. The study showed little difference in the performance of 2-year-old children and dogs, while 3-year-old children's performance was higher. Human adoption of some wolf behaviors. Bonn–Oberkassel dog. First dogs as a hunting technology. Dogs enter North America from Siberia. First dog breeds developed in Siberia. Dogs enter Japan.

Feral parrot: parrot that has adapted to life in an ecosystem to which it is not native. Many are descended from pets that have escaped or been deliberately released.

Red-masked parakeet (Psittacara erythrogenys): medium-sized parrot from Ecuador and Peru. It is popular as a pet and are known in aviculture as the cherry-headed conure or the red-headed conure. They are also considered the best talkers of all the conures.

Rose-ringed parakeet (Psittacula krameri): ring-necked parakeet, is a gregarious tropical Afro-Asian parakeet species that has an extremely large range. Both sexes have a distinctive green colour. Rose-ringed parakeets measure on average 40 cm in length, including the tail feathers, a large portion of their total length. One of the few parrot species that have successfully adapted to living in disturbed habitats, it has withstood the onslaught of urbanisation and deforestation. As a popular pet species, escaped birds have colonised a number of cities around the world; herbivorous and not migratory.

Kingston parakeets: feral rose-ringed parakeets that live in the suburbs around Kingston and Twickenham, South West London, England, numbering at least 6,000, with some estimates suggesting the UK population could be as high as 50,000 individuals.

Neuroscience

Category:Neuroscience

Category:Neural engineering

Category:Neurotechnology

Category:Neuroimaging

Category:Electroencephalography

Category:Biomedical cybernetics

Category:Computational neuroscience

Neuroscience Information Framework (NIF): repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources and provides many authoritative links throughout the neuroscience portal of wikipedia.

NeuroLex: dynamic lexicon of neuroscience concepts; structured as a semantic wiki, using Semantic MediaWiki

Soliton vs Hodgin-Huxley model:

Hodgkin–Huxley model: mathematical model (a type of scientific model) that describes how action potentials in neurons are initiated and propagated. It is a set of nonlinear ordinary differential equations that approximates the electrical characteristics of excitable cells such as neurons and cardiac myocytes.

Soliton model: proposes that the signals travel along the cell's membrane in the form of certain kinds of sound (or density) pulses known as solitons.

Behavioral contagion: propensity for certain behavior exhibited by one person to be copied by others either in the vicinity of the original user, or who have been exposed to media coverage describing the behavior of the original actor.

Neural top down control of physiology: direct regulation by the brain of physiological functions (in addition to smooth muscle and glandular ones). Regulation occurs through the sympathetic and parasympathetic system (the autonomic nervous system), and their direct innervation of body organs and tissues that starts in the brainstem. There is also a noninnervation hormonal control through the hypothalamus and pituitary (HPA). These lower brain areas are under control of cerebral cortex ones. Pavlovian conditioning shows that brain control over basic cell level physiological function can be learnt.

Mind uploading (whole brain emulation, mind transfer): hypothetical process of transferring or copying a conscious mind from a brain to a non-biological substrate by scanning and mapping a biological brain in detail and copying its state into a computer system or another computational device. The computer would have to run a simulation model so faithful to the original that it would behave in essentially the same way as the original brain, or for all practical purposes, indistinguishably.

Blue Brain Project (BBP): attempt to create a synthetic brain by reverse-engineering the mammalian brain down to the molecular level. Simulation of rat neocortical column (2 mm tall, 0.5 mm in diameter, 10⁸ synapses) was completed in 2006.12.

Human Brain Project (HBP): research project which aims to simulate (with supercomputers) and better understand the human brain. EU gave >1 bln € to this project.

Tonic–clonic seizure (formerly: grand mal seizures): type of generalized seizure that affects the entire brain; most commonly associated with epilepsy and seizures in general, though it is a misconception that they are the only type.

Electroconvulsive therapy (ECT; formerly: electroshock therapy): standard psychiatric treatment in which seizures are electrically induced in patients to provide relief from psychiatric illnesses. ECT is usually used as a last line of intervention for major depressive disorder, schizophrenia, mania and catatonia. Administered under anesthetic with a muscle relaxant. Although a large amount of research has been carried out, the exact mechanism of action of ECT remains elusive, and successful ECT is usually followed by medication treatment.

Brain stimulation reward: phenomenon in which direct stimulation of regions of the brain through either electrical or chemical means is rewarding and can serve as an operant reinforcer; stimulation activates the reward system and establishes response habits similar to those established by natural rewards such as food and water; stimulation of the lateral hypothalamus and other regions of the brain associated with natural reward was both rewarding as well as drive inducing. Relationship to natural rewards and drives: Strength of drive: Rats will perform lever-pressing at rates of several thousand responses per hour for days in order to obtain direct electrical stimulation of the lateral hypothalamus; Addiction: Rats and monkeys have been shown to work in a compulsive manner to achieve intravenous injections of stimulants, and when access to the drugs is not limited, they will self-administer the drugs to the point of severe weight loss and death.

Operant conditioning (instrumental conditioning): type of learning in which an individual's behavior is modified by its antecedents and consequences

Deep brain stimulation (DBS): surgical treatment involving the implantation of a medical device called a brain pacemaker, which sends electrical impulses to specific parts of the brain. Possible therapeutic benefits for chronic pain, Parkinson's, tremor, dystonia; sexual arousal; tested on patients with post-tramatic coma; could change behavior drastically. Despite the long history of DBS, its underlying principles and mechanisms are still not clear.

Wirehead (science fiction): when fiction meets DBS.

Brain stimulation reward: phenomenon in which direct stimulation of regions of the brain through either electrical or chemical means is rewarding and can serve as an operant reinforcer. The stimulation activates the reward system and establishes response habits similar to those established by natural rewards such as food and water.

Template:EEG

P300 (neuroscience): event related potential (ERP) component elicited in the process of decision making. It is considered to be an endogenous potential, as its occurrence links not to the physical attributes of a stimulus, but to a person's reaction to it. When recorded by electroencephalography (EEG), it surfaces as a positive deflection in voltage with a latency (delay between stimulus and response) of roughly 250 to 500 ms.

Nervous system

Category:Nervous system

Category:Animal nervous system

Category:Central nervous system

Category:Central nervous system disorders

Category:Systemic atrophies primarily affecting the central nervous system

Category:Neuromuscular disorders

Category:Amyotrophic lateral sclerosis

Category:Demyelinating diseases of CNS

Category:Multiple sclerosis

List of animals by number of neurons:

Whole nervous system:
1. Human 86,000,000,000 neurons; ~1.5×10¹⁴ Synapses for average adult
2. African elephant 257,000,000,000 neurons
Cerebral cortex:
1. Human 16,000,000,000 neurons
2. Long-finned pilot whale 37,200,000,000 neurons

Elephant cognition: Most contemporary ethologists view the elephant as one of the world's most intelligent animals. With a mass of just over 5 kg, an elephant's brain has more mass than that of any other land animal, and although the largest whales have body masses twenty times those of a typical elephant, a whale's brain is barely twice the mass of an elephant's brain. Elephants manifest a wide variety of behaviors, including those associated with grief, learning, mimicry, play, altruism, use of tools, compassion, cooperation, self-awareness, memory, and communication. Further, evidence suggests elephants may understand pointing: the ability to nonverbally communicate an object by extending a finger, or equivalent. It is thought they are equal with cetaceans and primates in this regard. Due to such claims of high intelligence and due to strong family ties of elephants, some researchers argue it is morally wrong for humans to cull them. The Ancient Greek philosopher, Aristotle, once said that the elephant was "the animal which surpasses all others in wit and mind."

Demyelinating disease: any disease affecting the nervous system where the myelin sheath surrounding neurons is damaged. This damage disrupts the transmission of signals through the affected nerves, resulting in a decrease in their conduction ability. Consequently, this reduction in conduction can lead to deficiencies in sensation, movement, cognition, or other functions depending on the nerves affected. Various factors can contribute to the development of demyelinating diseases, including genetic predisposition, infectious agents, autoimmune reactions, and other unknown factors. Proposed causes of demyelination include genetic predisposition, environmental factors such as viral infections or exposure to certain chemicals. Additionally, exposure to commercial insecticides like sheep dip, weed killers, and flea treatment preparations for pets, which contain organophosphates, can also lead to nerve demyelination. Chronic exposure to neuroleptic medications may also cause demyelination. Furthermore, deficiencies in vitamin B12 can result in dysmyelination.

Multiple sclerosis (MS, multiple cerebro-spinal sclerosis; Usual onset: Age 20–50): most common demyelinating disease, in which the insulating covers of nerve cells in the brain and spinal cord are damaged. This damage disrupts the ability of parts of the nervous system to transmit signals, resulting in a range of signs and symptoms, including physical, mental, and sometimes psychiatric problems. Specific symptoms can include double vision, visual loss, muscle weakness, and trouble with sensation or coordination. MS takes several forms, with new symptoms either occurring in isolated attacks (relapsing forms) or building up over time (progressive forms). While the cause is unclear, the underlying mechanism is thought to be either destruction by the immune system or failure of the myelin-producing cells. Proposed causes for this include genetics and environmental factors, such as viral infections. MS is usually diagnosed based on the presenting signs and symptoms and the results of supporting medical tests. No cure for multiple sclerosis is known. Treatments attempt to improve function after an attack and prevent new attacks.

ALS (amyotrophic lateral sclerosis, motor neurone disease (MND), Lou Gehrig's disease; Usual onset: 45 – 75 years): rare and terminal neurodegenerative disease that results in the progressive loss of motor neurons that control voluntary muscles. ALS is the most common form of the motor neuron diseases. Early symptoms of ALS include stiff muscles, muscle twitches, gradual increasing weakness, and muscle wasting. Limb-onset ALS begins with weakness in the arms or legs, while bulbar-onset ALS begins with difficulty in speaking or swallowing. Around half of people with ALS develop at least mild difficulties with thinking and behavior, and about 15% develop frontotemporal dementia. Motor neuron loss continues until the abilities to eat, speak, move, or, lastly, breathe are lost. Most cases of ALS (about 90% to 95%) have no known cause, and are known as sporadic ALS. However, both genetic and environmental factors are believed to be involved. The remaining 5% to 10% of cases have a genetic cause, often linked to a history of the disease in the family, and these are known as familial ALS (hereditary). There is no known cure for ALS. The goal of treatment is to slow the disease progression, and improve symptoms.The average survival from onset to death is two to four years, though this can vary, and about 10% of those affected survive longer than ten years.

Brain, mind, mind–body problem, consciousness

Category:Brain

Category:Cerebellum

Category:Mind

Category:Cognition

Category:Mental content

Category:Consciousness

Category:Cognition

Category:Mental health

Category:History of mental health

Category:Clinical psychology

Category:Psychiatry

Category:Psychotherapy

Category:Mental processes

Category:Psychology

Category:Psychiatry

Main regions of the vertebrate brain, shown for a shark and a human brain (the human brain is sliced along the midline). The two brains are not on the same scale.

Brain: organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It is located in the head, usually close to the sensory organs for senses such as vision. It is the most complex organ in a vertebrate's body. In a human, the cerebral cortex contains approximately 14–16 bln. neurons, and the estimated number of neurons in the cerebellum is 55–70 bln. Each neuron is connected by synapses to several thousand other neurons.

Anatomy:
- Evolution:
  - Generic bilaterian nervous system: There are a few types of existing bilaterians that lack a recognizable brain, including echinoderms and tunicates. It has not been definitively established whether the existence of these brainless species indicates that the earliest bilaterians lacked a brain, or whether their ancestors evolved in a way that led to the disappearance of a previously existing brain structure.
  - Invertebrates: Cephalopods such as the octopus and squid have the largest brains of any invertebrates.
  - Vertebrates: The first vertebrates appeared over 500 Mya, during the Cambrian period, and may have resembled the modern hagfish in form. Sharks appeared about 450 Mya, amphibians about 400 Mya, reptiles about 350 Mya, and mammals about 200 Mya. Each species has an equally long evolutionary history, but the brains of modern hagfishes, lampreys, sharks, amphibians, reptiles, and mammals show a gradient of size and complexity that roughly follows the evolutionary sequence. For mammals, the relationship between brain volume and body mass essentially follows a power law with an exponent of about 0.75. This formula describes the central tendency, but every family of mammals departs from it to some degree, in a way that reflects in part the complexity of their behavior. For example, primates have brains 5 to 10 times larger than the formula predicts. Predators tend to have larger brains than their prey, relative to body size. Blood vessels enter the central nervous system through holes in the meningeal layers. The cells in the blood vessel walls are joined tightly to one another, forming the blood–brain barrier, which blocks the passage of many toxins and pathogens (though at the same time blocking antibodies and some drugs, thereby presenting special challenges in treatment of diseases of the brain).
    - Mammals: The most obvious difference between the brains of mammals and other vertebrates is in terms of size. On average, a mammal has a brain roughly twice as large as that of a bird of the same body size, and ten times as large as that of a reptile of the same body size. Size, however, is not the only difference: there are also substantial differences in shape. The hindbrain and midbrain of mammals are generally similar to those of other vertebrates, but dramatic differences appear in the forebrain, which is greatly enlarged and also altered in structure. The cerebral cortex is the part of the brain that most strongly distinguishes mammals. In non-mammalian vertebrates, the surface of the cerebrum is lined with a comparatively simple three-layered structure called the pallium. In mammals, the pallium evolves into a complex six-layered structure called neocortex or isocortex. Several areas at the edge of the neocortex, including the hippocampus and amygdala, are also much more extensively developed in mammals than in other vertebrates.

Brainstem: posterior part of the brain, adjoining and structurally continuous with the spinal cord. In the human brain the brainstem includes the midbrain, the pons, and the medulla oblongata.

Pons: part of the brainstem, and in humans and other bipeds lies inferior to the midbrain, superior to the medulla oblongata and anterior to the cerebellum.

Schematic representation of the major anatomical divisions of the cerebellum.

Cerebellum: major feature of the hindbrain of all vertebrates. Although usually smaller than the cerebrum, in some animals such as the mormyrid fishes it may be as large as or even larger. In humans, the cerebellum plays an important role in motor control, and it may also be involved in some cognitive functions such as attention and language as well as in regulating fear and pleasure responses, but its movement-related functions are the most solidly established. The human cerebellum does not initiate movement, but contributes to coordination, precision, and accurate timing: it receives input from sensory systems of the spinal cord and from other parts of the brain, and integrates these inputs to fine-tune motor activity. Cerebellar damage produces disorders in fine movement, equilibrium, posture, and motor learning in humans. Its cortical surface is covered with finely spaced parallel grooves, in striking contrast to the broad irregular convolutions of the cerebral cortex. These parallel grooves conceal the fact that the cerebellar cortex is actually a continuous thin layer of tissue tightly folded in the style of an accordion. Within this thin layer are several types of neurons with a highly regular arrangement, the most important being Purkinje cells and granule cells. This complex neural organization gives rise to a massive signal-processing capability, but almost all of the output from the cerebellar cortex passes through a set of small deep nuclei lying in the white matter interior of the cerebellum.

Comparative anatomy and evolution: circuits in the cerebellum are similar across all classes of vertebrates, including fish, reptiles, birds, and mammals. There is also an analogous brain structure in cephalopods with well-developed brains, such as octopuses. This has been taken as evidence that the cerebellum performs functions important to all animal species with a brain. In amphibians, it is little developed, and in lampreys, and hagfish, the cerebellum is barely distinguishable from the brain-stem. Although the spinocerebellum is present in these groups, the primary structures are small, paired-nuclei corresponding to the vestibulocerebellum. The cerebellum is a bit larger in reptiles, considerably larger in birds, and larger yet in mammals. The large paired and convoluted lobes found in humans are typical of mammals, but the cerebellum is, in general, a single median lobe in other groups, and is either smooth or only slightly grooved. In mammals, the neocerebellum is the major part of the cerebellum by mass, but, in other vertebrates, it is typically the spinocerebellum. The cerebellum of cartilaginous and bony fishes is extraordinarily large and complex. In at least one important respect, it differs in internal structure from the mammalian cerebellum: The fish cerebellum does not contain discrete deep cerebellar nuclei. Instead, the primary targets of Purkinje cells are a distinct type of cell distributed across the cerebellar cortex, a type not seen in mammals. In mormyrid fish (a family of weakly electrosensitive freshwater fish), the cerebellum is considerably larger than the rest of the brain. The largest part of it is a special structure called the valvula, which has an unusually regular architecture and receives much of its input from the electrosensory system. The size of the human cerebellum, compared to the rest of the brain, has been increasing in size while the cerebrum decreased in size With both the development and implementation of motor tasks, visual-spatial skills and learning taking place in the cerebellum, the growth of the cerebellum is thought to have some form of correlation to greater human cognitive abilities. The lateral hemispheres of the cerebellum are now 2.7 times greater in both humans and apes than they are in monkeys. These changes in the cerebellum size cannot be explained by greater muscle mass. They show that either the development of the cerebellum is tightly linked to that of the rest of the brain or that neural activities taking place in the cerebellum were important during Hominidae evolution. Due to the cerebellum's role in cognitive functions, the increase in its size may have played a role in cognitive expansion.

Anatomy of the cerebellum: can be viewed at three levels. At the level of gross anatomy, the cerebellum consists of a tightly folded and crumpled layer of cortex, with white matter underneath, several deep nuclei embedded in the white matter, and a fluid-filled ventricle in the middle. At the intermediate level, the cerebellum and its auxiliary structures can be broken down into several hundred or thousand independently functioning modules or compartments known as microzones. At the microscopic level, each module consists of the same small set of neuronal elements, laid out with a highly stereotyped geometry.

Cerebellar vermis: located in the medial, cortico-nuclear zone of the cerebellum, which resides in the posterior fossa of the cranium. The primary fissure in the vermis curves ventrolaterally to the superior surface of the cerebellum, dividing it into anterior and posterior lobes. Functionally, the vermis is associated with bodily posture and locomotion.

Deep cerebellar nuclei: from lateral to medial, the four deep cerebellar nuclei are the dentate, emboliform, globose, and fastigii.

Disorders of consciousness: medical conditions that inhibit consciousness. Some define disorders of consciousness as any change from complete self-awareness to inhibited or absent self-awareness and arousal. This category generally includes minimally conscious state and persistent vegetative state, but sometimes also includes the less severe locked-in syndrome and more severe but rare chronic coma. Finally, brain death results in an irreversible disruption of consciousness.

Locked-in syndrome (pseudocoma): condition in which a patient is aware but cannot move or communicate verbally due to complete paralysis of nearly all voluntary muscles in the body except for vertical eye movements and blinking. The individual is conscious and sufficiently intact cognitively to be able to communicate with eye movements. The EEG is normal in locked-in syndrome. Total locked-in syndrome, or completely locked-in state (CLIS), is a version of locked-in syndrome wherein the eyes are paralyzed as well.

Minimally conscious state (MCS): disorder of consciousness distinct from persistent vegetative state and locked-in syndrome. Unlike persistent vegetative state, patients with MCS have partial preservation of conscious awareness.

Persistent vegetative state (PVS): disorder of consciousness in which patients with severe brain damage are in a state of partial arousal rather than true awareness. After four weeks in a vegetative state (VS), the patient is classified as in a persistent vegetative state. The vegetative state is a chronic or long-term condition. This condition differs from a coma: a coma is a state that lacks both awareness and wakefulness. Patients in a vegetative state may have awoken from a coma, but still have not regained awareness. In the vegetative state patients can open their eyelids occasionally and demonstrate sleep-wake cycles, but completely lack cognitive function. The vegetative state is also called a "coma vigil". The chances of regaining awareness diminish considerably as the time spent in the vegetative state increases. Persistent vegetative state is the standard usage for a medical diagnosis, made after numerous neurological and other tests, that due to extensive and irreversible brain damage a patient is highly unlikely ever to achieve higher functions above a vegetative state. This diagnosis does not mean that a doctor has diagnosed improvement as impossible, but does open the possibility, in the US, for a judicial request to end life support. Most PVS patients are unresponsive to external stimuli and their conditions are associated with different levels of consciousness. Some level of consciousness means a person can still respond, in varying degrees, to stimulation. A person in a coma, however, cannot. Many people emerge spontaneously from a vegetative state within a few weeks. The chances of recovery depend on the extent of injury to the brain and the patient's age – younger patients having a better chance of recovery than older patients.

Brain death: complete loss of brain function (including involuntary activity necessary to sustain life). It differs from persistent vegetative state, in which the person is alive and some autonomic functions remain. It is also distinct from an ordinary coma, whether induced medically or caused by injury and/or illness, even if it is very deep, as long as some brain and bodily activity and function remains; and it is also not the same as the condition known as locked-in syndrome. With the increasing ability of the medical community to resuscitate people with no respiration, heartbeat, or other external signs of life, the need for another definition of death occurred, raising questions of legal death. This gained greater urgency with the widespread use of life support equipment, as well as rising capabilities and demand for organ transplantation. In USA, if the patient is at or near death, the hospital must notify a transplant organization of the person's details and maintain the patient while the patient is being evaluated for suitability as a donor. The patient is kept on ventilator support until the organs have been surgically removed. If the patient has indicated in an advance health care directive that they do not wish to receive mechanical ventilation or has specified a do not resuscitate order and the patient has also indicated that they wish to donate their organs, some vital organs such as the heart and lungs may not be able to be recovered.

Beating heart cadaver: body that is pronounced dead in all medical and legal definitions, connected to a medical ventilator, and retains cardio-pulmonary functions. This keeps the organs of the body, including the heart, functioning and alive. As a result, the period of time in which the organs may be used for transplantation is extended. The heart contains pacemaker cells that will cause it to continue beating even when a patient is brain-dead. Other organs in the body do not have this capability and need the brain to be functioning to send signals to the organs to carry out their functions. A beating heart cadaver requires a ventilator to provide oxygen to its blood, but the heart will continue to beat on its own even in the absence of brain activity. This allows organs to be preserved for a longer period of time in the case of a transplant or donation.

Bayesian approaches to brain function: investigate the capacity of the nervous system to operate in situations of uncertainty in a fashion that is close to the optimal prescribed by Bayesian statistics. This term is used in behavioural sciences and neuroscience and studies associated with this term often strive to explain the brain's cognitive abilities based on statistical principles.

Sparse distributed memory (SDM): mathematical model of human long-term memory introduced by Pentti Kanerva in 1988 while he was at NASA Ames Research Center. It is a generalized random-access memory (RAM) for long (e.g., 1,000 bit) binary words. These words serve as both addresses to and data for the memory. The main attribute of the memory is sensitivity to similarity, meaning that a word can be read back not only by giving the original write address but also by giving one close to it, as measured by the number of mismatched bits (i.e., the Hamming distance between memory addresses).

Hierarchical temporal memory: unsupervised to semi-supervised online machine learning model developed by Jeff Hawkins and Dileep George of Numenta, Inc. that models some of the structural and algorithmic properties of the neocortex. HTM is a biomimetic model based on the memory-prediction theory of brain function described by Jeff Hawkins in his book On Intelligence. HTM is a method for discovering and inferring the high-level causes of observed input patterns and sequences, thus building an increasingly complex model of the world.

Connectome: comprehensive map of neural connections in the brain, and may be thought of as its "wiring diagram". More broadly, a connectome would include the mapping of all neural connections within an organism's nervous system. The term "connectome" is used primarily in scientific efforts to capture, map, and understand the organization of neural interactions within the brain. The ultimate goal of connectomics is to map the human brain.

Hemispheres

Hemispherectomy: very rare surgical procedure where one cerebral hemisphere (half of the brain) is removed or disabled.

Ahad Israfil: gunshot victim from Dayton, Ohio, remarkable for his recovery from an injury that destroyed most of one of his cerebral hemispheres.

Split-brain: lay term to describe the result when the corpus callosum connecting the two hemispheres of the brain is severed to some degree; surgical operation to produce this condition is called corpus callosotomy, and is usually a last resort to treat refractory epilepsy. After surgery, neuropsychological assessments are often performed to determine where functions of the brain are lateralized. For example, language is said to be lateralized in the left hemisphere while facial recognition is said to be lateralized in the right hemisphere. "Scientists have often wondered whether split-brain patients, who have had the two hemispheres of their brain surgically disconnected, are 'of two minds'" (Zilmer, 2001). Initially, partial callosotomies are performed; if this operation does not succeed, a complete callosotomy is performed to mitigate the risk of accidental physical injury by reducing the severity and violence of epileptic seizures.

Vision and brain

Category:Vision

Category:Face perception

Category:Visual perception

Category:Optical illusions

Blindsight: defined as the ability of people who are cortically blind due to lesions in their striate cortex, also known as primary visual cortex or V1, to respond to visual stimuli that they do not consciously see. There is signal processing all the way from the retinal ganglions to the visual cortex. Damage to visual cortex only leaves the other signal processing intact and the cortically blind can "see". Exact mechanism unknown.

Opponent process: color theory that states that the human visual system interprets information about color by processing signals from cones and rods in an antagonistic manner.

Face perception (facial perception): individual's understanding and interpretation of the face. Here, perception implies the presence of consciousness and hence excludes automated facial recognition systems. Although facial recognition is found in other species , this article focuses on facial perception in humans. The perception of facial features is an important part of social cognition. Information gathered from the face helps people understand each other's identity, what they are thinking and feeling, anticipate their actions, recognize their emotions, build connections, and communicate through body language. Developing facial recognition is a necessary building block for complex societal constructs. Being able to perceive identity, mood, age, sex, and race lets people mold the way we interact with one another, and understand our immediate surroundings. Though facial perception is mainly considered to stem from visual intake, studies have shown that even people born blind can learn face perception without vision. Studies have supported the notion of a specialized mechanism for perceiving faces. Overview: Traumatic brain injury and neurological illness: Theories about the processes involved in adult face perception have largely come from two sources: research on normal adult face perception and the study of impairments in face perception that are caused by brain injury or neurological illness. Novel optical illusions such as the Flashed Face Distortion Effect, in which scientific phenomenology outpaces neurological theory, also provide areas for research. Early development: infants; Ability to discern faces from other objects; Ability to detect emotion in the face; Ability to recognize familiar faces; Ability to 'mimic' faces. Ethnicity: Cross-race effect. Autism. Schizophrenia. Other animals. Artificial intelligence: Facial recognition system. Genetic basis.

Prosopagnosia (prósōpon, meaning "face", and agnōsía, meaning "non-knowledge"; face blindness): cognitive disorder of face perception in which the ability to recognize familiar faces, including one's own face (self-recognition), is impaired, while other aspects of visual processing (e.g., object discrimination) and intellectual functioning (e.g., decision-making) remain intact. The term originally referred to a condition following acute brain damage (acquired prosopagnosia), but a congenital or developmental form of the disorder also exists, with a prevalence rate of 2.5%. The specific brain area usually associated with prosopagnosia is the fusiform gyrus, which activates specifically in response to faces. The functionality of the fusiform gyrus allows most people to recognize faces in more detail than they do similarly complex inanimate objects. For those with prosopagnosia, the new method for recognizing faces depends on the less sensitive object-recognition system. The right hemisphere fusiform gyrus is more often involved in familiar face recognition than the left. It remains unclear whether the fusiform gyrus is only specific for the recognition of human faces or if it is also involved in highly trained visual stimuli.

Greeble (psychology): invented category of novel objects used as stimuli in psychological studies of object and face recognition. They were named by the psychologist Robert Abelson. The greebles were created for Isabel Gauthier's dissertation work at Yale, so as to share constraints with faces: they have a small number of parts in a common configuration.

Neurotransmitters

Category:Neurotransmitters

Monoamine neurotransmitter: contain one amino group that is connected to an aromatic ring by a two-carbon chain (-CH₂-CH₂-); derived from aromatic amino acids like phenylalanine, tyrosine, tryptophan, and the thyroid hormones by aromatic amino acid decarboxylase enzymes; function of monoamine is not clear but it is thought to trigger crucial components such as emotion, arousal, and cognition; drugs used to increase the effect of monoamine may be used to treat patients with psychiatric disorders, including depression, anxiety, and schizophrenia.

Optical illusions

Best Illusion of the Year Contest: annual recognition of the world's illusion creators awarded by the Neural Correlate Society. The contest was created in 2005 by professors Susana Martinez-Conde and Stephen Macknik as part of the European conference on Visual Perception in La Coruna, Spain. It has since transitioned to an online contest where everyone in the world is invited to submit illusions and vote for the winner. The contest decides on the most impressive perceptual or cognitive illusion of the year (unpublished, or published no earlier than the year prior to the most recent competition). An illusion is a perceptual or cognitive experience that does not match the physical reality (i.e. the perception of motion where no such motion physically exists) As human experience is generated indirectly by brain mechanisms that interact with the physical reality, the study of illusions offers insight into the neural bases of perception and cognition. The community includes neuroscientists, ophthalmologists, neurologists, and visual artists that create illusions to help discover the neural underpinnings of illusory perception.

Leaning tower illusion: However in the case of the two identical images of the Pisa tower, the corresponding outlines of the towers do not converge but run in parallel, and as a result the towers are perceived as non-parallel, i.e. as diverging.

Spinning Dancer

Intelligence, IQ

Category:Orcas

Category:Individual orcas

Mirror test: animals that have passed the mirror test: Cetaceans: Bottlenose dolphin (Tursiops truncatus), Killer whale (Orcinus orca) & false killer whales (Pseudorca crassidens); Primates: Bonobo (Pan paniscus), Chimpanzee (Pan troglodytes), Bornean orangutan (Pongo pygmaeus), Human (Homo sapiens); Proboscidea: Asian elephant (Elephas maximus); Birds: Eurasian magpie (Pica pica), Pigeons; Insects: ants (Myrmica sabuleti, Myrmica rubra and Myrmica ruginodis); Fish: Cleaner Wrasse. Animals that may pass: Gorillas, Fish: giant manta rays.

European Magpie (Pica pica): the most intelligent bird, one of the most intelligent animals. The pairs are monogamous, and remain together for the duration of their lives. Should one of the two die, the widow or widower will find a new partner from the stock of yearlings. Possible subspieces or neighboring species: Korean Magpie (Asian, Chinese Magpie), Yellow-billed Magpie (California), Black-billed Magpie (N. America)

Species	Simple brain-to-body ratio (E/S)^{[citation needed]}
small birds	1⁄12
human	1⁄40
mouse	1⁄40
dolphin	1⁄50
cat	1⁄100
chimpanzee	1⁄113
dog	1⁄125
frog	1⁄172
lion	1⁄550
elephant	1⁄560
horse	1⁄600
shark	1⁄2496
hippopotamus	1⁄2789

List of animals by number of neurons: Whole nervous system; Cerebral cortex.

Cephalization: considered an evolutionary trend, whereby nervous tissue, over many generations, becomes concentrated toward one end of an organism. This process eventually produces a head region with sensory organs.

Encephalization:

E=CS^{r}

; "E" is weight of the brain, "C" is cephalization factor, "S" is body weight, and "r" is the exponential constant. The exponential constant for primates is 0.28 and either 0.56 or 0.66 for mammals in general.

Encephalization quotient (EQ, encephalization level): measure of relative brain size defined as the ratio between actual brain mass and predicted brain mass for an animal of a given size, which is hypothesized to be a rough estimate of the intelligence of the animal. More refined than raw brain-to-body mass ratio by taking allometric effects. Ew(brain) = 0.12w(body)^2/3. EQ(human)=7.4-7.8, EQ(tucuxi dolphin)=4.56, EQ(bottlenose dolphin)=4.14, EQ(Orca)=2.57–3.3, EQ(chimp)=2.2–2.5, EQ(Raven)=2.49, EQ(Rhesus monkey)=2.1, EQ(Elephant)=1.13–2.36, EQ(Chinchilla)=1.34, EQ(dog)=1.17, EQ(cat)=1.00, EQ(mouse)=0.5

Dolphin intelligence

Cephalopod intelligence: measure of the cognitive ability of the cephalopod class of molluscs. The study of cephalopod intelligence also has an important comparative aspect in the broader understanding of animal cognition because it relies on a nervous system fundamentally different from that of vertebrates. In particular, the Coleoidea subclass (cuttlefish, squid, and octopuses) is thought to be the most intelligent invertebrates and an important example of advanced cognitive evolution in animals, though nautilus intelligence is also a subject of growing interest among zoologists. The scope of cephalopod intelligence and learning capability is controversial within the biological community, complicated by the inherent complexity of quantifying non-vertebrate intelligence. In spite of this, the existence of impressive spatial learning capacity, navigational abilities, and predatory techniques in cephalopods is widely acknowledged. Cephalopods have large, well-developed brains, and their brain-to-body mass ratio is the largest among the invertebrates, falling between that of endothermic and ectothermic vertebrates. Behavior: Predation: Unlike most other molluscs, all cephalopods are active predators (with the possible exceptions of the bigfin squid and vampire squid). Their need to locate and capture their prey has likely been the driving evolutionary force behind the development of their intelligence. Communication: Although believed to not be the most social of animals, many cephalopods are in fact highly social creatures; when isolated from their own kind, some species have been observed shoaling with fish. Learning. Problem-solving ability: The highly sensitive suction cups and prehensile arms of octopuses, squid, and cuttlefish allow them to hold and manipulate objects. However, unlike vertebrates, the motor skills of octopuses do not seem to depend upon mapping their body within their brains, as the ability to organize complex movements is not thought to be linked to particular arms. Protective legislation: Due to their intelligence, cephalopods are commonly protected by animal testing regulations that do not usually apply to invertebrates.

Species	EQ^[3]
Human	7.4–7.8
Dog	1.2
Bottlenose dolphin	5.3
Cat	1.0
Chimpanzee	2.2–2.5
Horse	0.9
Raven^[4]	2.49
Sheep	0.8
Rhesus monkey	2.1
Mouse	0.5
African elephant	1.3
Rat	0.4
Rabbit	0.4
Opossum	0.2

Heritability of IQ: IQ is a polygenic trait, however, certain single gene genetic disorders can severely affect intelligence, with phenylketonuria as an example. Estimates of heritability vary from below 0.5 to as high as 0.9.

Environment and intelligence: environmental influences: family, peer group, education, training and interventions, environmental enrichment; bio influences: nutrition, exposure to toxic chemicals and other substances (lead, Fetal alcohol spectrum disorder), birth complications (perinatal factors); development of genius; training: musical (Mozart effect: listening to classical music boosts IQ scores in specific area), chess (boosts math and comprehension performance).

G factor (psychometrics) ("general factor"): construct developed in psychometric investigations of cognitive abilities. g is highly heritable; g's biological correlates: brain size.

Genetic Studies of Genius (Terman Study of the Gifted): Terman: "At any rate, we have seen that intellect and achievement are far from perfectly correlated". Longitudinal study begun in 1921.

Flynn effect: substantial and long-sustained increase in intelligence test scores measured in many parts of the world.

Fertility and intelligence: Other correlates of IQ include income and educational attainment, which are also inversely correlated with fertility rate, and are to some degree heritable.

Old Tom (orca) (c. 1895 – 1930.09.17): killer whale (orca) known to whalers in the port of Eden, New South Wales, on the southeast coast of Australia. Old Tom was thought to be the leader of a pod of killer whales which helped the whalers by herding baleen whales into Twofold Bay. This pod was also known as "the killers of Eden".

Sleep

Category:Sleep

Category:Sleep physiology

Sleep (non-human): nematode C. elegans is the most primitive organism in which sleep-like states have been observed. Sleep in fish is not extensively studied; EEG pattern in reptilian sleep differs from what is seen in mammals and other animals; significant similarities between sleep in birds and sleep in mammals, which is one of the reasons for the idea that sleep in higher animals with its division into REM and NREM sleep has evolved together with warm-bloodedness (opinions partly differ about sleep in migratory birds); mammals: daily need for sleep is highest in carnivores, lower in omnivores and lowest in herbivores. Unihemispheric sleep: birds, some aquatic mammals, maybe certain species of lizards. Eared seals and whales show unihemispheric sleep; earless seals sleep bihemispherically like most mammals.

Torpor: umbrella-term used to categorize a state of regulated metabolic suppression in animals, typically to levels below what are normally essentially the minimum, so-called, basal metabolic rate (BMR); this does not exclude the possibility that torpor can be triggered from an elevated metabolic position and may terminate before reaching below BMR (e.g. diving).

Cognitive science, cognitive neuroscience, computational neuroscience, mental health, psychology, psychiatry

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User:Kazkaskazkasako/Books/EECS#Artificial intelligence (AI), machine learning
#Neuroscience
#Cognition: Cognitive science, cognitive neuroscience

}

Psychology

Category:Branches of psychology

Category:Applied psychology

Category:Clinical psychology

Category:Developmental psychology

Category:Psychoanalysis

Category:Psychotherapy

Category:Psychoanalysis

Category:Freudian psychology

Category:Autism

Category:Positive psychology

Category:Social psychology

Template:Psychology:

Template:Jungian psychology (Analytical psychology):

Psychometrics and Employment testing, Myers-Briggs Type Indicator, Keirsey Temperament Sorter

Personality test: Sexological testing, Online dating service & Comparison of online dating websites: even more subjective than psychology? Can few questions find the "personality type"?

Template:Psychology:

Basic science (psychology): concern of psychology as a basic science is in understanding the laws and processes that underlie behavior, cognition, and emotion. Abnormal psychology; Biological psychology (Neuropsychology, Physiological psychology, Cognitive neuroscience); Cognitive psychology; Developmental psychology; Experimental psychology; Evolutionary psychology; Mathematical psychology; Neuropsychology; Personality psychology; Psychophysics; Social psychology.

Differential psychology: studies the ways in which individuals differ in their behavior.

Evolutionary psychology: theoretical approach in the social and natural sciences that examines psychological structure from a modern evolutionary perspective. It seeks to identify which human psychological traits are evolved adaptations – that is, the functional products of natural selection or sexual selection in human evolution. Adaptationist thinking about physiological mechanisms, such as the heart, lungs, and immune system, is common in evolutionary biology. Some evolutionary psychologists apply the same thinking to psychology, arguing that the modularity of mind is similar to that of the body and with different modular adaptations serving different functions. Evolutionary psychologists argue that much of human behavior is the output of psychological adaptations that evolved to solve recurrent problems in human ancestral environments. Criticism of evolutionary psychology involves questions of testability, cognitive and evolutionary assumptions (such as modular functioning of the brain, and large uncertainty about the ancestral environment), importance of non-genetic and non-adaptive explanations, as well as political and ethical issues due to interpretations of research results.

Evolution of emotion: Evolution and natural selection has been applied to the study of human communication, mainly by Charles Darwin in his 1872 work, The Expression of the Emotions in Man and Animals. Darwin researched the expression of emotions in an effort to support his theory of evolution. He proposed that much like other traits found in animals, emotions also evolved and were adapted over time. His work looked at not only facial expressions in animals and specifically humans, but attempted to point out parallels between behaviors in humans and other animals. Primal emotions, such as fear, are associated with ancient parts of the brain and presumably evolved among our premammal ancestors. Filial emotions, such as a human mother's love for her offspring, seem to have evolved among early mammals. Social emotions, such as guilt and pride, evolved among social primates. Sometimes, a more recently evolved part of the brain moderates an older part of the brain, such as when the cortex moderates the amygdala's fear response. Evolutionary psychologists consider human emotions to be best adapted to the life our ancestors led in nomadic foraging bands.

Personality psychology: studies personality and its variation between individuals.

Applied psychology: Clinical psychology; Educational psychology; Forensic psychology and legal psychology; Health psychology; Human factors and ergonomics; Industrial and organizational psychology; Neuropsychology; Occupational health psychology; School psychology; Sport psychology (related to exercise psychology); Environmental psychology.

Asch conformity experiments: "When the confederates are not unanimous in their judgment, even if only one confederate voices a different opinion, participants are much more likely to resist the urge to conform than when the confederates all agree. This finding illuminates the power that even a small dissenting minority can have. Interestingly, this finding holds whether or not the dissenting confederate gives the correct answer. As long as the dissenting confederate gives an answer that is different from the majority, participants are more likely to give the correct answer."

Mass psychogenic illness (MPI; mass sociogenic illness): "the rapid spread of illness signs and symptoms affecting members of a cohesive group, originating from a nervous system disturbance involving excitation, loss or alteration of function, whereby physical complaints that are exhibited unconsciously have no corresponding organic aetiology"

Dancing mania (dancing plague, choreomania, St John's Dance, historically: St. Vitus' Dance; 14th-17th c.): social phenomenon that occurred primarily in mainland Europe.

Dancing Plague of 1518: case of dancing mania that occurred in Strasbourg, Alsace (then part of the Holy Roman Empire). Numerous people took to dancing for days without rest, and, over the period of about one month, some of the people died from heart attack, stroke, or exhaustion.

Tanganyika laughter epidemic (1962): outbreak of mass hysteria rumored to have occurred in or near the village of Kashasha on the western coast of Lake Victoria in the modern nation of Tanzania (formerly Tanganyika) near the border of Kenya.

Impostor syndrome (impostor phenomenon, fraud syndrome): psychological phenomenon in which people are unable to internalize their accomplishments.

Attribution (psychology): process by which individuals explain the causes of behavior and events

Positive psychology: branch of psychology that uses scientific understanding and effective intervention to aid in the achievement of a satisfactory life, rather than treating mental illness. Concerned with four topics: (1) positive experiences, (2) enduring psychological traits, (3) positive relationships and (4) positive institutions. Midlife crisis: researchers specify people in both their 20s and 70s are happier than during midlife, although the extent of happiness changes at different rates, e.g., feelings of stress and anger tend to decline after age 20, worrying drops after age 50, and enjoyment very slowly declines in adulthood but finally starts to rise after age 50. "Proven fact married people are happier than unmarried people". Happiness tended to spread through close relationships like friends, siblings, spouses, and next-door neighbors; researchers reported happiness spread more consistently than unhappiness through the network; "eight hugs a day, you'll be happier, and the world will be a better place".

Culture and positive psychology

Meaningful life: broad term encompassing a varied number of definitions having to do with the pursuit of life satisfaction. While the specific theories vary, there are two common aspects: a global way to understand one's life and the belief that life itself is meaningful. Those possessing a sense of meaning are generally found to have lower levels of negative emotions and lower risk of mental illness. Through the structured society we are able to create a symbolic immortality which can take various forms, e.g., monuments, theatrical productions, children, etc. Culture's order reduces death anxiety as it allows the individual to live up to the societal standards and in living up to such ideals; one is given self-esteem which counterbalances the mortal anxiety.

Carol Dweck: according to Dweck, individuals can be placed on a continuum according to their implicit views of where ability comes from. Some believe their success is based on innate ability; these are said to have a "fixed" theory of intelligence (fixed mindset). Others, who believe their success is based on hard work, learning, training and doggedness are said to have a "growth" or an "incremental" theory of intelligence (growth mindset). Dweck argues that the growth mindset will allow a person to live a less stressful and more successful life. For example, children given praise such as "good job, you're very smart" are much more likely to develop a fixed mindset, whereas if given compliments like "good job, you worked very hard" they are likely to develop a growth mindset.

Category:Mental states

Altered state of consciousness

Maslow's hierarchy of needs: theory in psychology proposed by Abraham Maslow in his 1943 paper “A Theory of Human Motivation” in Psychological Review. Maslow subsequently extended the idea to include his observations of humans' innate curiosity. His theories parallel many other theories of human developmental psychology, some of which focus on describing the stages of growth in humans. Maslow used the terms "physiological" (air, water, food, sleep, clothing, shelter, libido (sexual instinct)), "safety" (personal security, financial security, health & well-being), "belonging and love" (friendships, intimacy, family), "esteem", "self-actualization", and "self-transcendence" to describe the pattern that human motivations generally move through. The goal of Maslow's Theory is to attain the sixth level or stage: self transcendent needs. Maslow studied what he called exemplary people such as Albert Einstein, Jane Addams, Eleanor Roosevelt, and Frederick Douglass rather than mentally ill or neurotic people, writing that "the study of crippled, stunted, immature, and unhealthy specimens can yield only a cripple psychology and a cripple philosophy."

Flow (psychology): mental state of operation in which a person performing an activity is fully immersed in a feeling of energized focus, full involvement, and enjoyment in the process of the activity. In essence, flow is characterized by complete absorption in what one does. Flow has many of the same characteristics as (the positive aspects of) hyperfocus. However, hyperfocus is not always described in a positive light. Some examples include spending "too much" time playing video games or getting side-tracked and pleasurably absorbed by one aspect of an assignment or task to the detriment of the overall assignment.

Components (Jeanne Nakamura and Csíkszentmihályi):
1. Intense and focused concentration on the present moment
2. Merging of action and awareness
3. A loss of reflective self-consciousness
4. A sense of personal control or agency over the situation or activity
5. A distortion of temporal experience, one's subjective experience of time is altered
6. Experience of the activity as intrinsically rewarding, also referred to as autotelic experience
Additionally, psychology writer Kendra Cherry has mentioned three other components that Csíkszentmihályi lists as being a part of the flow experience:
1. "Immediate feedback"
2. Feeling that you have the potential to succeed
3. Feeling so engrossed in the experience, that other needs become negligible
History: Mihaly Csikszentmihályi and his fellow researchers began researching flow after Csikszentmihályi became fascinated by artists who would essentially get lost in their work. Artists, especially painters, got so immersed in their work that they would disregard their need for food, water and even sleep.
Mechanism: For the most part (except for basic bodily feelings like hunger and pain, which are innate), people are able to decide what they want to focus their attention on. However, when one is in the flow state, they are completely engrossed with the one task at hand and, without making the conscious decision to do so, lose awareness of all other things: time, people, distractions, and even basic bodily needs. This occurs because all of the attention of the person in the flow state is on the task at hand; there is no more attention to be allocated. The flow state has been described by Csikszentmihályi as the "optimal experience" in that one gets to a level of high gratification from the experience. Achieving this experience is considered to be personal and "depends on the ability" of the individual.
Education: around 2000, it came to the attention of Csíkszentmihályi that the principles and practices of the Montessori Method of education seemed to purposefully set up continuous flow opportunities and experiences for students.
Music: Musicians, especially improvisational soloists, may experience a state of flow while playing their instrument.
Sports; Religion and spirituality
Gaming: Flow is one of the main reasons that people play video games. It improves performance; calling the phenomenon "TV trance", a 1981 BYTE article discussed how "the best seem to enter a trance where they play but don't pay attention to the details of the game". The primary goal of games is to create entertainment through intrinsic motivation, which is related to flow; that is, without intrinsic motivation it is virtually impossible to establish flow. Through the balance of skill and challenge the player's brain is aroused, with attention engaged and motivation high. Thus, the use of flow in games helps foster an enjoyable experience which in turn increases motivation and draws players to continue playing. As such, game designers strive to integrate flow principles into their projects.
Outcomes: Positive experiences: Books by Csikszentmihályi suggest that enhancing the time spent in flow makes our lives more happy and successful. Flow experiences are predicated to lead to positive affect as well as to better performance. For example, delinquent behavior was reduced in adolescents after two years of enhancing flow through activities. Positive affect and life satisfaction: Several studies found that flow experiences and positive affect go hand in hand, and that challenges and skills above the individual's average foster positive affect. However, the causal processes underlying those relationships remains unclear at present. Performance and learning: Flow experiences imply a growth principle. When one is in a flow state, he or she is working to master the activity at hand. To maintain that flow state, one must seek increasingly greater challenges. Attempting these new, difficult challenges stretches one's skills. One emerges from such a flow experience with a bit of personal growth and great "feelings of competence and efficacy". By increasing time spent in flow, intrinsic motivation and self-directed learning also increases.
Criticism: Csikszentmihályi writes about the dangers of flow himself: ...enjoyable activities that produce flow have a potentially negative effect: while they are capable of improving the quality of existence by creating order in the mind, they can become addictive, at which point the self becomes captive of a certain kind of order, and is then unwilling to cope with the ambiguities of life.

Mindfulness: psychological process of bringing one's attention to experiences occurring in the present moment, which can be developed through the practice of meditation and other training. Large population-based research studies have indicated that the practice of mindfulness is strongly correlated with greater well-being and perceived health. Studies have also shown that rumination and worry contribute to mental illnesses such as depression and anxiety, and that mindfulness-based interventions are effective in the reduction of both rumination and worry. Meditation: Mindfulness meditation involves the process of developing the skill of bringing one’s attention to whatever is happening in the present moment. There are several meditation exercises designed to develop mindfulness meditation. One method is to sit on a straight-backed chair or sit cross-legged on the floor or a cushion, close one’s eyes and bring attention to either the sensations of breathing in the proximity of one’s nostrils or to the movements of the abdomen when breathing in and out.

Autism spectrum (autism spectrum disorder): a range of conditions classified as neurodevelopmental disorders in the DSM-5, published in 2013. Individuals diagnosed with autism spectrum disorder (ASD) must present two types of symptoms:

Deficits in social communication and social interaction
Restricted, repetitive patterns of behavior, interests or activities

Autism forms the core of the autism spectrum disorders. Asperger syndrome is closest to autism in signs and likely causes; unlike autism, people with Asperger syndrome have no significant delay in language development, according to the older DSM-4 criteria. Characteristics: Asperger syndrome was distinguished from autism in the DSM-IV by the lack of delay or deviance in early language development; individuals diagnosed with Asperger syndrome did not have significant cognitive delays; PDD-NOS was considered "subthreshold autism" and "atypical autism" because it was often characterized by milder symptoms of autism or symptoms in only one domain (such as social difficulties). Pathophysiology: neuroanatomical studies support the concept that autism may involve a combination of brain enlargement in some areas and reduction in others; autism may be caused by abnormal neuronal growth and pruning during the early stages of prenatal and postnatal brain development. Epidemiology: While rates of autism spectrum disorders are consistent across cultures, they vary greatly by gender, with boys affected far more frequently than girls; average male-to-female ratio for ASDs is 4.2:1, affecting 1 in 70 males, but only 1 in 315 females; females, however, are more likely to have associated cognitive impairment; among those with an ASD and intellectual disability, the sex ratio may be closer to 2:1.

High-functioning autism: term applied to people with autism who are deemed to be cognitively "higher functioning" (with an IQ of 70 or greater) than other people with autism. High-functioning autism is characterized by features very similar to those of Asperger syndrome. The defining characteristic most widely recognized by psychologists is a significant delay in the development of early speech and language skills, before the age of three years. Observable comorbidities associated with HFA include ADHD, Tourette syndrome, and possibly criminal behavior. While the association between HFA and criminal behavior is not completely characterized, several studies have shown that the features associated with HFA may increase the probability of engaging in criminal behavior.

Pervasive developmental disorder not otherwise specified (PDD-NOS)

Asperger syndrome: developmental disorder characterized by significant difficulties in social interaction and nonverbal communication, along with restricted and repetitive patterns of behavior and interests. As a milder autism spectrum disorder (ASD), it differs from other ASDs by relatively normal language and intelligence. There is no single treatment, and the effectiveness of particular interventions is supported by only limited data.

Erikson's stages of psychosocial development: as articulated in the second half of the 20th century by Erik Erikson, in collaboration with Joan Erikson, is a comprehensive psychoanalytic theory that identifies a series of eight stages, in which a healthy developing individual should pass through from infancy to late adulthood. All stages are present at birth, but only begin to unfold according to both a natural scheme and one's ecological and cultural upbringing. In each stage, the person confronts, and hopefully masters, new challenges. Each stage builds upon the successful completion of earlier stages. The challenges of stages not successfully completed may be expected to return as problems in the future.

Hope: Trust vs. Mistrust (oral-sensory, infancy, 0–2 years) Existential Question: Can I Trust the World?
Will: Autonomy vs. Shame/Doubt (early childhood, 2–4 years) Existential Question: Is It Okay to Be Me?
Purpose: Initiative vs. Guilt (locomotor-genital, preschool, 4–5 years) Existential Question: Is it Okay for Me to Do, Move, and Act?
Competence: Industry vs. Inferiority (latency, school age, 5–11 years) Existential Question: Can I Make it in the World of People and Things?
Fidelity: Identity vs. Role Confusion (adolescence, 12–18 years) Existential Question: Who Am I and What Can I Be?
Love: Intimacy vs. Isolation (early adulthood, 18-39 years) Existential Question: Can I Love?
Care: Generativity vs. Stagnation (adulthood, 40–64 years) Existential Question: Can I Make My Life Count?
Wisdom: ego integrity vs. despair (maturity, 65 – death) Existential Question: Is it Okay to Have Been Me?
Ninth stage Psychosocial Crises: All first eight stages in reverse quotient order

Lawrence Kohlberg's stages of moral development: constitute an adaptation of a psychological theory originally conceived by the Swiss psychologist Jean Piaget. Kohlberg began work on this topic while a psychology graduate student at the University of Chicago in 1958, and expanded upon the theory throughout his life. The theory holds that moral reasoning, the basis for ethical behavior, has six identifiable developmental stages, each more adequate at responding to moral dilemmas than its predecessor. Kohlberg followed the development of moral judgment far beyond the ages studied earlier by Piaget, who also claimed that logic and morality develop through constructive stages. Expanding on Piaget's work, Kohlberg determined that the process of moral development was principally concerned with justice, and that it continued throughout the individual's lifetime, a notion that spawned dialogue on the philosophical implications of such research. Kohlberg's scale is about how people justify behaviors and his stages are not a method of ranking how moral someone's behavior is. There should, however, be a correlation between how someone scores on the scale and how they behave, and the general hypothesis is that moral behaviour is more responsible, consistent and predictable from people at higher levels. Kohlberg's theory was initially developed based on empirical research using only male participants; Gilligan argued that it did not adequately describe the concerns of women. Kohlberg stated that women tend to get stuck at level 3, focusing on details of how to maintain relationships and promote the welfare of family and friends. Men are likely to move on to the abstract principles, and thus have less concern with the particulars of who is involved. Consistent with this observation, Gilligan's theory of moral development does not focus on the value of justice. She developed an alternative theory of moral reasoning based on the ethics of caring. Critics such as Christina Hoff Sommers, however, argued that Gilligan's research is ill-founded, and that no evidence exists to support her conclusion.

Social control: sociologists identify two basic forms of social control: 1. Informal means of control – Internalization of norms and values by a process known as socialization, which is defined as "the process by which an individual, born with behavioral potentialities of enormously wide range, is led to develop actual behavior which is confined to the narrower range of what is acceptable for him by the group standards". 2. Formal means of social control – External sanctions enforced by government to prevent the establishment of chaos or anomie in society. Some theorists, such as Émile Durkheim, refer to this form of control as regulation. Sociologist Edward A. Ross argues that belief systems exert a greater control on human behavior than laws imposed by government, no matter what form the beliefs take. Social control is considered to be one of the foundations of order within society. Informal sanctions may include shame, ridicule, sarcasm, criticism, and disapproval, which can cause an individual to stray towards the social norms of the society. In extreme cases sanctions may include social discrimination and exclusion. Informal social control usually has more effect on individuals because the social values become internalized, thus becoming an aspect of the individual's personality. Informal controls reward or punish acceptable or unacceptable behavior (i.e., deviance) and are varied from individual to individual, group to group, and society to society. Theorists such as Noam Chomsky have argued that systemic bias exists in the modern media. The marketing, advertising, and public relations industries have thus been said to utilize mass communications to aid the interests of certain political and business elites. Powerful ideological, economic and religious lobbyists have often used school systems and centralized electronic communications to influence public opinion.

Wilhelm Reich (1897.03.24–1957.11.03) was an Austrian psychoanalyst. Author of several influential books – most notably Character Analysis (1933), The Mass Psychology of Fascism (1933, Die Massenpsychologie des Faschismus) and The Sexual Revolution (1936) – Reich became known as one of the most radical practitioners of psychiatry.

His father was by all accounts a cold and jealous man. Both parents were Jewish, but decided against raising the boys as Jews. Reich and his brother, Robert, were brought up to speak only German, were punished for using Yiddish expressions and forbidden from playing with the local Yiddish-speaking children.
As an adult, Reich wrote extensively in his diary of his sexual precocity. He maintained that his first sexual experience was at the age of four when he tried to have sex with the family maid (with whom he shared a bed), that he would regularly watch the animals have sex, that he used a whip handle sexually on the horses while masturbating, and that he had almost daily sexual intercourse from the age of 11 with another of the servants. He wrote of regular visits to brothels, the first of which occurred when he was 15 years old, and said he was visiting them daily from the age of about 17. He also developed sexual fantasies about his mother, writing when he was 22 that he masturbated while thinking about her. It is impossible to judge the truth of these diary entries, but Reich's second daughter, psychiatrist Lore Reich Rubin, told Christopher Turner that she believed Reich had been a victim of child sexual abuse, and that this explained his lifelong interest in sex and childhood sexuality.
Orgastic potency, Rest cure in Switzerland (TB), Orgonomy

Primal scene (de: Urszene): initial witnessing by a child of a sex act, usually between the parents, that traumatizes the psychosexual development of that child. The scene witnessed may also occur between animals, and be displaced onto humans.

Jordan Peterson (1962.06.12-): Canadian professor of psychology, clinical psychologist, YouTube personality, and author. He began to receive widespread attention in the late 2010s for his views on cultural and political issues, often described as conservative. Born and raised in Alberta, Peterson obtained bachelor's degrees in political science and psychology from the University of Alberta and a PhD in clinical psychology from McGill University. After teaching and research at Harvard University, he returned to Canada in 1998 to permanently join the faculty of psychology at the University of Toronto. In 2016, Peterson released a series of YouTube videos criticizing the Act to amend the Canadian Human Rights Act and the Criminal Code (Bill C-16), passed by the Parliament of Canada to introduce "gender identity and expression" as prohibited grounds for discrimination. In October 2016 specifically, while on the University of Toronto's campus engaging in dialogue surrounding Bill C-16, a protester approached Peterson and filmed a video that was then released online, making it one of his most viral videos, subsequently propelling Peterson's image online. He argued that the bill would make the use of certain gender pronouns "compelled speech", and related this argument to a general critique of political correctness and identity politics. He subsequently received significant media coverage, attracting both support and criticism. Throughout 2019 and 2020, Peterson's work was obstructed by health problems in the aftermath of severe benzodiazepine withdrawal syndrome.

Maps of Meaning: The Architecture of Belief (1999): book by Canadian clinical psychologist and psychology professor Jordan Peterson. The book describes a theory for how people construct meaning, in a way that is compatible with the modern scientific understanding of how the brain functions. It examines the "structure of systems of belief and the role those systems play in the regulation of emotion", using "multiple academic fields to show that connecting myths and beliefs with science is essential to fully understand how people make meaning".

Motivation

Category:Organizational behavior

Category:Motivation

Self-determination theory: macro theory of human motivation and personality that concerns people's inherent growth tendencies and innate psychological needs. It is concerned with the motivation behind choices people make without external influence and interference.

Occupational burnout (job burnout): characterized by exhaustion, lack of enthusiasm and motivation, feelings of ineffectiveness, and also may have the dimension of frustration or cynicism, and as a result reduced efficacy within the workplace. Burnout is becoming a more common result as the modern workplace changes.

Boreout: management theory that posits that lack of work, boredom, and consequent lack of satisfaction are a common malaise affecting individuals working in modern organizations, especially in office-based white collar jobs.

Emotion

Category:Emotion

Category:Humour

Template:Emotion-footer

Contrasting and categorization of emotions: describes how emotions are thought to relate to each other. Various recent proposals of such groupings are described in the following sections.

Love

Joy

Pleasure: broad class of mental states that humans and other animals experience as positive, enjoyable, or worth seeking. It includes more specific mental states such as happiness, entertainment, enjoyment, ecstasy, and euphoria.

Happiness

Surprise

Boredom: boredom can be a symptom of clinical depression. Boredom related to drug abuse, pathological gambling (hypothesis that pathological gamblers seek stimulation to avoid states of boredom and depression).

I am lonely will anyone speak to me

Gallows humor (de:Galgenhumor): humor in the face of or about very unpleasant, serious, or painful circumstances. Any humor that treats serious matters, such as death, war, disease, crime, etc., in a light, silly or satirical fashion is considered gallows humor. Gallows humor is typically made by or about the victim of such a situation, but not the perpetrator of it.

Therapy, psychotherapy

Category:Therapy

Category:Psychotherapy

Category:Group psychotherapy

Category:Large-group awareness training

Category:Clinical psychology

Category:Mind control

Category:Psychological abuse

A satirical depiction of brainwashing by César Leal Jiménez.

Brainwashing (mind control, menticide, coercive persuasion, thought control, thought reform, re-education): concept that the human mind can be altered or controlled by certain psychological techniques. Brainwashing is said to reduce its subjects' ability to think critically or independently, to allow the introduction of new, unwanted thoughts and ideas into their minds, as well as to change their attitudes, values and beliefs. The term "brainwashing" was first used in English by Edward Hunter in 1950 to describe how the Chinese government appeared to make people cooperate with them. Research into the concept also looked at Nazi Germany, at some criminal cases in the United States, and at the actions of human traffickers. In the 1970s there was considerable scientific and legal debate, as well as media attention, about the possibility of brainwashing being a factor in the conversion of young people to some new religious movements, which were often referred to as cults at the time. It can also be a theme in science fiction and in political and corporate culture, but is not generally accepted as a scientific term (APA DSM-5). China and the Korean War: Thought reform in the People's Republic of China. USA: Project MKUltra (CIA mind control program). Legal cases: The brainwashing defense; Plagio. Human trafficking. Anti-cult movement.

Large-group awareness training (LGAT): activities usually offered by groups linked with the human potential movement which claim to increase self-awareness and bring about desirable transformations in individuals' personal lives. They are noted for being unconventional and often take place over several days. LGAT programs may involve several hundred people at a time. Forsyth and Corazzini cite Lieberman (1994) as suggesting "that at least 1.3 million Americans have taken part in LGAT sessions". The evolution of LGAT-providers. LGAT techniques: meditation, biofeedback, jargon, self-hypnosis, relaxation techniques, visualization, neuro-linguistic programming, yoga. LGATs and the anti-cult movement: anti-cult psychologist Dr Margaret Singer included large group awareness trainings as one example of what she called "brainwashing". Singer reworked much of the report material into the book Cults in Our Midst (1995, second edition: 2003), which she co-authored with Janja Lalich.

NXIVM: self-proclaimed USA multi-level marketing company based in Clifton Park, New York, a suburb of Albany, which offers personal and professional development seminars through its "Executive Success Programs" of large-group awareness training. The company has been widely described as a cult, and is alleged to have been a recruiting platform for a secret society (variously called "DOS" or "The Vow") in which women were branded and forced into sexual slavery. 2019.04 5 people associated with NXIVM—Mack, NXIVM co-founder Nancy Salzman, Lauren Salzman, Seagram heiress Clare Bronfman, and bookkeeper Kathy Russell—had pleaded guilty to various charges. Raniere was convicted in federal court of sex trafficking and racketeering on June 19, 2019. On September 30, 2020, Clare Bronfman became the first defendant sentenced in the case, when she was ordered to serve six years and nine months in federal prison.

Keith Raniere (1960.08.26-): USA felon and the founder of NXIVM. Convicted on all charges, Sentenced to 120 years.

Psychiatry

Category:Psychiatry

Category:Psychiatry-related fields

Category:Clinical psychology

Psychiatry: medical specialty devoted to the study, diagnosis, treatment, and prevention of mental disorders, among which are affective, behavioural, cognitive and perceptual abnormalities.

Rosenhan experiment: was a famous experiment done in order to determine the validity of psychiatric diagnosis, conducted by psychologist David Rosenhan and published by the journal Science in 1973 under the title "On being sane in insane places"; study is considered an important and influential criticism of psychiatric diagnosis. The study concluded "it is clear that we cannot distinguish the sane from the insane in psychiatric hospitals" and also illustrated the dangers of dehumanization and labeling in psychiatric institutions. Rosenhan and the other pseudopatients reported an overwhelming sense of dehumanization, severe invasion of privacy, and boredom while hospitalized.

Anti-psychiatry: view that psychiatric treatments are ultimately more damaging than helpful to patients. According to anti-psychiatry, psychiatry involves an unequal power relationship between doctor and patient, and a highly subjective diagnostic process, leaving too much room for opinions and interpretations. Dangerous treatments from before in medicine/psychiatry: electroconvulsive therapy, lobotomy, over-prescription of Valium and other sedatives; immediate concern lies in the significant increase in prescribing psychiatric drugs for children. Contemporary issues: freedom vs coercion, mind vs brain, nature vs nurture, and the right to be different. Some ex-patient groups have become anti-psychiatric, often referring to themselves as "survivors" rather than patients. Challenges to psychiatry: Civilization as a cause of distress; Normality and illness judgments (Asperger syndrome or autism: "neurodiversity" and "neurotypical"); Psychiatric labeling; Tool of social control (According to Franco Basaglia, Giorgio Antonucci and Bruce E. Levine, whose approach pointed out the role of psychiatric institutions in the control and medicalization of deviant behaviors and social problems, psychiatry is used as the provider of scientific support for social control to the existing establishment, and the ensuing standards of deviance and normality brought about repressive views of discrete social groups); Psychiatry and the pharmaceutical industry; Political abuse of psychiatry (USSR); "Therapeutic State" (Thomas Szasz: "modern man has no more right to be a madman than medieval man had a right to be a heretic because if once people agree that they have identified the one true God, or Good, it brings about that they have to guard members and nonmembers of the group from the temptation to worship false gods or goods", separation of church and state → separation of psychiatry and state); "Total Institution" (Goffman placed psychiatric hospitals in the same category as concentration camps, prisons, military organizations, orphanages, and monasteries; institutionalisation process socialises people into the role of a good patient, someone ‘dull, harmless and inconspicuous’). Psychiatry as pseudoscience and failed enterprise. 1990s+: Anti-psychiatry crusades have thus been charged with failing to put suffering individuals first, and therefore being similarly guilty of what they blame psychiatrists for; rise of anti-psychiatry in Italy was described by one observer as simply "a transfer of psychiatric control from those with medical knowledge to those who possessed socio-political power".

Psychiatric survivors movement (consumer/survivor/ex-patient movement)

Political abuse of psychiatry: abuse of psychiatry including one for political purposes is deliberate action of getting citizens certified, who, because of their mental condition, need neither psychiatric restraint nor psychiatric treatment. Psychiatrists have been involved in human rights abuses in states across the world when the definitions of mental disease were expanded to include political disobedience.

Political abuse of psychiatry in the Soviet Union

Psikhushka: Russian ironic diminutive for psychiatric hospital

Asylums (book) (1961 by Erving Goffman): was a key text in the development of deinstitutionalization.

Deinstitutionalisation (deinstitutionalization): process of replacing long-stay psychiatric hospitals with less isolated community mental health services for those diagnosed with a mental disorder or developmental disability.

Care in the Community: British policy of deinstitutionalization, treating and caring for physically and mentally disabled people in their homes rather than in an institution.

Psychiatric reform in Italy: after the passing of Basaglia Law in 1978 and terminated with the very end of the Italian state mental hospital system in 1998. Among European countries, Italy was the first to publicly declare its repugnance for a mental health care system which led to social exclusion and segregation.

Attention

Category:Attention

Default mode network (DMN): a large scale brain network of interacting brain regions known to have activity highly correlated with each other and distinct from other networks in the brain. DMN is most commonly shown to be active when a person is not focused on the outside world and the brain is at wakeful rest, such as during daydreaming and mind-wandering. But it is also active when the individual is thinking about others, thinking about themselves, remembering the past, and planning for the future. The network activates "by default" when a person is not involved in a task. Though the DMN was originally noticed to be deactivated in certain goal-oriented tasks and is sometimes referred to as the task-negative network, it can be active in other goal-oriented tasks such as social working memory or autobiographical tasks. The DMN has been shown to be negatively correlated with other networks in the brain such as attention networks.

Mental disorders

Category:Mental disorders

Category:Symptoms and signs of mental disorders

Category:Psychopathological syndromes

Category:Psychosis

Category:Delusional disorders

Diagnostic and Statistical Manual of Mental Disorders (DSM): provides a common language and standard criteria for the classification of mental disorders.

DSM-5 (2013.05.18)

Personality disorder

Trait theory: approach to the study of human personality; measurement of traits, which can be defined as habitual patterns of behavior, thought, and emotion; traits are relatively stable over time, differ across individuals (e.g. some people are outgoing whereas others are shy), and influence behavior. Virtually all trait models, and even ancient Greek philosophy, include extraversion vs. introversion as a central dimension of human personality; another prominent trait that is found in nearly all models is Neuroticism, or emotional instability.

Mental disorder (mental illness, psychiatric disorder): behavioral or mental pattern that causes significant distress or impairment of personal functioning. Such features may be persistent, relapsing and remitting, or occur as single episodes. The terms "mental breakdown" or "nervous breakdown" may be used by the general population to mean a mental disorder. The terms "nervous breakdown" and "mental breakdown" have not been formally defined through a medical diagnostic system such as the DSM-5 or ICD-10, and are nearly absent from scientific literature regarding mental illness.

Folie à deux: ('folly of two', or 'madness [shared] by two'; aka shared psychosis or shared delusional disorder (SDD)): psychiatric syndrome in which symptoms of a delusional belief, and sometimes hallucinations, are transmitted from one individual to another.

Neuroimaging

Category:Neuroimaging

Brainbow: process by which individual neurons in the brain can be distinguished from neighboring neurons using fluorescent proteins. By randomly expressing different ratios of red, green, and blue derivatives of green fluorescent protein in individual neurons, it is possible to flag each neuron with a distinctive color. This process has been a major contribution to the field of connectomics, or the study of neural connections in the brain.

CLARITY: method of making brain tissue transparent using acrylamide-based hydrogels built from within, and linked to, the tissue, and as defined in the initial paper, represents "transformation of intact biological tissue into a hybrid form in which specific components are replaced with exogenous elements that provide new accessibility or functionality". When accompanied with antibody or gene-based labeling, CLARITY enables highly detailed pictures of the protein and nucleic acid structure of organs, especially the brain. A series of chemical treatments must be applied to achieve transparency, in which the lipid content of the sample is removed, while almost all of the original proteins and nucleic acids are left in place. The purpose of this is to make the tissue transparent and thus amenable to detailed microscopic investigation of its constituent functional parts (which are predominantly proteins and nucleic acids). To accomplish this, the preexisting protein structure has to be placed in a transparent scaffolding which preserves it, while the lipid components are removed.

Human medicine and human biology

Category:Health sciences

Category:Medicine

Category:Medical specialties

Hippocratic Corpus (Corpus Hippocraticum; Hippocratic Collection): collection of around 60 early Ancient Greek medical works strongly associated with the physician Hippocrates and his teachings. The Hippocratic Corpus covers many diverse aspects of medicine, from Hippocrates' medical theories to what he devised to be ethical means of medical practice, to addressing various illnesses. Even though it is considered a singular corpus that represents Hippocratic medicine, they vary (sometimes significantly) in content, age, style, methods, and views practiced; therefore, authorship is largely unknown. Hippocrates began Western society's development of medicine, through a delicate blending of the art of healing and scientific observations. What Hippocrates was sharing from within his collection of works was not only how to identify symptoms of disease and proper diagnostic practices, but more essentially, he was alluding to his personable form of art, "The art of true living and the art of fine medicine combined."

All drugs prevent something, but also bring something; everything is drug: even food and water (too much water (drowning) can kill you!):

Triple-negative breast cancer#Oral contraceptive a risk factor: any breast cancer that does not express the genes for estrogen receptor (ER), progesterone receptor (PR) or Her2/neu

Template:Medicinal herbs & fungi (Medicinal herbs and fungi)

Template:Traditional Medicine

Alternative medicine

Traditional Chinese medicine

Chinese classic herbal formula

Kampo: Japanese study and adaptation of Traditional Chinese medicine

Kampo herb list

Kampo list

Patent medicine: medical compounds of questionable effectiveness sold under a variety of names and labels. E.g. "snake oil".

Information-theoretic death: destruction of the information within a human brain (or any cognitive structure capable of constituting a person) to such an extent that recovery of the original person is theoretically impossible by any physical means; distinct from clinical death and legal death.

Placebo: simulated or otherwise medically ineffectual treatment for a disease or other medical condition intended to deceive the recipient. Sometimes patients given a placebo treatment will have a perceived or actual improvement in a medical condition, a phenomenon commonly called the placebo effect. Expectancy and classical conditioning; placebo and brain → brain and body

Program in Placebo Studies (Beth Israel Deaconess Medical Center and the Harvard Medical School; 2011-): placebo response and the impact of medical ritual, the patient-physician relationship and the power of imagination, hope, trust, persuasion, compassion and empathic witnessing in the healing process.

Institute for Health Metrics and Evaluation (IHME): global health statistics and evaluation; core grant funding from the Bill & Melinda Gates Foundation and the state of Washington.

List of causes of death by rate

International Statistical Classification of Diseases and Related Health Problems (ICD): UN-sponsored WHO's "standard diagnostic tool for epidemiology, health management and clinical purposes"; designed as a health care classification system, providing a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease.

Alternative medicine (fringe medicine, pseudomedicine, questionable medicine): use and promotion of practices which are unproven, disproven, impossible to prove, or excessively harmful in relation to their effect — in the attempt to achieve the healing effects of medicine. They differ from experimental medicine in that the latter employs responsible investigation, and accepts results that show it to be ineffective. The scientific consensus is that alternative therapies either do not, or cannot, work. In some cases laws of nature are violated by their basic claims; in some the treatment is so much worse that its use is unethical. Alternative practices, products, and therapies range from only ineffective to having known harmful and toxic effects. Alternative medicine is a highly profitable industry, with a strong lobby. This fact is often overlooked by media or intentionally kept hidden, with alternative practice being portrayed positively when compared to "big pharma". The lobby has successfully pushed for alternative therapies to be subject to far less regulation than conventional medicine. Alternative therapies may even be allowed to promote use when there is demonstrably no effect, only a tradition of use. Regulation and licensing of alternative medicine and health care providers varies between and within countries. Despite laws making it illegal to market or promote alternative therapies for use in cancer treatment, many practitioners promote them. Alternative medicine is criticized for taking advantage of the weakest members of society. Critics state that "there is really no such thing as alternative medicine, just medicine that works and medicine that doesn't", that the very idea of "alternative" treatments is paradoxical, as any treatment proven to work is by definition "medicine".

Human reproduction and reproductive organs

Category:Human reproduction

Category:Obstetrics

Category:Obstetrical procedures

Category:Reproduction

Category:Women's health

{q.v. #Gender, sex, reproductive biology}

Template:Reproductive physiology (Human physiology and endocrinology of sexual reproduction)

Template:Menstrual cycle

Ovarian follicle atresia

Menopause:

Maternal age effect

Grandmother hypothesis

Blood–testis barrier (Sertoli cell barrier): physical barrier between the blood vessels and the seminiferous tubules of the animal testes; formed between Sertoli cells of the seminiferous tubule and as such isolates the further developed stages of germ cells from the blood.

Menstruation (mammal): shedding of the uterine lining (endometrium).

Evolution: Most female mammals have an estrous cycle, yet only ten primate species, four bats species, the elephant shrew, and one known species of spiny mouse have a menstrual cycle. As these groups are not closely related, it is likely that four distinct evolutionary events have caused menstruation to arise. It is speculated that menstruation is not a trait which provides any evolutionary advantage. Instead it is a side effect of spontaneous decidualization, which evolved in some placental mammals due to its advantages over non-spontaneous decidualization. Spontaneous decidualization allows for more maternal control in the maternal-fetal conflict by increasing selectivity over the implanted embryo. This may be necessary in humans and other primates, due to the abnormally large number of genetic disorders in these species. Since most aneuploidy events result in stillbirth or miscarriage, there is an evolutionary advantage to ending the pregnancy early, rather than nurturing a fetus that will later miscarry. There is evidence to show that some abnormalities in the developing embryo can be detected by cells in the uterus. This triggers epigenetic changes that prevent formation of the placenta, leaving the fetus to die and be removed in the next menstruation. This failsafe mode is not possible in species where decidualization is controlled by hormonal triggers from the embryo. This is sometimes referred to as the choosy uterus theory, and it is theorized that this positive outweighs the negative impacts of menstruation in species with high aneuploidy rates and hence a high number of 'doomed' embryos.

Immature ovum: cell that goes through the process of oogenesis to become an ovum. It can be an oogonium, an oocyte, or an ootid.

Oocyte (primary Oocyte; secondary Oocyte): female gametocyte or germ cell involved in reproduction. In other words, it is an immature ovum, or egg cell. An oocyte is produced in the ovary during female gametogenesis. The female germ cells produce a primordial germ cell (PGC), which then undergoes mitosis, forming oogonia. During oogenesis, the oogonia become primary oocytes. An oocyte is a form of genetic material that can be collected for cryoconservation.

Dictyate: prolonged resting phase in oogenesis. It occurs in the stage of meiotic prophase I in ootidogenesis. It starts late in fetal life and is terminated shortly before ovulation by the LH surge. Thus, although the majority of oocytes are produced in female fetuses before birth, these pre-eggs remain arrested in the dictyate stage until puberty commences and the cells complete ootidogenesis. In both mouse and human, oocyte DNA of older individuals has substantially more double-strand breaks than that of younger individuals.

Egg cell (ovum): female reproductive cell (gamete) in oogamous organisms. The egg cell is typically not capable of active movement, and it is much larger (visible to the naked eye) than the motile sperm cells.

Cumulus oophorus: cluster of cells (called cumulus cells) that surround the oocyte both in the ovarian follicle and after ovulation.

Corona radiata (embryology): innermost layer of the cumulus oophorus and is directly adjacent to the zona pellucida, the outer protective layer of the ovum; main purpose in many animals is to supply vital proteins to the egg cell.

Zona pellucida: glycoprotein layer surrounding the plasma membrane of mammalian oocytes. It is a vital constitutive part of the oocyte. The zona pellucida first appears in unilaminar primary oocytes. It is secreted by both the oocyte and the follicular cells.

Implantation (human embryo): stage of pregnancy at which the embryo adheres to the wall of the uterus. At this stage of prenatal development, the conceptus is called a blastocyst. It is by this adhesion that the embryo receives oxygen and nutrients from the mother to be able to grow.

Repeated implantation failure: failure of the embryo to implant onto the side of the uterus wall following IVF treatment. Regularly, this happens at 6-7 days after conception and involves the embedding of the growing embryo into the mothers uterus and a connection being formed. A successful implantation can be determined by using an ultrasound to view the sac which the baby grows in, inside the uterus. However, the exact definition of RIF is debated. Recently the most commonly accepted definition is when a women under 40 has gone through 3 unsuccessful cycles of IVF, when in each cycle 4 good quality eggs have been transferred. Contributing Maternal Factors: Congenital Uterine Abnormalities, Hox Genes, Fibroids, Endometrial Polyps, Intrauterine Adhesions, Thrombophilia. Embryonic Factors: Male Genetic Abnormalities (quality of the sperm that fertilizes an egg is a key contributor to the overall quality of the embryo. Abnormalities in DNA fragmentation and chromosomal arrangements are the main source of genetic deviation in males that can affect embryo quality), Female Genetic Abnormalities (Oocyte quality is also a main contributor to overall embryo quality since it is the DNA of the oocyte that is mainly involved in the first 3 days of embryo growth following fertilization), Zona Pellucida Dysfunction.

Decidualization: process that results in significant changes to cells of the endometrium in preparation for, and during, pregnancy. This includes morphological and functional changes (the decidual reaction) to endometrial stromal cells (ESCs), the presence of decidual leukocytes, and vascular changes to maternal arteries. The sum of these changes results in the endometrium changing into a structure called the decidua. In humans, the decidua is shed during the third phase of birth.

Repeated implantation failure (RIF): failure of the embryo to implant onto the side of the uterus wall following IVF treatment. Regularly, this happens at 6–7 days after conception and involves the embedding of the growing embryo into the mothers uterus and a connection being formed. A successful implantation can be determined by using an ultrasound to view the sac which the baby grows in, inside the uterus. Repeated implantation failure should not be confused with recurrent IVF failure. Recurrent IVF failure is a much more broad term and includes all repeated failures to get pregnant from IVF. Repeated implantation failure specifically refers to those failures due to unsuccessful implanting to the uterus wall. An unsuccessful implantation can be down to either problems with the mother or with the embryo. It is essential that the mother and embryo are able to communicate with each other during all stages of pregnancy, and an absence of this communication can lead to an unsuccessful implantation and a further unsuccessful pregnancy. Contributing Maternal Factors: Congenital Uterine Abnormalities, Hox Genes, Fibroids, Endometrial Polyps, Intrauterine Adhesions, Thrombophilia. Embryonic Factors: Male Genetic Abnormalities, Female Genetic Abnormalities, Zona Pellucida Dysfunction.

Template:Pregnancy

Prenatal:

Procedures:

Chorionic villus sampling (CVS): determine chromosomal or genetic disorders in the fetus; usually with FISH or PCR.

Amniocentesis (amniotic fluid test, AFT): chromosomal abnormalities and fetal infections, and also used for Sex Determination in which a small amount of amniotic fluid, which contains fetal tissues, is sampled from the amnion or amniotic sac surrounding a developing fetus, and the fetal DNA is examined for genetic abnormalities.

Molar pregnancy: abnormal form of pregnancy in which a non-viable fertilized egg implants in the uterus and will fail to come to term. A molar pregnancy is a gestational trophoblastic disease which grows into a mass in the uterus that has swollen chorionic villi. These villi grow in clusters that resemble grapes. It is characterized by the presence of a hydatidiform mole (or hydatid mole, mola hydatidosa). Molar pregnancies are categorized as partial moles or complete moles, with the word mole being used to denote simply a clump of growing tissue, or a growth. A complete mole is caused by a single sperm (90% of the time) or two (10% of the time) sperm combining with an egg which has lost its DNA. In the first case, the sperm then reduplicates, forming a "complete" 46 chromosome set. The genotype is typically 46,XX (diploid) due to the subsequent mitosis of the fertilizing sperm but can also be 46,XY (diploid). 46,YY (diploid) is not observed. In contrast, a partial mole occurs when a normal egg is fertilized by one or two sperm which then reduplicates itself, yielding the genotypes of 69,XXY (triploid) or 92,XXXY (tetraploid).

Cell-free fetal DNA: fetal DNA circulating freely in the maternal blood stream. It can be sampled by venipuncture on the mother. Studies have shown that cffDNA can first be observed as early as 7 weeks gestation, and the amount of cffDNA increases as the pregnancy progresses; no longer detectable in the maternal blood approximately 2 hours after birth; fragments approximately 200bp in size.

Microchimerism: presence of a small number of cells that originate from another individual and are therefore genetically distinct from the cells of the host individual. In humans (and perhaps in all Placentals) the most common form is fetomaternal microchimerism (also known as fetal cell microchimerism or fetal chimerism) whereby cells from a fetus pass through the placenta and establish cell lineages within the mother. Fetal cells have been documented to persist and multiply in the mother for several decades.

Human embryogenesis

Prenatal development

Zygote: eukaryotic cell formed by a fertilization event between two gametes. The zygote's genome is a combination of the DNA in each gamete, and contains all of the genetic information necessary to form a new individual. In multicellular organisms, the zygote is the earliest developmental stage. In single-celled organisms, the zygote can divide asexually by mitosis to produce identical offspring.

Cleavage (embryo): division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.

Morula: early stage embryo consisting of cells (called blastomeres) in a solid ball contained within the zona pellucida.[

Blastocyst: structure formed in the early development of mammals. It possesses an inner cell mass (ICM) which subsequently forms the embryo. The outer layer of the blastocyst consists of cells collectively called the trophoblast. This layer surrounds the inner cell mass and a fluid-filled cavity known as the blastocoele. The trophoblast gives rise to the placenta.

Male infertility crisis: name given to an observed increase in male infertility in recent decades. The earliest indications of this decrease first emerged in the 1970s. From this period, there has been a steady decline of 1.4% in sperm counts with an overall decline of 52.4% over approximately 40 years. The crisis is particularly prevalent in the West such as New Zealand, Australia, Europe and North America. A reduction in other parts of the world has yet to be observed. Hypotheses for the causes of the crisis is still subject to ongoing further research. Existing research cites lifestyle factors and the presence of hormone-disrupting chemicals, known as endocrine disruptors, in the environment.

Anogenital distance: distance from the midpoint of the anus to the genitalia, the underside of the scrotum or the vagina. It is considered medically significant for a number of reasons, in both humans and animals, including sex determination and as a marker of endocrine disruptor exposure. It is regulated by dihydrotestosterone, which can be disrupted by phthalates common in plastics. Such endocrine disruption may affect the development of the brain. Swan et al. report that the levels of phthalates associated with significant AGD reductions are found in approximately one-quarter of USA tested by CDC for phthalate body burdens. Women who had high levels of phthalates in their urine during pregnancy gave birth to sons who were ten times more likely to have shorter than expected AGDs.

Testicular dysgenesis syndrome (TDS): male reproduction-related condition characterized by the presence of symptoms and disorders such as hypospadias, cryptorchidism, poor semen quality, and testicular cancer. Causes: Genetic; Environmental: Exposure of a male fetus to substances that disrupt hormone systems, particularly chemicals that inhibit the action of androgens (male sex hormones) during the development of the reproductive system, has been shown to cause many of the characteristic TDS disorders. These include environmental estrogens and anti-androgens found in food and water sources that have been contaminated with synthetic hormones and pesticides used in agriculture. In historical cases, medicines given to pregnant women, like diethylstilbestrol (DES), have caused many of the features of TDS in fetuses exposed to this chemical during gestation. The impact of environmental chemicals is well documented in animal models. If a substance affects Sertoli and Leydig cell differentiation (a common feature of TDS disorders) at an early developmental stage, germ cell growth and testosterone production will be impaired; Lifestyle.

Parenthood, birth, children

Fecundity: actual reproductive rate of an organism or population, measured by the number of gametes (eggs), seed set, or asexual propagules. Fecundity is similar to fertility, the natural capability to produce offspring. A lack of fertility is infertility while a lack of fecundity would be called sterility.

Adaptation to extrauterine life: Perfusing its body by breathing independently instead of utilizing placental oxygen delivered via the umbilical cord is the first challenge of a newborn. At birth, the baby's lungs are filled with lung liquid, which is distinct from amniotic fluid. When the newborn is expelled from the birth canal, its central nervous system reacts to the sudden change in temperature and environment. This triggers it to take the first breath, within about 10 seconds after delivery. With the first breaths, there is a fall in pulmonary vascular resistance, and an increase in the surface area available for gas exchange. As the pulmonary circulation increases there is an equivalent reduction in the placental blood flow which normally ceases completely after about three minutes. These two changes result in a rapid redirection of blood flow into the pulmonary vascular bed, from approximately 4% to 100% of cardiac output. The increase in pulmonary venous return results in left atrial pressure being slightly higher than right atrial pressure, which closes the foramen ovale. Energy metabolism: Glycogen synthesis in the liver and muscle begins in the late second trimester of pregnancy, and storage is completed in the third trimester; Fat stores are the largest storage source of energy. At 27 weeks gestation, only 1% of a fetus' body weight is fat; At 40 weeks, that number increases to 16%. Temperature regulation

Multiple birth: culmination of one multiple pregnancy, wherein the mother delivers two or more offspring. A term most applicable to placental species, multiple births occur in most kinds of mammals, with varying frequencies.

List of multiple births: some of them are identical. With the use of reproductive technology such as fertility drugs and in vitro fertilization (IVF) twin and triplet births have become increasingly common.

Dionne quintuplets (born 1934.05.28): first quintuplets known to survive their infancy; born two months premature; identical sisters. Émilie and Marie shared an embryonic sac, Annette and Yvonne shared an embryonic sac, and it is believed that Cécile shared an embryonic sac with the miscarried sixth fetus. Each girl became emotionally the closest to whomever they shared a sac with; Cécile tended to be alone the most. All but Émilie were/are right-handed; all but Marie have/had a counter-clockwise whorl in their hair.

Lina Medina (1933.09.27-): youngest confirmed mother in medical history, giving birth at the age of five years, seven months and 17 days.

List of people with the most children: mother with the most children: 69 children to Mrs. and Mr. Feodor Vassilyev. Father with the most children can be in the 1000s, because of the medical sperm donation.

Meconium: earliest stool of a mammalian infant. Unlike later feces, meconium is composed of materials ingested during the time the infant spends in the uterus: intestinal epithelial cells, lanugo, mucus, amniotic fluid, bile, and water. Meconium, unlike later feces, is viscous and sticky like tar, its color usually being a very dark olive green; it is almost odorless. When diluted in amniotic fluid, it may appear in various shades of green, brown, or yellow. It should be completely passed by the end of the first few days after birth, with the stools progressing toward yellow (digested milk).

Twins

Category:Conjoined twins

Conjoined twins: Two contradicting theories exist to explain the origins of conjoined twins. The older theory is fission, in which the fertilized egg splits partially. The second and more generally accepted theory is fusion, in which a fertilized egg completely separates, but stem cells (which search for similar cells) find like-stem cells on the other twin and fuse the twins together. Conjoined twins share a single common chorion, placenta, and amniotic sac.

Parasitic twin

Vanishing twin (fetal resorption; twin embolisation syndrome or vanishing twin syndrome (VTS)): fetus in a multi-gestation pregnancy which dies in utero and is then partially or completely reabsorbed by the twin. "These very high resorption rates, which cannot be explained on the basis of the expected abortion rate, again suggest intense fetal competition for space, nutrition, or other factors during early gestation, with frequent loss or resorption of the other twin(s)."

Craniopagus parasiticus: rare type of craniopagus occurring in about 4 to 6 of 10,000,000 births; parasitic twin head with an undeveloped body is attached to the head of a developed twin.

Fetus in fetu: developmental abnormality in which a mass of tissue resembling a fetus forms inside the body.

Twin reversed arterial perfusion: rare complication of monochorionic twin pregnancies, involving an acardiac twin whose structural defects are incompatible with life, and an otherwise normal "pump" twin. Acardiac twin is a parasitic twin that fails to develop a head, arms and a heart.

Dicephalic parapagus twins: rare form of partial twinning where there are two heads side by side on one torso. Infants conjoined this way are sometimes called "two-headed babies" in popular media. If carried to term, most dicephalic twins are stillborn, or die soon after birth. A small number are known to have survived to adulthood. The extent to which limbs and organs are duplicated varies from case to case. One head may be only partially developed (anencephalic), or both may be complete. In some cases, two complete hearts are present as well, which improves their chances of survival. The total number of arms may be two, three or four. Their prospects are best if no attempt is made to separate them, except in cases where one twin is clearly dying.

Craniopagus twins: conjoined twins who are fused at the cranium; represents the rarest of congenital abnormalities only accounting for 2-6% of all conjoined twins; union in craniopagus twins may occur on any portion of the calvarium, but does not include either the face or the foramen magnum; thorax and abdomen are separate and each twin has its own ubilicus and umbilical cord. Genres of Craniopagus Twins: Partial; Total. If the parents choose to continue the pregnancy, mother and babies will be closely monitored throughout the pregnancy; in almost all cases a surgical procedure (C-section) delivery is planned often two to three weeks before the due date.

Chang and Eng Bunker (1811.05.11-1874.01.17): were conjoined twin brothers whose condition and birthplace became the basis for the term "Siamese twins". Chang and his wife had 10 children; Eng and his wife had 11. In time, the wives squabbled and eventually two separate households were set up just west of Mount Airy, North Carolina in the community of White Plains – the twins would alternate spending three days at each home.

Masha and Dasha Krivoshlyapova (1950.01.03-2003.04.17): Ischiopagus tripus conjoined twins from USSR/Russia. Masha and Dasha's mother, Yekaterina Krivoshlyapova, did not know she was having twins and spent two days and nights giving birth naturally. The doctors told her she had delivered a mutant (урод) and she was not shown the babies. The Soviet physiologist Pyotr Anokhin was studying the separate roles of the nervous system and the blood system on the body's ability to adjust to conditions such as prolonged sleep deprivation, extreme hunger, and extreme temperature change. Conjoined twins who shared a blood system but had separate nervous systems were ideal objects for research. He had put out an alert to all maternity hospitals in the USSR to be informed if any conjoined twins were born, and began studying Masha and Dasha within days of their birth. When the twins were born, their mother was told they required full-time care from the State. She agreed, but on the condition that she would keep custody and visit them regularly. A night nurse brought the twins in to see their mother and let her hold them. Scientists did not want her to keep custody of them so she was later told by one of Anokhin's physiologists that they had died of pneumonia. The twins were placed in the Academy of Medical Sciences Pediatric Institute, where a team of Anokhin's physiologists continued to carry out experiments on them for the following six years; Masha and Dasha's case is now considered a prolonged case of medical torture. This coincided with having been told by a medical commission which graded disability that they had been placed in the lowest grade, which meant that they would be kept for life in a retirement home (there were no homes for the disabled as the Soviet Union saw 'invalids' as flaws in the system) with no right to work or be independent in any way.

Lori and George Schappell (1961.09.18-): siblings are craniopagus conjoined twins joined at the head. Lori and George spent the first 24 years of their lives living in an institution in Reading, Pennsylvania, in which the majority of patients were suffering from severe intellectual disabilities. Although neither is intellectually disabled, George's physical condition required special care. A court decision was made that their parents would be unable to care for them properly and they were removed and institutionalized. In 2007, George, who was at that time known as Reba Schappell, stated that although assigned female at birth, he identified as male and changed his name to George.

Abby and Brittany Hensel (1990.03.07-): dicephalic parapagus twins, meaning that they are conjoined twins, each of whom has a separate head, but whose bodies are joined; several vital organs are doubled up; each twin has a separate heart (2 hearts in a shared circulatory system), stomach, spine, and spinal cord. By coordinating their efforts, they are able to walk, run, swim, and ride a bicycle normally—all tasks that they learned at a normal speed. 1 liver, Y-shaped small intestine, which experiences a slightly spastic double peristalsis at the juncture, 1 large intestine (one colon), 3 kidneys: 2 left, 1 right, 1 bladder, 1 set of reproductive organs.

Lakshmi Tatma

Krista and Tatiana Hogan (2006.10.25-): joined at the top, backs, and sides of their heads. There is evidence that the twins can see through each other's eyes due to brain conjoining. Their thalami are joined. At this time, Tatiana suffered from a sleep apnea condition that occasionally caused her to stop breathing for up to 20 seconds. A sleep apnea specialist, Dr. Fred Kozak, performed surgery on her and was able to successfully treat her sleep apnea. Not long after the surgery, her heart shrank to a more normal size and its rate dropped such that it no longer carried all of the burden of circulating blood for both brains.

Human (mammal?) hormones

Category:Hormones

Category:Hormones by functional axis

Category:Hormones of the hypothalamus-pituitary axis

Category:Hormones of the hypothalamus-pituitary-adrenal axis

Category:Hormones of the hypothalamus-pituitary-gonad axis

Category:Hormones of the hypothalamus-pituitary-thyroid axis

Category:Hormones of the somatotropic axis: Growth-hormone-releasing hormone, Somatostatin, Tesamorelin

Category:Human homeostasis

Endocrine system

Major neuroendocrine systems:

Hypothalamic–pituitary–adrenal axis (HPA axis): complex set of direct influences and feedback interactions among three components: the hypothalamus, the pituitary gland, and the adrenal glands. HPA axis is a major neuroendocrine system that controls reactions to stress and regulates many body processes, including digestion, the immune system, mood and emotions, sexuality, and energy storage and expenditure. It is the common mechanism for interactions among glands, hormones, and parts of the midbrain that mediate the general adaptation syndrome (GAS). While steroid hormones are produced mainly in vertebrates, the physiological role of the HPA axis and corticosteroids in stress response is so fundamental that analogous systems can be found in invertebrates and monocellular organisms as well.

Hypothalamic–pituitary–gonadal axis (HPG axis): because these glands often act in concert, physiologists and endocrinologists find it convenient and descriptive to speak of them as a single system. The HPG axis plays a critical part in the development and regulation of a number of the body's systems, such as the reproductive and immune systems. Fluctuations in this axis cause changes in the hormones produced by each gland and have various local and systemic effects on the body. In oviparous organisms (e.g. fish, reptiles, amphibians, birds), the HPG axis is commonly referred to as the hypothalamus-pituitary-gonadal-liver axis (HPGL-axis) in females. Many egg-yolk and chorionic proteins are synthesized heterologously in the liver, which are necessary for ovocyte growth and development. Examples of such necessary liver proteins are vitellogenin and choriogenin.

Hypothalamic–pituitary–thyroid axis (HPT axis): part of the neuroendocrine system responsible for the regulation of metabolism and also responds to stress. The hypothalamus senses low circulating levels of thyroid hormone (Triiodothyronine (T3) and Thyroxine (T4)) and responds by releasing thyrotropin-releasing hormone (TRH). The TRH stimulates the anterior pituitary to produce thyroid-stimulating hormone (TSH). The TSH, in turn, stimulates the thyroid to produce thyroid hormone until levels in the blood return to normal. Thyroid hormone exerts negative feedback control over the hypothalamus as well as anterior pituitary, thus controlling the release of both TRH from hypothalamus and TSH from anterior pituitary gland.

Thyroid hormone: triiodothyronine (T₃) and thyroxine (T₄); tyrosine-based hormones produced by the thyroid gland that are primarily responsible for regulation of metabolism; iodine is necessary for the production of T₃ and T₄; T₄:T₃=20:1 released into the blood; T₄ → T₃ (by deiodinases (5'-iodinase) inside the cells), T₃ is 3-4× more potent than T₄. These are further processed by decarboxylation and deiodination to produce iodothyronamine (T₁a) and thyronamine (T₀a); all three isoforms of the deiodinases are selenium-containing enzymes, thus dietary selenium is essential for T₃ production.

Renin–angiotensin system (RAS; renin-angiotensin-aldosterone system (RAAS)): hormone system that regulates blood pressure and water (fluid) balance.

Peptide hormone: have shorter amino acid chain lengths than protein hormones. These hormones have an effect on the endocrine system of animals, including humans. Most hormones can be classified as either amino acid–based hormones (amine, peptide, or protein) or steroid hormones. The former are water-soluble and act on the surface of target cells via second messengers; the latter, being lipid-soluble, move through the plasma membranes of target cells (both cytoplasmic and nuclear) to act within their nuclei. Preprohormones, peptide hormone precursors, are then processed in several stages, typically in the endoplasmic reticulum, including removal of the N-terminal signal sequence and sometimes glycosylation, resulting in prohormones. The prohormones are then packaged into membrane-bound secretory vesicles, which can be secreted from the cell by exocytosis in response to specific stimuli (e.g. an increase in Ca²⁺ and cAMP concentration in cytoplasm).

Proglucagon: protein that is cleaved from preproglucagon. Preproglucagon in humans is encoded by the GCG gene. Proglucagon is a precursor of glucagon, and several other components. It is generated in the alpha cells of the pancreas and in the intestinal L cells in the distal ileum and colon. Proglucagon itself is a protein with three repeats of slightly different secretin family hormones to be cleaved to form mature hormones.

Signal peptide (1-20) – removed from preproglucagon to form proglucagon
Glicentin (21–89)
Glicentin-related pancreatic polypeptide (GRPP, 21-50)
Oxyntomodulin (OXY or OXM, 53–89)
Glucagon (53–81)
Glucagon-like peptide 1 (GLP-1, 92–128)
Glucagon-like peptide 2 (GLP-2, 146–178)

Glucagon: peptide hormone, produced by alpha cells of the pancreas. It raises the concentration of glucose and fatty acids in the bloodstream and is considered to be the main catabolic hormone of the body. It is also used as a medication to treat a number of health conditions. Its effect is opposite to that of insulin, which lowers extracellular glucose.

Glucagon-like peptide-1: 30- or 31-amino-acid-long peptide hormone deriving from the tissue-specific posttranslational processing of the proglucagon peptide. It is produced and secreted by intestinal enteroendocrine L-cells and certain neurons within the nucleus of the solitary tract in the brainstem upon food consumption. The initial product GLP-1 (1–37) is susceptible to amidation and proteolytic cleavage, which gives rise to the two truncated and equipotent biologically active forms, GLP-1 (7–36) amide and GLP-1 (7–37).

Immunology, immune system

Category:Immunology

Category:Inflammations

Template:Inflammation

Processes:

Traditional:

Rubor (Flushing), Calor (Fever), Tumor (Swelling), Dolor (Pain), Functio laesa (loss of function, disturbance of function)

Inflammation: part of the complex biological response of body tissues to harmful stimuli, such as pathogens, damaged cells, or irritants, and is a protective response involving immune cells, blood vessels, and molecular mediators. The function of inflammation is to eliminate the initial cause of cell injury, clear out necrotic cells and tissues damaged from the original insult and the inflammatory process, and to initiate tissue repair.

Innate immune system: non-specific immune system or in-born immunity system, is an important subsystem of the overall immune system that comprises the cells and mechanisms that defend the host from infection by other organisms. The cells of the innate system recognize and respond to pathogens in a generic way, but, unlike the adaptive immune system, the system does not provide long-lasting immunity to the host.

Classical complement pathway: one of three pathways which activate the complement system, which is part of the immune system. The classical complement pathway is initiated by antigen-antibody complexes with the antibody isotypes IgG and IgM.

C-reactive protein: annular (ring-shaped), pentameric protein found in blood plasma, whose levels rise in response to inflammation. It is an acute-phase protein of hepatic origin that increases following interleukin-6 secretion by macrophages and T cells. Its physiological role is to bind to lysophosphatidylcholine expressed on the surface of dead or dying cells (and some types of bacteria) in order to activate the complement system via the C1Q complex. C-reactive protein was the first PRR to be identified.

Pattern recognition receptor (PRR): part of the innate immune system. They are proteins expressed by cells of the innate immune system to identify two classes of molecules: pathogen-associated molecular patterns (PAMPs), which are associated with microbial pathogens, and damage-associated molecular patterns (DAMPs), which are associated with cell components that are released during cell damage or death. They are also called primitive pattern recognition receptors because they evolved before other parts of the immune system, particularly before adaptive immunity. Membrane-bound PRRs: Receptor kinases; Toll-like receptors (TLR); The TLR signaling; C-type lectin receptors (CLR); CLR signaling; Cytoplasmic PRRs: NOD-like receptors (NLR); NLR signaling; NODs; NLRPs; RIG-I-like receptors (RLR); RLR signaling. Plant PRRs: Plants contain a significant number of PRRs that share remarkable structural and functional similarity with drosophila TOLL and mammalian TLRs. PRRs in human medicine.

Damage-associated molecular patterns (DAMPs; danger-associated molecular patterns, danger signals, alarmin): host biomolecules that can initiate and perpetuate a noninfectious inflammatory response. In contrast, pathogen-associated molecular patterns (PAMPs) initiate and perpetuate the infectious pathogen-induced inflammatory response. A subset of DAMPs are nuclear or cytosolic proteins. When released outside the cell or exposed on the surface of the cell following tissue injury, they move from a reducing to an oxidizing milieu, which results in their denaturation. Also, following necrosis (a kind of cell death), tumor DNA is released outside the nucleus, and outside the cell, and becomes a DAMP.

Acute-phase proteins (APPs): class of proteins whose concentrations in blood plasma either increase (positive acute-phase proteins) or decrease (negative acute-phase proteins) in response to inflammation. This response is called the acute-phase reaction (also called acute-phase response). The acute-phase reaction characteristically involves fever, acceleration of peripheral leukocytes, circulating neutrophils and their precursors. The terms acute-phase protein and acute-phase reactant (APR) are often used synonymously, although some APRs are (strictly speaking) polypeptides rather than proteins.

Adaptive immune system (acquired immune system, specific immune system): subsystem of the overall immune system that is composed of highly specialized, systemic cells and processes that eliminate pathogens or prevent their growth. The adaptive immune system is one of the two main immunity strategies found in vertebrates (the other being the innate immune system). Adaptive immunity creates immunological memory after an initial response to a specific pathogen, and leads to an enhanced response to subsequent encounters with that pathogen. This process of acquired immunity is the basis of vaccination. Like the innate system, the adaptive system includes both humoral immunity components and cell-mediated immunity components.

Human leukocyte antigen (HLA): system or complex is a gene complex encoding the major histocompatibility complex (MHC) proteins in humans. These cell-surface proteins are responsible for the regulation of the immune system in humans. The HLA gene complex resides on a 3 Mbp stretch within chromosome 6p21. HLA genes are highly polymorphic, which means that they have many different alleles, allowing them to fine-tune the adaptive immune system. HLAs corresponding to MHC class I (A, B, and C) which all are the HLA Class1 group present peptides from inside the cell. HLAs corresponding to MHC class II (DP, DM, DO, DQ, and DR) present antigens from outside of the cell to T-lymphocytes. HLAs corresponding to MHC class III encode components of the complement system. HLA may also be related to people's perception of the odor of other people, and may be involved in mate selection, as at least one study found a lower-than-expected rate of HLA similarity between spouses in an isolated community.

Antigenic escape (immune escape or immune evasion): occurs when the immune system of a human being ("host") is unable to respond to an infectious agent, or in other words that the host's immune system is no longer able to recognize and eliminate a virus or pathogen. This process can occur in a number of different ways of both a genetic and an environmental nature. Such mechanisms include homologous recombination, and manipulation and resistance of the host's immune responses.

Surgery

Category:Surgery

Category:Surgical specialties

Category:Cardiac surgery

Invasiveness of surgical procedures

The future surgeries are the least invasive, e.g.:

High-intensity focused ultrasound (HIFU, or sometimes FUS): highly precise medical procedure using high-intensity focused ultrasound to heat and destroy pathogenic tissue rapidly through ablation. Clinical HIFU is image-guided: Magnetic Resonance-guided Focused Ultrasound (MRgHIFU or MRgFUS); Ultrasound-guided Focused Ultrasound (USgFUS). Limited by the precision of imaging (MRI or US), by the precision of HIFU lenses and how HIFU travels and gets distorted in the tissues, and by the computational models how HIFU travels from the source to the destination (e.g. breathing/moving patient).

Coronary artery bypass surgery (heart bypass, bypass surgery): surgical procedure to restore normal blood flow to an obstructed coronary artery. Often indicated when coronary arteries have a 50 to 99 percent obstruction. The obstruction being bypassed is typically due to arteriosclerosis, atherosclerosis, or both.

Medical research

Category:Medical research

Category:Clinical research

Category:Animal testing

Great ape research ban: severe restrictions on the use of non-human great apes in research, is currently in place in NL, NZ, UK, SE, DE, AT.

Evidence-based practices

Category:Evidence-based practices

Category:Evidence-based medicine

Category:Systematic review

Evidence-based medicine (EBM): approach to medical practice intended to optimize decision-making by emphasizing the use of evidence from well-designed and well-conducted research. Although all medicine based on science has some degree of empirical support, EBM goes further, classifying evidence by its epistemologic strength and requiring that only the strongest types (coming from meta-analyses, systematic reviews, and randomized controlled trials) can yield strong recommendations; weaker types (such as from case-control studies) can yield only weak recommendations. The term was originally used to describe an approach to teaching the practice of medicine and improving decisions by individual physicians about individual patients. Use of the term rapidly expanded to include a previously described approach that emphasized the use of evidence in the design of guidelines and policies that apply to groups of patients and populations ("evidence-based practice policies"). 1996 David Sackett &co clarified the definition EBM "the conscientious, explicit and judicious use of current best evidence in making decisions about the care of individual patients."

Cochrane Collaboration: independent, non-profit, NGO consisting of a group of more than 31,000 volunteers in more than 120 countries. Formed to organize medical research information in a systematic way to facilitate the choices that health professionals, patients, policy makers and others face in health interventions according to the principles of evidence-based medicine. Conducts systematic reviews of randomized controlled trials of health-care interventions.

Cochrane Library: collection of databases in medicine and other healthcare specialties provided by the Cochrane Collaboration and other organizations. At its core is the collection of Cochrane Reviews, a database of systematic reviews and meta-analyses which summarize and interpret the results of medical research.

Systematic review: literature review focused on a research question that tries to identify, appraise, select and synthesize all high quality research evidence relevant to that question. Systematic reviews of high-quality randomized controlled trials are crucial to evidence-based medicine.

Epidemiology, epidemic, pandemic, infections

Category:Epidemiology

Category:Diseases and disorders

Category:Infectious diseases

Category:Zoonoses

Globalization and disease: Globalization, the flow of information, goods, capital, and people across political and geographic boundaries, has helped spread some of the deadliest infectious diseases known to humans. The spread of diseases across wide geographic scales has increased through history. Early diseases that spread from Asia to Europe were bubonic plague, influenza of various types, and similar infectious diseases. Specific diseases:

Plague: Bubonic plague Yersinia pestis
Measles: highly contagious airborne virus spread by contact with infected oral and nasal fluids
Typhus: rickettsia, transmitted to humans through lice. The main vector for typhus is the rat flea
Syphilis: STD, causes open sores, delirium and rotting skin, and is characterized by genital ulcers. Syphilis can also do damage to the nervous system, brain and heart. The disease can be transmitted from mother to child.
Smallpox: Variola virus, symptoms of the disease including hemorrhaging, blindness, back ache, vomiting, which generally occur shortly after the 12- to 17-day incubation period. The virus begins to attack skin cells, and eventually leads to an eruption of pimples that cover the whole body. As the disease progresses, the pimples fill up with pus or merge. Smallpox vaccine was developed in 1798 by Edward Jenner. By 1979 the disease had been completely eradicated, with no new outbreaks.
Leprosy: Mycobacterium leprae, chronic disease with an incubation period of up to five years. Symptoms often include irritation or erosion of the skin, and effects on the peripheral nerves, mucosa of the upper respiratory tract and eyes. The most common sign of leprosy are pale reddish spots on the skin that lack sensation.
Malaria: Plasmodium vivax, Plasmodium falciparum, generally transmitted to humans by mosquitoes between dusk and dawn. Mosquitoes use areas of standing water like marshes, wetlands, and water drums to breed.
Tuberculosis: Mycobacterium tuberculosis, generally spread when an infected person coughs and another person inhales the bacteria. Once inhaled TB frequently grows in the lungs, but can spread to any part of the body. Although TB is highly contagious, in most cases the human body is able to fend off the bacteria. But, TB can remain dormant in the body for years, and become active unexpectedly. Tuberculosis (TB) has been one of history’s greatest killers, taking the lives of over 3 mln people annually. It has been called the "white plague". According to the WHO, approximately fifty percent of people infected with TB today live in Asia. It is the most prevalent, life-threatening infection among AIDS patients.
HIV/AIDS: HIV and AIDS are among the newest and deadliest diseases. According to the World Health Organization, it is unknown where the HIV virus originated, but it appeared to move from animals to humans. It may have been isolated within many groups throughout the world. It is believed that HIV arose from another, less harmful virus, that mutated and became more virulent. The first two AIDS/HIV cases were detected in 1981. As of 2013, an estimated 1.3 mln persons in the United States were living with HIV or AIDS, almost 110,000 in the UK and an estimated 35 mln people worldwide are living with HIV”.
Ebola
Leptospirosis
Coronavirus (COVID-19) caused by SARS-CoV-2, and first appeared in Wuhan, China in November-December 2019; first reported as a pneumonia outbreak by the Chinese government. By December 31, 2019, the disease was confirmed to be a novel strain of coronavirus. The first death from this new strain of coronavirus was reported by the Chinese government in 2020.01.11. 2020.01.13, the first case of COVID-19 was reported outside of China.

List of epidemics

Plague (disease) (bacterium Yersinia pestis): symptoms include fever, weakness and headache. Usually this begins one to seven days after exposure. In the bubonic form there is also swelling of lymph nodes, while in the septicemic form tissues may turn black and die, and in the pneumonic form shortness of breath, cough and chest pain may occur. Bubonic and septicemic plague are generally spread by flea bites or handling an infected animal. The pneumonic form is generally spread between people through the air via infectious droplets. Diagnosis is typically by finding the bacterium in fluid from a lymph node, blood or sputum. After WWII, both USA and USSR developed means of weaponising pneumonic plague. Experiments included various delivery methods, vacuum drying, sizing the bacterium, developing strains resistant to antibiotics, combining the bacterium with other diseases (such as diphtheria), and genetic engineering. Scientists who worked in USSR bio-weapons programs have stated that the Soviet effort was formidable and that large stocks of weaponised plague bacteria were produced. Information on many of the Soviet and US projects are largely unavailable. Aerosolized pneumonic plague remains the most significant threat. The three types of plague are the result of the route of infection: bubonic plague, septicemic plague, and pneumonic plague.

Bubonic plague: one of three types of plague. One to seven days after exposure to the bacteria, flu-like symptoms develop. These symptoms include fever, headaches, and vomiting. Swollen and painful lymph nodes occur in the area closest to where the bacteria entered the skin. Occasionally, the swollen lymph nodes, known as buboes, may break open.

Timeline of plague

Epidemiology of plague: Globally about 600 cases are reported a year. In 2017 the countries with the most cases include the Democratic Republic of the Congo, Madagascar, and Peru. Local outbreaks of the plague are grouped into three plague pandemics, whereby the respective start and end dates and the assignment of some outbreaks to either pandemic are still subject to discussion.

Plague of Justinian (541-542; Yersinia pestis; part of the first plague pandemic): pandemic that afflicted the Eastern Roman (Byzantine) Empire, especially its capital Constantinople, the Sassanid Empire, and port cities around the entire Mediterranean Sea. One of the deadliest plagues in history, this devastating pandemic resulted in the deaths of an estimated 25 million (at the time of the initial outbreak that was at least 13% of the world's population) to 50 million people (in two centuries of recurrence). The principal historian during the 6th century, Procopius, viewed the pandemic as worldwide in scope. Genetic studies point to China as having been the primary source of the contagion. The plague returned periodically until the 8th century. The waves of disease had a major effect on the subsequent course of European history. Modern historians named this plague incident after the Eastern Roman Emperor Justinian I, who was emperor at the time of the initial outbreak; he contracted the disease himself but survived.

Second plague pandemic (Yersinia pestis): major series of epidemics of the plague that started with the Black Death, which reached mainland Europe in 1348 and killed up to a third of the population in the next four years. Although it died out in most places, it became epizootic and recurred regularly until the nineteenth century. A series of major plagues occurred in the late 17th century and it recurred in some places until the 19th. After this a new strain of the bacterium appeared as the third pandemic. The Second pandemic originated in or near China and was most likely spread by the Silk Road or by ship. It may have reduced world population from an estimated 450 mln. down to 350–375 mln. by the year 1400.

Black Death: one of the most devastating pandemics in human history, resulting in the deaths of an estimated 75 to 200 million people in Eurasia and peaking in Europe from 1346 to 1353. The bacterium Yersinia pestis, resulting in several forms of plague, is believed to have been the cause. The plague created a series of religious, social, and economic upheavals, which had profound effects on the course of European history. Black Death is thought to have originated in the dry plains of Central Asia, where it then travelled along the Silk Road, reaching Crimea by 1343. From there, it was most likely carried by Oriental rat fleas living on the black rats that were regular passengers on merchant ships, spreading throughout the Mediterranean and Europe.

Black Death in England: pneumonic plague pandemic, which reached England in June 1348. It was the first and most severe manifestation of the Second Pandemic, caused by Yersinia pestis bacteria. The term "Black Death" was not used until the late 17th century. The English government handled the crisis well, and the country did not experience the extreme reactions that were seen elsewhere in Europe. The most immediate consequence was a halt to the campaigns of the Hundred Years' War. In the long term, the decrease in population caused a shortage of labour, with subsequent rise in wages, resisted by the landowners, which caused deep resentment among the lower classes. The Peasants' Revolt of 1381 was largely a result of this resentment, and even though the rebellion was suppressed, in the long term serfdom was ended in England. The Black Death also affected artistic and cultural efforts, and may have helped advance the use of the vernacular. In 1361–62 the plague returned to England, this time causing the death of around 20% of the population. After this the plague continued to return intermittently throughout the 14th and 15th centuries, in local or national outbreaks. From this point on its effect became less severe, and one of the last outbreaks of the plague in England was the Great Plague of London in 1665–66.

1629–31 Italian plague: series of outbreaks of bubonic plague which ravaged northern and central Italy. This epidemic, often referred to as the Great Plague of Milan, claimed possibly one million lives, or about 25% of the population. This episode is considered one of the later outbreaks of the centuries-long pandemic of bubonic plague which began with the Black Death.

Great Northern War plague outbreak: During the Great Northern War (1700–1721), many towns and areas of the Circum-Baltic and East-Central Europe suffered from a severe outbreak of the plague with a peak from 1708 to 1712. This epidemic was probably part of a pandemic affecting an area from Central Asia to the Mediterranean. Most probably via Constantinople, it spread to Pińczów in southern Poland, where it was first recorded in a Swedish military hospital in 1702. The plague then followed trade, travel and army routes, reached the Baltic coast at Prussia in 1709, affected areas all around the Baltic Sea by 1711 and reached Hamburg by 1712. Therefore, the course of the war and the course of the plague mutually affected each other: while soldiers and refugees were often agents of the plague, the death toll in the military as well as the depopulation of towns and rural areas sometimes severely impacted the ability to resist enemy forces or to supply troops. This plague was the last to affect the Circum-Baltic, which had experienced several waves of the plague since the Black Death of the 14th century. However, for some areas, it was the most severe. People died within a few days of first showing symptoms. Especially on the eastern coast from Prussia to Estonia, the average death toll for wide areas was up to two thirds or three quarters of the population, and many farms and villages were left completely desolated. It is, however, hard to distinguish between deaths due to a genuine plague infection and deaths due to starvation and other diseases that spread along with the plague. While buboes are recorded among the symptoms, contemporary means of diagnosis were poorly developed, and death records are often unspecific, incomplete or lost. Some towns and areas were affected only for one year, while in other places the plague recurred annually throughout several subsequent years. In some areas, a disproportionally high death toll is recorded for children and women, which may be due to famine and the men being drafted. As the cause of the plague was unknown to contemporaries, with speculations reaching from religious causes over "bad air" to contaminated clothes, the only means of fighting the disease was containment, to separate the ill from the healthy. Cordons sanitaire were established around infected towns like Stralsund and Königsberg; one was also established around the whole Duchy of Prussia and another one between Scania and the Danish isles along the Sound, with Saltholm as the central quarantine station. "Plague houses" to quarantine infected people were established within or before the city walls, a notable example of the latter being the Charité of Berlin, which was, however, spared from the plague.

Spread in the Circum-Baltic 1708–1713: Prussia: Especially hard-hit were regions with a substantial non-German population: Masuria in the south as well as the eastern counties with a substantial Lithuanian peasant population. About 128,000 people died in the ämter (rural districts) of Insterburg, Memel, Ragnit and Tilsit, and the number of villages populated completely by Lithuanians sank from 1,830 before the plague to 35 thereafter. While indigenous, including Lithuanian population was included in the subsequent repopulation measures, the ethnic make-up of the province changed with the settlement of mostly German-speaking immigrants, most of whom were Protestants seeking refuge from religious prosecution ("Exulanten"). Lithuania, Livonia, Estonia: In the years 1710 and 1711, 190,000 People were infected half of which died. The main Lithuanian city, Vilnius (Wilno), suffered from the plague from 1709 to 1713. Between 23,000 and 33,700 people died in the city in 1709 and 1710; that number continued to rise in the following three years, when many of the starving from the Lithuanian countryside, which was ravaged by hunger and other diseases, took refuge within its walls. Finland, Gotland and Central Sweden: From Livonia and Estonia, refugees brought the plague to Central Sweden and Finland, at that time still an integral part of Sweden. In June 1710, most probably via a ship from Pernau, the plague arrived in Stockholm, where the health commission (Collegium Medicum) until 29 August denied that it was indeed the plague, despite buboes being visible on the bodies of victims from the ship and in the town. The plague raged in Stockholm until 1711, affecting primarily women (45.3% of the dead) and children (38.7% of the dead) in the poorer quarters outside the Old Town. Of Stockholm's approximately 55,000, inhabitants, about 22,000 did not survive the plague. Bremen, Bremen-Verden, Hamburg and Holstein.

1770–1772 Russian plague: last massive outbreak of plague in central Russia, claiming between 52 and 100 thousand lives in Moscow alone (1/6 to 1/3 of its population). The bubonic plague epidemic that originated in the Moldovan theatre of the 1768–1774 Russian-Turkish war in January 1770 swept northward through Ukraine and central Russia, peaking in Moscow in September 1771 and causing the Plague Riot. The epidemic reshaped the map of Moscow, as new cemeteries were established beyond the 18th-century city limits.

Third plague pandemic: designation of a major bubonic plague pandemic that began in Yunnan province in China in 1855. This episode of bubonic plague spread to all inhabited continents, and ultimately more than 12 million people died in India and China, with 10 million people killed in India alone. According to WHO, the pandemic was considered active until 1959, when worldwide casualties dropped to 200 per year. Casualty patterns indicate that waves of this late-19th-century/early-20th-century pandemic may have been from two different sources. The first was primarily bubonic and was carried around the world through ocean-going trade, through transporting infected persons, rats, and cargoes harboring fleas. The second, more virulent strain, was primarily pneumonic in character with a strong person-to-person contagion. This strain was largely confined to Asia, in particular Manchuria and Mongolia.

Plague of Cyprian: name given to a pandemic, probably of smallpox, that afflicted the Roman Empire from AD 250 onwards during the larger Crisis of the Third Century. It was still raging in 270, when it claimed the life of emperor Claudius II Gothicus. The plague caused widespread manpower shortages in agriculture and the Roman army.

1889–1890 pandemic ("Asiatic flu" or "Russian flu"): worldwide respiratory viral pandemic. It was the last great pandemic of the 19th century, and is among the deadliest pandemics in history. The pandemic killed about 1 mln. people out of a world population of about 1.5 bln. (0.067% of population).

World Health Organization (WHO; 1948.04.07): specialised agency of the United Nations that is concerned with world public health. Its predecessor, the Health Organisation, was an agency of the League of Nations. Since its establishment, it has played a leading role in the eradication of smallpox. Its current priorities include communicable diseases, in particular HIV/AIDS, Ebola, malaria and tuberculosis; the mitigation of the effects of non-communicable diseases such as sexual and reproductive health, development, and aging; nutrition, food security and healthy eating; occupational health; substance abuse; and driving the development of reporting, publications, and networking.

Category:World Health Organization

Category:Public health emergencies of international concern

Category:Global health

Coalition for Epidemic Preparedness Innovations (CEPI): foundation that takes donations from public, private, philanthropic, and civil society organisations, to finance independent research projects to develop vaccines against emerging infectious diseases. CEPI is focused on WHO "blueprint priority diseases", which include: MERS-CoV, SARS-CoV-2, the Nipah virus, the Lassa fever virus, and the Rift Valley fever virus, as well as the Chikungunya virus and the hypothetical, unknown pathogen "Disease X". CEPI investment also requires "equitable access" to the vaccines during outbreaks, although subsequent CEPI policy changes may have compromised this criteria. CEPI was conceived in 2015 and formally launched in 2017 at WEF in Davos, Switzerland. It was co-founded and co-funded with US$460 million from the Bill and Melinda Gates Foundation, the Wellcome Trust, and a consortium of nations composed of India, Germany, Japan and Norway, which EU (2019) and UK (2020) subsequently joined. CEPI is headquartered in Oslo, Norway.

Public Health Emergency of International Concern: formal declaration by WHO of "an extraordinary event which is determined to constitute a public health risk to other States through the international spread of disease and to potentially require a coordinated international response", formulated when a situation arises that is "serious, sudden, unusual or unexpected", which "carries implications for public health beyond the affected state's national border" and "may require immediate international action". Under the 2005 International Health Regulations (IHR), states have a legal duty to respond promptly to a PHEIC. Since 2009 there have been six PHEIC declarations: the 2009 H1N1 (or swine flu) pandemic, the 2014 polio declaration, the 2014 outbreak of Ebola in Western Africa, the 2015–16 Zika virus epidemic, the ongoing 2018–20 Kivu Ebola epidemic, and the ongoing 2019–20 coronavirus outbreak. The recommendations are temporary and require reviews every three months.

Subclinical infection (inapparent infection): infection that, being subclinical, is nearly or completely asymptomatic (no signs or symptoms). A subclinically infected person is thus an asymptomatic carrier of a microbe, intestinal parasite, or virus that usually is a pathogen causing illness, at least in some individuals. Many pathogens spread by being silently carried in this way by some of their host population. Such infections occur both in humans and nonhuman animals. An example of an asymptomatic infection is a mild common cold that is not noticed by the infected individual. Types of subclinical infections: Baylisascaris procyonis, Bordetella pertussis (Pertussis or whooping cough), Chlamydia pneumoniae, Chlamydia trachomatis (Chlamydia infection), Clostridium difficile, Cyclospora cayetanensis, Dengue virus, Dientamoeba fragilis, Entamoeba histolytica, enterotoxigenic Escherichia coli, Epstein-Barr virus, Group A streptococcal infection, Helicobacter pylori, Herpes simplex (oral herpes, genital herpes, etc.), HIV-1 (AIDS), Legionella pneumophila (Legionnaires' disease), measles viruses, Mycobacterium leprae (leprosy), Mycobacterium tuberculosis (tuberculosis), Neisseria gonorrhoeae (gonorrhoea), Neisseria meningitidis (Meningitis), nontyphoidal Salmonella, noroviruses, Poliovirus (Poliomyelitis), Plasmodium (Malaria), Rabies lyssavirus (Rabies), rhinoviruses (Common cold), Salmonella enterica serovar Typhi (Typhoid fever), SARS-COV-2 (COVID-19), Staphylococcus aureus, Streptococcus pneumoniae (Bacterial pneumonia), Treponema pallidum (syphilis). Host tolerance: Fever and sickness behavior and other signs of infection are often taken to be due to them. However, they are evolved physiological and behavioral responses of the host to clear itself of the infection. Instead of incurring the costs of deploying these evolved responses to infections, the body opts to tolerate an infection as an alternative to seeking to control or remove the infecting pathogen.

Asymptomatic carrier (healthy carrier, carrier): person or other organism that has become infected with a pathogen, but that displays no signs or symptoms. Although unaffected by the pathogen, carriers can transmit it to others or develop symptoms in later stages of the disease. Asymptomatic carriers play a critical role in the transmission of common infectious diseases such as typhoid (Salmonella enterica subsp. enterica, Serovar: S. typhimurium), C. difficile, influenzas, and HIV. While the mechanism of disease-carrying is still unknown, researchers have made progress towards understanding how certain pathogens can remain dormant in a human for a period of time. Types of asymptomatic carriers: When an individual transmits pathogens immediately following infection but prior to developing symptoms, they are known as an incubatory carrier. Humans are also capable of spreading disease following a period of illness. Typically thinking themselves cured of the disease, these individuals are known as convalescent carriers. Viral diseases such as hepatitis and poliomyelitis are frequently transmitted in this manner. Considered to be the classic asymptomatic carriers, "healthy carriers" never exhibit signs or symptoms of the disease, yet are capable of infecting others. Significance in disease transmission: e.g., a disease with a known low asymptomatic rate may lead to increased surveillance of symptomatic cases, whereas a higher asymptomatic rate could lead to more aggressive methods such as travel bans and compulsory quarantines, since the number of infectious, asymptomatic cases would be unknown. Possible explanations: exact explanation for asymptomatic carriage is unknown. Asymptomatic bacteriuria (Escherichia coli, Enterobacteriaceae, Pseudomonas aeruginosa, Enterococcus species, and group B streptococcus). Infectious diseases: Typhoid fever (Typhoid Mary); HIV; Epstein–Barr virus; Clostridium difficile; Chlamydia; Poliomyelitis; Tuberculosis (TB).

Mary Mallon (1869.09.23–1938.11.11; aka Typhoid Mary): Irish-born cook believed to have infected 51 people, three of whom died, with typhoid fever, and the first person in the United States identified as an asymptomatic carrier of the disease. Because she persisted in working as a cook, by which she exposed others to the disease, she was twice forcibly isolated by authorities, and died after a total of nearly three decades in isolation. From 1900 to 1907, Mallon worked as a cook in the New York City area for seven families. In 1900, she worked in Mamaroneck, New York, where, within two weeks of her employment, residents developed typhoid fever. In 1901, she moved to Manhattan, where members of the family for whom she worked developed fevers and diarrhea, and the laundress died. Mallon then went to work for a lawyer and left after seven of the eight people in that household became ill. In late 1906, one family hired a typhoid researcher named George Soper to investigate. Soper published the results on June 15, 1907, in the Journal of the American Medical Association. He believed Mallon might have been the source of the outbreak. Soper discovered that a female Irish cook, who fit the physical description he was given, was involved in all of the outbreaks. He was unable to locate her because she generally left after an outbreak began, without giving a forwarding address. Soper learned of an active outbreak in a penthouse on Park Avenue and discovered Mallon was the cook. Two of the household's servants were hospitalized, and the daughter of the family died of typhoid. The New York City Health Inspector determined she was a carrier. Under sections 1169 and 1170 of the Greater New York Charter, Mallon was held in isolation for three years at a clinic located on North Brother Island. In prison, she was forced to give stool and urine samples. Authorities suggested removing her gallbladder because they believed typhoid bacteria resided there. However, she refused as she did not believe she carried the disease. She was also unwilling to cease working as a cook. Eventually, Eugene H. Porter, the New York State Commissioner of Health, decided that disease carriers should no longer be kept in isolation and that Mallon could be freed if she agreed to stop working as a cook and take reasonable steps to prevent transmitting typhoid to others. On February 19, 1910, Mallon agreed that she was "prepared to change her occupation (that of a cook), and would give assurance by affidavit that she would upon her release take such hygienic precautions as would protect those with whom she came in contact, from infection." She was released from quarantine and returned to the mainland. Release and second quarantine (1915–1938)

Pathovar: bacterial strain or set of strains with the same or similar characteristics, that is differentiated at infrasubspecific level from other strains of the same species or subspecies on the basis of distinctive pathogenicity to one or more plant hosts.

Biovar: variant prokaryotic strain that differs physiologically and/or biochemically from other strains in a particular species. Morphovars (or morphotypes) are those strains that differ morphologically.Serovars (or serotypes) are those strains that have antigenic properties that differ from other strains.

Serotype (serovar): distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the subspecies level. A group of serovars with common antigens is called a serogroup or sometimes serocomplex.

Natural reservoir (disease reservoir, reservoir of infection): population of organisms or the specific environment in which an infectious pathogen naturally lives and reproduces, or upon which the pathogen primarily depends for its survival. A reservoir is usually a living host of a certain species, such as an animal or a plant, inside of which a pathogen survives, often (though not always) without causing disease for the reservoir itself. By some definitions a reservoir may also be an environment external to an organism, such as a volume of contaminated air or water. Identifying the natural reservoirs of infectious pathogens has proven useful in treating and preventing large outbreaks of disease in humans and domestic animals, especially those diseases for which no vaccine exists. In principle, zoonotic diseases can be controlled by isolating or destroying the pathogen's reservoirs of infection. For other pathogens, such as the ebolaviruses, the identity of the presumed natural reservoir remains obscure. Human reservoirs: poliomyelitis and smallpox. Animal reservoirs: common animal reservoirs include: bats, rodents, cows, pigs, sheep, swine, rabbits, raccoons, dogs, other mammals. Environmental reservoirs.

Zoonosis: infectious disease caused by a pathogen (an infectious agent, including bacteria, viruses, parasites, prions, etc) that has jumped from non-human animals (usually vertebrates) to humans. Major modern diseases such as Ebola virus disease and salmonellosis are zoonoses. HIV was a zoonotic disease transmitted to humans in the early part of the 20th century, though it has now mutated to a separate human-only disease. Most strains of influenza that infect humans are human diseases, although many strains of bird flu and swine flu are zoonoses; these viruses occasionally recombine with human strains of the flu and can cause pandemics such as the 1918 Spanish flu or the 2009 swine flu. Causes:

Farming, ranching and animal husbandry: Contact with farm animals can lead to disease in farmers or others that come into contact with infected farm animals.
Wild animal attacks: Rabies
Insect vectors
Pets: Feline zoonosis
Exhibition: Outbreaks of zoonoses have been traced to human interaction with and exposure to other animals at fairs, live animal markets, petting zoos, and other settings.
Hunting and bushmeat: HIV, COVID-19, SARS
Deforestation: The disruption of pristine forests driven by logging, mining, road building through remote places, rapid urbanisation and population growth is bringing people into closer contact with animal species they may never have been near before. The resulting transmission of disease from wildlife to humans, she says, is now "a hidden cost of human economic development".
Biodiversity loss and environmental degradation

Emerging infectious disease: whose incidence has increased recently (in the past 20 years), and could increase in the near future. Such diseases do not respect national boundaries. The minority that are capable of developing efficient transmission between humans can become major public and global concerns as potential causes of epidemics or pandemics. Their many impacts can be economic and societal, as well as clinical. Emerging infections account for at least 12% of all human pathogens. Re-emerging infectious disease, like tuberculosis (following drug resistance) or measles. Nosocomial (hospital-acquired) infections, such as methicillin-resistant Staphylococcus aureus are emerging in hospitals, and are extremely problematic in that they are resistant to many antibiotics. Of growing concern are adverse synergistic interactions between emerging diseases and other infectious and non-infectious conditions leading to the development of novel syndemics. Many EID are zoonotic.

Emergent virus: either newly appeared, notably increasing in incidence/geographic range or has the potential to increase in the near future. Emergent viruses are a leading cause of emerging infectious diseases and raise public health challenges globally, given their potential to cause outbreaks of disease which can lead to epidemics and pandemics. As well as causing disease, emergent viruses can also have severe economic implications. Recent examples include the SARS-related coronaviruses, which have caused the 2002-2004 outbreak of SARS (SARS-CoV-1) and the 2019–20 pandemic of COVID-19 (SARS-CoV-2). Other examples include the human immunodeficiency virus which causes HIV/AIDS; the viruses responsible for Ebola; the H5N1 influenza virus responsible for avian flu; and H1N1/09, which caused the 2009 swine flu pandemic (an earlier emergent strain of H1N1 caused the 1918 Spanish flu pandemic). Viral emergence in humans is often a consequence of zoonosis, which involves a cross-species jump of a viral disease into humans from other animals. As zoonotic viruses exist in animal reservoirs, they are much more difficult to eradicate and can therefore establish persistent infections in human populations. Emergent viruses should not be confused with re-emerging viruses or newly-detected viruses. A re-emerging virus is generally considered to be a previously appeared virus that is experiencing a resurgence, for example measles. Examples of emergent viruses: Influenza A, SARS-CoV, MERS-CoV, Bluetongue disease.

Disease X: placeholder name that was adopted by WHO in 2018.02 on their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. The WHO adopted the placeholder name to ensure that their planning was sufficiently flexible to adapt to an unknown pathogen (e.g., broader vaccines and manufacturing facilities).

Diarrhea (diarrhoea, diarrhœa): condition of having at least three loose, liquid, or watery bowel movements each day. It often lasts for a few days and can result in dehydration due to fluid loss. The most common cause is an infection of the intestines due to either a virus, bacterium, or parasite—a condition also known as gastroenteritis. These infections are often acquired from food or water that has been contaminated by feces, or directly from another person who is infected. The three types of diarrhea are: short duration watery diarrhea, short duration bloody diarrhea, and persistent diarrhea (lasting more than two weeks, which can be either watery or bloody). The short duration watery diarrhea may be due to cholera, although this is rare in the developed world. If blood is present, it is also known as dysentery. A number of non-infectious causes can result in diarrhea. These include lactose intolerance, irritable bowel syndrome, non-celiac gluten sensitivity, celiac disease, inflammatory bowel disease such as ulcerative colitis, hyperthyroidism, bile acid diarrhea, and a number of medications. In most cases, stool cultures to confirm the exact cause are not required.

Gastroenteritis (infectious diarrhea, gastro): inflammation of the gastrointestinal tract including the stomach and intestine. Symptoms may include diarrhea, vomiting, and abdominal pain. Fever, lack of energy, and dehydration may also occur. This typically lasts less than two weeks. Cause: Viral: Rotaviruses, noroviruses, adenoviruses, and astroviruses; Bacterial: Campylobacter jejuni, Escherichia coli, Salmonella, Shigella, Clostridium difficile, Staphylococcus aureus. Parasitic.

Rotavirus: genus of dsRNA viruses in the family Reoviridae. Rotaviruses are the most common cause of diarrhoeal disease among infants and young children. There are nine species of the genus, referred to as A, B, C, D, F, G, H, I and J. Rotavirus A, the most common species, causes more than 90% of rotavirus infections in humans.

Norovirus (winter vomiting disease): most common cause of gastroenteritis. Infection is characterized by non-bloody diarrhea, vomiting, and stomach pain. Fever or headaches may also occur. Symptoms usually develop 12 to 48 hours after being exposed, and recovery typically occurs within one to three days. Complications are uncommon, but may include dehydration, especially in the young, the old, and those with other health problems.

Coronavirus diseases, 'corona', 'COVID'

Template:COVID-19 pandemic

Crimson Contagion: joint exercise conducted 2019.01-08, in which numerous national, state and local, private and public organizations in USA participated, in order to test the capacity of the federal government and twelve states to respond to a severe pandemic of influenza originating in China. Scenario: According to the results of the coordinating draft report, dated 2019.10, the Crimson Contagion simulation registers 110 million infected Americans, 7.7 million hospitalizations, and 586,000 fatalities. Key findings: Federal government lacks sufficient funding to respond to a severe influenza pandemic; HHS had issues providing accurate and relevant information to hospitals and other public health organizations; Confusion between HHS, FEMA, and the Department of Homeland Security on which federal agency would take the lead in the crisis; USA lacks the production capacity to meet the demands for protective equipment and medical devices such as masks and ventilators imposed by a pandemic; States were unable to efficiently request resources due to the lack of a standardized request process.

Bat virome: assemblage of viruses associated with bats. Bats host a diverse array of viruses, including coronaviruses, filoviruses, lyssaviruses, and paramyxoviruses, among others. Several bat-borne viruses are considered important emerging viruses. These zoonotic viruses include the rabies virus, SARS-CoV, Marburg virus, Nipah virus, and Hendra virus. While research clearly indicates that SARS-CoV-2 originated in bats, it is unknown how it was transmitted to humans, or if an intermediate host was involved. It has been speculated that bats may have a role in the ecology of Ebola virus, though this is unconfirmed. Viral diversity: Bats are especially tolerant of viruses compared to terrestrial mammals. A single bat can host several different kinds of viruses without becoming ill, though some like the rabies virus can cause illness in bats. Most of the viruses harbored by bats are RNA viruses, though they are also known to have DNA viruses. A 2018 study found that bats have a dampened STING response compared to other mammals, which could allow them to respond to viral threats without over-responding. Additionally, bats lack several inflammasomes found in other mammals. While inflammation is an immune response to viruses, excessive inflammation is damaging to the body, and viruses like severe acute respiratory syndrome coronavirus (SARS-CoV) are known to kill humans by inducing excessive inflammation. Transmission to humans. Bats compared to other viral reservoirs: Bats, rodents, and primates all harbored significantly more zoonotic viruses (which can be transmitted to humans) than other mammal groups, though the differences among the aforementioned three groups were not significant (bats have no more zoonotic viruses than rodents and primates). Coronaviruses: In 2019, a food market that sold live wild game (a "wet market") in Wuhan, China was linked to the outbreak of SARS-CoV-2. Genetic analyses of SARS-COV-2 showed that it was highly similar to viruses found in horseshoe bats, with 96% similarity to a virus isolated from the intermediate horseshoe bat. Filoviruses (Marburgvirus and Ebolavirus): Marburg virus was first detected in the Egyptian fruit bat in 2007, and is now recognized as the natural reservoir of the virus. Lyssaviruses: rabies virus, Australian bat lyssavirus, and other related viruses; lyssaviruses are transmitted by mammals, most frequently through biting. All mammals are susceptible to lyssaviruses, though bats and carnivores are the most common natural reservoirs. Rabies virus exposure can be fatal in bats, though it is likely that the majority of individuals do not develop the disease after exposure. In non-bat mammals, exposure to the rabies virus almost always leads to death. Orthomyxoviruses include influenza. Paramyxoviruses: Henipavirus—Hendra virus and Nipah virus; horses are the intermediate host between flying foxes and humans of Hendra virus.

Severe acute respiratory syndrome–related coronavirus (SARSr-CoV): species of coronavirus that infects humans, bats and certain other mammals. It is an enveloped positive-sense single-stranded RNA virus that enters its host cell by binding to the angiotensin-converting enzyme 2 (ACE2) receptor. It is a member of the genus Betacoronavirus and subgenus Sarbecovirus. There are hundreds of other strains of SARS-CoV, all of which are only known to infect non-human species: bats are a major reservoir of many strains of SARS-related coronaviruses, and several strains have been identified in palm civets, which were likely ancestors of SARS-CoV. The SARS-related coronavirus was one of several viruses identified by WHO in 2016 as a likely cause of a future epidemic in a new plan developed after the Ebola epidemic for urgent R&D before and during an epidemic towards diagnostic tests, vaccines and medicines. The prediction came to pass with the COVID-19 pandemic.

Severe acute respiratory syndrome coronavirus (SARS-CoV-1): 2003.04.16 following the outbreak of SARS in Asia and secondary cases elsewhere in the world, WHO issued a press release stating that the coronavirus identified by a number of laboratories was the official cause of SARS. CDC in USA and National Microbiology Laboratory (NML) in Canada identified the SARS-CoV-1 genome in 2003.04. Scientists at Erasmus University in Rotterdam demonstrated that the SARS coronavirus fulfilled Koch's postulates thereby confirming it as the causative agent. In the experiments, macaques infected with the virus developed the same symptoms as human SARS victims.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): strain of coronavirus that causes COVID-19, the respiratory illness responsible for the COVID-19 pandemic; was previously referred to by its provisional name, 2019 novel coronavirus (2019-nCoV), and has also been called human coronavirus 2019 (HCoV-19 or hCoV-19). WHO declared the outbreak a Public Health Emergency of International Concern 2020.01.30, and a pandemic on 2020.03.11.

Timeline of the COVID-19 pandemic in 2019: first human cases of COVID-19 known to have been identified were in Wuhan, Hubei, China, in 2019.12.

Timeline of the COVID-19 pandemic in January 2020

Investigations into the origin of COVID-19: In 2021.01, the World Health Assembly (decision-making body of the World Health Organization, WHO) commissioned a study on the origins of the virus, to be conducted jointly between WHO experts and Chinese scientists. In 2021.03, the findings of this study were published online in a report to the WHO Commissioner-General. Echoing the assessment of most virologists, the report determined that the virus most likely had a zoonotic origin in bats, possibly transmitted through an intermediate host. It also stated that a laboratory origin for the virus was "extremely unlikely." 2021.07.22, the Chinese government had held a press conference in which Zeng Yixin, Vice Health Minister of the National Health Commission (NHC), said that China would not participate in a second phase of the WHO's investigation, denouncing it as "shocking" and "arrogant". In response to the WHO's June 2022 report, Chinese Foreign Ministry spokesperson Zhao Lijian called the lab leak theory "a lie concocted by anti-China forces for political purposes, which has nothing to do with science". Phase 2: In July 2021 China rejected WHO requests for greater transparency, cooperation, and access to data as part of Phase 2. On 16 July 2021, Foreign Ministry spokesperson Zhao Lijian declared that China's position was that future investigations should be conducted elsewhere and should focus on cold chain transmission and the US military's labs. ... He (Zeng Yixin) elaborated "In some aspects, the WHO's plan for next phase of investigation of the coronavirus origin doesn't respect common sense, and it's against science. It's impossible for us to accept such a plan."

Peter Daszak: British zoologist, consultant and public expert on disease ecology, in particular on zoonosis. He is the president of EcoHealth Alliance, a nonprofit non-governmental organization that supports various programs on global health and pandemic prevention. Daszak was involved in investigations into the initial outbreak which eventually developed into the COVID-19 pandemic and became a member of the World Health Organization team sent to investigate the origins of the COVID-19 pandemic in China. This became controversial due to Daszak's previous activities with the Wuhan Institute of Virology, perceived by some as a conflict of interest.

Shi Zhengli (1964.05.26): Chinese virologist who researches SARS-like coronaviruses of bat origin. Shi directs the Center for Emerging Infectious Diseases at the Wuhan Institute of Virology (WIV). In 2017, Shi and her colleague Cui Jie discovered that the SARS coronavirus likely originated in a population of cave-dwelling horseshoe bats in Xiyang Yi Ethnic Township, Yunnan. She came to prominence in the popular press as "Batwoman" during the COVID-19 pandemic for her work with bat coronaviruses.

Variants of SARS-CoV-2: 2020.12: GISAID—referring to SARS-CoV-2 as hCoV-19—identified seven clades (O, S, L, V, G, GH, and GR); Nextstrain identified five (19A, 19B, 20A, 20B, and 20C). 2020.11 issue of International Journal of Infectious Diseases, Guan et al. identified five global clades (G₆₁₄, S₈₄, V₂₅₁, I₃₇₈ and D₃₉₂). Rambaut et al. proposed the term "lineage" in a 2020 article in Nature Microbiology; 2020.12: there have been five major lineages (A, B, B.1, B.1.1, and B.1.777) identified.

SARS-CoV-2 Alpha variant (lineage B.1.1.7; VOC-202012/01; UK variant, British variant): variant of SARS-CoV-2. The variant was first detected in 2020.11 from a sample taken in September, during the COVID-19 pandemic in the United Kingdom; it began to spread quickly by mid-December, and is correlated with a significant increase in SARS-CoV-2 infections in UK. This increase is thought to be at least partly because of one or more mutations in the virus's spike protein. The variant is also notable for having more mutations than normally seen. One of the most important changes in B.1.1.7 seems to be N501Y, a change from asparagine (N) to tyrosine (Y) in amino-acid position 501. This is because of its position inside the spike protein's receptor-binding domain (RBD)—more specifically inside the receptor-binding motif (RBM), a part of the RBD —which binds human ACE2. 2021.02.02, Public Health England reported that they had detected "[a] limited number of B.1.1.7 VOC-202012/01 genomes with E484K mutations", which they dubbed Variant of Concern 202102/02 (VOC-202102/02). This mutation is also present in the 501.V2 variant and in Lineage B.1.1.248 and may reduce vaccine effectiveness. Detection: Backwards tracing using genetic evidence suggests B.1.1.7 emerged in September 2020 and then circulated at very low levels in the population until mid-November. The increase in cases linked to the variant first became apparent in late November when Public Health England (PHE) was investigating why infection rates in Kent were not falling despite national restrictions. PHE then discovered a cluster linked to this variant spreading rapidly into London and Essex.

Cluster 5: outbreak of a mutated variant of the SARS-CoV-2 virus. It was discovered in Northern Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. 2020.11.04 it was announced that the mink population in Denmark would be culled in order to prevent possible spread of this mutation, and that a lockdown and travel restrictions would be introduced in seven municipalities of Northern Jutland in order to prevent the mutation from spreading widely (which could compromise national or international responses to the COVID-19 pandemic). WHO has stated that Cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies". Denmark's State Serum Institute (SSI) warned that the mutation was unlikely to respond to COVID-19 vaccines under development.

Mink industry in Denmark: 40% world's pelts, making Denmark the largest producer of mink skins in the world. Ranked third in Denmark's agricultural export items of animal origin, fur and mink skins have a yearly export value of about EUR 0,5 billion. Kopenhagen Fur, located in Copenhagen, is the world's largest fur auction house; annually, it sells approximately 14 million Danish mink skins produced by 2,000 Danish fur farmers, and 7 million mink skins produced in other countries. Mink produced in Denmark is considered to be the finest in the world and is ranked by grade, with the best being Saga Royal, followed by Saga, Quality 1, and Quality 2. 2020.11 a mutated strain of COVID-19 known as "cluster 5" was detected among minks, leading the Danish Government to order the culling of 17 million minks in order to prevent a resurgence in COVID-19 cases.

501.V2 variant (B.1.351 lineage; South African COVID-19 variant): first detected in the Nelson Mandela Bay metropolitan area of the Eastern Cape province of South Africa and reported by the country's health department 2020.12.18. Researchers and officials reported that the prevalence of the variant was higher among young people with no underlying health conditions, and by comparison with other variants it is more frequently resulting in serious illness in those cases. The South African health department also indicated that the variant may be driving the second wave of the COVID-19 pandemic in the country due to the variant spreading at a more rapid pace than other earlier variants of the virus. 3 mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y, K417N, and E484K. N501Y mutation has also been detected in the United Kingdom (Variant of Concern 202012/01), but not mutations E484K and K417N.

Lineage P.1 (a 20J/501Y.V3, (VOC-202101/02), colloquially Brazil(ian) variant): has 17 amino acid changes, ten of which are in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T. This variant of SARS-CoV-2 was first detected by the National Institute of Infectious Diseases, Japan, in 2021.01.06 in four people who had arrived in Tokyo having visited Amazonas, Brazil, four days earlier. It was subsequently declared to be in circulation in Brazil. At least some vaccines were found to be significantly less effective than against other variants. P.1 has also been called 'B.1.1.28.1', although strictly only three sublevels are permitted in the PANGO Lineage system of nomenclature, hence the designation 'P.1'.

SARS-CoV-2 Omicron variant: first reported to WHO from South Africa in 2021.11.24. The variant has an unusually large number of mutations, several of which are novel (also known as autapomorphy), and several of which affect the spike protein used for most vaccine targeting at the time of its discovery. This level of variation has led to concerns regarding transmissibility, immune system evasion, and vaccine resistance. As a result, the variant was rapidly designated as being "of concern", and travel restrictions were introduced by several countries to limit or slow its international spread. International response: In response, South African Minister of Health Joe Phaahla defended his country's handling of the pandemic and said that travel bans went against the "norms and standards" of WHO.

Solidarity trial: for treatments is a multinational Phase III-IV clinical trial organized by WHO and partners to compare four untested treatments for hospitalized people with severe COVID-19 illness. The trial was announced 2020.03.18, and as of 2020.07.01, nearly 5,500 patients in 21 countries had been recruited to participate in the trial.

COVID-19 vaccine: By mid-December 2020, 57 vaccine candidates were in clinical research, including 40 in Phase I–II trials and 17 in Phase II–III trials. National regulatory authorities have approved six vaccines for public use: two RNA vaccines (tozinameran from Pfizer–BioNTech and mRNA-1273 from Moderna), two conventional inactivated vaccines (BBIBP-CorV from Sinopharm and CoronaVac from Sinovac), and two viral vector vaccines (Gam-COVID-Vac from the Gamaleya Research Institute and AZD1222 from the University of Oxford and AstraZeneca).

Tozinameran (Pfizer–BioNTech COVID-19 vaccine)

MRNA-1273 (Moderna COVID-19 vaccine)

AZD1222 (ChAdOx1 nCoV-19): COVID-19 vaccine developed by Oxford University and AstraZeneca given by intramuscular injection, using as a vector the modified chimpanzee adenovirus ChAdOx1.

Gam-COVID-Vac (Гам-КОВИД-Вак; Sputnik V (V for vaccine)): COVID-19 vaccine candidate developed by the Gamaleya Research Institute of Epidemiology and Microbiology, and registered 2020.08.11 by the Russian Ministry of Health. Seven countries (India, Brazil, Uzbekistan, Mexico, Nepal, Egypt and Kazakhstan) ordered millions of Sputnik V doses from Russia as of 2020.11. In December 2020, the Gamaleya Institute published preliminary data on 22,714 participants of its phase III trials. The study is a randomised, double-blind, placebo-controlled, multi-centre clinical trial involving 40,000 volunteers and is scheduled to run until May 2021. Supplies for the global market being produced by partners in India, Brazil, China, South Korea, Hungary, and other countries. Gam-COVID-Vac is a viral two-vector vaccine based on two human adenoviruses — a common cold virus — containing the gene that encodes the spike protein (S) of SARS-CoV-2 to stimulate an immune response. The recombinant adenovirus types 26 and 5 are both used as vectors in the vaccine. They were biotechnology-derived and contain the SARS-CoV-2 S protein cDNA.

Long COVID (post-COVID-19 syndrome, post-acute sequelae of SARS-CoV-2, chronic COVID syndrome): condition characterized by long-term sequelae appearing or persisting after the typical convalescence period of COVID-19. Long COVID can affect nearly every organ system, with sequelae including respiratory system disorders, nervous system and neurocognitive disorders, mental health disorders, metabolic disorders, cardiovascular disorders, gastrointestinal disorders, malaise, fatigue, musculoskeletal pain, and anemia. A wide range of symptoms are commonly reported, including fatigue, headaches, shortness of breath, anosmia (loss of smell), parosmia (distorted smell), muscle weakness, low fever and cognitive dysfunction.

COVID-19 lab leak theory: proposal that SARS-CoV-2 (the virus that caused the COVID-19 pandemic) originated from a laboratory in Wuhan, China. Central to the idea is the fact that the Wuhan Institute of Virology (WIV) is in the same city as the pandemic's earliest known outbreak. The theory gained support because of suspicions about the secrecy of the Chinese government's response. Scientists from WIV had previously collected SARS-related coronaviruses from bats; allegations that they also performed undisclosed risky work on such viruses is central to some versions of the idea.

Influenza, flu

GISAID: global science initiative and primary source that provides open-access to genomic data of influenza viruses and the coronavirus responsible for the COVID-19 pandemic. 2020.01.10 the first whole-genome sequences including the first vaccines and the first diagnostic tests to detect SARS-CoV-2 were uploaded to GISAID. GISAID facilitates genomic epidemiology and real-time surveillance to monitor the emergence of new COVID-19 viral strains across the planet. Since its establishment in 2008 as an alternative to sharing avian influenza data via conventional public-domain archives, GISAID is recognized for incentivizing rapid exchange of outbreak data during the H1N1 pandemic in 2009, the H7N9 epidemic in 2013, and the COVID-19 pandemic in 2020. GISAID was recognized for its importance to global health by G20 health ministers in 2017, and in 2020 the World Health Organization chief scientist called the data-science initiative "a game changer". Correspondence letter published in the journal Nature in 2006: global initiative on sharing avian influenza data. The Initiative came together in a way that gives credit to those submitting data and makes substantial efforts to work with and include them in collaborative analyses on viral sequence data, "further tipping the scales in favor of collaboration". The notion of sharing not just data, but also the benefits of resulting research, represented a "paradigm shift" that puts contributors from higher and lower resource environments on more equal footing.

Vaccination

Category:Vaccination

Category:Vaccination-related organizations

Vaccine hesitancy: delay in acceptance, or refusal of vaccines despite the availability of vaccine services. The term covers outright refusals to vaccinate, delaying vaccines, accepting vaccines but remaining uncertain about their use, or using certain vaccines but not others. "Anti-vaccinationism" refers to total opposition to vaccination; in more recent years, anti-vaccinationists have been known as "anti-vaxxers" or "anti-vax'". Vaccine hesitancy is complex and context-specific, varying across time, place and vaccines. It can be influenced by factors such as lack of proper scientifically-based knowledge and understanding about how vaccines are made or how vaccines work, complacency, convenience, or even fear of needles. There is an overwhelming scientific consensus that vaccines are generally safe and effective. Vaccine hesitancy often results in disease outbreaks and deaths from vaccine-preventable diseases.

GAVI (Gavi, the Vaccine Alliance): public–private global health partnership with the goal of increasing access to immunisation in poor countries. GAVI brings together developing country and donor governments, the WHO, UNICEF, the World Bank, the vaccine industry in both industrialised and developing countries, research and technical agencies, civil society, the Bill & Melinda Gates Foundation and other private philanthropists. GAVI has observer status at the World Health Assembly. GAVI currently supports the immunization of almost half the world's children, giving it power to negotiate better prices for the world's poorest countries and remove the commercial risks that manufacturers faced in serving this market. In 2020.09, GAVI was announced as one of the organisations leading the Covax vaccine allocation plan, created to ensure that any new COVID-19 vaccine would be shared equally between the world's richest and poorest countries.

Malaria vaccine: Approved vaccines:

RTS,S: The first approved vaccine for malaria is RTS,S, known by the brand name Mosquirix. As of April 2023, the vaccine has been given to 1.5 million children living in areas with moderate-to-high malaria transmission. It requires at least three doses in infants by age 2, and a fourth dose extends the protection for another 1–2 years. The vaccine reduces hospital admissions from severe malaria by around 30%.
R21/Matrix-M: most effective malaria vaccine is R21/Matrix-M, with 77% efficacy shown in initial trials. It is the first vaccine that meets WHO's goal of a malaria vaccine with at least 75% efficacy. It was developed through a collaboration involving the Jenner Institute at the University of Oxford, the Kenya Medical Research Institute, the London School of Hygiene and Tropical Medicine, Novavax, and the Serum Institute of India. Ghana's Food and Drugs Authority approved the use of the R21 vaccine in 2023.04, for use in children aged between five months to three years old. The Serum Institute of India is preparing to produce between 100–200 million doses of the vaccine per year, and is constructing a vaccine factory in Accra, Ghana. Following Ghana's decision, Nigeria provisionally approved the R21 vaccine.

Agents under development: Nanoparticle enhancement of RTS,S; PfSPZ vaccine

Human microbiome

Category:Microbiomes

Category:Gut flora

Template:Microbiota

Human microbiota: aggregate of microorganisms that resides on or within any of a number of human tissues and biofluids, including the skin, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and gastrointestinal tracts. They include bacteria, archaea, protists, fungi and viruses. Though micro-animals also live on the human body, they are typically excluded from this definition.

Human Microbiome Project: USA NIH initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans (the Human microbiome).

Uterine microbiome: commensal, nonpathogenic, bacteria present in a healthy uterus, amniotic fluid and endometrium and the specific environment which they inhabit. It has been only recently confirmed that the uterus and its tissues are not sterile. Uterus has been found to possess its own characteristic microbiome that differs significantly from the vaginal microbiome. Despite its close spatial connection with the vagina, the microbiome of the uterus more closely resembles the commensal bacteria found in the oral cavity. In addition, the immune system is able to differentiate between those bacteria normally found in the uterus and those that are pathogenic. Hormonal changes have an effect on the microbiota of the uterus.

Toxicology

Category:Toxicology

Toxidrome (portmanteau of toxic and syndrome): syndrome caused by a dangerous level of toxins in the body. The term was coined in 1970 by Mofenson and Greensher. It is often the consequence of a drug overdose. Common symptoms include dizziness, disorientation, nausea, vomiting, and oscillopsia. A toxidrome may indicate a medical emergency requiring treatment at a poison control center. Aside from poisoning, a systemic infection may also lead to a toxidrome. Anticholinergic; Cholinergic; Hallucinogenic; Opiate; Sedative/hypnotic; Sympathomimetic.

Nutrition

Category:Nutrition

Category:Diets

Category:High-fat diets

Category:Low-carbohydrate diets

Category:Eating behaviors

Category:Food and drink

Category:Food science

Category:Flavors

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Postprandial somnolence (food coma, carb coma): normal state of drowsiness or lassitude following a meal. Postprandial somnolence has two components: a general state of low energy related to activation of the parasympathetic nervous system in response to mass in the gastrointestinal tract, and a specific state of sleepiness caused by hormonal and neurochemical changes related to the rate at which glucose enters the bloodstream and its downstream effects on amino acid transport in the central nervous system.

Glycemic index: number associated with a particular type of food that indicates the food's effect on a person's blood glucose (also called blood sugar) level.

Glycemic load: of food is a number that estimates how much the food will raise a person's blood glucose level after eating it. One unit of glycemic load approximates the effect of consuming one gram of glucose.

Ketogenic diet: high-fat, adequate-protein, low-carbohydrate diet that in medicine is used primarily to treat difficult-to-control (refractory) epilepsy in children. The diet forces the body to burn fats rather than carbohydrates. Normally, the carbohydrates contained in food are converted into glucose, which is then transported around the body and is particularly important in fuelling brain-function.

Acetoin (3-hydroxybutanone, acetyl methyl carbinol): colorless liquid with a pleasant, buttery odor, chiral. The form produced by bacteria is (R)-acetoin. Food ingredients: Acetoin, along with diacetyl, is one of the compounds that gives butter its characteristic flavor. Because of this, manufacturers of partially hydrogenated oils typically add artificial butter flavor – acetoin and diacetyl – (along with beta carotene for the yellow color) to the final product.

Cancer

Category:Cancer

Category:Oncology

Warburg effect: Plant physiology: decrease of photosynthesis by high oxygen concentrations. Oncology: observation that most cancer cells predominantly produce energy by a high rate of glycolysis followed by lactic acid fermentation in the cytosol, rather than by a comparatively low rate of glycolysis followed by oxidation of pyruvate in mitochondria as in most normal cells.

Warburg hypothesis (Warburg theory of cancer): postulates that the driver of tumorigenesis is an insufficient cellular respiration caused by insult to mitochondria. The Warburg hypothesis was that the Warburg effect was the root cause of cancer. The current popular opinion is that cancer cells ferment glucose while keeping up the same level of respiration that was present before the process of carcinogenesis, and thus the Warburg effect would be defined as the observation that cancer cells exhibit glycolysis with lactate secretion and mitochondrial respiration even in the presence of oxygen.

History of cancer chemotherapy: era of cancer chemotherapy began in the 1940s with the first use of nitrogen mustards and folic acid antagonist drugs.

Peto's paradox: observation, named after English statistician and epidemiologist Richard Peto, that at the species level, the incidence of cancer does not appear to correlate with the number of cells in an organism. For example, the incidence of cancer in humans is much higher than the incidence of cancer in whales. This is despite the fact that a whale has many more cells than a human. If the probability of carcinogenesis were constant across cells, one would expect whales to have a higher incidence of cancer than humans. Writing an overview of the multistage model of cancer, Peto noted that, on a cell-for-cell basis, humans were much less susceptible to cancer than mice: "A man has 1000 times as many cells as a mouse... and we usually live at least 30 times as long as mice..." Peto went on to suggest that evolutionary considerations were likely responsible for varying per-cell carcinogenesis rates across species. Evidence: Within members of the same species, cancer risk and body size appear to be positively correlated, even once other risk factors are controlled for. Across species, however, the relationship breaks down. Evolutionary considerations: The evolution of multicellularity has required the suppression of cancer to some extent, and connections have been found between the origins of multicellularity and cancer. In order to build larger and longer-lived bodies, organisms required greater cancer suppression. Evidence suggests that large organisms such as elephants have more adaptations that allow them to evade cancer. 2015.10 two independent studies showed that elephants have 20 copies of tumor suppressor gene TP53 in their genome, where humans and other mammals have only one. Additional research showed 14 copies of the gene present in the DNA of preserved mammoths, but only one copy of the gene in the DNA of manatees and hyraxes, the elephant's closest living relatives. Metabolic and cell size considerations: Maciak and Michalak argue that cell size is not uniform across mammalian species, making body size an imperfect proxy for the number of cells in an organism. (For example, the volume of an individual red blood cell of an elephant is roughly four times that of one from a common shrew). Furthermore, larger cells divide more slowly than smaller ones, a difference which compounds exponentially over the life-span of the organism. Fewer cell divisions means fewer opportunities for cancer mutations, and mathematical models of cancer incidence are highly sensitive to cell-division rates. Additionally, larger animals generally have lower basal metabolic rates, following a well-defined inverse logarithmic relationship. Consequently, their cells will incur less damage over time per unit of body mass. Combined, these factors may explain much of the apparent paradox.

Hospital

Category:Health care

Category:Types of health care facilities

Category:Mayo Clinic

Mayo Clinic: nonprofit medical practice and medical research group based in Rochester, Minnesota. It is the first and largest integrated nonprofit medical group practice in the world, employing more than 3,800 physicians and scientists and 50,900 allied health staff. The practice specializes in treating difficult cases through tertiary care. It spends over $500 million a year on research.

Cohort studies, longitudinal study

Category:Cohort studies

Grant Study: part of the Study of Adult Development at Harvard Medical School. It is a 75-year longitudinal study of 268 physically- and mentally-healthy Harvard college sophomores from the classes of 1939–1944. It has run in tandem with a study called "The Glueck Study," which included a second cohort of 456 disadvantaged nondelinquent inner-city youths who grew up in Boston neighborhoods between 1940 and 1945. The subjects were all male, white and of American nationality. The men continue to be studied to this day.

Longitudinal study: correlational research study that involves repeated observations of the same variables over long periods of time — often many decades. It is a type of observational study. Longitudinal studies are often used in psychology to study developmental trends across the life span, and in sociology to study life events throughout lifetimes or generations.

Medical works, medical manuals

Category:Academic works about medicine

Category:Reference works in medicine

Category:Medical manuals

Category:Medical literature

De Medicina: 1st-century medical treatise by Aulus Cornelius Celsus, a Roman encyclopedist and possibly (but not likely) a practicing physician. It is the only surviving section of a much larger encyclopedia; only small parts still survive from sections on agriculture, military science, oratory, jurisprudence and philosophy. De Medicina draws upon knowledge from ancient Greek works, and is considered the best surviving treatise on Alexandrian medicine. Its "encyclopedic arrangement follows the tripartite division of medicine at the time as established by Hippocrates and Asclepiades — diet, pharmacology, and surgery."

Aulus Cornelius Celsus: Roman encyclopaedist, known for his extant medical work, De Medicina. Nothing is known about the life of Celsus.

Health information on the Internet

Health information on Wikipedia

Gerontology, ageing, immortality, longevity

Category:Old age

Category:Gerontology

Category:Life extension

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Longevity: sometimes used as a synonym for "life expectancy" in demography - however, the term "longevity" is sometimes meant to refer only to especially long-lived members of a population, whereas "life expectancy" is always defined statistically as the average number of years remaining at a given age. For example, a population's life expectancy at birth is the same as the average age at death for all people born in the same year (in the case of cohorts). Longevity is best thought of as a term for general audiences meaning 'typical length of life' and specific statistical definitions should be clarified when necessary.

Blue Zone: regions of the world where Dan Buettner claims people live much longer than average. The term first appeared in his November 2005 National Geographic magazine cover story, "The Secrets of a Long Life". Buettner identified five regions as "Blue Zones" (a term he trademarked): Okinawa (Japan); Sardinia (Italy); Nicoya (Costa Rica); Icaria (Greece); and among the Seventh-day Adventists in Loma Linda, California.

Gompertz–Makeham law of mortality: states that the human death rate is the sum of an age-independent component (the Makeham term, named after William Makeham) and an age-dependent component (the Gompertz function, named after Benjamin Gompertz), which increases exponentially with age. In a protected environment where external causes of death are rare (laboratory conditions, low mortality countries, etc.), the age-independent mortality component is often negligible. In this case the formula simplifies to a Gompertz law of mortality. In 1825, Benjamin Gompertz proposed an exponential increase in death rates with age.

Negligible senescence: lack of symptoms of aging in some organisms. Negligibly senescent organisms do not have measurable reductions in their reproductive capability with age, or measurable functional decline with age. Death rates in negligibly senescent organisms do not increase with age as they do in senescent organisms. Turtles, for example, were once thought to lack senescence, but more extensive observations have found evidence of decreasing fitness with age.

Strategies for Engineered Negligible Senescence (SENS): term coined by British biogerontologist Aubrey de Grey for the diverse range of regenerative medical therapies, either planned or currently in development, for the periodical repair of all age-related damage to human tissue with the ultimate purpose of maintaining a state of negligible senescence in the patient, thereby postponing age-associated disease for as long as the therapies are reapplied.

Cryonics: ≤−196°C of a human corpse, with the hope that resuscitation may be possible in the future. Cryopreservation of humans is not reversible with present technology; cryonicists hope that medical advances will someday allow cryopreserved people to be revived. Immersion in liquid nitrogen at a temperature of −196 °C (77 K) is often used for convenience.

Suspended animation: inducement of a temporary cessation or decay of main body functions, including the brain, to a hypometabolic state in order to try to preserve its mental and physiological capabilities. Procedure has been associated with a lethargic state in nature when animals or plants appear, over a period, to be dead but then can wake up or prevail without suffering any harm. This has been termed in different contexts hibernation, dormancy or anabiosis (this last in some aquatic invertebrates and plants in scarcity conditions). Since the 1970s, induced hypothermia has been performed for some open-heart surgeries as an alternative to heart-lung machines. Hypothermia, however, provides only a limited amount of time in which to operate and there is a risk of tissue and brain damage for prolonged periods. Cryonics operates under a fundamentally distinct paradigm from suspended animation in that it depends on future technology as part of its premise for working. It is not currently possible to preserve mental capacities and memories by this method and only cells and microorganisms are currently revivable. Scientific possibilities: Temperature-induced: Hypothermic range; Chemically induced.

Deep hypothermic circulatory arrest (DHCA): surgical technique that involves cooling the body to temperatures between 20°C to 25°C, and stopping blood circulation and brain function for up to one hour. It is used when blood circulation to the brain must be stopped because of delicate surgery within the brain, or because of surgery on large blood vessels that lead to or from the brain. DHCA is used to provide a better visual field during surgery due to the cessation of blood flow. DHCA is a form of carefully managed clinical death in which heartbeat and all brain activity cease. A key principle of DHCA is total inactivation of the brain by cooling, as verified by "flatline" isoelectric EEG, also called electrocerebral silence (ECS). Instead of a continuous decrease in activity as the brain is cooled, electrical activity decreases in discontinuous steps. In the human brain, a type of reduced activity called burst suppression occurs at a mean temperature of 24 °C, and electrocerebral silence occurs at a mean temperature of 18 °C. The achievement of measured electrocerebral silence has been called "a safe and reliable guide" for determining cooling required for individual patients, and verification of electrocerebral silence is required prior to stopping blood circulation to begin a DHCA procedure. Hippocrates used snow and ice to surface cool wounded patients to prevent excessive bleeding. People who are to undergo DHCA surgery are placed on cardiopulmonary bypass (CPB), a procedure that uses an external heart-lung machine that can artificially replace the function of the heart and lungs. A portion of the circulating blood supply is removed and stored for later replacement, with the remaining blood diluted by added fluids with the objective of reducing viscosity and clotting tendencies at cold temperature. The remaining diluted blood is cooled by the heart-lung machine until hypothermia causes the heart to stop beating normally, after which the blood pump of the heart-lung machine continues blood circulation through the body. Corticosteroids are typically given 6–8 hours before surgery as it has shown to have neuroprotective properties to decrease risk of neurological dysfunction by decreasing the release of inflammatory cytokines. Glucose is eliminated from all intravenous solutions to reduce the risk of hyperglycemia. Post-operative hyperthermia is associated with adverse outcomes. Patients are completely rewarmed before discontinuing CPB, but temperature remain labile despite rewarming efforts which requires close monitoring in the ICU.

Emergency Preservation and Resuscitation: experimental medical procedure where an emergency department patient is cooled into suspended animation for an hour to prevent incipient death from ischemia, such as the blood loss following a shooting or stabbing. EPR uses hypothermia, drugs, and fluids to "buy time" for resuscitative surgery.

Audrey Smith (1915.05.21–1981.06.03): British cryobiologist, who discovered the use of glycerol to protect human red blood cells during freezing.

Emergency medicine

Category:Emergency medicine

Category:Wilderness medicine

Triage: process of determining the priority of patients' treatments based on the severity of their condition. This rations patient treatment efficiently when resources are insufficient for all to be treated immediately. The term comes from the French verb trier, meaning to separate, sift or select. Triage may result in determining the order and priority of emergency treatment, the order and priority of emergency transport, or the transport destination for the patient. Those responsible for the removal of the wounded from a battlefield or their care afterwards would divide the victims into three categories:

Those who are likely to live, regardless of what care they receive;
Those who are unlikely to live, regardless of what care they receive;
Those for whom immediate care might make a positive difference in outcome.

Wilderness medicine (practice): providing "vital emergency care in remote settings" is a rapidly evolving field and is of increasing importance as more people engage in hiking, climbing, kayaking and other potentially hazardous activities in the backcountry. A primary focus of the field is the evaluation, prioritization (triage), preliminary treatment of acute injuries or illnesses which occur in those environments and the emergency evacuation of victims.

Human diseases and disorders

Category:Human diseases and disorders

Non-alcoholic fatty liver disease (Metabolic (dysfunction) associated fatty liver disease (MAFLD); NAFLD): excessive fat build-up in the liver without another clear cause such as alcohol use. There are two types; non-alcoholic fatty liver (NAFL) and metabolic dysfunction–associated steatohepatitis (formerly non-alcoholic steatohepatitis (NASH)), with the latter also including liver inflammation. Non-alcoholic fatty liver disease is less dangerous than NASH and usually does not progress to NASH or liver cirrhosis. When NAFLD does progress to NASH, it may eventually lead to complications such as cirrhosis, liver cancer, liver failure, or cardiovascular disease. Obesity and type 2 diabetes are strong risk factors for NAFLD. NAFLD is the most common liver disorder worldwide and is present in approximately 25% of the world's population. It is also very common in developed nations, such as USA, and affected about 75 to 100 million Americans in 2017. Over 90% of obese, 60% of diabetic, and up to 20% normal-weight people develop it. NAFLD is the leading cause of chronic liver disease and the second most common reason for liver transplantation in the US and Europe as of 2017. NAFLD affects about 20 to 25% of people in Europe. In USA, estimates suggest between 30 and 40% of adults have NAFLD, and about 3 to 12% of adults have NASH.

Veterinary medicine

Category:Veterinary medicine

Drugs, pharmaceutical drugs (medication, medicine)

Category:Drugs

Category:Drugs by mechanism of action

Category:Drugs with unknown mechanisms of action

Category:Drugs by target organ system

Category:Drugs acting on the gastrointestinal system and metabolism

Category:Antiobesity drugs

Category:Veterinary drugs

Category:World Health Organization essential medicines

Medication (medicament, medicine, pharmaceutical drug, medicinal drug, simply drug): drug used to diagnose, cure, treat, or prevent disease. Drug therapy (pharmacotherapy) is an important part of the medical field and relies on the science of pharmacology for continual advancement and on pharmacy for appropriate management.

WHO Model List of Essential Medicines (Essential Medicines List; EML): published by WHO, contains the medications considered to be most effective and safe to meet the most important needs in a health system. The list is frequently used by countries to help develop their own local lists of essential medicines. As of 2016, more than 155 countries have created national lists of essential medicines based on the World Health Organization's model list. This includes both developed and developing countries. About 25% of items are in the complementary list.

WHO Model List of Essential Medicines for Children (EMLc): published by WHO, contains the medications considered to be most effective and safe in children up to twelve years of age to meet the most important needs in a health system.

Xenobiotic: chemical substance found within an organism that is not naturally produced or expected to be present within the organism. It can also cover substances that are present in much higher concentrations than are usual. Natural compounds can also become xenobiotics if they are taken up by another organism, such as the uptake of natural human hormones by fish found downstream of sewage treatment plant outfalls, or the chemical defenses produced by some organisms as protection against predators.

Semaglutide (Ozempic, Wegovy, Rybelsus): antidiabetic medication used for the treatment of type 2 diabetes and an anti-obesity medication used for long-term weight management, developed by Novo Nordisk in 2012. It is a peptide similar to the hormone glucagon-like peptide-1 (GLP-1), modified with a side chain. It can be administered by subcutaneous injection or taken orally. Semaglutide is a glucagon-like peptide-1 receptor agonist. The most common side effects include nausea, vomiting, diarrhea, abdominal pain, and constipation. In 2017.12, the injectable version with the brand name Ozempic was approved for use by people with diabetes in USA, and, in 2018.01, in Canada. In 2018.02, authorization was granted in EU, in 2018.03 in Japan, and in 2019.08 in Australia.

Metformin (Glucophage): main first-line medication for the treatment of type 2 diabetes, particularly in people who are overweight. It is also used in the treatment of polycystic ovary syndrome. It is sometimes used as an off-label adjunct to lessen the risk of metabolic syndrome in people who take antipsychotics. Metformin is not associated with weight gain and is taken by mouth. Metformin is generally well tolerated. Common adverse effects include diarrhea, nausea, and abdominal pain. It has a small risk of causing low blood sugar. High blood lactic acid level is a concern if the medication is used in overly large doses or prescribed in people with severe kidney problems. It is not recommended in those with significant liver disease. Metformin is a biguanide antihyperglycemic agent. It works by decreasing glucose production by the liver, by increasing the insulin sensitivity of body tissues, and by increasing GDF15 secretion, which reduces appetite and caloric intake. Metformin was discovered in 1922. French physician Jean Sterne began the study in humans in the 1950s. It was introduced as a medication in France in 1957 and USA in 1995. It is on the World Health Organization's List of Essential Medicines.

Botany, plant biology

Category:Botany

Template:Plant classification (Supergroup)

Archaeplastida
- Rhodelphidia
- Rhodophyta (red algae)
- Glaucophyta
- incertae sedis: Algospongia
- Viridiplantae or Plantae s.s. (green algae & land plants)
Embryophyta (and plants) or Plantae sensu strictissimo
- Bryophytes
  - Marchantiophyta (liverworts)
  - Anthocerotophyta (hornworts)
  - Bryophyta (mosses)
- Polysporangiophytes
  - Protracheophytes
  - Tracheophytes (vascular plants)

Archaeplastida (Plantae sensu lato): major group of eukaryotes, comprising the photoautotrophic red algae (Rhodophyta), green algae, land plants, and the minor group glaucophytes. It also includes the non-photosynthetic lineage Rhodelphidia, a predatorial (eukaryotrophic) flagellate that is sister to the Rhodophyta, and probably the microscopic picozoans. The Archaeplastida have chloroplasts that are surrounded by two membranes, suggesting that they were acquired directly through a single endosymbiosis event by feeding on a cyanobacterium. All other groups which have chloroplasts, besides the amoeboid genus Paulinella, have chloroplasts surrounded by three or four membranes, suggesting they were acquired secondarily from red or green algae. Unlike red and green algae, glaucophytes have never been involved in secondary endosymbiosis events. The cells of the Archaeplastida typically lack centrioles and have mitochondria with flat cristae. They usually have a cell wall that contains cellulose, and food is stored in the form of starch. However, these characteristics are also shared with other eukaryotes. The main evidence that the Archaeplastida form a monophyletic group comes from genetic studies, which indicate their plastids probably had a single origin. This evidence is disputed. Based on the evidence to date, it is not possible to confirm or refute alternative evolutionary scenarios to a single primary endosymbiosis. Photosynthetic organisms with plastids of different origin (such as brown algae) do not belong to the Archaeplastida.

Glaucophyte: are a small group of rare freshwater microscopic algae. Together with the red algae (Rhodophyta) and the green algae plus land plants (Viridiplantae or Chloroplastida), they form the Archaeplastida. However, the relationships among the red algae, green algae and glaucophytes are unclear, in large part due to limited study of the glaucophytes. The glaucophytes are of interest to biologists studying the development of chloroplasts because some studies suggest they may be similar to the original algal type that led to green plants and red algae in that they may be basal Archaeplastida. The chloroplasts of glaucophytes are known as 'cyanelles' or 'cyanoplasts'. Unlike the chloroplasts in other organisms, they have a peptidoglycan layer, believed to be a relic of the endosymbiotic origin of plastids from cyanobacteria. Glaucophytes contain the photosynthetic pigment chlorophyll a.

Botany

Turgor pressure: force within the cell that pushes the plasma membrane against the cell wall.

Viridiplantae ('green plants'): clade of eukaryotic organisms made up of the green algae, which are primarily aquatic, and the land plants (embryophytes), which emerged within them.

Embryophyte: most familiar group of green plants that form vegetation on earth. Living embryophytes include hornworts, liverworts, mosses, ferns, lycophytes, gymnosperms and flowering plants, and emerged from Charophyte green algae. The Embryophyta are informally called land plants because they live primarily in terrestrial habitats, while the related green algae are primarily aquatic. All are complex multicellular eukaryotes with specialized reproductive organs. The name derives from their innovative characteristic of nurturing the young embryo sporophyte during the early stages of its multicellular development within the tissues of the parent gametophyte. With very few exceptions, embryophytes obtain their energy by photosynthesis, that is by using the energy of sunlight to synthesize their food from carbon dioxide and water.

Bryophyte: group of land plants, sometimes treated as a taxonomic division, that contains three groups of non-vascular land plants (embryophytes): the liverworts, hornworts and mosses. In the strict sense, Bryophyta consists of the mosses only. Bryophytes are characteristically limited in size and prefer moist habitats although they can survive in drier environments. Bryophytes produce enclosed reproductive structures (gametangia and sporangia), but they do not produce flowers or seeds. They reproduce sexually by spores and asexually by fragmentation or the production of gemmae. Though bryophytes were considered a paraphyletic group in recent years, almost all of the most recent phylogenetic evidence supports the monophyly of this group, as originally classified by Wilhelm Schimper in 1879.

Vascular plant (Latin vasculum: duct; higher plants): form a large group of plants (c. 308,312 accepted known species [2016]) that are defined as those land plants that have lignified tissues (the xylem) for conducting water and minerals throughout the plant; include the clubmosses, horsetails, ferns, gymnosperms (including conifers) and angiosperms (flowering plants).

Spermatophyte: comprise those plants that produce seeds, hence the alternative name seed plants.

Flowering plant (angiosperms): most diverse group of land plants, with 416 families, approx. 13,164 known genera and a total of c. 295,383 known species [2016].

Pinophyta (Coniferophyta or Coniferae, conifers): division of vascular land plants containing a single class, Pinopsida. They are gymnosperms, cone-bearing seed plants. All extant conifers are perennial woody plants with secondary growth. The great majority are trees, though a few are shrubs. While tropical rainforests have more biodiversity and turnover, the immense conifer forests of the world represent the largest terrestrial carbon sink. Conifers are of great economic value for softwood lumber and paper production.

Gnetophyta

Transpiration: process of water movement through a plant and its evaporation from aerial parts, such as leaves, stems and flowers. Water is necessary for plants but only a small amount of water taken up by the roots is used for growth and metabolism. The remaining 97–99.5% is lost by transpiration and guttation. Leaf surfaces are dotted with pores called stomata, and in most plants they are more numerous on the undersides of the foliage. The stomata are bordered by guard cells and their stomatal accessory cells (together known as stomatal complex) that open and close the pore. Transpiration occurs through the stomatal apertures, and can be thought of as a necessary "cost" associated with the opening of the stomata to allow the diffusion of carbon dioxide gas from the air for photosynthesis. Transpiration also cools plants, changes osmotic pressure of cells, and enables mass flow of mineral nutrients and water from roots to shoots. Mass flow of liquid water from the roots to the leaves is driven in part by capillary action, but primarily driven by water potential differences. If the water potential in the ambient air is lower than the water potential in the leaf airspace of the stomatal pore, water vapor will travel down the gradient and move from the leaf airspace to the atmosphere. This movement lowers the water potential in the leaf airspace and causes evaporation of liquid water from the mesophyll cell walls. This evaporation increases the tension on the water menisci in the cell walls and decrease their radius and thus the tension that is exerted on the water in the cells. Because of the cohesive properties of water, the tension travels through the leaf cells to the leaf and stem xylem where a momentary negative pressure is created as water is pulled up the xylem from the roots. In taller plants and trees, the force of gravity can only be overcome by the decrease in hydrostatic (water) pressure in the upper parts of the plants due to the diffusion of water out of stomata into the atmosphere. Water is absorbed at the roots by osmosis, and any dissolved mineral nutrients travel with it through the xylem.

Soil plant atmosphere continuum: pathway for water moving from soil through plants to the atmosphere.

Transpiration stream: uninterrupted stream of water and solutes which is taken up by the roots and transported via the xylem vessels to the leaves where it evaporates into the air/apoplast-interface of the substomatal cavity. It is driven by capillary action and in some plants by root pressure. The main driving factor is the difference in water potential between the soil and the substomatal cavity caused by transpiration.

Pressure bomb (pressure chamber, Scholander bomb): instrument with which it is possible to measure the approximate water potential of plant tissues. A leaf attached to a stem is placed inside a sealed chamber and pressurised gas is added to the chamber slowly. As the pressure increases at some point sap will be forced out of the xylem and will be visible at the cut end of the stem. The pressure that is required to do so is equal and opposite to the water potential of the leaf.

Water potential: potential energy of water per unit volume relative to pure water in reference conditions. Water potential quantifies the tendency of water to move from one area to another due to osmosis, gravity, mechanical pressure, or matrix effects such as capillary action (which is caused by surface tension).

Vascular tissue

Vascular bundle

Xylem: transport water from roots to shoot and leaves, but it also transports some nutrients.

Cohesion-tension theory of intermolecular attraction that explains the process of water flow upwards (against the force of gravity) through the xylem of plants. Water is constantly lost through transpiration from the leaf. When one water molecule is lost another is pulled along by the processes of cohesion and tension. Transpiration pull, utilizing capillary action and the inherent surface tension of water, is the primary mechanism of water movement in plants.

Phloem: carries organic nutrients (known as photosynthate), in particular, sucrose, a sugar, to all parts of the plant where needed. Unlike xylem (which is composed primarily of dead cells), the phloem is composed of still-living cells that transport sap.

Plant to plant communication via mycorrhizal networks: with other plants of the same or different species. Mycorrhizal networks allow for the transfers of signals and cues between plants which influence the behavior of the connected plants by inducing morphological or physiological changes. The chemical substances which act as these signals and cues are referred to as infochemicals. These can be allelochemicals, defensive chemicals or nutrients. Allelochemicals are used by plants to interfere with the growth or development of other plants or organisms, defensive chemicals can help plants in mycorrhizal networks defend themselves against attack by pathogens or herbivores, and transferred nutrients can affect growth and nutrition.

Plant cognition: study of the mental capacities of plants. It explores the idea that plants are capable of responding to and learning from stimuli in their surroundings in order to choose and make decisions that are most appropriate to ensure survival. In 2012, Paco Calvo Garzón and Fred Keijzer published evidence that plants exhibited structures equivalent to (1) action potentials (2) neurotransmitters and (3) synapses. Also, they stated that a large part of plant activity takes place underground, and that the notion of a 'root brain' was first mooted by Charles Darwin in 1880.

Plant disease resistance: protects plants from pathogens in two ways: by pre-formed structures and chemicals, and by infection-induced responses of the immune system. Relative to a susceptible plant, disease resistance is the reduction of pathogen growth on or in the plant (and hence a reduction of disease), while the term disease tolerance describes plants that exhibit little disease damage despite substantial pathogen levels. Common disease resistance mechanisms: Pre-formed structures and compounds; Inducible post-infection plant defenses. Immune system: plant immune system carries two interconnected tiers of receptors, one most frequently sensing molecules outside the cell and the other most frequently sensing molecules inside the cell. Both systems sense the intruder and respond by activating antimicrobial defenses in the infected cell and neighboring cells. In some cases, defense-activating signals spread to the rest of the plant or even to neighboring plants. The two systems detect different types of pathogen molecules and classes of plant receptor proteins; Pattern-triggered immunity; Effector triggered immunity; R genes and R proteins; Effector biology; RNA silencing and systemic acquired resistance elicited by prior infections; Species-level resistance. Signaling mechanisms. Plant breeding for disease resistance

Systemic acquired resistance: "whole-plant" resistance response that occurs following an earlier localized exposure to a pathogen. SAR is analogous to the innate immune system found in animals, and there is evidence that SAR in plants and innate immunity in animals may be evolutionarily conserved.

Crop diversity: variance in genetic and phenotypic characteristics of plants used in agriculture. Over the past 50 years, there has been a major decline in two components of crop diversity; genetic diversity within each crop and the number of species commonly grown.

Hand-pollination (mechanical pollination): technique that can be used to pollinate plants when natural or open pollination is either undesirable or insufficient. This method of pollination is done by manually transferring pollen from the stamen of one plant to the pistil of another. Pears grown in Hanyuan County, China have been hand-pollinated since the 1980s, because they can't be pollinated with other varieties that have different flowering times; also, lice infestation requires the use of many insecticide sprays, which causes local beekeepers to refuse to lend beehives.

Materially engineered artificial pollinators: experimental radiowave-controlled micro-drones that use ionic liquid gels for artificial pollination without living insects.

RoboBee: tiny robot capable of partially untethered flight, developed by a research robotics team at Harvard University. The culmination of twelve years of research, RoboBee solved two key technical challenges of micro-robotics. Engineers invented a process inspired by pop-up books that allowed them to build on a sub-millimeter scale precisely and efficiently. To achieve flight, they created artificial muscles capable of beating the wings 120 times per second.

Gametophyte: one of the two alternating multicellular phases in the life cycles of plants and algae. It is a haploid multicellular organism that develops from a haploid spore that has one set of chromosomes. The gametophyte is the sexual phase in the life cycle of plants and algae. It develops sex organs that produce gametes, haploid sex cells that participate in fertilization to form a diploid zygote which has a double set of chromosomes. Cell division of the zygote results in a new diploid multicellular organism, the second stage in the life cycle known as the sporophyte.

Sporophyte: diploid multicellular stage in the life cycle of a plant or alga which produces asexual spores. This stage alternates with a multicellular haploid gametophyte phase. Bryophytes (mosses, liverworts and hornworts) have a dominant gametophyte phase on which the adult sporophyte is dependent for nutrition. The embryo sporophyte develops by cell division of the zygote within the female sex organ or archegonium, and in its early development is therefore nurtured by the gametophyte. Because this embryo-nurturing feature of the life cycle is common to all land plants they are known collectively as the embryophytes. Most algae have dominant gametophyte generations, but in some species the gametophytes and sporophytes are morphologically similar (isomorphic). An independent sporophyte is the dominant form in all clubmosses, horsetails, ferns, gymnosperms, and angiosperms that have survived to the present day.

Dioicy (/daɪˈoʊəsi/): sexual system where archegonia and antheridia are produced on separate gametophytes. It is one of the two main sexual systems in bryophytes. Both dioicous (/daɪˈoʊəkəs/) and monoicous gametophytes produce gametes in gametangia by mitosis rather than meiosis, so that sperm and eggs are genetically identical with their parent gametophyte. 68% of liverwort species, 57% to 60% of moss species, and 40% of hornwort species are dioicous. Dioicy also occurs in algae such as Charales and Coleochaetales. It is also prevalent in brown algae.

Monoicy (/mɒˈnoʊəsi/): sexual system in haploid plants (mainly bryophytes) where both sperm and eggs are produced on the same gametophyte, in contrast with dioicy, where each gametophyte produces only sperm or eggs but never both. Role in survival: There can be both selective advantages and selective disadvantages for organisms that are monoicous or dioicous. Monoicous bryophytes can easily reproduce sexually, since both sexes can be found on the same organism. On the other hand, this can lead to inbreeding and reduce genetic variation within populations. Dioicous organisms necessarily exchange genes with other organisms of the species during sexual reproduction, increasing heterozygosity and variability (given a sufficiently large variable mating population). If isolated, however, organisms may only reproduce asexually, which could present a severe selective disadvantage over time. Bryophyte sperm dispersal can therefore be key to species longevity, particularly in dioicous species. While sperm dispersal is typically passive, with sperm dispersing through water, certain species exhibit very active dispersal mechanisms, such as aerial dispersal recently described in the liverwort Conocephalum conicum.

Plant taxonomy

Template:List of systems of plant taxonomy

Angiosperm Phylogeny Group: refers to an informal international group of systematic botanists who came together to try to establish a consensus on the taxonomy of flowering plants (angiosperms) that would reflect new knowledge about plant relationships discovered through phylogenetic studies.

APG III system (Angiosperm Phylogeny Group III system)

APG IV system: of flowering plant classification is the fourth version of a modern, mostly molecular-based, system of plant taxonomy for flowering plants (angiosperms) being developed by the Angiosperm Phylogeny Group (APG). It was published in 2016, seven years after its predecessor the APG III system was published in 2009, and 18 years after the first APG system was published in 1998. Compared to the APG III system, the APG IV system recognizes five new orders (Boraginales, Dilleniales, Icacinales, Metteniusales and Vahliales), along with some new families, making a total of 64 angiosperm orders and 416 families.

Asterids (APG IV system (2016)): clade (a monophyletic group). Common examples include the forget-me-nots, nightshades (including potatoes, eggplants, tomatoes, peppers and tobacco), the common sunflower, petunias, morning glory and sweet potato, coffee, lavender, lilac, olive, jasmine, honeysuckle, ash tree, teak, snapdragon, sesame, psyllium, garden sage, and table herbs such as mint, basil, and rosemary.

Cornales: Plants within the Cornales usually have four-parted flowers, drupaceous fruits, and inferior gynoecia topped with disc-shaped nectaries.

Ericales: large and diverse order of dicotyledons, including, for example, tea, persimmon, blueberry, Brazil nut, and azalea. The order includes trees, bushes, lianas, and herbaceous plants. Together with ordinary autophytic plants, the Ericales include chlorophyll-deficient mycoheterotrophic plants (e.g., Sarcodes sanguinea) and carnivorous plants (e.g., genus Sarracenia).

Euasterids:

Lamiids

Solanales: Family Solanaceae (nightshade family; includes Nolanaceae as well as potatoes, eggplants, tomatoes, chilli peppers, tobacco, and petunias); Family Convolvulaceae (morning glory and sweet potato); Families Montiniaceae, Sphenocleaceae, Hydroleaceae.

Potato: Potatoes are the world's fourth-largest food crop, following maize (corn), wheat, and rice. The green leaves and green skins of tubers exposed to the light are toxic. In the Andes, where the species is indigenous, some other closely related species are cultivated. Potatoes were introduced to Europe in the second half of the 16th century by the Spanish. Wild potato species can be found throughout the Americas from the United States to southern Chile. The potato was originally believed to have been domesticated independently in multiple locations, but later genetic testing of the wide variety of cultivars and wild species proved a single origin for potatoes in the area of present-day southern Peru and extreme Northwestern Bolivia (from a species in the Solanum brevicaule complex), where they were domesticated approximately 7,000–10,000 years ago.

Campanulids

Mycology

Category:Mycology

Category:Fungi

Category:Fungus ecology

Mycology: branch of biology concerned with the study of fungi, including their genetic and biochemical properties, their taxonomy and their use to humans as a source for tinder, traditional medicine, food, and entheogens, as well as their dangers, such as toxicity or infection. Mycology branches into the field of phytopathology, the study of plant diseases, and the two disciplines remain closely related because the vast majority of plant pathogens are fungi.

Mycorrhiza (Greek μύκης mýkēs, "fungus", and ῥίζα rhiza, "root"; pl. mycorrhizae, mycorrhiza or mycorrhizas): mutual symbiotic association between a fungus and a plant. The term mycorrhiza refers to the role of the fungus in the plant's rhizosphere, its root system. Mycorrhizae play important roles in plant nutrition, soil biology, and soil chemistry. In a mycorrhizal association, the fungus colonizes the host plant's root tissues, either intracellularly as in arbuscular mycorrhizal fungi (AMF or AM), or extracellularly as in ectomycorrhizal fungi. The association is sometimes mutualistic. In particular species or in particular circumstances, mycorrhizae may have a parasitic association with host plants.

Mycorrhizal network (common mycorrhizal networks): underground hyphal networks created by mycorrhizal fungi that connect individual plants together and transfer water, carbon, nitrogen, and other nutrients and minerals. The formation of these networks is context-dependent, and can be influenced by factors such as soil fertility, resource availability, host or myco-symbiont genotype, disturbance and seasonal variation. By analogy to the many roles intermediated by the World Wide Web in human communities, the many roles that mycorrhizal networks appear to play in woodland have earned them a colloquial nickname: the Wood Wide Web.

Microbiology

Category:Microbiology

Category:Archaea

Category:Bacteriology

Category:Microorganisms

Category:Phytopathology

Category:Prokaryotes

Category:Virology

{q.v. #Protozoa, protista, single cell eukaryotes}

DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea): superphylum of Extremophile Archaea.

Archaea: superphylum - TACK - has been proposed that includes the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota. This superphylum may be related to the origin of eukaryotes.

Proteoarchaeota (TACK): proposed archaeal kingdom.

Template:Growth media

Thioglycolate broth: multipurpose, enriched, differential medium used primarily to determine the oxygen requirements of microorganisms. Sodium thioglycolate in the medium consumes oxygen and permits the growth of obligate anaerobes. This, combined with the diffusion of oxygen from the top of the broth, produces a range of oxygen concentrations in the medium along its depth. The oxygen concentration at a given level is indicated by a redox-sensitive dye such as resazurine that turns pink in the presence of oxygen. This allows the differentiation of obligate aerobes, obligate anaerobes, facultative anaerobes, microaerophiles, and aerotolerant organisms.

Prokaryote, bacteria, archaea, bacteriology

Nucleoid (nucleus-like) is an irregularly shaped region within the cell of a prokaryote that contains all or most of the genetic material, called genophore. The genome of prokaryotic organisms generally is a circular, double-stranded piece of DNA, of which multiple copies may exist at any time. The length of a genome widely varies, but generally is at least a few million base pairs. As in all cellular organisms, length of the DNA molecules of bacterial and archaeal chromosomes is very large compared to the dimensions of the cell, and the genomic DNA molecules must be compacted to fit.

Mycobacterium: aerobic and nonmotile bacteria (except: Mycobacterium marinum, which has been shown to be motile within macrophages); characteristically acid-alcohol-fast; lack of an outer cell membrane; all share a characteristic cell wall, thicker than in many other bacteria, which is hydrophobic, waxy, and rich in mycolic acids. Adapt readily to growth on very simple substrates, using ammonia or amino acids as nitrogen sources and glycerol as a carbon source in the presence of mineral salts. Some species can be very difficult to culture, have extremely long reproductive cycles — M. leprae, may take more than 20 days to proceed through one division cycle; availability of genetic manipulation techniques still lags far behind that of other bacterial species

Tuberculosis: common, and in many cases lethal, infectious disease caused by various strains of mycobacteria, usually Mycobacterium tuberculosis; typically attacks the lungs, but can also affect other parts of the body; most infections are asymptomatic and latent, but about one in ten latent infections eventually progresses to active disease which, if left untreated, kills more than 50% of those so infected; classic symptoms of active TB infection are a chronic cough with blood-tinged sputum, fever, night sweats, and weight loss (the latter giving rise to the formerly prevalent term "consumption"); multiple drug-resistant tuberculosis (MDR-TB) infections. 1/3rd of the world's population is thought to have been infected with M. tuberculosis, with new infections occurring in about 1% of the population each year. ~80% of the population in many Asian and African countries test positive in tuberculin tests, while only 5–10% of USA population tests positive. More people in the developing world contract tuberculosis because of compromised immunity, largely due to high rates of HIV infection and the corresponding development of AIDS.

Mycobacterium tuberculosis: most recent common ancestor of the M. tuberculosis complex evolved ~40,000 years ago.

Multi-drug-resistant tuberculosis

Extensively drug-resistant tuberculosis

Totally drug-resistant tuberculosis

Lipoarabinomannan (LAM): glycolipid, and a virulence factor associated with M. tuberculosis; inactivate macrophages and scavenge oxidative radicals

Mycolic acid: long fatty acids found in the cell walls of Mycobacterium sp.; major component of the cell wall

Leprosy (Hansen's disease (HD)): left untreated, leprosy can be progressive, causing permanent damage to the skin, nerves, limbs and eyes. Contrary to folklore, leprosy does not cause body parts to fall off, although they can become numb or diseased as a result of secondary infections; these occur as a result of the body's defenses being compromised by the primary disease

Mycobacterium leprae (Hansen’s coccus spirilly): intracellular, pleomorphic, acid-fast bacterium; culture takes several weeks to mature; obligate intracellular parasite; longest doubling time of all known bacteria, and has thwarted every effort at culture in the laboratory

Mycobacterium lepromatosis: discovered in 2008; species is distinct from Mycobacterium leprae; causes diffuse Lepromatous leprosy (DLL)

Leprosy stigma

Leper colony (leprosarium, lazar house): in 2001, government-run leper colonies in Japan came under judicial scrutiny, leading to the determination that the Japanese government had mistreated the patients, and the District Court ordered Japan to pay compensation to former patients

National Hansen's Disease Museum (Japan)

Bacterial microcompartment

Carboxysome: bacterial microcompartments that contain enzymes involved in carbon fixation; made of polyhedral protein shells about 80 to 140 nm in diameter; thought to concentrate carbon dioxide to overcome the inefficiency of RuBisCO; found in all cyanobacteria and many chemotrophic bacteria that fix carbon dioxide

Escherichia coli: Gram-negative, facultatively anaerobic, rod-shaped bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms). Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in their hosts, and are occasionally responsible for product recalls due to food contamination. The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2, and preventing colonization of the intestine with pathogenic bacteria.

Escherichia coli in molecular biology: Gram-negative gammaproteobacterium commonly found in the lower intestine of warm-blooded organisms (endotherms). The descendants of two isolates, K-12 and B strain, are used routinely in molecular biology as both a tool and a model organism. Strains: Escherich's isolate; K-12; B strain; C strain; W strain.

Escherichia coli O104:H4

Escherichia coli O157:H7

Escherichia coli (molecular biology)

Taxon in disguise: in bacteriology, a species, genus or higher unit of biological classification whose evolutionary history reveals has evolved from another unit of similar or lower rank, making the parent unit paraphyletic. This happens when rapid evolution makes a new species appear radically different from the ancestral group, so that it is not (initially) recognised as belonging to the parent phylogenetic group, leaving the latter an evolutionary grade. The bacterial genus Shigella is the cause of bacillary dysentery, a potentially severe infection that claim the lives of over a million people annually. The genus (S. dysenteriae, S. flexneri, S. boydii, S. sonnei) have evolved from the common intestinal bacterium Escherichia coli, rendering that species parephyletic. E. coli itself can also cause serious dysentery, but the difference in the genetic makeup between the E. coli and Shigella causes different medical conditions and symptoms.

Candidatus Desulforudis audaxviator: monospecific genus of bacteria that lives in groundwater at depths from 1.5–3 km below the Earth's surface. The name comes from a quotation from Jules Verne's novel Journey to the Center of the Earth, where the hero, Professor Lidenbrock, finds a secret inscription in Latin: Descende, audax viator, et terrestre centrum attinges (Descend, bold traveller, and you will attain the center of the Earth). Desulforudis audaxviator is the only bacterium found in water samples obtained 2.8 km underground in the Mponeng gold mine in South Africa; survives on chemical food sources derived from the radioactive decay of minerals in the surrounding rock. This makes it one of the few known organisms that does not depend on sunlight for nourishment, and the only species known to be alone in its ecosystem. It has genes for extracting carbon from dissolved carbon dioxide and for nitrogen fixation. It may also have acquired genes from a species of archaea by horizontal gene transfersurvives on chemical food sources derived from the radioactive decay of minerals in the surrounding rock. This makes it one of the few known organisms that does not depend on sunlight for nourishment, and the only species known to be alone in its ecosystem. It has genes for extracting carbon from dissolved carbon dioxide and for nitrogen fixation. It may also have acquired genes from a species of archaea by horizontal gene transfer. Analyses of water from the bacteriums' habitat show that the water is very old and has not been diluted by surface water, indicating the bacterium have been isolated from Earth's surface for several million years. The source of the hydrogen needed for their respiration comes from the decomposition of water by radioactive decay of uranium, thorium and potassium. The radiation allows for the production of sulphur compounds the bacteria can use as a high-energy food source. "Ca. D. audaxviator" not only survives in a complete absence of organic compounds, light, and oxygen, but also in temperatures as high as 60 °C and pH 9.3. The physiology that enables it to live in these extreme conditions is a tribute to its unusually large genome, consisting of 2157 genes instead of the 1500 of its peers. If conditions become unfavorable for normal life, "Ca. D. audaxviator" is able to encyst, safeguarding its DNA from heat, extreme pH, and the lack of water.

Cupriavidus metallidurans: non-spore-forming, Gram-negative bacterium which is adapted to survive several forms of heavy metal stress. It is of industrial importance and used for heavy metal remediation and sensing. It is an aerobic chemolithoautotroph, facultatively able to grow in a mineral salts medium in the presence of H₂, O₂, and CO₂ without an organic carbon source. The energy-providing subsystem of the cell under these conditions is composed only of the hydrogenase, the respiratory chain, and the F1F0-ATPase. It is able to degrade xenobiotics even in the presence of high heavy metal concentrations. Finally, strain CH34 is adapted to the outlined harsh conditions by a multitude of heavy-metal resistance systems that are encoded by the two indigenous megaplasmids pMOL28 and pMOL30 on the bacterial chromosome(s).

Delftia acidovorans: Gram-negative, motile, non-sporulating, rod-shaped bacterium known for its ability to biomineralize gold and bioremediation characteristics. It was first isolated from soil in Delft, Netherlands. Metabolism. Biomineralization: Au³⁺ is reduced extracellularly by the non-ribosomal secondary metabolite delftibactin. Bioremediation and biomanufacturing: capable of converting toxic metals like selenium and chromium ions into harmless products. Role in disease: Delftia acidovorans is an emergent opportunistic pathogen that demonstrates antibiotic resistance. The infection can cause bacteremia, keratitis, pneumonia, empyema, otitis, and peritonitis.

Borderline life

Category:Prions

Biological dark matter: informal term for unclassified or poorly understood genetic material. This genetic material may refer to genetic material produced by unclassified microorganisms. By extension, biological dark matter may also refer to the un-isolated microorganism whose existence can only be inferred from the genetic material that they produce. Up to 99% of all living microorganisms cannot be cultured, so few functional insights exist about the metabolic potential of these organisms. Sequences that are believed to be derived from unknown microbes are referred to as the 'Microbial Dark Matter, the 'Dark Virome', or 'Dark Matter Fungi' Such sequences are not rare. It has been estimated that in material from humans, between 40 and 90% of viral sequences are from Dark Matter. Other studies have suggested the existence of 264 new viral genera, discovered in publicly available databases, and a study of human blood suggested that 42% of people have at least one previously unknown virus each, adding up to 19 different new genera. A comprehensive study of DNA sequences from multiple human samples inferred the existence of 4,930 species of microbes of which 77% were previously unreported. Health-related findings include a prophage that might be associated with cirrhosis of the liver, and seven novel sequences from children with type-1 diabetes that have characteristics of viruses.

Ultramicrobacteria (0.3-0.2 µm): many, if not all, of these small bacteria are dormant forms of larger cells that allow survival under starvation conditions

Nanobe: tiny filamental structure first found in some rocks and sediments.

Prion: infectious agent thought to be the cause of the transmissible spongiform encephalopathies (TSEs). It is composed entirely of protein material, called PrP (short for prion protein), that can fold in multiple, structurally distinct ways, at least one of which is transmissible to other prion proteins, leading to disease that is similar to viral infection. This would be in contrast to all other known infectious agents (virus/bacteria/fungus/parasite) which must contain nucleic acids (either DNA, RNA, or both).

Transmissible spongiform encephalopathy (TSE): group of progressive, invariably fatal, conditions that are associated with prions and affect the brain (encephalopathies) and nervous system of many animals, including humans, cattle, and sheep. According to the most widespread hypothesis, they are transmitted by prions, though some other data suggest an involvement of a Spiroplasma infection. Mental and physical abilities deteriorate and many tiny holes appear in the cortex causing it to appear like a sponge when brain tissue obtained at autopsy is examined under a microscope. The disorders cause impairment of brain function, including memory changes, personality changes and problems with movement that worsen chronically. Transmission occurs when healthy animals consume tainted tissues from others with the disease. In the 1980s and 1990s, bovine spongiform encephalopathy spread in cattle in an epidemic fashion. This occurred because cattle were fed the processed remains of other cattle, a practice now banned in many countries. In turn, consumption (by humans) of bovine-derived foodstuff which contained prion-contaminated tissues resulted in an outbreak of the variant form of Creutzfeldt–Jakob disease in the 1990s and 2000s. Prions cannot be transmitted through the air or through touching or most other forms of casual contact. However, they may be transmitted through contact with infected tissue, body fluids, or contaminated medical instruments. Normal sterilization procedures such as boiling or irradiating materials fail to render prions non-infective. TSEs of humans include Creutzfeldt–Jakob disease (sCJD, fCJD, iCJD, vCJD), Gerstmann–Sträussler–Scheinker syndrome, fatal insomnia, kuru, variably protease-sensitive prionopathy. Cause: Genetics; Protein-only hypothesis; Multi-component hypothesis; Spiroplasma hypothesis; Viral hypothesis.

PRNP (Major prion protein; PrP): the only known example of a prion protein. In humans, it is encoded by the PRNP gene.

Creutzfeldt–Jakob disease (CJD): degenerative neurological disease that is incurable and invariably fatal. Caused by infectious PRNP. CDC: the defective protein can be transmitted by contaminated harvested human brain products, corneal grafts (in at least one reported case), dural grafts or electrode implants (acquired or iatrogenic form (iCJD)); it can be familial (fCJD); or it may appear for the first time in the patient (sporadic form: sCJD); in the familial form, a mutation occurs in the gene for PrP, PRNP; 10%-15% of CJD cases are familial.

Gerstmann–Sträussler–Scheinker syndrome: very rare, usually familial, fatal neurodegenerative disease that affects patients from 20 to 60 years in age. A change in codon 102 from proline to leucine on chromosome 20, has been found in PRNP of most affected individuals.

Fatal familial insomnia: extremely rare autosomal dominant inherited prion disease of the brain; almost always caused by a mutation to the protein PrP^C, but can also develop spontaneously in patients with a non-inherited mutation variant called sporadic fatal insomnia.

Kuru (disease): incurable degenerative neurological disorder endemic to tribal regions of Papua New Guinea. Now widely accepted that kuru was transmitted among members of the Fore tribe of Papua New Guinea via funerary cannibalism. Prion-resistant genetic variant of PRNP G127V.

Virology, viruses, viroids

Category:Viruses

Category:Virology

Category:Viroids

Non-cellular life: life that exists without a cellular structure for at least part of its life cycle. Historically, most (descriptive) definitions of life postulated that a living organism must be composed of one or more cells, but this is no longer considered necessary, and modern criteria allow for forms of life based on other structural arrangements. The primary candidates for non-cellular life are viruses. A minority of biologists consider viruses to be living organisms, but most do not. Their primary objection is that no known viruses are capable of autonomous reproduction: they must rely on cells to copy them. However, the recent discovery of giant viruses that possess genes for part of the required translation machinery has raised the prospect that they may have had extinct ancestors that could evolve and replicate independently.

Virus: small infectious agent that replicates only inside the living cells of an organism. Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants, and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, about 5,000 virus species have been described in detail, although there are millions of types. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. These viral particles, also known as virions, consist of: (i) the genetic material made from either DNA or RNA, long molecules that carry genetic information; (ii) a protein coat, called the capsid, which surrounds and protects the genetic material; and in some cases (iii) an envelope of lipids that surrounds the protein coat. The shapes of these virus particles range from simple helical and icosahedral forms for some virus species to more complex structures for others. The average virion is about one one-hundredth the size of the average bacterium. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity. Viruses are considered by some to be a life form, because they carry genetic material, reproduce, and evolve through natural selection, but lack key characteristics (such as cell structure) that are generally considered necessary to count as life. Because they possess some but not all such qualities, viruses have been described as "organisms at the edge of life", and as replicators.

Virology: study of viruses; structure, classification and evolution, their ways to infect and exploit host cells for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy; virology is considered to be a subfield of microbiology or of medicine.

Virus, Baltimore Classification. Classes I-VII (Legend: ss = single stranded; ds = double stranded)

Baltimore classification: developed by David Baltimore, is a virus classification system that groups viruses into families, depending on their type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds), ...) and their method of replication.

I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)
II: ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses)
III: dsRNA viruses (e.g. Reoviruses)
IV: (+)ssRNA viruses (+ strand or sense) RNA (e.g. Picornaviruses, Togaviruses)
V: (−)ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxoviruses, Rhabdoviruses)
VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses)
VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle (e.g. Hepadnaviruses)

RNA virus: ICTV classifies RNA viruses as those that belong to Group III, Group IV or Group V of the Baltimore classification system of classifying viruses and does not consider viruses with DNA intermediates in their life cycle as RNA viruses. Mutation rate about 10⁶ times faster than DNA viruses, "because viral RNA polymerases lack the proof-reading ability of DNA polymerases". ssRNA, sometimes dsRNA. Ribovirus: explicitly excludes retroviruses (DNA intermediate).

Provirus: virus genome that is integrated into the DNA of a host cell. In the case of bacterial viruses (bacteriophages), proviruses are often referred to as prophages. A latent infection may become productive in response to changes in the host's environmental conditions or health; the provirus may be activated and begin transcription of its viral genome. This can result in the destruction of its host cell because the cell's protein synthesis machinery is hijacked to produce more viruses. {q.v. Endogenous retrovirus}

Positive-sense single-stranded RNA virus (+)ssRNA virus, group IV): virus that uses positive sense single stranded RNA as its genetic material. (+)ssRNA viruses account for a large fraction of known viruses, including many pathogens such as the hepacivirus C, West Nile virus, dengue virus, SARS and MERS coronaviruses, and SARS-CoV-2 as well as less clinically serious pathogens such as the rhinoviruses that cause the common cold. Positive-sense ssRNA viruses have genetic material that can function both as a genome and as messenger RNA; it can be directly translated into protein in the host cell by host ribosomes; viral replication complexes (VRCs) formed in association with intracellular membranes. All positive-sense ssRNA virus genomes encode RNA-dependent RNA polymerase (RdRP), a viral protein that synthesizes RNA from an RNA template. Recombination. Genome: Coronaviruses have the largest known RNA genomes, up to 32kb in length, and likely possess replication proofreading mechanisms in the form of a proofreading exoribonuclease, non-structural protein 14, that is otherwise not found in RNA viruses.

Retrovirus: type of RNA virus that inserts a copy of its genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Notable human retroviruses include HIV-1 and HIV-2, the cause of the disease AIDS. Main virion components are: envelope, RNA, proteins (gag proteins, protease, Pol proteins, env proteins). Classification: Group VI viruses: use virally encoded reverse transcriptase, an RNA-dependent DNA polymerase, to produce DNA from the initial virion RNA genome. Group VII viruses: both families have DNA genomes contained within the invading virus particles. The DNA genome is transcribed into both mRNA, for use as a transcript in protein synthesis, and pre-genomic RNA, for use as the template during genome replication. Group VI and VII are exogenous retroviruses. Endogenous retroviruses are not formally included in this classification system.

Subfamily Orthoretrovirinae:
- Genus Alpharetrovirus; including Avian leukosis virus and Rous sarcoma virus
- Genus Betaretrovirus; including Mouse mammary tumour virus
- Genus Gammaretrovirus; including Murine leukemia virus and Feline leukemia virus
- Genus Deltaretrovirus; including Bovine leukemia virus and the cancer-causing Human T-lymphotropic virus
- Genus Epsilonretrovirus
- Genus Lentivirus; including HIV 1 and Simian immunodeficiency virus and Feline immunodeficiency virus
Subfamily Spumaretrovirinae:
- Genus Bovispumavirus
- Genus Equispumavirus
- Genus Felispumavirus
- Genus Prosimiispumavirus
- Genus Simian foamy virus (Simiispumavirus)

Viral evolution: Viruses have short generation times, and many—in particular RNA viruses—have relatively high mutation rates (on the order of one point mutation or more per genome per round of replication for RNA viruses). This elevated mutation rate, when combined with natural selection, allows viruses to quickly adapt to changes in their host environment. In addition, most viruses provide many offspring, so any mutated genes can be passed on to many offspring quickly. Studies at the molecular level have revealed relationships between viruses infecting organisms from each of the three domains of life, and viral proteins that pre-date the divergence of life and thus the last universal common ancestor; genomes of most vertebrate species contain hundreds to thousands of sequences derived from ancient retroviruses

Paleovirology (viral fossils): regions of genomes that originate from ancient germline integration of viral genetic material

Endogenous viral element (EVE): DNA sequence derived from a virus, and present within the germline of a non-viral organism; may be entire viral genomes (proviruses), or fragments of viral genomes.

Endogenous retrovirus (ERV; HERV: Human Endogenous Retrovirus): endogenous viral elements in the genome that closely resemble and can be derived from retroviruses. They are abundant in the genomes of jawed vertebrates, and they comprise up to 5–8% of the human genome (lower estimates of ~1%). ERVs are a subclass of a type of gene called a transposon, which can be packaged and moved within the genome to serve a vital role in gene expression and in regulation. Can play an active role in shaping genomes; long terminal repeat (LTR) sequences that flank ERV genomes frequently act as alternate promoters and enhancers, often contributing to the transcriptome by producing tissue-specific variants. 64% of known LTR-promoted transcription variants are expressed in reproductive tissues. Retroelements in general are largely prevalent in rapidly evolving, mammal-specific gene families whose function is largely related to the response to stress and external stimuli: class I & class II MHC genes. Majority of ERVs that occur in vertebrate genomes are ancient, inactivated by mutation, and have reached genetic fixation in their host species. HERVs comprise: 98,000 ERV elements; fragments make up nearly 8%; no HERVs capable of replication had been identified [2005], containing major deletions or nonsense mutations. HERV-K (HML2) family of viruses has been active since the divergence of humans and chimpanzees; makes up less than 1% of HERV elements but is one of the most studied; has even been active in the past few hundred thousand years, e.g., some human individuals carry more copies of this virus family than others; two members of HERV-K(HML2), HERV-K106 and HERV-K116, were active in the last 800,000 years and that HERV-K106 may have infected modern humans 150kya; absence of known infectious members of the HERV-K(HML2) family, and the lack of elements with a full coding potential within the published human genome sequence, suggests to some that the family is less likely to be active at present

ERVWE1 (HERV-W_7q21.2 provirus ancestral Env polyprotein; syncytin; enverin): in humans, and other mammals, intact env proteins called syncytins are responsible for the formation and function of syncytiotrophoblasts; been suggested that the selection and fixation of these proteins for this function have played a critical role in the evolution of viviparity. Distinct, syncytin-like genes have been identified in primates, rodents, lagomorphs, carnivores, and ungulates, with integration dates ranging from 10-85 mya. Syncytins: retroviral envelope proteins have been exapted to produce a protein that is expressed in the placental syncytiotrophoblast, and is involved in fusion of the cytotrophoblast cells to form the syncytial layer of the placenta; syncytiotrophoblast: responsible for maintaining nutrient exchange and protecting the developing fetus from the mother's immune system

ERV-Fc: was an ERV, or a genus or family of them, related to the modern murine leukemia virus. It was active and infectious among many species of mammals in several orders, jumping species more than 20 times between about 33 million and about 15 million years ago, in the Oligocene and early Miocene, in all large areas of the world except for Australia and Antarctica. After about 15 million years ago, it became extinct as an active infectious virus, perhaps due to its hosts developing inherited resistance to it, but inactive damaged copies and partial copies and fragments of its DNA survive as inclusions in the hereditary nuclear DNA of many species of mammals, some in different orders, including humans and other great apes. That has let interspecies jump routes of the spreading virus be tracked, and timed by the molecular clock in their extant descendants, but with gaps where trails were lost by passing through infected animals who left no extant descendants or by loss of the integrated sequence in some lineages.

Evolution of influenza: virus causing influenza is one of the best known pathogens found in various species. In particular, the virus is found in birds as well as mammals including horses, pigs, and humans.

Template:Retroviruses:

Blubervirales: Hepadnaviridae
Ortervirales:
- (ssRNA-RT viruses): Belpaoviridae, Metaviridae, Pseudoviridae, Retroviridae
- (dsDNA-RT viruses): Caulimoviridae
ERV

Nucleocytoplasmic large DNA viruses: proposed order of dsDNA viruses, notable for containing the Megavirales or giant viruses. There are nine families of NCLDVs that all share certain genomic and structural characteristics; however, it is uncertain whether the similarities of the different families of this group have a common viral ancestor. One feature of this group is a large genome and the presence of many genes involved in DNA repair, DNA replication, transcription, and translation. Typically, viruses with smaller genomes do not contain genes for these processes. Most of the viruses in this family also replicate in both the host's nucleus and cytoplasm, thus the name nucleocytoplasmic.

Pithovirus (genome: ): 1.5 µm in length and 0.5 µm in diameter; infects amoebas; double-stranded DNA virus; viable specimen was found in a 30,000-year-old ice core harvested from permafrost in Siberia.

Mimiviridae: family of viruses. Amoeba and other protists serve as natural hosts.

Mimivirus (genome: 1,181,404 bp): Amoeba serve as their natural hosts. This genus contains a single identified species named Acanthamoeba polyphaga mimivirus. Mimivirus has a large and complex genome compared with most other viruses.

Mamavirus: large and complex virus in the Group I family mimiviridae. Virus is exceptionally large, and larger than many bacteria. Like mimivirus, mamavirus was isolated from an amoeba in a cooling tower. The mimiviridae were not discovered until recently because of their size; when filtered the mimiviridae stay with the bacteria which led scientists to believe they were also bacteria.

Cafeteria roenbergensis virus: giant virus that infects the marine bicosoecid flagellate Cafeteria roenbergensis, a member of the microzooplankton community. 300 nm diameter outer protein shell with icosahedral symmetry, an underlying lipid membrane, and an inner core that contains the genome. The first virus to be found with a mechanosensitive ion channel protein, which may protect the genome from osmotic damage.

Pandoravirus (genome: 1.9-2.5 Mb)

Megavirus (genome: 1,259,197 bp)

Virophage: small, double-stranded DNA viral phages that require the co-infection of another virus. The co-infecting viruses are typically giant viruses. Virophages rely on the viral replication factory of the co-infecting giant virus for their own replication. One of the characteristics of virophages is that they have a parasitic relationship with the co-infecting virus. Their dependence upon the giant virus for replication often results in the deactivation of the giant viruses. The virophage may improve the recovery and survival of the host organism.

Sputnik virophage: subviral agent that reproduces in amoeba cells that are already infected by a certain helper virus; Sputnik uses the helper virus's machinery for reproduction and inhibits replication of the helper virus. At its discovery in a Paris water-cooling tower in 2008 Sputnik was the first known satellite virus that inhibited replication of its helper virus and thus acted as a parasite of that virus. In analogy to the term bacteriophage it was called a virophage.

Satellite (biology): subviral agent composed of nucleic acid that depends on the co-infection of a host cell with a helper virus for its replication.

Viroid: smallest infectious pathogens known. They are composed solely of a short strand of circular, single-stranded RNA that has no protein coating. All known viroids are inhabitants of higher plants, in which most cause diseases, ranging in economic importance. Although viroids are composed of nucleic acid, they do not code for any protein. The viroid's replication mechanism uses RNA polymerase II, a host cell enzyme normally associated with synthesis of messenger RNA from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid's RNA as a template. Some viroids are ribozymes, having catalytic properties that allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.

Virusoid: circular single-stranded RNA(s) dependent on viruses for replication and encapsidation. The genome of virusoids consist of 200–400 nts and does not code for any proteins. Virusoids are essentially viroids that have been encapsulated by a helper virus coat protein. They are thus similar to viroids in their means of replication (rolling circle replication) and due to the lack of genes, but they differ in that viroids do not possess a protein coat. They encode a hammerhead ribozyme.

Capsid: protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic material of the virus. Icosahedral: T-number - representative of the size and complexity of the capsids; Prolate; Helical.

Virus-like particle (VLPs): molecules that closely resemble viruses, but are non-infectious because they contain no viral genetic material. They can be naturally occurring or synthesized through the individual expression of viral structural proteins, which can then self assemble into the virus-like structure.

Virome: collection of nucleic acids, both RNA and DNA, that make up the viral community associated with a particular ecosystem or holobiont. The word is derived from virus and genome and first used by Forest Rohwer and colleagues to describe viral shotgun metagenomes. All macro-organisms have viromes that include bacteriophage and viruses. Viromes are important in the nutrient and energy cycling, development of immunity, and a major source of genes through lysogenic conversion.

T7 RNA polymerase: from T7 bacteriophage catalyzes the formation of RNA from DNA in the 5'→ 3' direction. Related proteins: T7 polymerase is a representative member of the single-subunit DNA-dependent RNAP (ssRNAP) family. Other members include phage T3 and SP6 RNA polymerases, the mitochondrial RNA polymerase (POLRMT), and the chloroplastic ssRNAP. The ssRNAP family is structurally and evolutionarily distinct from the multi-subunit family of RNA polymerases (including bacterial and eukaryotic sub-families). In contrast to bacterial RNA polymerases, T7 polymerase is not inhibited by the antibiotic rifampicin. This family is related to single-subunit reverse transcriptase and DNA polymerase.

Negative-strand RNA virus (−ssRNA viruses; Baltimore: Group V; Phylum: Negarnaviricota): group of related viruses that have negative-sense, single-stranded genomes made of ribonucleic acid. They have genomes that act as complementary strands from which mRNA is synthesized by the viral enzyme RNA-dependent RNA polymerase (RdRp). During replication of the viral genome, RdRp synthesizes a positive-sense antigenome that it uses as a template to create genomic negative-sense RNA. Negative-strand RNA viruses also share a number of other characteristics: most contain a viral envelope that surrounds the capsid, which encases the viral genome, −ssRNA virus genomes are usually linear, and it is common for their genome to be segmented. Descended from a common ancestor that was a double-stranded RNA (dsRNA) virus, and they are considered to be a sister clade of reoviruses, which are dsRNA viruses.

Rhabdoviridae: vertebrates (including mammals and humans), invertebrates, plants, fungi and protozoans serve as natural hosts.

Lyssavirus (Greek λύσσα lyssa "rage, fury, rabies"): genus of RNA viruses in the family Rhabdoviridae, order Mononegavirales. Mammals, including humans, can serve as natural hosts. The genus Lyssavirus includes the rabies virus traditionally associated with the disease of the same name. Genomes are linear, around 11kb in length.

HIV

Subtypes of HIV: One of the obstacles to treatment of the human immunodeficiency virus is its high genetic variability. HIV can be divided into two major types, HIV type 1 (HIV-1) and HIV type 2 (HIV-2). HIV-1 is related to viruses found in chimpanzees and gorillas living in western Africa, while HIV-2 viruses are related to viruses found in the endangered west African primate sooty mangabey. The HIV-1 group M viruses predominate and are responsible for the AIDS pandemic. Group M can be further subdivided into subtypes based on genetic sequence data. Some of the subtypes are known to be more virulent or are resistant to different medications. Likewise, HIV-2 viruses are thought to be less virulent and transmissible than HIV-1 M group viruses, although HIV-2 is known to cause AIDS.

History of HIV/AIDS: originated in non-human primates in Sub-Saharan Africa and was transferred to humans during the late 19th or early 20th century. Two types: HIV-1 and HIV-2. The pandemic strain of HIV-1 is closely related to a virus found in the chimpanzees of the subspecies Pan troglodytes troglodytes, which lives in the forests of the Central African nations of Cameroon, Equatorial Guinea, Gabon, Republic of Congo (or Congo-Brazzaville), and Central African Republic. HIV-2 is less transmittable and is largely confined to West Africa, along with its closest relative, a virus of the sooty mangabey (Cercocebus atys atys), an Old World monkey inhabiting southern Senegal, Guinea-Bissau, Guinea, Sierra Leone, Liberia, and western Ivory Coast.

Timeline of early HIV/AIDS cases

Timeline of HIV/AIDS

HIV-1:

HIV Rev response element (RRE): highly structured, ~350 nucleotide RNA segment present in the Env coding region of unspliced and partially spliced viral mRNAs; in the presence of the HIV-1 accessory protein Rev, HIV-1 mRNAs that contain the RRE can be exported from the nucleus to the cytoplasm for downstream events such as translation and virion packaging.

Long-term nonprogressor: individuals infected with HIV, who maintain a CD4 count greater than 500 without antiretroviral therapy with a detectable viral load. Many of these patients have been HIV positive for 30 years without progressing to the point of needing to take medication in order not to develop AIDS. They have been the subject of a great deal of research, since an understanding of their ability to control HIV infection may lead to the development of immune therapies or a therapeutic vaccine. The classification "Long-term non-progressor" is not permanent, because some patients in this category have gone on to develop AIDS. Long-term nonprogressors typically have viral loads under 10,000 copies /mL blood, do not take antiretrovirals, and have CD4+ counts within the normal range. Most people with HIV not on medication have viral loads which are much higher. It is estimated that around 1 in 500 people with HIV are long-term nonprogressors. Without the symptoms of AIDS, many LTNP patients may not know they are infected.

Science software, medical software

Category:Science software

Category:Medical software

Category:Health software

Category:Health care software

Template:Free healthcare software

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Template:Free healthcare software

Bioethics

Category:Bioethics

Category:Medical ethics

Wrongful birth: legal cause of action in some common law countries in which the parents of a congenitally diseased child claim that their doctor failed to properly warn of their risk of conceiving or giving birth to a child with serious genetic or congenital abnormalities. Wrongful conception (vasectomy, tubal ligation, or other sterilization procedure); Wrongful adoption.

Wrongful life: name given to a legal action in which someone is sued by a severely disabled child (through the child's legal guardian) for failing to prevent the child's birth.

Maternal-fetal conflict: obstetric conflict, occurs when a pregnant woman's (maternal) interests conflict with the interests of her baby (fetus). Legal and ethical considerations involving women's rights and the rights of the fetus as a patient and future child, have become more complicated with advances in medicine and technology. Fetus: Fetus as a patient, Defining a healthy fetus. Maternal-fetal relationship: Experience, circumstance, and shared interest; Protection of the fetus. Physician role: Mediating the conflict and honoring the patient. Legal issues: Legal inequalities.

Medical ethics and law

Category:Medical ethics

Category:Ethically disputed medical practices

Category:Circumcision

Beneficence (ethics): concept in research ethics that states that researchers should have the welfare of the research participant as a goal of any clinical trial or other research study. The antonym of this term, maleficence, describes a practice that opposes the welfare of any research participant. According to the Belmont Report, researchers are required to follow two moral requirements in line with the principle of beneficence: do not harm and maximize possible benefits for research while minimizing any potential harm on others. There are many different precedents in medicine and research for conducting a cost–benefit analysis and judging whether a certain action would be a sufficient practice of beneficence, and the extent to which treatments are acceptable or unacceptable is under debate.

Primum non nocere ("first, do no harm"): Non-maleficence, which is derived from the maxim, is one of the principal precepts of bioethics that all students in healthcare are taught in school and is a fundamental principle throughout the world. Another way to state it is that, "given an existing problem, it may be better not to do something, or even to do nothing, than to risk causing more harm than good." It reminds healthcare personnel to consider the possible harm that any intervention might do. It is invoked when debating the use of an intervention that carries an obvious risk of harm but a less certain chance of benefit.

{q.v. User:Kazkaskazkasako/Books/History#Classical Greece : Kynodesme}

Foreskin restoration: process of expanding the skin on the penis to reconstruct an organ similar to the foreskin, which has been removed by circumcision or injury. Foreskin restoration is primarily accomplished by stretching the residual skin of the penis, but surgical methods also exist. Restoration creates a facsimile of the foreskin, but specialized tissues removed during circumcision cannot be reclaimed. History: In the Greco-Roman world intact genitals, including the foreskin, were considered a sign of beauty, civility, and masculinity. In Classical Greek and Roman societies (8th century BC to 6th century AD), exposure of the glans was considered disgusting and improper, and did not conform to the Hellenistic ideal of gymnastic nudity. Men with short foreskins would wear the kynodesme to prevent exposure. As a consequence of this social stigma, an early form of foreskin restoration known as epispasm was practiced among some Jews in Ancient Rome (8th century BC to 5th century AD). Foreskin restoration is of ancient origin and dates back to the reign of the Roman Emperor Tiberius (AD 14-37), when surgical means were taken to lengthen the foreskin of individuals born with either a short foreskin that did not cover the glans completely or a completely exposed glans as a result of circumcision. Again, during WWII some European Jews sought foreskin restoration to avoid Nazi persecution.

Restoration device: device used for applying tension to skin during the process of non-surgical foreskin restoration. Those who use such a device employ the technique of tissue expansion, which causes new skin to grow. History: Until the 2nd century AD, the Pondus Judaeus was used among some circumcised males. It was a replacement for more painful techniques known at the time. This device was a bronze sheath used to expand the foreskin, which at the time was not fully excised. Its effectiveness became limited after circumcisions were modified to eliminate its use (Tushmet 1965).

Futile medical care: continued provision of medical care or treatment to a patient when there is no reasonable hope of a cure or benefit. One could say that it is impossible to reach a firm definition of futile medical care, because this would depend upon universal agreement about the point at which there is no further benefit to intervention, and different involved parties may always disagree about the amount and type of benefit under discussion. For instance, a cancer patient may be willing to undergo yet more chemotherapy with a very expensive medication for the benefit of a few weeks of life, while medical staff, the insurance company, and close relatives may all feel otherwise, for different reasons.

Baby Doe Law (Baby Doe Amendment; 1984): set forth specific criteria and guidelines for the treatment of seriously ill and/or disabled newborns, regardless of the wishes of the parents.

Template:Medical ethics cases:

David Vetter ("David, the bubble boy"; 1971.09.21-1984.02.22): severe combined immunodeficiency; a few months after unmatched bone marrow transplant from his sister Katherine, he died from Burkitt's lymphoma due to the dormant Epstein-Barr virus in the donor bone marrow.

Model organisms

Template:Model Organisms:

Schizosaccharomyces pombe (fission yeast) & Saccharomyces cerevisiae (budding yeast):

Schizosaccharomyces pombe#Comparison with budding yeast (Saccharomyces cerevisiae)

diverged 300-600 mya
cerevisiae: 250 introns; pombe: ~5000
cerevisiae: 16 chromosomes; pombe: 3
cerevisiae: often diploid; pombe: often haploid
cerevisiae: in G1 phase (cell cycle) for an extended period (G1-S transition tightly controlled); pombe: in G2 (G2-M transition tightly controlled)
both share genes with higher eukaryotes that they do not share with each other: pombe: RNAi machinery genes; cerevisiae has greatly simplified heterochromatin compared to pombe; cerevisiae has well-developed peroxisomes, while pombe does not
cerevisiae: small point centromere of 125 bp, and sequence-defined replication origins of about the same size; pombe: large, repetitive centromeres (40–100 kb) more similar to mammalian centromeres, and degenerate replication origins of at least 1kb

Saccharomyces Genome Database

Saccharomyces boulardii (S. cerevisiae var. boulardii): tropical yeast first isolated from lychee and mangosteen fruit peel in 1923 by French scientist Henri Boulard. Although early reports claimed distinct taxonomic, metabolic, and genetic properties, S. boulardii is genetically a grouping of S. cerevisiae strains, sharing >99% genomic relatedness. S. boulardii is sometimes used as a probiotic with the purpose of introducing beneficial microbes into the large and small intestines and conferring protection against pathogens. It grows at 37 °C. In healthy patients, S. boulardii has been shown to be nonpathogenic and nonsystemic (it remains in the gastrointestinal tract rather than spreading elsewhere in the body).

Thermus thermophilus: Gram negative eubacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely thermophilic, with an optimal growth temperature of about 65 °C. rTth DNA polymerase is a recombinant thermostable DNA polymerase derived from Thermus thermophilus, with optimal activity at 70-80 °C, used in some PCR applications; this enzyme possesses efficient reverse transcriptase activity in the presence of manganese.

Dormancy

Dormancy: period in an organism's life cycle when growth, development, and (in animals) physical activity are temporarily stopped. This minimizes metabolic activity and therefore helps an organism to conserve energy. Dormancy tends to be closely associated with environmental conditions. Organisms can synchronize entry to a dormant phase with their environment through predictive or consequential means. Predictive dormancy occurs when an organism enters a dormant phase before the onset of adverse conditions. For example, photoperiod and decreasing temperature are used by many plants to predict the onset of winter. Consequential dormancy occurs when organisms enter a dormant phase after adverse conditions have arisen. This is commonly found in areas with an unpredictable climate. While very sudden changes in conditions may lead to a high mortality rate among animals relying on consequential dormancy, its use can be advantageous, as organisms remain active longer and are therefore able to make greater use of available resources.

Animals: Hibernation, Diapause, Aestivation, Brumation.

Diapause: delay in development in response to regular and recurring periods of adverse environmental conditions. It is a physiological state with very specific initiating and inhibiting conditions. The mechanism is a means of surviving predictable, unfavorable environmental conditions, such as temperature extremes, drought, or reduced food availability. Diapause is observed in all the life stages of arthropods, especially insects.

Embryonic diapause (delayed implantation): reproductive strategy used by approximately 100 different mammals in seven or eight different orders. In embryonic diapause, the embryonic blastocyst does not immediately implant in the uterus after sexual reproduction has created the zygote, but rather remains in a state of dormancy. Little to no development takes place while the embryo remains unattached to the uterine wall. As a result, the normal gestation period is extended for a species-specific time. Some mammals that undergo embryonic diapause include rodents, bears, armadillos, mustelids (e.g. weasels and badgers), and marsupials (e.g. kangaroos). Some groups only have one species that undergoes embryonic diapause, such as the roe deer in the order Artiodactyla.

Plants: survival strategy exhibited by many plant species, which enables them to survive in climates where part of the year is unsuitable for growth, such as winter or dry seasons. Seeds: when a mature and viable seed under a favorable condition fails to germinate, it is said to be dormant. Seed dormancy is referred to as embryo dormancy or internal dormancy and is caused by endogenous characteristics of the embryo that prevent germination. Trees: Vernalization
Bacteria: can survive adverse conditions such as temperature, desiccation, and antibiotics by forming endospores, cysts, or states of reduced metabolic activity lacking specialized cellular structures. Up to 80% of the bacteria in samples from the wild appear to be metabolically inactive —many of which can be resuscitated. Such dormancy is responsible for the high diversity levels of most natural ecosystems.
Viruses: dormancy, in its rigid definition, does not apply to viruses, as they are not metabolically active. However, some viruses such as poxviruses and picornaviruses, after entering the host, can become latent for long periods of time, or even indefinitely until they are externally activated. Herpesviruses, for example, can become latent after infecting the host, and after years they can activate again if the host is under stress or exposed to ultraviolet radiation.

Seed dormancy: evolutionary adaptation that prevents seeds from germinating during unsuitable ecological conditions that would typically lead to a low probability of seedling survival. Dormant seeds do not germinate in a specified period of time under a combination of environmental factors that are normally conducive to the germination of non-dormant seeds. Many species of plants have seeds that delay germination for many months or years, and some seeds can remain in the soil seed bank for more than 50 years before germination. Some seeds have a very long viability period, and the oldest documented germinating seed was nearly 2000 years old based on radiocarbon dating. Exogenous dormancy: caused by conditions outside the embryo and is often broken down into three subgroups: Physical dormancy: impermeable seed coat is known as physical dormancy; Mechanical dormancy: seed coats or other coverings are too hard to allow the embryo to expand during germination; Chemical dormancy: includes growth regulators etc., that are present in the coverings around the embryo. Endogenous dormancy: caused by conditions within the embryo itself, and it is also often broken down into three subgroups: physiological dormancy, morphological dormancy and combined dormancy. Secondary dormancy.

Soil seed bank: natural storage of seeds, often dormant, within the soil of most ecosystems. The study of soil seed banks started in 1859 when Charles Darwin observed the emergence of seedlings using soil samples from the bottom of a lake. The first scientific paper on the subject was published in 1882 and reported on the occurrence of seeds at different soil depths. Weed seed banks have been studied intensely in agricultural science because of their important economic impacts; other fields interested in soil seed banks include forest regeneration and restoration ecology.

Biotechnology

Category:Biotechnology

Category:Pharmaceutical industry

{q.v. #Health care}

Biomolecular engineering: application of engineering principles and practices to the purposeful manipulation of molecules of biological origin. Biomolecular engineers integrate knowledge of biological processes with the core knowledge of chemical engineering in order to focus on molecular level solutions to issues and problems in the life sciences. Biomolecular engineers purposefully manipulate carbohydrates, proteins, nucleic acids and lipids within the framework of the relation between their structure, function and properties and in relation to applicability to such areas as environmental remediation, crop and livestock production, biofuel cells and biomolecular diagnostics. Attention is also given to the rudiments of engineered biomolecules in cell signaling, cell growth kinetics, biochemical pathway engineering and bioreactor engineering.

In vitro compartmentalization (IVC): emulsion-based technology that generates cell-like compartments in vitro. These compartments are designed such that each contains no more than one gene. When the gene is transcribed and/or translated, its products (RNAs and/or proteins) become 'trapped' with the encoding gene inside the compartment. By coupling the genotype (DNA) and phenotype (RNA, protein), compartmentalization allows the selection and evolution of phenotype. Some combinations of surfactants used to generate oil-surfactant mixture are mineral oil / 0.5% Tween 80 / 4.5% Span 80 / sodium deoxycholate and a more heat stable version, light mineral oil / 0.4% Tween 80 / 4.5% Span 80 / 0.05% Triton X-100. In vitro transcription/translation; Breaking emulsion and coupling of genotype and phenotype

Host cell protein (HCPs): process-related protein impurities that are produced by the host organism during biotherapeutic manufacturing and production. During the purification process, a majority of produced HCPs are removed from the final product (>99% of impurities removed). However, residual HCPs still remain in the final distributed pharmaceutical drug. HCPs may cause immunogenicity in individuals or reduce the potency, stability or overall effectiveness of a drug. National regulatory organisations, such as the FDA and EMA provide guidelines on acceptable levels of HCPs that may remain in pharmaceutical products before they are made available to the public. Currently, the acceptable level of HCPs in pharmaceutical drugs range from 1-100ppm (1–100 ng/mg product). However, the accepted level of HCPs in a final product is evaluated on a case-by-case basis, and depends on multiple factors including: dose, frequency of drug administration, type of drug and severity of disease.

Classification, taxonomy, systematics

Category:Scientific classification

Category:Morphology

Category:Morphology (biology)

Category:Scientific nomenclature

Category:Classification systems

Category:Taxonomy

Category:Borderline life

Category:Phylogenetics {also q.v. Category:Evolutionary biology}

Template:Taxonomic ranks: Main ones: Domain, Kingdom, Phylum/Division, Class, Order, Family, Tribe, Genus, Species.

Taxonomy (biology): academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups; groups created through this process are referred to as taxa (singular taxon). Father of modern taxonomy: Carolus Linnaeus. Taxonomic descriptions; Classifying organisms: Phylogenetics and cladistics, Phenetics.

Biological classification (scientific classification in biology): method of taxonomy used to group and categorize organisms into groups such as genus or species

Systematics: study of the diversification of living forms, both past and present, and the relationships among living things through time; used to understand the evolutionary history of life on Earth.

Synonym (taxonomy): scientific name that applies to a taxon that (now) goes by a different scientific name, although zoologists use the term somewhat differently. Differences between zoology and botany.

Monophyly: "A satisfactory and comprehensive cladistic definition of a species or genus is in fact impossible, and reflects the impossibility of seamlessly impressing a gradualistic model of continual change over the 'quantum' Linnean model, where species have defined boundaries, and intermediaries between species cannot be accommodated". Then comes paraphyly, polyphyly... Quantum physics vs classical physics; (mathematical) logics vs complete & consistent

Evolutionary grade {q.v. Taxon in disguise}: in alpha taxonomy, a grade refers to a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.

Gene Ontology (GO): major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. AmiGO is a web-based application that allows users to query, browse and visualize ontologies and gene product annotation data. In addition, it also has a BLAST tool, tools allowing analysis of larger data sets, and an interface to query the GO database directly. There is a significant body of literature on the development and use of GO, and it has become a standard tool in the bioinformatics arsenal. Their objectives have three aspects: building gene ontology, assigning ontology to gene/gene products and developing software and databases for the first two objects.

Structural Classification of Proteins: SCOP, manual classification

CATH: CATH Protein Structure Classification

Organizations and nomenclature:

International Code of Zoological Nomenclature (ICZN or ICZN Code): Principles: Principle of Binominal Nomenclature, Principle of Priority, Principle of Coordination, Principle of the First Reviser, Principle of Homonymy (name of each taxon must be unique), Principle of Typification.

International Commission on Zoological Nomenclature (ICZN)

ZooBank: open access website intended to be the official ICZN (Commission) registry of zoological nomenclature; proposed: 2005; live: 2006.08.10 :: 1.5 mln species. LSIDs

International Code of Nomenclature for algae, fungi, and plants (ICN; before 2011.07: International Code of Botanical Nomenclature (ICBN))

Biological classification

{q.v. #Evolutionary biology, chemistry}

Taxonomical root node	Two superdomains (controversial)	Two empires	Three domains	Five Dominiums^[6]	Five kingdoms	Six kingdoms	Eocyte hypothesis
Biota / Vitae / Life	Acytota / Aphanobionta non-cellular life			Virusobiota (Viruses, Viroids)
	Acytota / Aphanobionta non-cellular life			Prionobiota (Prions)
	Cytota cellular life	Prokaryota / Procarya (Monera)	Bacteria	Bacteria	Monera	Eubacteria	Bacteria
		Prokaryota / Procarya (Monera)	Archaea	Archaea	Monera	Archaebacteria	Archaea including eukaryotes
		Eukaryota / Eukarya			Protista
					Fungi
					Plantae
					Animalia

Cavalier-Smith's system of classification: The classification system of life introduced by British zoologist Thomas Cavalier-Smith involves systematic arrangements of all life forms on earth. Following and improving the classification systems introduced by Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy. His classification has been a major foundation in modern taxonomy, particularly with revisions and reorganisations of kingdoms and phyla. Cavalier-Smith has published extensively on the classification of protists.

Species problem: mixture of difficult, related questions that often come up when biologists define the word "species". E.g. what works well for some organism (e.g., birds) will be useless for others (e.g., bacteria). When to recognize a new species, for example when new data indicate that one previously described species actually may include two or more separately evolving groups, each of which could possibly be recognized as a separate species. Jody Hey: "result of two conflicting motivations by biologists: 1) to categorize and identify organisms; 2) to understand the evolutionary processes that give rise to species".

Ring species: connected series of neighboring populations, each of which can interbreed with closely sited related populations, but for which there exist at least two "end" populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each "linked" species. Such non-breeding, though genetically connected, "end" populations may co-exist in the same region thus closing a "ring". Formally, the issue is that interfertile ("able to interbreed") is not a transitive relation – if A can breed with B, and B can breed with C, it does not follow that A can breed with C – and thus does not define an equivalence relation.

Template:Mammal hybrids: some are through natural and some through artificial insemination.

Three-domain system: biological classification introduced by Carl Woese et al. in 1977 that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Woese argued that, on the basis of differences in 16S rRNA genes, these two groups and the eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings, and this nomenclature was widely used until the term "domain" was adopted in 1990.

Eukaryotes

Eukaryote (Greek εὖ (eu, "well" or "true") + κάρυον (karyon, "nut" or "kernel")): any organism whose cells have a cell nucleus and other organelles enclosed within membranes. Eukaryotes belong to the domain Eukaryota or Eukarya, and can be unicellular or multicellular organisms. The defining feature that sets eukaryotic cells apart from prokaryotic cells (Bacteria and Archaea) is that they have membrane-bound organelles, especially the nucleus, which contains the genetic material enclosed by the nuclear membrane. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus. In addition, plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many kinds of tissue and cell types. Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. The domain Eukaryota appears to be monophyletic, and makes up one of the domains of life in the three-domain system. Eukaryotes evolved approximately 1.6–2.1 billion years ago, during the Proterozoic eon.

Bikont ("two flagella")

Diaphoretickes (Plants+HC+SAR megagroup): Archaeplastida; Cryptista; Haptista; SAR supergroup; Telonemia; Where Chromista is used as a taxon, its member groups all fall within Diaphoretickes.

Plants+HC clade

Archaeplastida: Red algae (Rhodophyta), Glaucophytes (glaucocystophytes), Plantae

Hacrobia (cryptomonads-haptophytes assemblage; CCTH (standing for Cryptophyta, Centrohelida, Telonemia and Haptophyta); "Eukaryomonadae"): proposed monophyletic grouping of unicellular eukaryotes that are not included in the SAR supergroup

SAR supergroup: clade that includes stramenopiles (heterokonts), alveolates, and Rhizaria.

Excavata

Apusozoa: comprising several genera of flagellate protozoa; occur in soils and aquatic habitats, where they feed on bacteria; grouped together based on the presence of an organic shell or theca under the dorsal surface of the cell.

Unikont: have a single emergent flagellum, or are amoebae with no flagella

Amoebozoa

Opisthokont

Holozoa: includes animals and their closest single-celled relatives, but excludes fungi

Mesomycetozoea (DRIP clade, or Ichthyosporea): small group of protists, mostly parasites of fish and other animals

Filozoa: monophyletic grouping; include animals along with their nearest unicellular relatives (those organisms which are more closely related to animals than to fungi or Mesomycetozoa)

Filasterea

Choanoflagellate

Metazoa or "Animalia"

Holomycota

Fungus (pl.: fungi or funguses)

Nucleariid: group of amoebae with filose pseudopods, known mostly from soils and freshwater; distinguished from the superficially similar vampyrellids mainly by having mitochondria with discoid cristae.

Incertae sedis ("of uncertain placement"; unclassified)

Template:Hacrobia (Supergroup)

SAR supergroup: clade that includes stramenopiles (heterokonts), alveolates, and Rhizaria.

Halvaria

Template:Heterokont (Heterokonta or Stramenopiles) (Supergroup)

Heterokont (Heterokonta, Heterokontae or Heterokontophyta; stramenopiles ("S")): group of protists. The group is a major line of eukaryotes. Most are algae, ranging from the giant multicellular kelp to the unicellular diatoms, which are a primary component of plankton. Other notable members of the Stramenopiles include the (generally) parasitic oomycetes, including Phytophthora, which caused the Great Famine of Ireland, and Pythium, which causes seed rot and damping off.

Ochrophyta: group of mostly photosynthetic heterokonts. Their plastid is of red algal origin.

Brown algae (Phaeophyceae): large group of multicellular algae, including many seaweeds located in colder waters within the Northern Hemisphere. Brown algae are the major seaweeds of the temperate and polar regions. They are dominant on rocky shores throughout cooler areas of the world. Most brown algae live in marine environments, where they play an important role both as food and as a potential habitat. For instance, Macrocystis, a kelp of the order Laminariales, may reach 60 m in length and forms prominent underwater kelp forests. Kelp forests like these contain a high level of biodiversity. Another example is Sargassum, which creates unique floating mats of seaweed in the tropical waters of the Sargasso Sea that serve as the habitats for many species. Many brown algae, such as members of the order Fucales, commonly grow along rocky seashores. Some members of the class, such as kelps, are used by humans as food. Brown algae are unique among heterokonts in developing into multicellular forms with differentiated tissues, but they reproduce by means of flagellated spores and gametes that closely resemble cells of other heterokonts. Genetic studies show their closest relatives to be the yellow-green algae.

Stramenopile: clade of organisms distinguished by the presence of stiff tripartite external hairs. In most species, the hairs are attached to flagella, in some they are attached to other areas of the cellular surface, and in some they have been secondarily lost (in which case relatedness to stramenopile ancestors is evident from other shared cytological features or from genetic similarity). Stramenopiles represent one of the three major clades in the SAR supergroup, along with Alveolata and Rhizaria. History and the Heterokont problem.

Template:Alveolata (Supergroup) Alveolate

Acavomonidia
Ciliophora (Ciliates)
Colponemidia
Myzozoa

Alveolate (Alveolata; meaning "with cavities"): group of protists, considered a major clade and superphylum within Eukarya.

Ciliate (Ciliophora): group of protozoans characterized by the presence of hair-like organelles called cilia, which are identical in structure to eukaryotic flagella, but are in general shorter and present in much larger numbers, with a different undulating pattern than flagella. Cilia occur in all members of the group (although the peculiar Suctoria only have them for part of their life-cycle) and are variously used in swimming, crawling, attachment, feeding, and sensation. Ciliates are an important group of protists, common almost anywhere there is water — in lakes, ponds, oceans, rivers, and soils. About 4,500 unique free-living species have been described, and the potential number of extant species is estimated at 27,000–40,000.

Myzozoa

Apicomplexa: large phylum of parasitic alveolates. Most of them possess a unique form of organelle that comprises a type of plastid called an apicoplast, and an apical complex structure. The organelle is an adaptation that the apicomplexan applies in penetration of a host cell. The Apicomplexa are unicellular and spore-forming. All species are obligate endoparasites of animals, except Nephromyces, a symbiont in marine animals, originally classified as a chytrid fungus. Motile structures such as flagella or pseudopods are present only in certain gamete stages. Malaria (Plasmodium), Toxoplasmosis (Toxoplasma gondii)

Template:Rhizaria (Supergroup)

Rhizaria: vary considerably in form, but for the most part they are amoeboids with filose, reticulose, or microtubule-supported pseudopods; many produce shells or skeletons, which may be quite complex in structure, and these make up the vast majority of protozoan fossils. Nearly all have mitochondria with tubular cristae.

Template:Amoebozoa (Supergroup)

Amoebozoa: pseudopodia are characteristically blunt and finger-like, called lobopodia

Template:Opisthokont protists (Opisthokonta) (Supergroup) = Animal + Fungi

Opisthokont (Choanozoa; "Fungi/Metazoa group"; ὀπίσθιος (opísthios) = "rear, posterior" + κοντός (kontós) = "pole" i.e. "flagellum"): broad group of eukaryotes, including both the animal and fungus kingdoms, together with the eukaryotic microorganisms that are sometimes grouped in the paraphyletic phylum Choanozoa (conventionally assigned to the protist "kingdom"); generally recognized as a monophyletic clade, and it is thought to be a basal Obazoa clade, sister of the Apusomonadida – Breviata clade. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants, because opisthokonts have a triple fusion of carbamoyl phosphate synthetase, dihydroorotase, and aspartate carbamoyltransferase that is not present in plants, and plants have a fusion of thymidylate synthase and dihydrofolate reductase not present in the opisthokonts. Animals and fungi are also more closely related to amoebas than they are to plants, and plants are more closely related to the SAR supergroup of protists than they are to animals or fungi. Animals and fungi are both heterotrophs, unlike plants, and while fungi are sessile like plants, there are also sessile animals.

Template:Excavata

Discoba
- Discicristata
  - Euglenozoa
  - Percolozoa
- Jakobea
- Tsukubamonada
Loukozoa (+ Ancyromonads)

Excavate (Excavata): major subgroup of unicellular eukaryotes; introduced by Thomas Cavalier-Smith in 2002 as a new phylogenetic category, it contains a variety of free-living and symbiotic forms, and also includes some important parasites of humans. Excavates were formerly considered to be included in the now obsolete Protista kingdom. They are classified based on their flagellar structures, and they are considered to be the oldest members (basal lineage) of flagellated organisms. Discoba or JEH (Tsukubea, Euglenozoa, Heterolobosea (Percolozoa), Jakobea), Metamonada or POD (Preaxostyla, Fornicata, Parabasalia), Neolouka (Malawimonas). Excavate relationships are still uncertain; it is possible that they are not a monophyletic group.

Euglenozoa

Protozoa, protista, single cell eukaryotes

Obsolete:

Protist: any eukaryotic organism that is not an animal, plant or fungus. The protists do not form a natural group, or clade, but are often grouped together for convenience, like algae or invertebrates. In cladistic systems, there are no equivalents to the taxa Protista or Protoctista, both terms referring to a paraphyletic group which spans the entire eukaryotic tree of life. In cladistic classification, the contents of Protista are distributed among various supergroups (SAR, Archaeplastida, Excavata, Opisthokonta, etc.) and "Protista", Protoctista and "Protozoa" are considered obsolete.

Chromalveolata: eukaryote supergroup present in a major classification of 2005, then regarded as one of the six major groups within the eukaryotes. It is a refinement of the kingdom Chromista, first proposed by Thomas Cavalier-Smith in 1981. Chromalveolata was proposed to represent the organisms descended from a single secondary endosymbiosis involving a red alga and a bikont. The plastids in these organisms are those that contain chlorophyll c. However, the monophyly of the Chromalveolata has been increasingly challenged. Thus, two papers published in 2008 have phylogenetic trees in which the chromalveolates are split up, and recent studies continue to support this view.

Protozoa: informal term for single-celled eukaryotes, either free-living or parasitic, which feed on organic matter such as other microorganisms or organic tissues and debris. Historically, the protozoa were regarded as "one-celled animals", because they often possess animal-like behaviors, such as motility and predation, and lack a cell wall, as found in plants and many algae. Although the traditional practice of grouping of protozoa with animals is no longer considered valid, the term continues to be used in a loose way to identify single-celled organisms that can move independently and feed by heterotrophy. Modern ultrastructural, biochemical, and genetic techniques have shown that protozoa, as traditionally defined, belong to widely divergent lineages distributed across the eukaryotic tree of life, and can no longer be regarded as "primitive animals". For this reason, the terms "protists", "Protista" or "Protoctista" are sometimes preferred for the high-level classification of eukaryotic microorganisms.

Radiolaria (Radiozoa): protozoa of diameter 0.1–0.2 mm that produce intricate mineral skeletons, typically with a central capsule dividing the cell into the inner and outer portions of endoplasm and ectoplasm. The elaborate mineral skeleton is usually made of silica. They are found as zooplankton throughout the global ocean. As zooplankton, radiolarians are primarily heterotrophic, but many have photosynthetic endosymbionts and are, therefore, considered mixotrophs. The skeletal remains of some types of radiolarians make up a large part of the cover of the ocean floor as siliceous ooze. Due to their rapid change as species and intricate skeletons, radiolarians represent an important diagnostic fossil found from the Cambrian onwards.

Provora: proposed supergroup of eukaryotes made up of predatory microbes, "devouring voracious protists". It was reported that ten strains were isolated and cultured in 2022. They are predators of other microorganisms. Their discovery was very delayed, compared to other microorganisms in their environments, due to their rarity. Their 18S is very different from that of other eukaryotes, thus they were taxonomically placed in a separate supergroup.

Organelles

Category:Organelles

{q.v. #Protein complexes}

Archæplastida

Excavata

Chromalveolata

Rhizaria ^a

Paulinella

Edit

acetyl-CoA carboxylase

replication origin regions

tRNA

small RNA

ribosomal protein

replication origin regions

atp-dependent protease

ribosomal proteins

tRNAs

nicotiana tabacum

edit · image

Plastid: major double-membrane organelle found in the cells of plants, algae, and some other eukaryotic organisms. Plastids are the site of manufacture and storage of important chemical compounds used by the cell. They often contain pigments used in photosynthesis, and the types of pigments present can change or determine the cell's color. Most plants inherit the plastids from only one parent. In general, angiosperms inherit plastids from the female gamete, whereas many gymnosperms inherit plastids from the male pollen. Algae also inherit plastids from only one parent. The plastid DNA of the other parent is, thus, completely lost.

Chloroplast: organelles, specialized compartments, in plant and algal cells; main role of chloroplasts is to conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight and converts it and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat.

Biomolecular condensate: class of non-membrane bound organelles and organelle subdomains. As with other organelles, biomolecular condensates are specialized subunits of the cell. However, unlike many organelles, biomolecular condensate composition is not controlled by a bounding membrane. Instead they can form through a range of different processes, the most well-known of which is phase separation of proteins, RNA and other biopolymers into colloids, liquid crystals, solid crystals or aggregates.

Health care

Category:Health care

Category:Health care industry

Category:Pharmaceutical industry

Category:Pharmaceutics

Category:Pharmacology

Drug design (rational drug design): inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves the design of molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it. Drug design frequently but not necessarily relies on computer modeling techniques. This type of modeling is sometimes referred to as computer-aided drug design. Finally, drug design that relies on the knowledge of the three-dimensional structure of the biomolecular target is known as structure-based drug design.

Fragment-based lead discovery (FBLD; fragment-based drug discovery, FBDD): identifying small chemical fragments, which may bind only weakly to the biological target, and then growing them or combining them to produce a lead with a higher affinity.

Pharmaceutics, Pharmacology

Category:Pharmacology

Category:Drugs

Category:Biopharmaceuticals

Category:Drug safety

Category:Pharmaceutical industry

Category:Drug discovery

Category:Pharmacokinetics

Category:Pharmacology literature

Category:Pharmacopoeias

Category:Pharmaceutics

Category:Clinical research

Category:Medical manuals

Category:Pharmacopoeias

Category:Medical literature

Category:Pharmacopoeias

{q.v. User:Kazkaskazkasako/Books/Physical sciences#Medicinal chemistry}

Pharmacopoeia (from the obsolete typography pharmacopœia, literally, “drug-making”): book containing directions for the identification of compound medicines, and published by the authority of a government or a medical or pharmaceutical society. History: major initial works in the field are considered to be the Edwin Smith Papyrus in Egypt, Pliny’s pharmacopoeia and De Materia Medica (Περὶ ὕλης ἰατρικῆς), a five-volume book originally written in Greek by Pedanius Dioscorides. The latter is considered to be precursor to all modern pharmacopoeias, and is one of the most influential herbal books in history. In fact it remained in use until about CE 1600. The Canon of Medicine of Avicenna in 1025, and works by Ibn Zuhr (Avenzoar) in the 12th century (and printed in 1491), and Ibn Baytar in the 14th century. The Shen-nung pen ts'ao ching (Divine Husbandman's Materia Medica) is the earliest known Chinese pharmacopoeia. City pharmacopoeia origins. London; National pharmacopoeia origins; Supranational and international harmonization (EU, Japan, USA, WHO). Medical preparations, uses, and dosages. List of national and supranational pharmacopoeias.

Martindale: The Complete Drug Reference: listing some 6,000 drugs and medicines used throughout the world, including details of over 180,000 proprietary preparations. It also includes almost 700 disease treatment reviews.

International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH): project that brings together the regulatory authorities of Europe, Japan and USA and experts from the pharmaceutical industry in the three regions to discuss scientific and technical aspects of pharmaceutical product registration; reduce or eliminate the need to duplicate the testing carried out during the research and development of new medicines by recommending ways to achieve greater harmonisation in the interpretation and application of technical guidelines and requirements for product registration. Harmonisation would lead to a more economical use of human, non-human animal and material resources, and the elimination of unnecessary delay in the global development and availability of new medicines while maintaining safeguards on quality, safety, and efficacy, and regulatory obligations to protect public health.

International Society for Pharmacoepidemiology (ISPE): launched officially by Stanley A. Edlavitch, David E. Lilienfeld, and Hugh A. Tilson in 1989 during the Fifth International Conference on Pharmacoepidemiology (ICPE) in Minneapolis. ISPE is the only international acting society dealing with the topics of pharmacoepidemiology in the context of pharmacovigilance or drug safety; the International Society for Pharmacoeconomics and Outcomes Research (ISPOR) addresses outcomes research epidemiology. The society has organized yearly conferences since its foundation. The society's office is located in Bethesda, Maryland, and its executive director is Mark Epstein. A number of the major figures in drug safety and pharmacovigilance have served as its Presidents, and its Officers and Trustees have been drawn from the leadership of the pharmacoepidemiology community.

Parenteral Drug Association (PDA): international non-profit industry trade group for pharmaceutical and biopharmaceutical manufacturers headquartered in Bethesda, MD, USA, with offices in Berlin, Germany, and Singapore. Leading global provider of science, technology, regulatory information, and education for the bio/pharmaceutical community. Since its founding as a non-profit in 1946, PDA has been committed to developing scientifically sound, practical technical information and resources to advance science and regulation through the expertise of our more than 10,500 members worldwide.

Biopharmaceutical (biologic(al) medical product, biologic): any pharmaceutical drug product manufactured in, extracted from, or semisynthesized from biological sources. Different from totally synthesized pharmaceuticals, they include vaccines, whole blood, blood components, allergenics, somatic cells, gene therapies, tissues, recombinant therapeutic protein, and living medicines used in cell therapy. Biologics can be composed of sugars, proteins, nucleic acids, or complex combinations of these substances, or may be living cells or tissues. They (or their precursors or components) are isolated from living sources—human, animal, plant, fungal, or microbial. They can be used in both human and animal medicine. Some regulatory agencies use the terms biological medicinal products or therapeutic biological product to refer specifically to engineered macromolecular products like protein- and nucleic acid-based drugs, distinguishing them from products like blood, blood components, or vaccines, which are usually extracted directly from a biological source. Biopharmaceutics is pharmaceutics that works with biopharmaceuticals. Biopharmacology is the branch of pharmacology that studies biopharmaceuticals.

Excipient: substance formulated alongside the active ingredient of a medication, included for the purpose of long-term stabilization, bulking up solid formulations that contain potent active ingredients in small amounts (thus often referred to as "bulking agents", "fillers", or "diluents"), or to confer a therapeutic enhancement on the active ingredient in the final dosage form, such as facilitating drug absorption, reducing viscosity, or enhancing solubility. Excipients can also be useful in the manufacturing process, to aid in the handling of the active substance concerns such as by facilitating powder flowability or non-stick properties, in addition to aiding in vitro stability such as prevention of denaturation or aggregation over the expected shelf life. The selection of appropriate excipients also depends upon the route of administration and the dosage form, as well as the active ingredient and other factors. Often, more excipient is found in a final drug formulation than active ingredient, and practically all marketed drugs contain excipients. Relative versus absolute inactivity: in basic research and clinical trials excipients are sometimes included in the control substances in order to minimize confounding, reflecting that otherwise, the absence of the active ingredient would not be the only variable involved, because absence of excipient cannot always be assumed not to be a variable; Such studies are called excipient-controlled or vehicle-controlled studies.

Experiments, research, laboratory

Category:Experiments

Category:Research

In vitro

In vivo

In silico: "performed on computer or via computer simulation"

Laboratory (lab)

Wet laboratory (wet lab)

Lab-on-a-chip

Society for Laboratory Automation and Screening (SLAS): formed in 2010 as a merger between the Association for Laboratory Automation and the Society for Biomolecular Sciences. SLAS is a global organization that exists to provide forums for education and information exchange to encourage the study of, and improve the science and practice of, laboratory automation and screening.

Journal of Laboratory Automation (1996-): bimonthly peer-reviewed scientific journal published by SLAS; covers a wide range of technologies including sample processing (liquid handling, sample storage, sample analysis, and system integration), microfluidics (design, applications, and integration), and informatics (data acquisition and management, electronic laboratory notebooks, and integration).

Journal of Biomolecular Screening: peer-reviewed scientific journal published by SAGE Publications on behalf of SLAS; covers scientific and technical applications and advances in areas such as lab automation and robotics, virtual screening, and high throughput screening.

Operant conditioning chamber (Skinner box): laboratory apparatus used in the experimental analysis of behavior to study animal behavior.

Long-term experiment: runs through a long period of time, in order to test a hypothesis or observe a phenomenon that takes place at an extremely slow rate. Several agricultural field experiments have run for more than 100 years, but much shorter experiments may qualify as "long-term" in other disciplines.

Scientific equipment, laboratory equipment

Category:Scientific equipment

Category:Laboratory equipment

Category:Laboratory equipment manufacturers

Bruker Corporation: USA manufacturer of scientific instruments for molecular and materials research, as well as for industrial and applied analysis. The company was founded in 1960.09.07, in Karlsruhe, Germany as Bruker-Physik AG by five people, one of them being Günther Laukien, who was a professor at the University of Karlsruhe at the time. The name Bruker originates from co-founder Emil Bruker, as Günther Laukien himself was formally not allowed to commercialize his research whilst being a professor. Bruker produced Nuclear Magnetic Resonance Spectroscopy (NMR) and EMR spectroscopy equipment then.

Scientific modeling, artificial life

Category:Scientific modelling

Category:Artificial life

Category:Artificial life models

Category:Digital organisms

Category:Self-replication

Category:Virtual pets

Category:Notation {q.v. User:Kazkaskazkasako/Books/All#Systems science, systems}

{q.v.

} Biological systems, ecosystems, engineering and scientifically modeled systems are complex systems at the intersection of EECS, physical and life sciences. 3D printing in various senses, from plastics to cell printing. Data science and machine learning deal with these complex systems and huge amounts of data. Artificial intelligence.

OpenWorm: international open science project to simulate the roundworm Caenorhabditis elegans at the cellular level in silico. Although the long term goal is to model all 959 cells of the C. elegans, the first stage is to model the worm's locomotion by simulating the 302 neurons and 95 muscle cells.

WormBase: online biological database about the biology and genome of C. elegans and contains information about other related nematodes. Sequence curation: Genome sequence; Gene structure models (Gene prediction programs give a reasonable set of gene structures, but the best of them only predict about 80% of the complete gene structures correctly. They have difficulty predicting genes with unusual structures, as well as those with a weak translation start signal, weak splice sites or single exon genes. They can incorrectly predict a coding gene model where the gene is a pseudogene and they predict the isoforms of a gene poorly, if at all.);

WormBook: open access, comprehensive collection of original, peer-reviewed chapters covering topics related to the biology of the nematode worm C. elegans.

Xenobot: named after the African clawed frog (Xenopus laevis), are synthetic lifeforms that are designed by computers to perform some desired function and built by combining together different biological tissues. Xenobots built to date have been less than 1 millimeter (0.039 inches) wide and composed of just two things: skin cells and heart muscle cells, both of which are derived from stem cells harvested from early (blastula stage) frog embryos. Xenobots have been designed to walk, swim, push pellets, carry payloads, and work together in a swarm to aggregate debris scattered along the surface of their dish into neat piles. They can survive for weeks without food and heal themselves after lacerations.

Self-replication

{q.v.

}

Biology: self replication with error (evo-devo) is life.

Cognition

Category:Cognition

Category:Cognitive science

Category:Heuristics

Category:Problem solving

Category:Decision-making

Category:Decision theory

Cognition: "the mental action or process of acquiring knowledge and understanding through thought, experience, and the senses". It encompasses many aspects of intellectual functions and processes such as: attention, the formation of knowledge, memory and working memory, judgment and evaluation, reasoning and "computation", problem solving and decision making, comprehension and production of language. Cognitive processes use existing knowledge and generate new knowledge. Cognitive processes are analyzed from different perspectives within different contexts, notably in the fields of linguistics, anesthesia, neuroscience, psychiatry, psychology, education, philosophy, anthropology, biology, systemics, logic, and computer science → cognitive science. Psychology: Piaget's theory of cognitive development. Metacognition. Improving cognition: Physical exercise, Dietary supplements, Pleasurable social stimulation, Other methods.

Satisficing: decision-making strategy or cognitive heuristic that entails searching through the available alternatives until an acceptability threshold is met. The term satisficing, a portmanteau of satisfy and suffice, was introduced by Herbert A. Simon in 1956, although the concept was first posited in his 1947 book Administrative Behavior. Simon used satisficing to explain the behavior of decision makers under circumstances in which an optimal solution cannot be determined. He maintained that many natural problems are characterized by computational intractability or a lack of information, both of which preclude the use of mathematical optimization procedures. He observed in his Nobel Prize in Economics speech that "decision makers can satisfice either by finding optimum solutions for a simplified world, or by finding satisfactory solutions for a more realistic world. Neither approach, in general, dominates the other, and both have continued to co-exist in the world of management science".

Cognitive science, cognitive neuroscience

Category:Cognitive science

Category:Cognitive neuroscience

Category:Mental processes

Category:Thought

Category:Magical thinking

Category:Psycholinguistics

Category:Attention

Category:Neuropsychology

Category:Neuropsychological assessment

Category:Memory

Cognitive science: interdisciplinary scientific study of the mind and its processes; includes research on intelligence and behavior, especially focusing on how information is represented, processed, and transformed (in faculties such as perception, language, memory, reasoning, and emotion) within nervous systems (human or other animal) and machines (e.g. computers). Multiple research disciplines, including psychology, artificial intelligence, philosophy, neuroscience, linguistics, and anthropology.

Computational neuroscience (theoretical neuroscience): study of brain function in terms of the information processing properties of the structures that make up the nervous system. It is an interdisciplinary science that links the diverse fields of neuroscience, cognitive science, and psychology with EECS, mathematics, and physics. Computational neuroscience is distinct from psychological connectionism and from learning theories of disciplines such as machine learning, neural networks, and computational learning theory in that it emphasizes descriptions of functional and biologically realistic neurons (and neural systems) and their physiology and dynamics. Major topics: Single-neuron modeling; Development, axonal patterning, and guidance; Sensory processing; Memory and synaptic plasticity; Behaviors of networks (connections are, unlike most ANNs, sparse and usually specific); Cognition, discrimination, and learning; Consciousness; Computational clinical neuroscience.

Center for Applied Rationality: organisation based in the San Francisco Bay Area, Berkeley, CA whose focus is to "[take] the results of cognitive science research, and turn them into techniques that people can practice and use in their own lives." It was created in mid-2012, by Julia Galef a statistician, writer, and prominent figure in the skeptic movement, Anna Salamon, an ex-researcher from NASA and the Machine Intelligence Research Institute, and two Mathematics PhD holders, Michael Smith and Andrew Critch. CFAR develops and tests strategies of cognitive tools and triggers that are known from research in the field of cognitive science on how people form and change their beliefs.

Autobiographical memory: memory system consisting of episodes recollected from an individual's life, based on a combination of episodic (personal experiences and specific objects, people and events experienced at particular time and place) and semantic (general knowledge and facts about the world) memory. Event-specific knowledge (ESK) is vividly detailed information about individual events, often in the form of visual images and sensory-perceptual features. Originating events (events that mark the beginning of a path towards long-term goals), turning points (events that re-direct plans from original goals), anchoring events (events that affirm an individuals beliefs and goals) and analogous events (past events that direct behaviour in the present) are all event specific memories that will resist memory decay. The sensory-perceptual details held in ESK, though short-lived, are a key component in distinguishing memory for experienced events from imagined events. Unlike lifetime periods and general events, ESK are not organized in their grouping or recall; instead, they tend to simply 'pop' into the mind. Remember vs. Know: source of a remembered memory is attributed to personal experience; source of a known memory is attributed to an external source, not personal memory.

Source-monitoring error: type of memory error where a specific recollected experience is incorrectly determined to be the source of a memory. These errors are most prevalent in elderly individuals and young children.

Remember versus know judgements: different processes are involved in remembering something versus knowing whether it is familiar.

Neural correlates of consciousness (NCC): constitute the minimal set of neuronal events and mechanisms sufficient for a specific conscious percept. Neuroscientists use empirical approaches to discover neural correlates of subjective phenomena; that is, neural changes which necessarily and regularly correlate with a specific experience. Neurobiological approach to consciousness. Level of arousal and content of consciousness. The neuronal basis of perception. Global disorders of consciousness. Forward versus feedback projections.

Software, internet, databases

{q.v.

}

Academic, research, science games:

NanoMission: serious game by PlayGen for Wellcome Trust and FEI in order to teach the player about the world of nanomedicine. Advergame

Computations, CS, IT, bioinformatics (BioInfo), computational biology (Comp Bio)

Critical Assessment of Prediction of Interactions

Critical Assessment of Techniques for Protein Structure Prediction

PHYLIP ((PHYLogeny Inference Package)): free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies).

Open Bioinformatics Foundation: BioPython

Bioconductor: based on statistical R programming language

List of mass spectrometry software: Proteomics software; Database search algorithms; De novo sequencing algorithms; Homology searching algorithms; MS/MS peptide quantification.

Bioinformatics

Category:Bioinformatics

Category:Phylogenetics

Category:Metagenomics

Category:Bioinformatics

Category:Mathematical and theoretical biology

Category:Systems biology

Category:Biological systems

Category:Computational science

{q.v. }@ecosystems (SYSTEMS)

Genome Reference Consortium (GRC): international collective of academic and research institutes with expertise in genome mapping, sequencing, and informatics, formed to improve the representation of reference genomes. At the time the human reference (Human Genome Project) was initially described, it was clear that some regions were recalcitrant to closure with existing technology. Initially the focus lies with the Human and the Mouse reference genomes, but in mid-late 2010 full maintenance and improvement of the Zebrafish genome sequence was also added to the GRC. The goal of the Consortium is to correct the small number of regions in the reference that are currently misrepresented, to close as many remaining gaps as possible and to produce alternative assemblies of structurally variant loci when necessary. 2015.06 the major assembly release for human, mouse and zebrafish are GRCh38, GRCm38 and GRCz10 respectively.

Multiple sequence alignment (MSA): sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.

Clustal: widely used MSA program. ClustalW: command line; ClustalX: GUI; Clustal Omega: increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours (command line, protein-only).

Stockholm format: MSA format used by Pfam and Rfam to disseminate protein and RNA sequence alignments

Chemistry Development Kit (CDK; GNU LGPL; Java): library for Chemoinformatics and Bioinformatics. Wrappers: Python, Ruby.

Pfam: database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. Clans: Over time both sequence and residue coverage have increased, and as families have grown, more evolutionary relationships have been discovered, allowing the grouping of families into clans. Clans were first introduced to the Pfam database in 2005. They are groupings of related families that share a single evolutionary origin, as confirmed by structural, functional, sequence and HMM comparisons. {q.v. TrEMBL}

Rfam: database containing information about ncRNA families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the EBI. Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. These MSAs become more useful with the addition of secondary structure information

General feature format (.GFF): file format used for describing genes and other features of DNA, RNA and protein sequences.

Metagenomics (environmental genomics, ecogenomics, community genomics): study of genetic material recovered directly from environmental samples. Early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before. Recent studies use either "shotgun" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities.

Orphan gene (ORFans, especially in microbial literature): genes without detectable homologues in other lineages. Orphan genes differ in that they are lineage-specific with no known history of shared duplication and rearrangement outside of their specific species or clade.

Modelling biological systems (theoretical biology, dry biology, biomathematics): significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems, including cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks), to both analyze and visualize the complex connections of these cellular processes. Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.

Artificial life (ALife or A-Life): field of study wherein researchers examine systems related to natural life, its processes, and its evolution, through the use of simulations with computer models, robotics, and biochemistry. The discipline was named by Christopher Langton, an American theoretical biologist, in 1986. In 1987 Langton organized the first conference on the field, in Los Alamos, New Mexico. There are three main kinds of alife, named for their approaches: soft from software, hard from hardware, wet from biochemistry. Artificial life researchers study traditional biology by trying to recreate aspects of biological phenomena.

Homology modeling (comparative modeling): constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template").

Deep biosphere: part of the biosphere that resides below the first few meters of the surface. It extends down at least 5 kilometers below the continental surface and 10.5 kilometers below the sea surface, at temperatures that may reach beyond 120 °C which is comparable to the maximum temperature where a metabolically active organism has been found. It includes all three domains of life and the genetic diversity rivals that on the surface. The first indications of deep life came from studies of oil fields in the 1920s, but it was not certain that the organisms were indigenous until methods were developed in the 1980s to prevent contamination from the surface. Samples are now collected in deep mines and scientific drilling programs in the ocean and on land. Deep observatories have been established for more extended studies. There is very little energy at greater depths, so metabolisms are up to a million times slower than at the surface. Cells may live for thousands of years before dividing and there is no known limit to their age. The term is "surface chauvinism". Gold wrote, "In retrospect, it is not hard to understand why the scientific community has typically sought only surface life in the heavens. Scientists have been hindered by a sort of 'surface chauvinism.'". Deep underground mines, for example South African gold mines and the Pyhäsalmi copper and zinc mine in Finland, have provided opportunities to sample the deep biosphere.

Bioinformatics software

Category:Bioinformatics software

{q.v.

}

Databases (DBs), classification, data files: phys, chem, bio, ...

Category:Biological databases

{q.v. #Sequencing and interpretation, genomes, human genomes}

Biocurator (scientific curators, data curators or annotators): professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases. Employ shared biomedical ontologies; consistent use of nomenclatures (e.g. HUGO, IUBMB: EC number). International Society for Biocuration (ISB) was founded in 2008.

Bioinformatic Harvester: uses many DBs to gather bio/chem/(phys) data

Enzyme Commission number (EC number; enzyme nomenclature): numerical classification scheme for enzymes, based on the chemical reactions they catalyze; every EC number is associated with a recommended name for the corresponding enzyme-catalyzed reaction. EC numbers do not specify enzymes but enzyme-catalyzed reactions. If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number. Furthermore, through convergent evolution, completely different protein folds can catalyze an identical reaction (these are sometimes called non-homologous isofunctional enzymes) and therefore would be assigned the same EC number. By contrast, UniProt identifiers uniquely specify a protein by its amino acid sequence.

RefSeq (Reference Sequence): open access, annotated and curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products; built by NCBI, provides only a single record for each natural biological molecule (i.e. DNA, RNA or protein) for major organisms ranging from viruses to bacteria to eukaryotes. NC: Complete genomic molecules; NG: Incomplete genomic region; NM: mRNA; NR: ncRNA; NP: Protein; XM: predicted mRNA model; XR: predicted ncRNA model; XP: predicted Protein model (eukaryotic sequences); WP: predicted Protein model (prokaryotic sequences).

Entrez: federated search engine over many DBs: PubMed (Medline, PubMed Central), OMIM & OMIA, (Nucleotide (SNP, Gene, HomoloGene, Genome), Taxonomy, Protein, Structure), many other

Mendelian Inheritance in Man (OMIM): diseases with genetic component (nature vs. nurture), links to genes in human genome

BLAST (Basic Local Alignment Search Tool): Bio-sequences: protein, nucleotides (DNA (genomic), RNA). Algorithm, scoring matrix, "training" the algorithm.

UniProt (Universal Protein resource; launched in 2003.12): comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. In 2002, these joined forces as UniProt Consortium: European Bioinformatics Institute (EBI (UK), @EMBL) + the Swiss Institute of Bioinformatics (SIB) + Protein Information Resource (PIR (US)). SIB: ExPASy; PIR (@Georgetown University Medical Center in Washington, DC, USA): Margaret Dayhoff's Atlas of Protein Sequence and Structure, first published in 1965.

UniProtKB (UniProt Knowledgebase):

UniProtKB/Swiss-Prot: contains reviewed, manually annotated entries by biocurators. Aim: to provide all known relevant information about a particular protein.

UniProtKB/TrEMBL: contains unreviewed, automatically annotated entries; introduced in response to increased dataflow resulting from genome projects, as the time- and labour-consuming manual annotation process of UniProtKB/Swiss-Prot could not be broadened to include all available protein sequences.

UniParc (UniProt Archive): comprehensive and non-redundant database, which contains all the protein sequences from the main, publicly available protein sequence databases. Identical sequences are merged, regardless of whether they are from the same or different species. Each sequence is given a stable and unique identifier (UPI), making it possible to identify the same protein from different source databases. UniParc contains only protein sequences, with no annotation.

UniRef (UniProt Reference Clusters): consists of three databases of clustered sets of protein sequences from UniProtKB and selected UniParc records: UniRef100 (identical sequences, 100% sequence identity), UniRef90 (at least 90%), UniRef50 (at least 50% sequence identity). This clustering of sequences enables faster sequence searches and reduces DB size.

UniMes (UniProt Metagenomic and Environmental Sequences): metagenomic and environmental data.

Other UniProt related:

ExPASy: proteomics: sequence (domains), structure (functional sites), protein families, 2D gel electrophoresis analysis. By SIB; collaborates with EMBL-EBI.

NeXtProt: knowledge platform on human proteins; comprehensive resource that provides a variety of types of information on human proteins, such as their function, subcellular location, expression, interactions and role in diseases. Major part of the information obtained from the UniProt Swiss-Prot database, but gradually being complemented by data originating from high-throughput studies with an emphasis on proteomics

BRENDA (BRaunschweig ENzyme DAtabase): enzymes

International HapMap Project: organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation.

HUGO Gene Nomenclature Committee (HGNC) {http://www.genenames.org/}: approves a unique and meaningful name for every known human gene based on a query of experts. In addition to a long name, the HGNC also assigns an abbreviation (referred to as symbol) to every gene.

Information Hyperlinked over Proteins: (iHOP) genes, proteins, RNA as hyperlinks in PubMed abstracts

KEGG: collection of DBs: genomes, enzymatic pathways , biological chemicals ("pathway intermediates")

WikiPathways: community resource for contributing and maintaining content dedicated to biological pathways. built using MediaWiki software, a custom graphical pathway editing tool (PathVisio) and integrated BridgeDb databases covering major gene, protein, and metabolite systems.

Protein Information Resource: PIR; bioinfo DB: genomic and proteomic (+RNA?)

Ensembl: the ultimate resource to genomes, genomics and genetics. Retrieval of genomic information

Vertebrate and Genome Annotation Project (Vega): annotated genomes of human, mouse, zebrafish, pig, dog. Built upon Ensembl

Protein Data Bank (PDB): 3D structural data repository of large (bio)molecules, e.g. DNA, RNA, protein, sugars, lipids (small inorganics are excluded). X-ray, NMR, EM, hybrid data. File format. Classification projects: Gene Ontology, SCOP, CATH.

Crystallographic Information File: standard text file format for representing crystallographic information, promulgated by IUCr. Closely related is mmCIF, macromolecular CIF, which is intended as an alternative to PDB file format. Also closely related is Crystallographic Information Framework, a broader system of exchange protocols based on data dictionaries and relational rules expressible in different machine-readable manifestations, including, but not restricted to, Crystallographic Information File and XML.

EM Data Bank (Electron Microscopy Data Bank (EMDB)): from 2011.12.20 EMDB joined PDB archive.

Worldwide Protein Data Bank (wwPDB): organization that maintains the archive of macromolecular structure; mission: to maintain a single PDB Archive of macromolecular structural data that is freely and publicly available to the global community. 4 members: Research Collaboratory for Structural Bioinformatics Protein Database (RCSB PDB), Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj), Biological Magnetic Resonance Data Bank (BMRB).

Orientations of Proteins in Membranes database (OPM) {http://opm.phar.umich.edu/}: spatial positions of membrane protein structures with respect to the lipid bilayer. However, structures of many membrane-associated proteins are not included in the database if they can not be computationally predicted.

Ki Database: binding affinities (K_i) of chemical compounds for biomacromolecules (proteins: receptors, transporters, ion channels, enzymes)

OvidSP: health science DBs search interface

InterPro {http://www.ebi.ac.uk/interpro/}: database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them; signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models) which describe protein families, domains or sites.

Pfam ↑

PRINTS: collection of so-called "fingerprints"; provides both a detailed annotation resource for protein families, and a diagnostic tool for newly-determined sequence.

TIGRFAMs: database of protein families designed to support manual and automated genome annotation.

Superfamily database (SUPERFAMILY; {http://supfam.org/SUPERFAMILY/}): database of structural and functional annotation for all proteins and genomes

PROSITE {http://prosite.expasy.org/}: entries describing the protein families, domains and functional sites as well as amino acid patterns, signatures, and profiles in them; manually curated by a team of the Swiss Institute of Bioinformatics and tightly integrated into Swiss-Prot protein annotation

Transporter Classification database (TCDB): IUBMB approved classification system for membrane transport proteins including ion channels; designed to be analogous to the EC number system for classifying enzymes, but it also uses phylogenetic information.

GeneCards: database of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes; developed and maintained by the Crown Human Genome Center at the Weizmann Institute of Science.

Human Protein Atlas (HPA): Swedish-based program started in 2003 with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. The version 18 (2017.12.01) consists of three separate parts, each focusing on a particular aspect of the genome-wide analysis of the human proteins; the Tissue Atlas showing the distribution of the proteins across all major tissues and organs in the human body, the Cell Atlas showing the subcellular localization of proteins in single cells, and finally the new Pathology Atlas showing the impact of protein levels for survival of patients with cancer.

Tissue Atlas: contains information regarding the expression profiles of human genes both on the mRNA and protein level. The protein expression data is derived from antibody-based protein profiling using immunohistochemistry. Altogether 76 different cell types, corresponding to 44 normal human tissue types, have been analyzed and the data is presented as pathology-based annotation of protein expression levels. All underlying images of immunohistochemistry stained normal tissues are available as high-resolution images in the normal tissue atlas.
Cell Atlas: provides high-resolution insights into the spatial distribution of proteins within cells. The protein expression data is derived from antibody-based profiling using immunofluorescence confocal microscopy. A panel of 56 cell lines, selected to represent various cell populations in different organs of the human body, forms the basis of the Cell Atlas. In this cell line panel the mRNA expression of all human genes have been characterized using deep RNA-sequencing. The subcellular distribution of proteins is investigated in a subset of the cell lines, and classified into 32 different organelles and fine cellular structures.
Pathology Atlas: is based on the analysis of 17 main cancer types using data from 8,000 patients. In addition, a new concept for showing patient survival data is introduced, called Interactive Survival Scatter plots, and the atlas includes more than 400,000 such plots. A national supercomputer center was used to analyze more than 2.5 petabytes of underlying publicly available data from the Cancer Genome Atlas (TCGA) to generate more than 900,000 survival plots describing the consequence of RNA and protein levels on clinical survival. The Pathology Atlas also contains 5 million pathology-based images generated by the Human Protein Atlas consortium.

Comparative Toxicogenomics Database (CTD): public website and research tool that curates scientific data describing relationships between chemicals, genes, and human diseases.

Reactome: free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism.

Bionumbers: free-access database of quantitative data in biology designed to provide the scientific community with access to the large amount of data now generated in the biological literature. BioNumbers project performs literature-based curation of various sources. It is a regularly updated online resource that contains >6,000 entries from ~1,000 distinct references. Examples of data include transcription and translation rates, organism and organelle sizes, metabolites concentrations and growth rates.

Wikis

Proteopedia: Wiki of proteins, RNA, DNA and other molecules. All PDB entries.

Other DBs: arts, humanities, ...

EServer.org

Publication (article)

Publication bias: bias with regard to what is likely to be published, among what is available to be published; one problematic and much-discussed bias is the tendency of researchers, editors, and pharmaceutical companies to handle the reporting of experimental results that are positive (i.e. showing a significant finding) differently from results that are negative (i.e. supporting the null hypothesis) or inconclusive, leading to a misleading bias in the overall published literature. The file drawer effect, or file drawer problem, is that many studies in a given area of research may be conducted but never reported, and those that are not reported may on average report different results from those that are reported.

Data publication: practice consisting in preparing certain data or data set(s) for public use thus to make them available to everyone to use as they wish. This practice is an integral part of the open science movement. There is a large and multidisciplinary consensus on the benefits resulting from this practice. The main goal is to elevate data to be first class research outputs.

Data paper: “scholarly publication of a searchable metadata document describing a particular on-line accessible dataset, or a group of datasets, published in accordance to the standard academic practices”. Their final aim being to provide “information on the what, where, why, how and who of the data”.

Repositories for data publication:

Figshare: online digital repository where researchers can preserve and share their research outputs, including figures, datasets, images, and videos. It is free to upload content and free to access, in adherence to the principle of open data. Researchers can upload all of their research outputs to Figshare, thus making them publicly available. Users can upload files in any format and items are attributed a DOI.

Dryad (repository): international disciplinary repository of data underlying scientific and medical publications.

PANGAEA (data library): Data Publisher for Earth & Environmental Science is a digital data library and a data publisher for earth system science. Data can be georeferenced in time (date/time or geological age) and space (latitude, longitude, depth/height).

[gigadb.org (GIGA)ⁿ DB]: repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles.

Retraction Watch: blog that reports on retractions of scientific papers. The blog was launched in August 2010 and is produced by science writers Ivan Oransky (Vice President and Global Editorial Director of MedPage Today) and Adam Marcus (editor of Gastroenterology & Endoscopy News).

Dedicated search engines of published papers

List of academic databases and search engines: representative list of major databases and search engines useful in an academic setting for finding and accessing articles in academic journals, repositories, archives, or other collections of scientific and other articles.

Microsoft Academic Search: free public search engine for academic papers and literature, developed by Microsoft Research for the purpose of algorithms research in object-level vertical search, data mining, entity linking, and data visualization. Although largely functional, the service is not intended to be a production web site and may be taken offline in the future when the research goals of the project have been met.

ArXiv {physics, mathematics, CS, nonlinear sciences, quantitative bio, statistics}

Social Science Research Network (SSRN): website devoted to the rapid dissemination of scholarly research in the social sciences and humanities. SSRN was founded in 1994 by Michael Jensen and Wayne Marr, both financial economists. Academic papers in PDF can be uploaded directly to the site by authors and are then available for worldwide free downloading. Publishers and institutions can upload papers and charge a fee for readers to download them. In economics, and to some degree in law (especially in the field of law and economics), almost all papers are now first published as preprints on SSRN and/or other paper distribution networks such as Research Papers in Economics (RePEc) before being submitted to an academic journal.

CiteSeer: replaced by CiteSeer^X.

Google scholar

JSTOR: originally containing digitized back issues of academic journals, it now also includes books and primary sources, and current issues of journals;

LexisNexis {law}

Science.gov: gateway to US government scientific and technical information and research

Scopus (SciVerse Scopus, @Elsevier): bibliographic database containing abstracts and citations for academic journal articles.

Pubget: by Copyright Clearance Center (CCC).

PubMed (1996.01): free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at NIH maintains the database as part of the Entrez information retrieval system. Indexed with MeSH.

PubMed identifier (PMID): unique number assigned to each PubMed record; there is a similar PMCID (PMC). Assignment of a PMID or PMCID to a publication tells the reader nothing about the type or quality of the content. PMIDs are assigned to letters to the editor, editorial opinions, op-ed columns, and any other piece that the editor chooses to include in the journal, as well as peer-reviewed papers. The existence of the identification number is also not proof that the papers have not been retracted for fraud, incompetence, or misconduct. The announcement about any corrections to original papers may be assigned a PMID.

MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online): bibliographic database of life sciences and biomedical information. MEDLARS (Medical Literature Analysis and Retrieval System) is a computerised biomedical bibliographic retrieval system, launched by NLM in 1964.

United States National Library of Medicine (NLM): operated by USA federal government; world's largest medical library; collections include >7 mln. books, journals, technical reports, manuscripts, microfilms, photographs, and images on medicine and related sciences, including some of the world's oldest and rarest works. Institute within NIH.

National Center for Biotechnology Information (NCBI): part of NLM, branch of NIH. NCBI houses a series of databases relevant to biotechnology and biomedicine and an important resource for bioinformatics tools and services. GenBank; PubMed. All these databases are available online through the Entrez search engine. BLAST.

PubChem: database of chemical molecules and their activities against biological assays. The system is maintained by NCBI. As of 2017.11.01: Compounds, 93.9 mln entries (up from 54 mln entries in 2014.09), contains pure and characterized chemical compounds; Substances, 236 mln entries (up from 163 mln entries in 2014.09), contains also mixtures, extracts, complexes and uncharacterized substances. BioAssay, bioactivity results from 1.25 mln (up from 6000 in 2014.09) high-throughput screening programs with several million values.

MedlinePlus: online information service produced by US NLM; provides curated consumer health information in English and Spanish

Index Medicus

GoPubMed: mashup; Gene Ontology (GO) and Medical Subject Headings (MeSH) serve as "Table of contents" in order to structure the millions of articles of the MEDLINE database.

PubMed Central: free digital database of full-text scientific literature in biomedical and life sciences. It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by NLM as an online archive of biomedical journal articles.

Europe PubMed Central (Europe PMC; till 2012.11.01: UK PubMed Central): launched in 2007 as the first ‘mirror’ site to PMC

PubMed Central Canada (PMC Canada; 2009-)

Zasshi Kiji Sakuin (雑誌記事索引, "Japanese Periodicals Index"): searchable database of scholarly articles in Japanese

American Chemical Society (ACS): scientific society based in USA that supports scientific inquiry in the field of chemistry. Founded in 1876 at New York University, the ACS currently has more than 158,000 members at all degree levels and in all fields of chemistry, chemical engineering, and related fields.

Chemical Abstracts Service (CAS): division of ACS; source of chemical information; CAS is located in Columbus, Ohio, USA. In 2005, the ACS was criticized for opposing the creation of PubChem, which is an open access chemical database developed by the NIH's NCBI. The ACS raised concerns that the publicly supported PubChem database would duplicate and unfairly compete with their existing fee-based CAS and argued that the database should only present data created by the Molecular Libraries Screening Center initiative of the NIH. The ACS lobbied members of USA Congress to rein in PubChem and hired outside lobbying firms to try to persuade congressional members, the NIH, and the Office of Management and Budget (OMB) against establishing a publicly funded database. The ACS was unsuccessful, and as of 2012 PubChem is the world's largest free chemical database.

SciFinder: database of chemical and bibliographic information. Originally a client application, a web version was released in 2008. It has a graphical interface, and can be searched for chemical structures and reactions as well as literature in chemistry and related disciplines. The client version is for chemists in commercial organizations.

CAS Registry Number (CAS RN, CAS Number): unique identification number assigned by CAS in USA to every chemical substance described in the open scientific literature. It includes all substances described from 1957 through the present, plus some substances from as far back as the early 1800s. It is a chemical database that includes organic and inorganic compounds, minerals, isotopes, alloys, mixtures, and nonstructurable materials (UVCBs, substances of unknown or variable composition, complex reaction products, or biological origin). CAS RNs are generally serial numbers (with a check digit), so they do not contain any information about the structures themselves the way SMILES and InChI strings do. The registry maintained by CAS is an authoritative collection of disclosed chemical substance information. It identifies more than 182 million unique organic and inorganic substances and 68 million protein and DNA sequences, plus additional information about each substance. It is updated with around 15,000 additional new substances daily.

Guerilla Open Access Manifesto: document written by Aaron Swartz in 2008 that supports the Open Access movement. The goal of the Open Access movement is to remove barriers and paywalls that may prohibit the general public from accessing scientific research publications. Aaron Swartz, the creator of the Guerilla manifesto, was an activist who fought against the restrictions that were placed on scholarly articles and for the right of all people to have access to scientific research.

Sci-Hub: shadow library website that provides free access to millions of research papers and books, without regard to copyright, by bypassing publishers' paywalls in various ways. Sci-Hub was founded in Kazakhstan by Alexandra Elbakyan in 2011, in response to the high cost of research papers behind paywalls (see Serials crisis). The site is extensively used worldwide. In September 2019, the site's owners said that it served approximately 400,000 requests per day. Sci-Hub and Elbakyan were sued twice for copyright infringement in the United States, in 2015 and 2017, and lost both cases by default, leading to loss of some of its Internet domain names. The site has cycled through different domain names since then. Sci-Hub has been lauded by some in the scientific, academic, and publishing communities for providing access to knowledge generated by the scientific community, which is usually funded by taxpayers (government grants) and with zero royalties paid to the authors. Publishers have criticized it for violating copyright, reducing the revenue of publishers, and potentially being linked to activities compromising universities' network security, though the cybersecurity threat posed by Sci-Hub may have been exaggerated by publishers.

Library.nu

The Pirate Bay (TPB): online index of digital content of entertainment media and software. Founded in 2003 by Swedish think tank Piratbyrån, The Pirate Bay allows visitors to search, download, and contribute magnet links and torrent files, which facilitate peer-to-peer, file sharing among users of the BitTorrent protocol.

Japanese Historical Text Initiative (JHTI): Japanese historical documents and English translations. It is part of the Center for Japanese Studies at the University of California at Berkeley.

ISI Web of Knowledge: search engine, citation index, who is highly cited and why ("popular research")

Scirus (2001.04.1): comprehensive science-specific search engine

Technical writing styles

Technical writing:

Style guide R

Template:Styles : writing, formatting, citing, other examples according to defined "standard" styles

Wikipedia:Manual of Style: q.v. User:Kazkaskazkasako/Books/Wikipedia#Manual of Style

Punctuation

Citation, references, SW, reference management

{q.v.:

}

Parenthetical referencing and Wikipedia:Parenthetical referencing: "author-date" and "author-title"

Comparison of reference management software:

Internet browser integration

Zotero (AGPL; by Roy Rosenzweig Center for History and New Media (CHNM)): Firefox (original add-on); Zotero Standalone can be integrated into Google Chrome, Safari.

Mendeley (on ~2013.04 Elsevier bought): proprietary; main competitor to Zotero. Based on Qt, runs on Windows, Mac, Linux, iOS (iPhone, iPad).

Papers (software) (on ~2012.11 Springer bought): initially only Mac OS X and iOS (iPhone, iPad), in 2012.02.14 on Windows. iTunes-like look & feel.

ReadCube: desktop and browser-based program for managing, annotating, and accessing academic research articles. It is proprietary, but available for free. Initially launched for 3 years in an open beta, it provides access to research materials through partnerships with several publishing companies including the Nature Publishing Group, Frontiers and John Wiley & Sons. Articles are available for digital download and rental for 48 hours.

Social bookmarking of papers/articles: CiteULike, Connotea (NPG)

No integration into Internet browser:

EndNote (Thomson Reuters): the granddaddy of all current reference management software.

Aigaion, JabRef, RefDB, Refbase, BibDesk (Mac OS X)

Template:Reference management software: web-based reference management (OS independent, only browser is needed)

Comparison of notetaking software: Evernote, Microsoft OneNote

Citavi: reference management program for MS Windows. Popular in DE.

Citation Style Language: open XML-based language to describe the formatting of citations and bibliographies. Used by Zotero, Mendeley, Papers.

Citation analysis: examination of the frequency, patterns, and graphs of citations in documents. It uses the directed graph of citations — links from one document to another document — to reveal properties of the documents. A typical aim would be to identify the most important documents in a collection. A classic example is that of the citations between academic articles and books. For another example, judges of law support their judgements by referring back to judgements made in earlier cases. An additional example is provided by patents which contain prior art, citation of earlier patents relevant to the current claim.

Publishers (groups), journals, information management, publications

Category:Academic publishing

Category:Academic journals

Category:Technical communication

Category:Peer review

Category:Open access (publishing)

Diamond open access

IMRAD (introduction, methods, results, and discussion)

Academic journal

Review journal

Review article: attempt to summarize the current state of understanding on a topic; analyze or discuss research previously published by others, rather than reporting new experimental results.

Template:Reed Elsevier:

Elsevier

ScienceDirect

Cell Press: imprint of Elsevier

Trends (journals)

Science (journal)

Template:Holtzbrinck

Georg von Holtzbrinck Publishing Group (also: Die Zeit (50%), Handelsblatt, Der Tagesspiegel.):

Nature Publishing Group (NPG)

Macmillan Publishers Ltd (The Macmillan Group)

Proceedings of the National Academy of Sciences (PNAS): by USA NAS

Public Library of Science & Template:PLoS:

Plos one - multidisciplinary, comparable to Nature, Science, PNAS...

Annual Reviews (publisher): reviews of particular topics

Annual Review of Biochemistry: sets the standard for review articles in biological chemistry and molecular biology.

Knowable Magazine: non-profit, editorially independent online publication from science publisher Annual Reviews that discusses scientific discoveries and the significance of scholarly work in a journalistic style. The magazine uses information from Annual Reviews' 51 review journals as springboards for stories on topics such as health & disease, society, geography, environment and other science-related material, linking back to scholarly sources. As a nonprofit publication, Knowable Magazine is supported by grants from the Gordon and Betty Moore Foundation and the Alfred P. Sloan Foundation.

Wiley-Blackwell: Microscopy Research and Technique

Cold Spring Harbor Laboratory Press (1933-): CSH monographs, CSH perspectives

RNA (journal) (1995.03-2003: Cambridge University Press; 2003-: CSHL Press): published on behalf of the RNA Society.

Cambridge University Press (1534- granted letters patent by Henry VIII): world's oldest publishing house, and the second largest university press in the world.

Springer Nature: British German academic publishing company created by the May 2015 merger of Springer Science+Business Media and Holtzbrinck Publishing Group's Nature Publishing Group, Palgrave Macmillan, and Macmillan Education.

Springer Science+Business Media (part of Springer Nature since 2015): global publishing company that publishes books, e-books and peer-reviewed journals in science, technical and medical (STM) publishing. Springer also hosts a number of scientific databases, including SpringerLink, Springer Protocols, and SpringerImages. 2015.01.15 Holtzbrinck Publishing Group / Nature Publishing Group and Springer Science+Business Media announced a merger. The transaction was concluded in 2015.05 and a new joint venture company, Springer Nature, was formed, with Holtzbrinck having the majority 53% share and BC Partners retaining 47% interest in the company.

BioMed Central (BMC): UK-based, for-profit scientific open access publisher. BioMed Central publishes over 250 scientific journals. All BioMed Central journals are only published online. BioMed Central describes itself as the first and largest open access science publisher. It is owned by Springer Nature.

Template:Thomson Reuters: business data provider and was created by the Thomson Corporation's purchase of Reuters Group on 17 April 2008. Owned 53% by Thomson family. Thomson Reuters is Canada's "leading corporate brand".

Thomson Scientific & Healthcare: split in 2006: Thomson Healthcare + Thomson Scientific. In 2008 both were renamed due to the merger and in 2009 both were merged back into Healthcare & Science unit of the Professional Division of Thomson Reuters, now [12/02/09] called IP & Science (includes also: Legal and Tax & Accounting).

Wolters Kluwer: global information services and publishing company. In 1987 formed by friendly merger of Kluwer Publishers and Wolters Samson (to defend against hostile takeover by Elsevier).

Health & Pharma Solutions: Ovid Technologies: access to online (health science) bibliographic databases, journals and other products; once produced MEDLINE; new DB search interface OvidSP in 2007. SilverPlatter (SilverPlatter Information, Inc.): produced commercial reference databases on CD-ROMs; now part of Ovid.

other: Financial & Compliance Services; Legal & Regulatory; Tax & Accounting.

Journal of Visualized Experiments (JoVE; 2006-): publishing biological, medical, chemical, and physical research in video format.

Frontiers Media: academic publisher of peer-reviewed open access scientific journals currently active in science, technology, and medicine. It was founded in 2007 by a group of neuroscientists, including Henry and Kamila Markram, and later expanded to other academic fields. Frontiers is based in Lausanne, Switzerland. Frontiers Media was, controversially, included in Jeffrey Beall's list of potential predatory open access publishers and has been accused of using email spam. The publisher has "a history of badly handled and controversial retractions and publishing decisions".

Royal Society of Chemistry: learned society (professional association) in UK with the goal of "advancing the chemical sciences"; formed in 1980 from the merger of the Chemical Society, the Royal Institute of Chemistry, the Faraday Society and the Society for Analytical Chemistry with a new Royal Charter and the dual role of learned society and professional body.

List of Royal Society of Chemistry journals

Lab on a Chip (journal): any aspect of miniaturisation at the micro and nano scale

Simons Foundation: private foundation established in 1994 by Marilyn and James Harris Simons with offices in New York City. The foundation -- one of the largest charitable organizations in the US, with assets of over $4 billion in 2019 -- makes grants in "four program areas: mathematics and physical sciences; life sciences; autism research; and education & outreach." In 2016, the foundation launched the Flatiron Institute, a multidisciplinary academic research entity focused on computation.

Quanta Magazine (2012-): ditorially independent online publication of the Simons Foundation covering developments in physics, mathematics, biology and computer science. In November 2018, MIT Press published two collections of articles from Quanta Magazine, Alice and Bob Meet the Wall of Fire and The Prime Number Conspiracy.

Aggregators:

Faculty of 1000: recent research papers evaluated by "over 2000 biological researchers by interestingness"

Plagiarism:

VroniPlag Wiki & de:VroniPlag Wiki (2011.03.28-): wiki at Wikia that examines and documents the extent of plagiarism in German theses (Doctoral, MD, Master, Law...).

de:GuttenPlag Wiki: for Karl-Theodor zu Guttenberg's de:Verfassung und Verfassungsvertrag

Bibliometrics

Category:Bibliometrics

Scientometrics: science of measuring and analysing science. In practice, scientometrics is often done using bibliometrics which is a measurement of the impact of (scientific) publications. Fathers of scientometrics: Derek J. de Solla Price and Eugene Garfield. One significant finding in the field is a principle of cost escalation to the effect that achieving further findings at a given level of importance grow exponentially more costly in the expenditure of effort and resources. However, new methods in search, machine learning and data mining are showing that is not the case for many information retrieval and extraction based problems (what about robotization?).

Impact factor (IF): measure reflecting the average number of citations to articles published in science and social science journals. Frequently used as proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones. Devised by Eugene Garfield, the founder of ISI (now part of Thomson Reuters). Spoofs of IF: "A short history of SHELX" (by University of Göttingen crystallographer George Sheldrick); reviews have much higher per article IF than an article/letter about original research. Articles providing new tools (e.g. software (esp. FOSS), new biochemical method (e.g. SDS-PAGE, Bradford assay)) have much higher IFs than articles about new phys/chem/bio phenomena.

Bibliometrics: set of methods to quantitatively analyze scientific and technological literature. Citation analysis and content analysis. Trying to make automatic tools to make citation indexes and to use these to distribute scientific funding, grant tenures...

Altmetrics: new metrics proposed as an alternative to the widely used Journal Impact Factor; covers not just citation counts, but also other aspects of the impact of a paper, such as how many data and knowledge bases refer to the article, article views, downloads, or mentions in social media and news media. Counting cites in: Wikipedia; saved by users using CiteULike, Mendeley.

Be objective

Jan Hendrik Schön

Bogdanov Affair

Scientific wikis

Scholarpedia: English-language online wiki-based encyclopedia that uses the same MediaWiki software as Wikipedia, but has features more commonly associated with open-access online academic journals. Articles are written by invited expert authors and are subject to peer review. Scholarpedia lists the real names and affiliations of all authors, curators and editors involved in an article, however, the peer review process (which can suggest changes or additions, and has to be satisfied before an article can appear) is anonymous. Focus fields: computational neuroscience, dynamical systems, computational intelligence, physics and astrophysics.

Openness and competition

Open notebook science

Openwetware

Presentation(s)

Edward Tufte#Criticism of PowerPoint: PowerPoint - useful or not? Handouts and reading vs. only speaking? Q&A session?

Reference works, encyclopedias

Category:Reference works

Category:Encyclopedias

{q.v. User:Kazkaskazkasako/Books/All#Science writers, encyclopedists}

Natural History (Pliny): early encyclopedia in Latin by Pliny the Elder, who died in 79 AD. one of the largest single works to have survived from the Roman Empire to the modern day and purports to cover all ancient knowledge; cover topics including astronomy, mathematics, geography, ethnography, anthropology, human physiology, zoology, botany, agriculture, horticulture, pharmacology, mining, mineralogy, sculpture, painting, and precious stones. The work is dedicated to the emperor Titus, son of Pliny's close friend, the emperor Vespasian, in the first year of Titus's reign. It is the only work by Pliny to have survived and the last that he published. He began it in 77, and had not made a final revision at the time of his death during the AD 79 eruption of Vesuvius.

Suda massive 10th-century Byzantine encyclopedia of the ancient Mediterranean world. Encyclopedic lexicon, written in Greek, with 30,000 entries, many drawing from ancient sources that have since been lost, and often derived from medieval Christian compilers. The articles on literary history are especially valuable; these entries supply details and quotations from authors whose works are otherwise lost.

History of the Encyclopædia Britannica: 1st edition (1771); 2nd (1783); 3rd (1797). Piracy of Britannica: Dobson's Encyclopædia (1789-1798) and Moore's Dublin Edition, Encyclopædia Britannica. The 4th (1800-1810), 5th (1817), and 6th (1823) editions are virtually the same as each other. 7th (1827; 1830-1842): new work, first edition to include a general index for all articles. 8th (1860): thorough revision. 9th (1875-1889): W. Robertson Smith addressed the historical interpretation of the Bible; first to include a significant article about women ("Women, Law Relating to"); evolution was listed for the first time, in the wake of Charles Darwin's writings; 8,500 sold in Britain and 45,000 in USA, but in spite of this, several hundred thousand cheaply produced pirated copies were also sold in USA. American editions (10th-14th): 11th (1903-1910). 15th (1st ed.: 1974-1984)

ARKive: "promoting the conservation of the world's threatened species, through the power of wildlife imagery"; locating and gathering films, photographs and audio recordings of the world's species into a centralised digital archive

Wikispecies

Encyclopedia of Life (EOL; 2008.02.26-): free, online collaborative encyclopedia intended to document all of the 1.9 million living species known to science

Biodiversity Heritage Library (BHL; 2005-): consortium of natural history and botanical libraries that cooperate to digitize and make accessible the legacy literature of biodiversity held in their collections and to make that literature available for open access and responsible use as a part of a global “biodiversity commons". Since 2009, the BHL has expanded globally.

Integrated Taxonomic Information System (ITIS): partnership designed to provide consistent and reliable information on the taxonomy of biological species

Catalogue of Life: started in 2001.06 by ITIS and Species 2000; planned to become a comprehensive catalogue of all known species of organisms on Earth

Species 2000: federation of database organizations across the world

Urban Dictionary: satirical crowdsourced online dictionary of slang words and phrases that was founded in 1999 as a parody of Dictionary.com by then-college freshman Aaron Peckham. Anyone with either a Facebook or Gmail account can make a submission to the dictionary, and it is claimed that all entries are reviewed by volunteers.

Funding (agencies), companies, government, politics, scientific societies, institutes

Science policy

List of wealthiest charitable foundations (charitable foundations, private foundations and other charitable organizations):

Howard Hughes Medical Institute (HHMI) (endowment=16.1 bln USD)

Janelia Farm Research Campus (opened in 2006)

Category:Foundations

Category:Foundations by subject

Category:Medical and health foundations

Category:Medical and health foundations in the United States

Category:Bill & Melinda Gates Foundation

Foundation (nonprofit)

Wellcome Trust (est. 1936): biomedical research charity based in London, UK; legacies from the pharmaceutical magnate Sir Henry Wellcome to fund research to improve human and animal health. The aim of the Trust is to "achieve extraordinary improvements in health by supporting the brightest minds", and in addition to funding biomedical research it supports the public understanding of science. Endowment of around £18 bln. The Trust has been described by the Financial Times as the United Kingdom's largest provider of non-governmental funding for scientific research and one of the largest providers in the world; in the field of medical research, it is the world's second-largest private funder after the Bill & Melinda Gates Foundation.

Bill & Melinda Gates Foundation (BMGF; 2000-; endowment of US$46.8 bln as of 2018; merging of the William H. Gates Foundation and the Gates Learning Foundation): largest private foundation in the world, founded by Bill and Melinda Gates; largest transparently operated private foundation in the world. Primary aims of the foundation are, to enhance healthcare and reduce extreme poverty across the globe, and to expand educational opportunities and access to information technology in the USA. Foundation is controlled by its three trustees: Bill Gates, Melinda Gates, and Warren Buffett. Other principal officers include Chief Executive Officer Mark Suzman.

J. Craig Venter Institute: non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The Institute was the result of consolidating four organizations: the Center for the Advancement of Genomics, The Institute for Genomic Research (TIGR), the Institute for Biological Energy Alternatives, and the J. Craig Venter Science Foundation Joint Technology Center. It has facilities in Rockville, Maryland and La Jolla, California.

Craig Venter (1946.10.14-): USA biotechnologist, biochemist, geneticist, and businessman. He is known for being involved with sequencing the second human genome and assembled the first team to transfect a cell with a synthetic chromosome. Venter founded Celera Genomics, The Institute for Genomic Research (TIGR) and the J. Craig Venter Institute (JCVI). He was the co-founder of Human Longevity Inc., served as its CEO until 2017, and is executive chairman of the board of directors. Career: EST controversy; Human Genome Project; Global Ocean Sampling Expedition; Synthetic genomics; Individual human genome: 2007.09.04 a team led by Sam Levy published the first complete diploid genome of an individual human—Venter's own DNA sequence; Human Longevity, Inc.: Human Longevity's mission is to extend healthy human lifespan by the use of high-resolution big data diagnostics from genomics, metabolomics, microbiomics, and proteomics, and the use of stem cell therapy. In a 2007 interview with New Scientist when asked "Assuming you can make synthetic bacteria, what will you do with them?", Venter replied: "Over the next 20 years, synthetic genomics is going to become the standard for making anything. The chemical industry will depend on it. Hopefully, a large part of the energy industry will depend on it. We really need to find an alternative to taking carbon out of the ground, burning it, and putting it into the atmosphere. That is the single biggest contribution I could make."

Grantsmanship

United States of America

National Institutes of Health (NIH): agency of United States Department of Health and Human Services; primary agency of the United States government responsible for biomedical and health-related research (Main provider of funds for biomedical research).

National Science Foundation (NSF); fundamental research and education in all the non-medical fields of science and engineering

National Institute of Standards and Technology (NIST): agency of United States Department of Commerce. Very few funds to keep measurement standards.

Non-money giving organization:

United States National Academy of Sciences (NAS): corporation in the United States whose members serve pro bono as "advisers to the nation on science, engineering, and medicine." Publishes PNAS.

American Association for the Advancement of Science (AAAS): council of AAAS has some elected delegates where at least 2 are from US NAS.

Sage Bionetworks: nonprofit organization in Seattle that promotes open science and patient engagement in the research process. Sage Bionetworks was founded in 2009 as a spinout of Merck & Co., who released software, hardware, intellectual property, and staff connected to its Rosetta Inpharmatics unit.

Stephen Friend (1953.12.10-) is an American physician, scientist, entrepreneur and innovator. He is an authority in the field of cancer biology and a pioneer in the field of the genetics of gene expression, integrating system biology approaches to complex diseases. He is the president, co-founder and director of Sage Bionetworks.

Andrew Kasarskis (1972.11.02-): His focus is on improving health outcomes through better data mining, and his research program includes sequencing-based pathogen surveillance; pharmacogenomics; electronic health records; and systems biology of sleep, behavior, and stress. Kasarskis is known for directing the first class that allowed medical and PhD students to fully sequence and analyze their own genomes, along with co-instructors Michael Linderman, George Diaz, Ali Bashir, and Randi Zinberg. He has said that courses like this will be critical for training teams of people capable of performing this type of analysis in a medical setting. He chose whole genome sequencing because he expects the more limited exome sequencing will not be a relevant technological approach in the long term.

Eric Schadt (1965.01.31): Schadt’s work combines supercomputing and advanced computational modeling with diverse biological data to understand the relationship between genes, gene products, other molecular features such as cells, organs, organisms, and communities and their impact on complex human traits such as disease. He is known for calling for a shift in molecular biology toward a network-oriented view of living systems to complement the reductionist, single-gene approaches that currently dominate biology to more accurately model the complexity of biological systems. Demonstrating the ability to infer causal relationships among features in high dimensional data using DNA variation information, Schadt and his colleagues at Merck began reconstructing predictive networks that were shown to be causally associated with disease, leading to the idea of targeting networks, not single genes, to effectively treat common disorders such as Alzheimer’s disease, obesity, and most forms of cancer. A Merck spokesman said that the papers Schadt began publishing based on this genetic network data “changed the way people looked at disease”.

Santa Fe Institute: independent, nonprofit theoretical research institute located in Santa Fe (New Mexico, United States) and dedicated to the multidisciplinary study of the fundamental principles of complex adaptive systems, including physical, computational, biological, and social systems.

European Union

EU: European Research Area (ERA) ⇒ European Research Council (ERC) similar to NSF: Framework Programmes for Research and Technological Development funds research in ERA.

European Molecular Biology Laboratory (EMBL): established in 1974 by many EU members at that time (Western part of current EU); the main Laboratory in Heidelberg, and Outstations in Hinxton (EBI), Grenoble, Hamburg, and Monterotondo near Rome.

European Bioinformatics Institute (EBI; 1992-): lots of DBs

European Science Foundation (ESF; 1974-): association of 72 member organizations devoted to scientific research in 30 European countries; independent, non-governmental, non-profit organisation that facilitates cooperation and collaboration in European research and development, European science policy and science strategy. Together represent €25 bln funding.

Central European Institute of Technology (CEITEC; Brno, Czech Republic): European centre of excellence in the fields of life sciences and advanced materials and technologies; nanotechnologies and microtechnologies, structural biology, genomics and proteomics going into advanced materials and medicine.

de:Kategorie:Begabtenförderungswerk

Alfried Krupp von Bohlen und Halbach Foundation & de:Alfried Krupp von Bohlen und Halbach-Stiftung

de:Fonds der Chemischen Industrie

Boehringer Ingelheim Fonds

Germany

DE: de:Deutsche Forschungsgemeinschaft (DFG):

Fraunhofer Society: 1/3rd from gov, 2/3rds from contract work, either for government sponsored projects or from industry

Max Planck Society (Max-Planck-Gesellschaft zur Förderung der Wissenschaften Eingetragener Verein, MPG): federal and state (Länder) gov. funding

Forschungszentrum Jülich: Ernst Ruska-Centre does HRTEM (FEI Titan, JEOL TEMs)

Helmholtz Association of German Research Centres:

German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

DESY (Deutsches Elektronen Synchrotron), collaborates in International Linear Collider (ILC, under planning/building, 2010), European x-ray free electron laser (Eu XFEL) (being built, 2010)

Alfred-Wegener-Institut für Polar- und Meeresforschung (AWI), German Center for Neurodegenerative Diseases (DZNE) [being built, 2010], Max Delbrück Center for Molecular Medicine Berlin-Buch (MDC), Forschungszentrum Dresden-Rossendorf (FZD)

United Kingdom

Template:Science and technology in the United Kingdom

UK Research councils: Arts and Humanities Research Council (AHRC), Biotechnology and Biological Sciences Research Council (BBSRC), Economic and Social Research Council (ESRC), Engineering and Physical Sciences Research Council (EPSRC), Medical Research Council (MRC), Natural Environment Research Council (NERC), Particle Physics and Astronomy Research Council (PPARC), Science and Technology Facilities Council (STFC)

Royal Society of Chemistry (RSC): learned society (professional association) in UK with the goal of "advancing the chemical sciences." Formed in 1980.

Canada

Category:Canada Research Chairs

Canada Research Chair (CRC; 2000-): prestigious Canadian university research professorships created through the Canada Research Chairs Program; created to attract world best scholars in various disciplines to be part of CA university system. $300 million is spent annually to attract and retain outstanding scholars and scientists. Tier 1 Chairs – tenable for seven years and renewable indefinitely, are for outstanding researchers acknowledged by their peers as world leaders in their fields; Tier 2 Chairs – tenable for five years and renewable once, are for exceptional emerging researchers, acknowledged by their peers as having the potential to lead in their field.

Middle East, Western Asia

King Abdullah University of Science and Technology (KAUST): public research university located in Thuwal, Saudi Arabia; built and operated for the first three years by Saudi Aramco. Focuses exclusively on graduate education and research, using English as the official language of instruction. Biological and Environmental Sciences and Engineering; Computer, Electrical, and Mathematical Sciences and Engineering; and Physical Sciences and Engineering

Scientific societies

International:

International Association of Academies (IAA; 1899-1913): was an academy designed for the purpose of linking the various Academies around the world, of which the first meeting was held in Paris, FR, in 1900.

Template:International Council for Science (ICSU, formerly International Council of Scientific Unions): formed in 1931; international co-operation in the advancement of science. One of the oldest non-governmental organizations in the world and represents the evolution and expansion of two earlier bodies known as the IAA (1899-1913/14) and the International Research Council (IRC; 1919-1931). Members are national scientific bodies (e.g. academy of science of country X), and international scientific unions.

The international scientific unions (also members of ICSU; [member since]):

IUPAC (1922)

International Astronomical Union (IAU; [1922])

International Mathematical Union (IMU; [1922])

(IUGS; [1922])

International Union of Biological Sciences (IUBS; founded in 1919; [1925]): promotes the biological sciences internationally.

International Union of Crystallography (IUCr; [1947])

International Union of Biochemistry and Molecular Biology (IUBMB; formed as International Union of Biochemistry in [1955])

EU

European Molecular Biology Organization (EMBO); publications: Molecular Systems Biology, EMBO Journal, EMBO Reports

European Life Scientist Organisation (ELSO) absorbed by EMBO, end 2008

Federation of European Biochemical Societies (FEBS); publications: FEBS Journal, FEBS Letters and Molecular Oncology

Companies

Pharma (according to size {human count}):

Bayer: chemical and pharmaceutical
Hoffmann–La Roche (aka Roche): pharmaceuticals and diagnostics; holding company: Roche Holding AG
Boehringer Ingelheim

Science hoax

Dihydrogen monoxide parody (DHMO; hydroxyl acid, hydrogen oxide; Dihydrogen monoxide hoax)

Companies in life sciences, genetics

Illumina (company) (1998.04-): USA corporation, that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. The company provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California. Illumina's technology had purportedly by 2013 reduced the cost of sequencing a human genome to US$4,000, down from a price of US$1 million in 2007.

Francis deSouza (1970.12.02-; 2 children): USA entrepreneur and business executive who is the President and CEO of Illumina Corporation.

BGI Group: Chinese genome sequencing company, headquartered in Shenzhen, Guangdong, China. It was formed in 1999 to participate in the Human Genome Project, and is the world's largest genetics research center. It is the world's leader in gene-sequencing services, also sequencing genomes of other animals, plants and microorganisms.

Human communication

Category:Human communication

Category:Intrapersonal communication

Human communication (anthroposemiotics): field dedicated to understanding how humans communicate. Human communication is grounded in cooperative and shared intentions. Our ability to communicate with one another cannot be possible without an understanding of what we are referencing or thinking about. Because we are unable to fully understand another's perspective, there needs to be a creation of commonality through a shared mindset and/or viewpoint. The field of communication is very diverse. There are multiple layers to what communication is and how we use its different sectors and features as human beings. Humans have communicatory abilities other animals do not. For example, we are able to communicate about time and place as though they are solid objects. Humans communicate to request help, to inform others, and to share attitudes for bonding. Communication is a joint activity largely dependent on the ability to maintain common attention. We share relevant background knowledge and joint experience in order to communicate content and coherence in exchanges. The evolution of human communication took place over a long period of time. We evolved from simple pointing and hand gestures to the use of spoken language.

Intrapersonal communication: process by which an individual communicates within themselves, acting as both sender and receiver of messages, and encompasses the use of unspoken words to consciously engage in self-talk and inner speech.

Brave New World, transhumanism

Category:Transhumanism

Category:Singularitarianism

Category:Transhumanist organizations

Category:Futurology

Category:Artificial intelligence

Category:Existential risk from artificial general intelligence

Category:Doomsday scenarios

Category:Human extinction

Category:Existential risk

{q.v.

}

Intracytoplasmic sperm injection

Designer baby

Reprogenetics

Human enhancement

Transhumanism: Dehumanization ("Frankenstein complex")

Outline of transhumanism

@Transhumanism: Wikipedia:Articles for deletion/Postbiological evolution: form of evolution which has transitioned from a biological paradigm, driven by the propagation of genes, to a nonbiological (e.g., cultural or technological) paradigm, presumably driven by some alternative replicator, and potentially resulting in the extinction, obsolescence, or trophic reorganization of the former. Researchers anticipating a postbiological universe tend to describe this transition as marked by the maturation and potential convergence of high technologies, such as artificial intelligence or nanotechnology. Cultural evolution moves at a much faster rate than biological evolution and this is one reason why it isn’t very well understood. Intelligence Principle.

Accelerating change: perceived increase in the rate of technological change throughout history, which may suggest faster and more profound change in the future and may or may not be accompanied by equally profound social and cultural change.

Technological singularity: hypothesis that the invention of artificial superintelligence will abruptly trigger runaway technological growth, resulting in unfathomable changes to human civilization. According to this hypothesis, an upgradable intelligent agent (such as a computer running software-based artificial general intelligence) would enter a "runaway reaction" of self-improvement cycles, with each new and more intelligent generation appearing more and more rapidly, causing an intelligence explosion and resulting in a powerful superintelligence that would, qualitatively, far surpass all human intelligence. John von Neumann first used the term "singularity" (c. 1950s), in the context of technological progress causing accelerating change: "The accelerating progress of technology and changes in the mode of human life, give the appearance of approaching some essential singularity in the history of the race beyond which human affairs, as we know them, could not continue". Criticisms: Steven Pinker, Jared Diamond, Theodore Modis, William Nordhaus, Jaron Lanier, The Economist.

Superintelligence: hypothetical agent that possesses intelligence far surpassing that of the brightest and most gifted human minds. "Superintelligence" may also refer to a property of problem-solving systems (e.g., superintelligent language translators or engineering assistants) whether or not these high-level intellectual competencies are embodied in agents that act in the world. A superintelligence may or may not be created by an intelligence explosion and associated with a technological singularity.

Background: Although technological progress has been accelerating in most areas (though slowing in some), it has been limited by the basic intelligence of the human brain, which has not, according to Paul R. Ehrlich, changed significantly for millennia. However, with the increasing power of computers and other technologies, it might eventually be possible to build a machine that is significantly more intelligent than humans. If a superhuman intelligence were to be invented—either through the amplification of human intelligence or through artificial intelligence—it would bring to bear greater problem-solving and inventive skills than current humans are capable of. Such an AI is referred to as Seed AI because if an AI were created with engineering capabilities that matched or surpassed those of its human creators, it would have the potential to autonomously improve its own software and hardware or design an even more capable machine. This more capable machine could then go on to design a machine of yet greater capability. These iterations of recursive self-improvement could accelerate, potentially allowing enormous qualitative change before any upper limits imposed by the laws of physics or theoretical computation set in. It is speculated that over many iterations, such an AI would far surpass human cognitive abilities.
Intelligence explosion: possible outcome of humanity building AGI. AGI may be capable of recursive self-improvement, leading to the rapid emergence of artificial superintelligence (ASI), the limits of which are unknown, shortly after technological singularity is achieved.
Other manifestations: Emergence of superintelligence; Non-AI singularity; Speed superintelligence.
Plausibility: Most proposed methods for creating superhuman or transhuman minds fall into one of two categories: intelligence amplification of human brains and artificial intelligence (AI). The many speculated ways to augment human intelligence include bioengineering, genetic engineering, nootropic drugs, AI assistants, direct brain–computer interfaces and mind uploading. These multiple paths to an intelligence explosion makes a singularity more likely, as they would all have to fail for a singularity not to occur. Speed improvements: Exponential growth; Accelerating change. Algorithm improvements: compares it to the changes that human intelligence brought: humans changed the world thousands of times more rapidly than evolution had done, and in totally different ways. Similarly, the evolution of life was a massive departure and acceleration from the previous geological rates of change, and improved intelligence could cause change to be as different again. <...> An abundance of accumulated hardware that can be unleashed once the software figures out how to use it has been called "computing overhang." Criticisms
Potential impacts: Uncertainty and risk: According to Eliezer Yudkowsky, a significant problem in AI safety is that unfriendly artificial intelligence is likely to be much easier to create than friendly AI; Next step of sociobiological evolution; Implications for human society.
Hard vs. soft takeoff
Immortality

Institute for Ethics and Emerging Technologies (IEET): "technoprogressive think tank" that seeks to contribute to understanding of the likely impact of emerging technologies on individuals and societies by "promoting and publicizing the work of thinkers who examine the social implications of scientific and technological advance". It was incorporated in the United States in 2004, as a non-profit 501(c)(3) organization, by philosopher Nick Bostrom and bioethicist James Hughes. The institute aims to influence the development of public policies that distribute the benefits and reduce the risks of technological change; being among the transhumanist groups that "play a strong role in the academic arena". The IEET works with Humanity Plus (also founded and chaired by Bostrom and Hughes, and previously known as the World Transhumanist Association), an international non-governmental organization with a similar mission but with an activist rather than academic approach. A number of technoprogressive thinkers are offered honorary positions as IEET Fellows.

Humanity+ (World Transhumanist Association): international organization which advocates the ethical use of emerging technologies to enhance human capacities.

Posthuman: concept originating in the fields of science fiction, futurology, contemporary art, and philosophy that literally means a person or entity that exists in a state beyond being human. The concept addresses questions of ethics and justice, language and trans-species communication, social systems, and the intellectual aspirations of interdisciplinarity. Post-posthumanism and post-cyborg ethics. According to transhumanist thinkers, a posthuman is a hypothetical future being "whose basic capacities so radically exceed those of present humans as to be no longer unambiguously human by our current standards." Posthumans primarily focus on cybernetics, the posthuman consequent and the relationship to digital technology. The emphasis is on systems. Posthuman god: idea that posthumans, being no longer confined to the parameters of human nature, might grow physically and mentally so powerful as to appear possibly god-like by present-day human standards. This notion should not be interpreted as being related to the idea portrayed in some science fiction that a sufficiently advanced species may "ascend" to a higher plane of existence—rather, it merely means that some posthuman beings may become so exceedingly intelligent and technologically sophisticated that their behaviour would not possibly be comprehensible to modern humans, purely by reason of their limited intelligence and imagination.

Dataism: mindset or philosophy created by the emerging significance of Big Data. It was first used by David Brooks in the New York Times in 2013. More recently, the term has been expanded to describe what social scientist Yuval Noah Harari has called an emerging ideology or even a new form of religion, in which 'information flow' is the 'supreme value'. Harari goes on to argue that Dataism, like any other religion, has practical commandments. A Dataist should want to "maximise dataflow by connecting to more and more media", and believes that freedom of information is "the greatest good of all". Harari also argues that Aaron Swartz, who took his life in 2013 after being prosecuted for releasing hundreds of thousands of scientific papers from the JSTOR archive online for free, could be called the "first martyr" of Dataism. Writing in the Financial Times, Harari argued that Dataism presents an existential challenge to the dominant moral ideology of Humanism, which sees human feelings as the ultimate authority in the world: "humanism is now facing an existential challenge and the idea of “free will” is under threat... Once Big Data systems know me better than I know myself, authority will shift from humans to algorithms." Harari predicts that the logical conclusion of this process is that eventually humans will give algorithms the authority to make the most important decisions in their lives, such as who to marry and which career to pursue.

Global catastrophic risk: hypothetical future event which could damage human well-being on a global scale, even crippling or destroying modern civilization. An event that could cause human extinction or permanently and drastically curtail humanity's potential is known as an existential risk. Examples of technology risks are hostile artificial intelligence and destructive biotechnology or nanotechnology. Insufficient or malign global governance creates risks in the social and political domain, such as a global war, including nuclear holocaust, bioterrorism using genetically modified organisms, cyberterrorism destroying critical infrastructure like the electrical grid; or the failure to manage a natural pandemic. Problems and risks in the domain of earth system governance include global warming, environmental degradation, including extinction of species, famine as a result of non-equitable resource distribution, human overpopulation, crop failures and non-sustainable agriculture. Examples of non-anthropogenic risks are an asteroid impact event, a supervolcanic eruption, a lethal gamma-ray burst, a geomagnetic storm destroying electronic equipment, natural long-term climate change, hostile extraterrestrial life, or the predictable Sun transforming into a red giant star engulfing the Earth.

Why The Future Doesn't Need Us (in 2000.04 issue of Wired magazine, by Bill Joy (then Chief Scientist at Sun Microsystems)): he argues (quoting the sub title) that "Our most powerful 21st-century technologies — robotics, genetic engineering, and nanotech — are threatening to make humans an endangered species." Rather than relinquishment of artificial general intelligence, McGinnis argues for a kind of differential technological development in which friendly artificial intelligence is advanced faster than other kinds.

Superintelligence: hypothetical agent that possesses intelligence far surpassing that of the brightest and most gifted human minds. "Superintelligence" may also refer to a property of problem-solving systems (e.g., superintelligent language translators or engineering assistants) whether or not these high-level intellectual competencies are embodied in agents that act in the world. A superintelligence may or may not be created by an intelligence explosion and associated with a technological singularity. University of Oxford philosopher Nick Bostrom defines superintelligence as "any intellect that greatly exceeds the cognitive performance of humans in virtually all domains of interest". Following Hutter and Legg, Bostrom treats superintelligence as general dominance at goal-oriented behavior, leaving open whether an artificial or human superintelligence would possess capacities such as intentionality (cf. the Chinese room argument) or first-person consciousness (cf. the hard problem of consciousness).

Simulation hypothesis: contends that reality is in fact a simulation (most likely a computer simulation), of which we, the simulants, are totally unaware. Some versions rely on the development of simulated reality, a fictional technology. The hypothesis has been a central plot device of many science fiction stories and films.

Template:Existential risk from artificial intelligence

Concepts: Accelerating change, AI box, AI takeover, Control problem, Existential risk from artificial general intelligence, Friendly artificial intelligence, Instrumental convergence, Intelligence explosion, Machine ethics, Superintelligence, Technological singularity
Organizations: Allen Institute for AI, Center for Applied Rationality, Center for Human-Compatible Artificial Intelligence, Centre for the Study of Existential Risk, DeepMind, Foundational Questions Institute, Future of Humanity Institute, Future of Life Institute, Humanity+, Institute for Ethics and Emerging Technologies, Leverhulme Centre for the Future of Intelligence, Machine Intelligence Research Institute, ✓OpenAI
People: Scott Alexander, ✓Nick Bostrom, Eric Drexler, ✓Sam Harris, ✓Stephen Hawking, Bill Hibbard, Bill Joy, ✓Elon Musk, Steve Omohundro, Huw Price, Martin Rees, Stuart J. Russell, Jaan Tallinn, Max Tegmark, Frank Wilczek, Roman Yampolskiy, Andrew Yang, Eliezer Yudkowsky
Other: Artificial intelligence as a global catastrophic risk, Controversies and dangers of artificial general intelligence, Ethics of artificial intelligence, Suffering risks, Human Compatible, Open Letter on Artificial Intelligence, Our Final Invention, The Precipice, ✓Superintelligence: Paths, Dangers, Strategies, Do You Trust This Computer?

Existential risk from artificial general intelligence: hypothesis that substantial progress in AGI could result in human extinction or some other unrecoverable global catastrophe for humanity. The existential risk ("x-risk") school argues as follows: The human species currently dominates other species because the human brain has some distinctive capabilities that other animals lack. If AI surpasses humanity in general intelligence and becomes "superintelligent", then it could become difficult or impossible for humans to control. Just as the fate of the mountain gorilla depends on human goodwill, so might the fate of humanity depend on the actions of a future machine superintelligence. Concerns about superintelligence have been voiced by leading computer scientists and tech CEOs such as Geoffrey Hinton, Alan Turing, Elon Musk, and OpenAI CEO Sam Altman. In 2022, a survey of AI researchers found that some researchers believe that there is a 10 percent or greater chance that our inability to control AI will cause an existential catastrophe (more than half the respondents of the survey, with a 17% response rate). Two sources of concern are the problems of AI control and alignment: that controlling a superintelligent machine, or instilling it with human-compatible values, may be a harder problem than naïvely supposed. Many researchers believe that a superintelligence would resist attempts to shut it off or change its goals (as such an incident would prevent it from accomplishing its present goals) and that it will be extremely difficult to align superintelligence with the full breadth of important human values and constraints. In contrast, skeptics such as computer scientist Yann LeCun argue that superintelligent machines will have no desire for self-preservation. A third source of concern is that a sudden "intelligence explosion" might take an unprepared human race by surprise. To illustrate, if the first generation of a computer program that is able to broadly match the effectiveness of an AI researcher can rewrite its algorithms and double its speed or capabilities in six months, then the second-generation program is expected to take three calendar months to perform a similar chunk of work. In this scenario the time for each generation continues to shrink, and the system undergoes an unprecedentedly large number of generations of improvement in a short time interval, jumping from subhuman performance in many areas to superhuman performance in virtually all domains of interest. Empirically, examples like AlphaZero in the domain of Go show that AI systems can sometimes progress from narrow human-level ability to narrow superhuman ability extremely rapidly.

History: One of the earliest authors to express serious concern that highly advanced machines might pose existential risks to humanity was the novelist Samuel Butler, who wrote the following in his 1863 essay Darwin among the Machines.
General argument: The three difficulties; Bostrom's argument; Possible scenarios: AI takeover (An AI takeover is a hypothetical scenario in which AI becomes the dominant form of intelligence on Earth, as computer programs or robots effectively take the control of the planet away from the human species.); Anthropomorphic arguments; Definition of "intelligence".
Sources of risk: AI alignment problem; Difficulty of specifying goals; Difficulties of modifying goal specification after launch; Instrumental goal convergence; Orthogonality thesis; Other sources of risk: Ethics of artificial intelligence, Artificial intelligence arms race, and Global catastrophic risk.
Perspectives: Endorsement; Skepticism; Intermediate views; Popular reaction;
Mitigation: Views on banning and regulation

Future of Life Institute (FLI): nonprofit organization that works to reduce global catastrophic and existential risks facing humanity, particularly existential risk from advanced AI. The Institute's work is made up of three main strands: grantmaking for risk reduction, educational outreach, and advocacy within UN, US government and EU institutions. Its founders include MIT cosmologist Max Tegmark and Skype co-founder Jaan Tallinn, and its advisors include entrepreneur Elon Musk. In 2018, FLI drafted a letter calling for "laws against lethal autonomous weapons". Signatories included Elon Musk, Demis Hassabis, Shane Legg, and Mustafa Suleyman. Starting in 2017, FLI offered an annual Future of Life Award, with the first awardee being Vasili Arkhipov. Also in 2017, FLI released Slaughterbots, a short arms-control advocacy film. FLI released a sequel in 2021. In 2018, FLI drafted a letter calling for "laws against lethal autonomous weapons". Signatories included Elon Musk, Demis Hassabis, Shane Legg, and Mustafa Suleyman. In March 2023, FLI drafted a letter calling on major AI developers to agree on a verifiable six-month pause of any systems "more powerful than GPT-4" and to use that time to institute a framework for ensuring safety; or, failing that, for governments to step in with a moratorium. The letter said: "recent months have seen AI labs locked in an out-of-control race to develop and deploy ever more powerful digital minds that no-one - not even their creators - can understand, predict, or reliably control". The letter referred to the possibility of "a profound change in the history of life on Earth" as well as potential risks of AI-generated propaganda, loss of jobs, human obsolescence, and society-wide loss of control. Prominent signatories included Elon Musk, Steve Wozniak, Evan Sharp, Chris Larsen, and Gary Marcus; AI lab CEOs Connor Leahy and Emad Mostaque; politician Andrew Yang; deep-learning pioneer Yoshua Bengio; and intellectual Yuval Noah Harari.

Futures studies (futurism, futurology)

Category:Futures studies

Category:Futures studies organizations

Category:Long Now Foundation

Futures studies (futures research, futurology): systematic, interdisciplinary and holistic study of social and technological advancement, and other environmental trends, often for the purpose of exploring how people will live and work in the future. Unlike the physical sciences where a narrower, more specified system is studied, futurology concerns a much bigger and more complex world system. The methodology and knowledge are much less proven than in natural science and social sciences like sociology and economics. There is a debate as to whether this discipline is an art or science, and it is sometimes described as pseudoscience.

The Millennium Project: think tank that publishes a State of the Future report. It was established in 1996 under the American Council for the United Nations University. By 2007 it had become a part of the World Federation of United Nations Associations By 2009 it had become independent.

Future of Humanity Institute: interdisciplinary research centre at the University of Oxford investigating big-picture questions about humanity and its prospects. It was founded in 2005 as part of the Faculty of Philosophy and the Oxford Martin School. Its director is philosopher Nick Bostrom, and its research staff and associates include futurist Anders Sandberg, engineer K. Eric Drexler, economist Robin Hanson, and Giving What We Can founder Toby Ord. History: Nick Bostrom established the Institute in November 2005 as part of the Oxford Martin School, then the James Martin 21st Century School. In 2018, the Open Philanthropy Project recommended a grant of up to approximately £13.4 million to FHI over three years, with a large portion conditional on successful hiring. Existential risk. Anthropic reasoning: Anthropic arguments FHI has studied include the doomsday argument, which claims that humanity is likely to go extinct soon because it is unlikely that one is observing a point in human history that is extremely early. Instead, present-day humans are likely to be near the middle of the distribution of humans that will ever live. Bostrom has also popularized the simulation argument. A recurring theme in FHI's research is the Fermi paradox, the surprising absence of observable alien civilizations. Robin Hanson has argued that there must be a "Great Filter" preventing space colonization to account for the paradox. That filter may lie in the past, if intelligence is much more rare than current biology would predict; or it may lie in the future, if existential risks are even larger than is currently recognized. Human enhancement and rationality.

Nick Bostrom (1973.03.10-): Swedish philosopher at the University of Oxford known for his work on existential risk, the anthropic principle, human enhancement ethics, superintelligence risks, the reversal test, and consequentialism. He holds a PhD from the London School of Economics (2000). In 2011, he founded the Oxford Martin Programme on the Impacts of Future Technology, and he is currently the founding director of the Future of Humanity Institute at Oxford University. Forecasts (when): with 10% confidence is 2024 (mean 2034, st. dev. 33 years), with 50% confidence is 2050 (mean 2072, st. dev. 110 years), and with 90% confidence is 2070 (mean 2168, st. dev. 342 years).

Superintelligence: Paths, Dangers, Strategies (2014): argues that if machine brains surpass human brains in general intelligence, then this new superintelligence could replace humans as the dominant lifeform on Earth. Sufficiently intelligent machines could improve their own capabilities faster than human computer scientists, and the outcome could be an existential catastrophe for humans.

Robin Hanson (1959.08.28-): associate professor of economics at George Mason University and a research associate at the Future of Humanity Institute of Oxford University. He is known for his work on idea futures and markets, and he was involved in the creation of the Foresight Institute's Foresight Exchange and DARPA's FutureMAP project. Hanson received a BS in physics from the University of California, Irvine in 1981, an MS in physics and an MA in Conceptual Foundations of Science from the University of Chicago in 1984, and a PhD in social science from Caltech in 1997 for his thesis titled Four puzzles in information and politics: Product bans, informed voters, social insurance, and persistent disagreement. Before getting his PhD he researched artificial intelligence, Bayesian statistics and hypertext publishing at Lockheed, NASA, and elsewhere. A 2003 article in Fortune examined Hanson's work, noting, among other things, that he is a proponent of cryonics and that his ideas have found some acceptance among extropians on the Internet. He has since written extensively on the topic. Hanson also coined the term Great Filter, referring to whatever prevents "dead matter" from becoming an expanding and observable intelligent civilization. He was motivated to seek his doctorate so that his theories would reach a wider audience. Hanson has written a book, The Age of Em, concerning his views on brain emulation and its eventual impact on society.

Anders Sandberg (1972.07.11-): Swedish researcher, science debater, futurist, transhumanist and author. He holds a PhD in computational neuroscience from Stockholm University, and is currently a Senior Research Fellow at the Future of Humanity Institute at the University of Oxford.

Long Now Foundation (1996.01.04-): USA non-profit organization based in San Francisco that seeks to start and promote a long-term cultural institution. It aims to provide a counterpoint to what it views as today's "faster/cheaper" mindset and to promote "slower/better" thinking. The Long Now Foundation hopes to "creatively foster responsibility" in the framework of the next 10,000 years. In a manner somewhat similar to the Holocene calendar, the foundation uses 5-digit dates to address the Year 10,000 problem (e.g., by writing the current year "02023" rather than "2023"). Clock of the Long Now. Rosetta Project: preserve all languages that have a high likelihood of extinction over the period from 2000 to 2100. These include many languages whose native speakers number in the thousands or fewer. Other languages with many more speakers are considered by the project to be endangered because of the increasing importance of English as an international language of commerce and culture. Long Bet Project: to propose and keep track of bets on long-term events and stimulate discussion about the future. The Long Now Foundation describes The Long Bet Project as a "public arena for enjoyably competitive predictions, of interest to society, with philanthropic money at stake."

Companies in biotech and pharma

Moderna (ModeRNA Therapeutics (2010–2018)): pharmaceutical and biotechnology company based in Cambridge, Massachusetts, that focuses on RNA therapeutics, primarily mRNA vaccines. The company's name is derived from the terms "modified", "RNA", and "modern". The company's only commercial product is the Moderna COVID-19 vaccine, marketed as Spikevax. The company has 45 treatment and vaccine candidates, of which 38 have entered clinical trials. Candidates include possible vaccines for influenza, HIV, respiratory syncytial virus, Epstein–Barr virus, the Nipah virus, chikungunya, human metapneumovirus, varicella zoster virus, as well as a cytomegalovirus vaccine, a Zika virus vaccine funded by the Biomedical Advanced Research and Development Authority, and three cancer vaccines. The company's pipeline also includes a cell therapy-based treatment: a relaxin fusion protein being developed to treat acute decompensated heart failure. It also includes candidates that use OX40 ligand, interleukin 23, IL36G, and interleukin 12 for cancer immunotherapy, specifically treatment of breast cancer, urothelial carcinoma, lymphoma, and melanoma. Also being developed by Moderna is a regenerative medicine treatment that encodes vascular endothelial growth factor A to stimulate blood vessel growth for patients with myocardial ischemia.

^ ^a ^b Shafee, Thomas; Lowe, Rohan (2017). "Eukaryotic and prokaryotic gene structure". WikiJournal of Medicine. 4 (1). doi:10.15347/wjm/2017.002. ISSN 2002-4436.
^ Jefferson, T. A.; Leatherwood, S.; Webber, M. A. (1994). Marine Mammals of the World. Food and Agriculture Department of the United Nations. pp. 1–2. ISBN 978-92-5-103292-3. OCLC 30643250.
^ Roth, Gerhard; Dicke, Ursula (May 2005). "Evolution of the brain and intelligence". Trends in Cognitive Sciences. 9 (5): 250–7. doi:10.1016/j.tics.2005.03.005. PMID 15866152. S2CID 14758763.
^ Emery, Nathan J (29 January 2006). "Cognitive ornithology: The evolution of avian intelligence". Philosophical Transactions of the Royal Society B: Biological Sciences. 361 (1465): 23–43. doi:10.1098/rstb.2005.1736. PMC 1626540. PMID 16553307.
^ Csikszentmihalyi M (1997). Finding Flow: The Psychology of Engagement with Everyday Life (1st ed.). New York: Basic Books. p. 31. ISBN 978-0-465-02411-7.
^ Luketa, Stefan (2012). "New views on the megaclassification of life" (PDF). Protistology. 7 (4): 218–237.

[ShafeeLowe2017-1] Shafee, Thomas; Lowe, Rohan (2017). "Eukaryotic and prokaryotic gene structure". WikiJournal of Medicine. 4 (1). doi:10.15347/wjm/2017.002. ISSN 2002-4436.

[2] Jefferson, T. A.; Leatherwood, S.; Webber, M. A. (1994). Marine Mammals of the World. Food and Agriculture Department of the United Nations. pp. 1–2. ISBN 978-92-5-103292-3. OCLC 30643250.

[Roth2005-3] Roth, Gerhard; Dicke, Ursula (May 2005). "Evolution of the brain and intelligence". Trends in Cognitive Sciences. 9 (5): 250–7. doi:10.1016/j.tics.2005.03.005. PMID 15866152. S2CID 14758763.

[pmid16553307-4] Emery, Nathan J (29 January 2006). "Cognitive ornithology: The evolution of avian intelligence". Philosophical Transactions of the Royal Society B: Biological Sciences. 361 (1465): 23–43. doi:10.1098/rstb.2005.1736. PMC 1626540. PMID 16553307.

[Finding_Flow-5] Csikszentmihalyi M (1997). Finding Flow: The Psychology of Engagement with Everyday Life (1st ed.). New York: Basic Books. p. 31. ISBN 978-0-465-02411-7.

[6] Luketa, Stefan (2012). "New views on the megaclassification of life" (PDF). Protistology. 7 (4): 218–237.

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