User talk:Hankwbass/Group 5

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Genomics

Please leave your critique review here

I think the intro paragraph could be rearranged in a way that makes it flow a little better. The fourth sentence, "Genomics aims at the collective characterization and quantification of genes, which direct the production of proteins with the assistance of enzymes and messenger molecules," goes into detail about proteins kind of prematurely, which leads to the fourth and fifth sentence and less pertinent info on proteins and mutations. I suggest removing the material on proteins and mutations and making the sixth sentence ("In contrast to genetics...") the fourth sentence. This would keep the focus on what genomics is, the big picture. AndrewBrowning (talk) 22:28, 10 April 2017 (UTC)

I agree with this change. The genomics introduction needs revision, and currently it goes from being very broad to very specific rather abruptly. Changing the fourth sentence as AndrewBrowning suggests is a good idea. Additionally, the intro paragraph can be split into two parts for easier reading. The first half of the paragraph describes the study of genomics, while the second half deals with genomics in application. I think these two halves would serve better as separate paragraphs. The split can be made in between either the third and fourth sentences or the fourth and fifth. Abbystewart (talk) 22:53, 19 April 2017 (UTC)

I believe that the section "early sequencing efforts" lacks information and is quite vague with the different efforts and publications that took place. I think that each effort/publication should have had a short summary explaining research that was found and what was accomplished. I think that the first sentence should say: Rosalind Franklin's confirmation of the helical structure of DNA was one of the earliest sequencing efforts. In 1951, Rosalind and an fellow student named Raymond Gosling, were able to capture two high-resolution photos of crystallized DNA fibers. "Franklin used two different fibers of DNA, one more highly hydrated than the other. From this she deduced the basic dimensions of DNA strands, and that the phosphates were on the outside of what was probably a helical structure." AlejandroArias (talk) 09:31, 21 April 2017 (UTC)

The "DNA-sequencing technology developed" section could benefit from the addition of information about 454 Pyrosequencing. "In the pyrosequencing approach, DNA is isolated, fragmented, ligated to special adapters, and separated into single strands. Emulsion PCR is then carried out for clonal amplification." 454 pyrosequencing has the ability to sequence multiple individual samples simultaneously "using the barcoding multiplex approach, in which unique sequences are incorporated into the primers and barcoded amplicons are generated". The benefit of the barcoding multiplex approach is that "both sampling depth (number of sequences per sample) and breadth (number of samples or individuals analyzed)" are more broad than traditional methods. an13c (talk) 08:13, 21 April 2017 (UTC)

The subsection "Assembly" could use clarification by providing more information about EST and rearranging the paragraph to provide a well-structured summary of assembly in association to shotgun sequencing. Tc16e (talk) 15:29, 21 April 2017 (UTC)

Recombinant DNA

The first section of the Recombinant DNA wiki should clearly and definitively state that Recombinant DNA allows big groups of single genes to be isolated from a pool of up to millions of genes. Also, genes which are isolated may be manipulated or modified and, from their initial source be reintroduced into a range of cell types by the mechanism of transformation. These are two fundamental reasons why Recombinant DNA is such a valuable technique in the field of genetics. --Austinjak (talk) 04:21, 27 April 2017 (UTC)

The second paragraph of this page is little weak and could use some added information as well as clarification. The first sentence could use minor edits, "Recombinant DNA is the general name for a piece of DNA that has been created in vitro by the combination of at least two DNA strands from different sources." I also propose adding more information to the last sentence of this paragraph. Maybe something as follows, "Bacterial plasmids are a popular form of cloning vector. To form a recombinant DNA molecule, the host vector and donor DNA both contain a specific palindromic sequence called a restriction site that attracts the same restriction enzyme. The enzyme cuts the strands into DNA fragments, each containing sticky (cohesive) or blunt ends. The host and donor ends are then bonded by another enzyme, DNA ligase, to form the new recombinant DNA molecule." This would be a brief overview for readers who only read the first few paragraphs, a more in depth description of this process would go in the "Creation" section. Jackierodz518 (talk) 04:03, 11 April 2017 (UTC)

    I agree with Jackierodz518 that the second paragraph is in need of clarification. I would reword the second sentence to say something along the lines of "Recombinant DNA is the general name...by the combination of DNA material in the form of a template strand from one source and a vector from a different source." This helps specify what is needed specifically for recombinant DNA to be made. AndrewBrowning (talk) 03:25, 12 April 2017 (UTC)

I agree with Jackierodz518 that the last sentence of the second paragraph could be more insightful as stated above or so that it may have its own paragraph providing a summary of the basic procedures of R-DNA technology and the construction of R-DNA.Tc16e (talk) 13:58, 21 April 2017 (UTC)

I think changing the first sentence of the second paragraph to what Jackierodz518 suggests is a good idea. The proposed sentence provides more information, comes across as more factual, and allows for smoother reading. Specifically, "...DNA strands from two different sources," provides for a better understanding of recombinant DNA than the current, "...combination of at least two strands." Knowing that the strands are from different sources is vital to understanding the concept of recombinant DNA, so this is important to mention in the beginning of the article. Abbystewart (talk) 23:13, 19 April 2017 (UTC)

In the first sentence of this page, recombinant DNA is abbreviated by "rDNA." I suggest either differentiating between recombinant DNA and ribosomal DNA, which are both abbreviated by rDNA, or removing the abbreviation altogether to avoid confusion. AndrewBrowning (talk) 22:27, 10 April 2017 (UTC)

I definitely agree with this edit. Using the abbreviation 'rRNA' can be easily confused with ribosomal RNA.--Austinjak (talk) 13:44, 27 April 2017 (UTC)

I think this is a good idea. I hadn't heard of rRNA in reference to recombinant DNA before reading this article. Abbystewart (talk) 03:15, 16 April 2017 (UTC)

I was confused when I read rDNA as well. I have never heard of recombinant DNA being abbreviated as rDNa. I think this should be changed as it would be very confusing to viewers. Res13k (talk) 15:21, 18 April 2017 (UTC)

I agree that rDNA does not specify recombinant DNA, which could confuse the reader. Defining all the terms being used in the explanation of the creation, as well as, any other subsection, at the beginning of the article would be helpful for readers to follow along.Kellsonp (talk) 02:26, 22 April 2017 (UTC)

I believe that the last sentence of the second paragraph should be removed and/or replaced. Instead, a third paragraph should form providing a summary of R-DNA technology and the construction of R-DNA because this information is equally important and can be beneficial to readers understanding of the creation of R-DNA. It should be able to answer the question “What R-DNA technology and how?”. I suggest beginning it with “R-DNA technology introduces fragments of DNA from one organism into a different organism.“ Following that sentence would then include information briefing isolation of DNA, restriction, ligation, and the introduction into new cells. A beneficial reference to this would be Chaudhuri, Keya (1 January 2013). "Recombinant DNA Technology". The Energy and Resources Institute (TERI). Tc16e (talk) 14:08, 21 April 2017 (UTC)

I think the first paragraph of the Recombinant DNA article can be revised to read something along the lines of "The construction of recombinant DNA is possible due to the universality of the genetic code," rather than the current last two sentences which read, "Recombinant DNA is possible because DNA molecules from all organisms share the same chemical structure. They differ only in the nucleotide sequence within that identical overall structure." This revision will help the sentence to flow better, and an in-text link for the genetic code wikipedia article will provide more information regarding the matter. Abbystewart (talk) 03:11, 16 April 2017 (UTC)

   This would be helpful. Saying that "...DNA molecules from all organisms share the same chemical structure..." sounds a little too broad and doesn't address B-DNA or rhinoviruses. AndrewBrowning (talk) 23:31, 17 April 2017 (UTC)

The third paragraph of the lead section is a bit "wordy" and can be revised to be more clear and concise. Currently, it reads, "The DNA sequences used in the construction of recombinant DNA molecules can originate from any species. For example, plant DNA may be joined to bacterial DNA, or human DNA may be joined with fungal DNA. In addition, DNA sequences that do not occur anywhere in nature may be created by the chemical synthesis of DNA, and incorporated into recombinant molecules. Using recombinant DNA technology and synthetic DNA, literally any DNA sequence may be created and introduced into any of a very wide range of living organisms." The examples are more or less equivalent, and so having two in the lead section is somewhat unnecessary. Minor edits can help improve the last sentence to sound more factual. I suggest something along the lines of, "The construction of recombinant DNA molecules may contain DNA sequences originating from any species. For example, plant DNA may be joined to bacterial DNA. Additionally, DNA sequences that do not occur in nature may be created by Oligonucleotide synthesis and incorporated into recombinant molecules." Abbystewart (talk) 03:38, 16 April 2017 (UTC)

I agree after the third paragraph has too many words and not enough factual information. The paragraph should be changed to be more concise and factual. I also agree that taking out one of the examples would make the paragraph better. The last sentence says " Using recombinant DNA technology and synthetic DNA, literally any DNA sequence may be created and introduced into any of a very wide range of living organisms." This sentence should be changed, the language sounds very casual and not very factual. It should be reworded to say something along the lines of "Through the use of recombinant DNA technology and synthetic DNA almost any DNA sequence can be created. These DNA sequences may then be introduced into a large range of living organisms." Res13k (talk) 01:05, 19 April 2017 (UTC)

I agree with Res13k as the last sentence of the third paragraph should include stronger vocabulary rather than using intensifiers to back up our content. The word "literally" should be taken out from the last sentence of the third paragraph as it comes off too casual and unprofessional. How about "a multitude of"? Csf14c (talk) 18:47, 20 April 2017 (UTC)

I agree with Res13k that the third paragraph could be more concise by providing a general idea of species that R-DNA can originate from instead of providing a single example and going further into details based off of that one specific example. Also, Csf14c is correct in regards to the vocabulary being unprofessional. Great substitutions for "literally" could be "a plethora of or a variety of".Tc16e (talk) 14:18, 21 April 2017 (UTC)

The third paragraph most definitely uses to many words without putting its point across. It discusses how recombinant DNA can be constructed from “any species”, this should be more specific and describe why DNA from altering species may be combined. “Recombinant DNA is formed from two or more species with altering DNA. Their DNA strands are “cut and glued” together, creating a new recombinant DNA strand. DNA is the universal genetic material and therefore it is chemically consistent across species, allowing for compatibility between two phenotypically unlike species. Synthetic DNA sequences may also be produced via oligonucleotide synthesis (chemical synthesis of short DNA sequences) and combined with naturally produced DNA to assemble recombinant DNA." ElizaBarrett (talk) 09:56, 19 April 2017 (UTC)

I concur that the third paragraph feels like a run-on sentence and I didn't quite feel like it did a good job in actually discussing why and how DNA from altering species is combined. The text that is followed in your comment is a better overall description of how rDNA can be formed and generated from "any species (too vague)."Dsg14c (talk) 20:02, 20 April 2017 (UTC)

The second paragraph of the "Uses" section begins with the following sentence: "The most common application of recombinant DNA is in basic research, in which the technology is important to most current work in the biological and biomedical sciences." I suggest changing "The most common..." to "An additional..." or something of that nature because the first paragraph of the section describes commercial and medical purposes as a wide use. Also, removing the word "basic," as it implies that the work being done in this field is simplistic, may improve the text. I suggest removing the latter part of the sentence starting with "...in which the..." and replacing it with the second sentence of the paragraph to follow up the introduction of research at the beginning of the sentence. Combining all of these suggestions may produce something like: "An additional application of recombinant DNA is in modern research, in which it is used to identify, map, sequence, and determine the function of genes."AndrewBrowning (talk) 23:13, 17 April 2017 (UTC)

I agree with the removal of the word "basic" in front of research. Perhaps the original poster meant something along the lines of primary research, but the current descriptor marginalizes the work. I don't know if changing "most common application" to "an additional application" is completely necessary, because stating that recombinant DNA is mostly used in biological/biomedical research might be a significant detail. Abbystewart (talk) 23:31, 19 April 2017 (UTC)

I agree with Jackierodz518 that the second paragraph of the page needs more depth, however even the Creation section does not have an as in depth explanation of how recombinant dna is created regarding the restriction enzymes in cutting, and DNA ligase in building back together.  Maybe we should place Jackierodz518's edits in the Creation section rather than the intro. Thokalath19 (talk) 03:23, 20 April 2017 (UTC)

I think the following content from the first paragraph should be rearranged in wording to make it correct with syntax. "Recombinant DNA is possible because DNA molecules from all organisms share the same chemical structure. They differ only in the nucleotide sequence within that identical overall structure." The phrase should rather read, "Recombinant DNA is possible because DNA molecules from all organisms share the same chemical structure, but differ in the nucleotide sequence within that identical overall structure." By doing this, you compact the main idea into one sentence and get to the point quicker. Csf14c (talk) 18:31, 20 April 2017 (UTC)

The second sentence should be revised, because the statement is a bit untrue. DNA molecules from all organisms do not share the same chemical structure. rDNA is usually used to note ribosomal DNA, so I would suggest that recombinant DNA is abbreviated another way to avoid confusion. Also Under the "Creation" tab, there should be a caption under the image that describes the process of gene cloning. Under the "Uses" tab, I would describe the GloFish a little more by describing how it has different fluorescent color proteins from sea organisms and how it was marketed as the world's first genetically modified pet. Under the "Controversy" tab, as a famous example, I would include how RNA silencing technology allowed for the shelf life of foods to be increased (Flavr Savr tomato). The "History" section of this page needs a lot more expanding.

Bjb15e (talk) 02:07, 23 April 2017 (UTC)

[citation needed]

In the fourth paragraph of the recombinant DNA article, it states "Expression of foreign proteins requires the use of specialized expression vectors and often necessitates significant restructuring by foreign coding sequences." but a citation is missing. I believe this abstract offers a good source on the matter. Wes.kosater (talk) 20:10, 8 April 2017 (UTC)

Good catch; here's the source cited. Bendig MM. The production of foreign proteins in mammalian cells. Genet. Eng. 1988;7:91–127. La15d (talk) 22:54, 20 April 2017 (UTC)

History

I would add information to the History section of Recombinant DNA. I propose more information about major contributors to the discovery of recombinant DNA. "In 1978, Werner Arber, Daniel Nathans, and Hamilton O. Smith received the Nobel Prize in Physiology or Medicine for their discovery of restriction enzymes which proved to be groundbreaking tools in the study of recombinant DNA." Jackierodz518 (talk) 03:38, 9 April 2017 (UTC)

Keeping in mind that our audience is large and varying, this is a good addition. Many existing Wikipedia articles include an extensive History section, so this edit can help make this article more considerable among articles. Abbystewart (talk) 23:30, 19 April 2017 (UTC)

I agree with Jackierodz518 and think it would also benefit the article to include AquAdvantage salmon. According to Nature, it is the first animal modified with recombinant DNA technology to be approved for consumption from the FDA. Wes.kosater (talk) 23:48, 11 April 2017 (UTC)

I agree with both Jackierodz518 and Abbystewart that more information needs to be added to the History section. I believe that having more background information/history, will give readers a better understanding of the material. In addition, I think that information should be added regarding all of the money hungry corporations that wanted to capitalize on Stanley N. Cohen and Herbert W. Boyle's work, which led to the birth of the Biotech Industry. AlejandroArias (talk) 18:58, 20 April 2017 (UTC)

After the first sentence I would add: "In 1971, Douglas Berg isolated the first plasmid bacterial cloning vector, λdvgal 120 and Robert Pollack voiced his concern about the potential biohazards of cloning. I would continue with another sentence and say: A year later in 1972, David Jackson, Peter Lobban, and A. D. Kaiser developed a method, which allowed the joining of DNA's in vitro and Jackson and colleagues created the first chimeric DNA in vitro. AlejandroArias (talk) 09:59, 21 April 2017 (UTC) Followed by: "In 1973 for the first time S.Cohen and H. Boyer developed a recombinant plasmid, which after using as vector replicated well within a bacterial host."

I agree that adding these sentences after the first sentence would be beneficial. The extreme lack of information in the History section can confuse lots of readers. These sentences will supplement the reader with important historical information that is needed to understand the timeline of recombinant DNA and recombinant DNA technologies.Dja13e (talk) 18:39, 21 April 2017 (UTC)

The history section needs significant expansion. Peter Lobban’s contributions to the field of Recombinant DNA should be further described. I would add information about the methods that were used to create human insulin and any complications that the scientists encountered. For example, contamination was an initial problem that caused the scientists to test many trials. Bjb15e (talk) 01:58, 24 April 2017 (UTC)

Properties of Organisms containing recombinant DNA

The first sentence of this section needs revision. The statement "In most cases, organisms containing recombinant DNA have apparently normal phenotypes" is vague and oddly worded. It appears that "apparently normal phenotypes" is implying that an observable change to the phenotype is expected, but not observed. Regardless, this statement should be revised. The section could be improved if instead it began with "Most organisms containing recombinant DNA despite having a change in genotype display no change in phenotype." Ngrab14 (talk) 23:40, 20 April 2017 (UTC)

The second paragraph needs a slight revision. The second sentence of the second paragraph states "Gross phenotypic changes are not the norm, unless the recombinant gene has been chosen and modified so as to generate biological activity in the host organism", and this could be a little confusing to the average reader. The article should define "gross phenotypic changes", for not everybody knows what is meant by that. Also it is unclear what is meant when the article says "unless the recombinant gene is chosen". The article should change the wording so as to make it more reader friendly.Dja13e (talk) 17:11, 21 April 2017 (UTC)

I did not think that the first sentence of this paragraph was too confusing, but I do agree that what Ngrab14 proposed is much clearer and easier to understand. As for the second paragraph, Dja13e is right that it needs revision. I think that the content of first two sentences are good but they are too wordy and might flow better if they were reorganized. I would rewrite them, but since the content does not need editing, only rewording, the sentences would sound too similar. The last sentence mentions that toxicity is a phenotype, but it is very confusing to understand. I think the author meant that if a gene is over expressed, then the recombinant DNA could become toxic to the host organism. If so, then this sentence should also be reworded for comprehensiveness. Jackierodz518 (talk) 01:16, 25 April 2017 (UTC)

Creation

It would definitely be helpful to list the typical steps of a representative gene cloning experiment: (1) isolation of DNA from an organism which contains the 'target gene' and is cut with a restriction endonuclease. (2) to digest the source DNA, a DNA cloning vector is cut with the same restriction endonuclease used. only one of these restriction endonuclease sites is present and viable in the cloning vector. (3) T4 DNA ligase is mixed with the two DNA samples. the enzymatic creation of phosphodiester bonds at the ends of DNA strands generate various combinations of DNA molecules, including vector DNA and DNA from the source organism. (4) E. coli or other host cells are transformed with DNA molecules from the ligase reaction, producing some cells that carry vector–insert DNA constructs. the vector may be replicated in the host cell because of its DNA sequence (origin of replication), and the entire construct is preserved. E. coli uptaking of DNA is aided by electroporation, CaCl2–heat shock treatment, or other means. in some cases conjugative and mobilization functions of plasmids are utilized to transfer a plasmid–gene construct to a bacterium that is not easily transformed.--Austinjak (talk) 05:38, 04/25/2017 (UTC)

It is important to add in this section, near the end when PCR has already been mentioned, that the major advantage of using PCR methods directly to sequence genomic or complex mixtures of DNAs (instead of amplifying and cloning before sequencing) is that only one single sequence needs to be determined when PCR is utilized. An average of sequences of the target DNA present in the solution will be obtained by the data. Versus, when sequencing "PCR clones" at least four determined data sets are neccesary to actually distinguish the location of point mutations; also several data sets are necessary to effectively determine is during cycling "phase disruption has occurred. Further, PCR-mediated recombinants have been referred to as "phase disruptions" in several reports which link their production to PCR products that terminate early.--Austinjak (talk) 04:36, 27 April 2017 (UTC)

I also think it is useful to mention that human insulin used to treat diabetes was the first commercial pharmaceutical produced using Recombinant DNA technology. --Austinjak (talk) 04:47, 27 April 2017 (UTC)

Somewhere in the second paragraph of the "Creation" section of the Recombinant DNA page I would add the fact that there are about 4000 restriction enzymes, each of which bind to their own specific sequence of nucleotides or restriction site. There are four types of restriction enzymes with Type II being the most abundant. The abundance of restriction endonucleases allows for the plasmid to be cut at a variety of sites for differentiation in gene expression and an assortment of recombinant DNA molecules. Jackierodz518 (talk) 04:21, 11 April 2017 (UTC)

In the second paragraph it mentions ligase cloning and Gibson assembly, but does not explain what they are. I think they should include the definitions of each that can be found on other wikipedia pages. For example "Gibson Assembly [[1]] is a molecular cloning method which allows for the joining of multiple DNA fragments in a single, isothermal reaction." and " Ligation (Ligase Cloning) [[2]] is the joining of two nucelic acid fragments through the action of an enzyme." Both should include links to the other wikipedia page so the reader can find out more information about each subject. Res13k (talk) 00:36, 19 April 2017 (UTC)

In the first paragraph of the "Creation" section the method of Polymerase Chain Reaction (PCR) is discussed briefly as a means to amplify DNA by copying an existing sequence and to replicate DNA of a test tube. Even though this is a good intro description into the realm PCR, it is very brief and forgets about crucial aspects of PCR that are needed to be discussed extensively. First, I would propose that PCR eliminates the need to use host cells for cloning and that PCR can amplify even the smallest of DNA sequences/samples . The process includes three major continuous steps including: primer annealing, denaturation and extension. Without the separation of strands from denaturation, you would not be able to anneal specific primers. Lastly, PCR demands two oligonucleotide primers, one complementary to the 5' end of the first strand of the target DNA to be amplified and another complementary to the 3' end of the second strand. Dsg14c (talk) 19:32, 20 April 2017 (UTC)

→→ @ Dsg14c I agree that PCR needs to be detailed a little more extensively on this wiki; even mentioning the basic "primer annealing, denaturation, and extension" would effectively give readers a better understanding of Recombinant DNA. --Austinjak (talk) 04:40, 27 April 2017 (UTC)

The explanation of how recombinant DNA is created is more of a brief overview of general cloning, without any specificity or in depth details related to recombinant DNA and it's formation. I would start out by separating the section into the various steps that goes into creation, so that it is easier to follow and understand the process. These steps could be isolating donor/vector DNA, Cutting DNA with the use of restriction enzymes, Joining the DNA, and then, Amplifying the Recombinant DNA and then, describing each step a little further. An addition of figure might assist readers in this section, as well. I think it would be helpful to define the Donor DNA as well. Maybe saying something at the beginning of the section such as "The DNA donated by the organism being studied is called the Donor DNA." If vocabulary is addressed first, it will be easier for the reader to follow along by only using those words instead of an explanation each time. Kellsonp (talk) 02:19, 22 April 2017 (UTC) — Preceding unsigned comment added by Kellsonp (talk • contribs) 02:00, 22 April 2017 (UTC)

There should be a step-by-step explanation of Polymerase Chain Reaction included in this section. PCR is one of the most notable reactions in recombinant DNA and by including a graphic, this will allow for readers to better visualize this mechanism. [3] — Preceding unsigned comment added by Csf14c (talk • contribs) 02:35, 22 April 2017 (UTC)

I agree with the above proposed edits Pco11 (talk) 03:38, 28 April 2017 (UTC) (pco11)

Recombinant DNA uses

Recombinant DNA is used in research for cystic fibrosis, so this can be added among the list of uses in the article. This additional subsection could read something like, "Gene therapy is under development for treatment of cystic fibrosis. While few attempts have reached clinical efficacy, current studies like the UK Cystic Fibrosis Gene Therapy Consortium are working to use recombinant DNA methods to establish the clinical benefits of gene therapy in cystic fibrosis treatment. Abbystewart (talk) 19:41, 16 April 2017 (UTC)

I agree, recombinant DNA has been used to make groundbreaking discoveries in regards to cystic fibrosis. One study published in the Mayo Clinic Proceedings Journal found that "as a result of recent advances in molecular genetics, carrier testing is now available as a clinical assay in a limited number of laboratories." This is important because it shows that laboratories are using recombinant DNA to test whether someone is a carrier for cystic fibrosis.Dja13e (talk) 17:34, 21 April 2017 (UTC)

Recombinant Human Insulin

This section of the page lacks professionalism and is overtly vague, specifically referring to ‘a variety of different recombinant insulin preparations are in widespread use’. Instead, the article should read more like “Used to treat insulin-dependent diabetes (Type I), insulin was originally harvested from pig and cattle pancreases. However with the use of rDNA, the human insulin gene may be inserted into either Escherichia coli or Saccharomyces cerevisiae via transformation, rendering an insulin factory.ElizaBarrett (talk) 02:08, 20 April 2017 (UTC)

I agree, changes should be made to this section, it is not easy to follow and lacks substance. The revisions made above would make a lot more sense and help the section seem more polished. ash15d 01:38, 21 April 2017 (UTC) — Preceding unsigned comment added by AviyaHayon (talk • contribs)

Because the use of recombinant DNA in the making of human insulin is the most commonly known application, I would add more information on this topic and clarify what is already said. I would add "Because individuals who are diabetic do not have the ability to make their own insulin, they have to get insulin through other means. This is why most diabetics require insulin injections. Before the widespread usage and application of recombinant DNA, insulin was taken from animals, such as pigs. By using recombinant DNA to help produce human insulin, this eliminates the need for animals and allows its widespread use across the pharmaceutical industry." Kellsonp (talk) 02:22, 22 April 2017 (UTC) — Preceding unsigned comment added by Kellsonp (talk • contribs) 02:17, 22 April 2017 (UTC) Golden Rice

In this section, some information can be added, such as statistics on those in need of golden rice and where it is being used. The Golden Rice Project states "providing children that have Vitamin A Deficiency with golden rice could prevent about a third of all under-five deaths, which amounts up to 2.7 million children that could be saved from dying unnecessarily." Golden rice is being used in developing nations already but the costs are very high to keep the programs going.Dja13e (talk) 19:17, 21 April 2017 (UTC)

Herbicide Resistant Crops

There is very little information in this section. The article states "These crops are in commercial use in several countries", but that is not very specific. Instead the article should list the different countries that are utilizing herbicide resistant crops. Also, the article does not go into detail about the limitations of herbicide resistant crops. For instance, if a farmer constantly uses glyphosate each year to kill weeds, then the weeds could develop a resistance and then another problem arises.Dja13e (talk) 18:30, 21 April 2017 (UTC)

I agree that this section could be expanded - herbicide resistant crops are widely used and an important application of genetic engineering. --Austinjak (talk) 15:02, 27 April 2017 (UTC)

Insect-Resistant Crops Some information could be added to this section. Specifically, information about insect-resistant crops impact on non-target insects. Insects that are beneficial to the environment are not the target of insect-resistance, but the beneficial insects can still die as a result of insect-resistance. Even though negative impacts of insect-resistant crops have been shown, the positive impacts far outweigh the negative ones. Further studies can be done on the non-target insects involved.Dja13e (talk) 19:02, 21 April 2017 (UTC)

Biopolymers ('Uses' section) I think biopolymers should be mentioned in the 'Uses' section of the Recombinant DNA wiki page. These polymers have properties that are useful to pharmaceutical, manufacturing, and food-processing industries. Synthetic polymers have been replaced with biological polymers using Recombinant DNA technologies, enhancing their structural and physical characteristics, decreasing manufacturing costs, and increase yields. Xanthan gum, Melanin, rubber, polyhydroxyalkanoates, and hyaluronic acid are examples of biopolymers produced using Recombinant DNA technology. By providing hyperlinks, excessive details about each biopolymer can be avoided - but these are important commercial products that are synthesized by recombinant microorganisms. --Austinjak (talk) 14:45, 27 April 2017 (UTC)

Genomics "See also"

In this section I would add some more relevant areas of genomics such as metabolomics, taxicogenomics, transcriptomics, and pharmacogenomics. The "omics" revolution is constantly growing so it will be necessary to update this list every so often. Ideally, these words would be linked to a page with a more in depth explanation about that area. Jackierodz518 (talk) 01:37, 18 April 2017 (UTC)

This is a good idea! One of the things about Wikipedia that makes it so unique and user-friendly is that the in-text Wiki links can guide the reader to new and expanding information. Adding information for curious readers to read after viewing this article will help establish the Genomics article among others on Wikipedia. Abbystewart (talk) 23:52, 19 April 2017 (UTC)

I also think this idea is much better than what is already written because it would provide way more information regarding genomics that are beneficial to the reader. Dsg14c (talk) 22:11, 20 April 2017 (UTC)

Some other relevant areas that I would add are bacteriophage genomics and cyanobacteria genomics. I agree that this list is not extensive enough for how fast the "omics" are growing and how relevant it is in modern and future technology, medicine, etc. Mav15f (talk) 04:50, 24 April 2017 (UTC)

Human Genomics

There is no information under the Human Genomic section. I think that a lot of information could be added here such as the 1000 Genomes Project, the controversy of the Personal Genome Project, and the Cancer Genome Atlas. The 1000 Genome Project was completed in 2015 and contains data from 2,504 individuals over 26 populations all over the world with the goal of collecting a variety of human genomes . The Personal Genome Project takes advantage of the low cost of human genome sequencing with the intention of providing individuals with the ability to sequence their DNA. This project could have medical benefits for early detection of heritable diseases. Although there are medical benefits, there is a fear of fraud among participants. The Cancer Genome Atlas focuses on mutations in the order of nucleotides in specific genes that make an individual more prone to an impairment in the cell cycle. This information could lead to early detection of mutations that could eventually lead to cancer. Jackierodz518 (talk) 02:50, 18 April 2017 (UTC)

I agree with Jackie; I think there are a lot more applications of genomics that we can put under this subsection. Maybe a subsection on IVF and the concept of 'designer babies' that has caused a lot of controversy in respect to selecting for genetic traits such as gender and disease risk. I'm also surprised CRISPR doesn't have a link in this page; maybe we could do a subsection and introduce the CRISPR concept since it has its own detailed wikipedia page?La15d (talk) 03:49, 20 April 2017 (UTC)

I also agree with Jackie considering this is such a huge topic and they simply just direct us to another page when we can add some more information about it. This section could probably even go under the Applications of Genetics section because it could potentially discuss how the field is being used rather than just what human genomics is. I also think CRISPR should be mentioned in this section because it would flow very nicely. Kristenmarchena (talk) 21:39, 21 April 2017 (UTC)

I believe that the Human Genomic section should incorporate some information about the History of Celera Corporation. The Celera Corporation also set out to sequence the entire human genome through shotgun sequencing. The funding for the Celera Human Genome project ($300 Million) was one-tenth that of the publicly funded Human Genome Project ($3 Billion). Both the public and parallel projects of sequencing the human genome drove competition resulting in a faster than expected result. — Preceding unsigned comment added by Thokalath19 (talk • contribs) 02:59, 20 April 2017 (UTC)

Genome analysis

I was thinking for the 'Sequencing' subsection we could make an outline of the overall steps for Sanger sequencing. This is more of an opinion rather than something that needs to be fixed; I just think an outline would make the material a lot easier to digest since it's really dense at the moment. I had to use other sources to fully understand it when I tried to do the CR La15d (talk) 03:49, 20 April 2017 (UTC)

I was just thinking about how difficult it was to get a good definition/understanding of Sanger sequencing from the article when I was doing the critique report. An outline is a good idea; having the steps listed provides clarity while giving all the necessary information. I think most people looking up and reading about Sanger sequencing are looking for a definition and the method, so this will be very useful. Do you have an outline drafted? Abbystewart (talk) 17:55, 20 April 2017 (UTC)

This page does a really great job at explaining it: http://www.techcouncil.org/the-sanger-dna-sequencing-methods-1

"1.The region of DNA to be sequenced is amplified in some way and then denatured to produce single stranded DNA.

2.A sequencing primer is annealed to the single stranded DNA.

3.Dideoxynucleotide chain termination DNA sequencing then takes advantage of the fact that a growing chain of nucleotides, extending in the 5’ to 3’ direction, will terminate if, instead of ::a conventional deoxynucleotide, a 2’3’ dideoxynucleotide becomes incorporated. By performing four separate reactions, each containing a DNA polymerase and a small amount of one of the four ::dideoxynucleotides in addition to all four deoxynucleotides, four separate sets of chain-terminated fragments can be produced.

4.Following the replication/termination step, these chain terminated fragments will remain bound to the single stranded DNA molecule which has acted as a template. By heating these partially ::double stranded molecules and adding a denaturing agent such as formamide, the single stranded chain termination molecules can be released from their template and separated using high ::resolution denaturing gel electrophoresis.

5.The sequence of the original region of DNA is then finally deduced by examining the relative positions of the dideoxynucleotide chain termination products in the four lanes of the ::denaturing gel." I was thinking we can condense it in our own words to make a more digestible outline and source this pageLa15d (talk) 19:26, 20 April 2017 (UTC)

I completely agree on the fact that it is extremely hard to comprehend Sangar sequencing from the article. Mainly because the paragraph is very wordy and it jumps around too much. I think the outline is perfect and puts the sequence more in order and makes each job easier to understand. I think somewhere before or even with the description of the sequence, we can add better or more clear definitions of words like primer, chain termination, etc. because that was also hard to find definitions for in the critique report. Kristenmarchena (talk) 20:13, 21 April 2017 (UTC)

I noticed that the "Sequencing Pipelines and Databases" subsection is somewhat vague and lacks more detail on how computational pipelines have an important application in genomics. Though it briefly states that it is due to "the need for reproducibility and efficient management of the large amount of data associated with genome projects", I think more information on this is necessary. Specifically, I think that the article must expand on how sequencing pipelines and databases are changing and improving to work with the large amount of data associated with genome projects. For example, this article which describes how a research group "examined every gene and feature of the Drosophila genome and manually improved the quality of the annotations" taking into account and tackling 3 pre-requisites: "first, a computational pipeline and a database capable of both monitoring the pipeline's progress and storing the raw analysis; second, an additional database to provide the curators with a complete, compact and salient collection of evidence and to store the annotations generated by the curators; and third, an editing tool for the curators to create and edit annotations based on this evidence" Mav15f (talk) 04:33, 24 April 2017 (UTC)

Citations

I recall doing the CR and having certain citation links being either dead-links or redirecting to another article entirely; I'll check tomorrow which ones they were when I get my sheet back. I think we should go through and make sure that all the citations are up to date and actually functioning. La15d (talk) 03:49, 20 April 2017 (UTC)

"Kaiser O, Bartels D, Bekel T, Goesmann A, Kespohl S, Pühler A, Meyer F (Dec 2003). "Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique" (PDF). Journal of Biotechnology. 106 (2–3): 121–33. doi:10.1016/j.jbiotec.2003.08.008. PMID 14651855." This is one of the references that leads to "page not found". Will keep an eye out for others Res13k (talk) 00:47, 19 April 2017 (UTC)

Number 12 on the Recombinant DNA article is a "page not found," too: "Donna U. Vogt and Mickey Parish. (1999) Food Biotechnology in the United States: Science, Regulation, and Issues." This citation either needs to be revised with the link to the actual article or it needs to be removed. Abbystewart (talk) 18:12, 20 April 2017 (UTC)

I went through the articles online that are used and I think this is the only one that doesn't give a page for the Recombinant DNA article. Abbystewart (talk) 18:21, 20 April 2017 (UTC)

Although we are doing edits on Recombinant DNA I think I'll still make an edit on the Genomics page because 82 for example leads to a dead-link as well; it needs to be updated with a link to article or removed.. Church GM, Regis E (2012). Regenesis : how synthetic biology will reinvent nature and ourselves. New York: Basic Books. ISBN 9780465021758.La15d (talk) 18:17, 20 April 2017 (UTC)

Recombinant DNA/Source 17/Fernandez, M.; Hosey, R. (2009). "Performance-enhancing drugs snare nonathletes, too". The Journal of family practice. 58 (1): 16–23. PMID 19141266./ Doesn't lead to article; it links to a publication database with the title of the article but you have to click around to eventually find the article. I suggest we redirect the link to the actual abstract page: http://www.mdedge.com/jfponline/article/63418/performance-enhancing-drugs-snare-nonathletes-too La15d (talk) 18:41, 20 April 2017 (UTC)

Recombinant DNA/Source 6/ Russell, David W.; Sambrook, Joseph (2001). Molecular cloning: a laboratory manual. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory. ISBN 0-87969-576-5./ Although it is a book source, there is a full pdf of the article online. Suggest redirect to article page - http://www.cshlpress.com/pdf/sample/2013/MC4/MC4FM.pdf La15d (talk) 18:52, 20 April 2017 (UTC)

I think this one is a book. You can click on the linked ISBN and Wikipedia gives you the option of finding it on Google, Amazon, or Open Library. Abbystewart (talk) 19:13, 20 April 2017 (UTC)

Gotcha; the link I included above actually has the full text so we can still include the current citation but maybe add the link as an additional reference if someone wanted to view it online. Btw can you check Source 17; the link it leads me to is a blank abstract page with only the title and authors; clicking around brings you to the abstract on another link so I suggest we just change the link to the one with the abstract already dincluded La15d (talk) 19:17, 20 April 2017 (UTC)

I didn't see your link before--my bad! I checked out source 17 and you're right. It leads to a blank page with the title and authors but otherwise it's pretty insignificant. I found the same link you did for the actual article, and I agree that it's a good idea to change the link to lead to the full article. I'm slightly confused on what you mean for source 6, though. Did you find an online source with the full text for the book, or are you referring to source 17 when you write that the link can be added as an additional reference? Abbystewart (talk) 19:27, 20 April 2017 (UTC)

Sorry I didn't explain it that well! For source 6, I found a full pdf of the textbook online. Although it is a textbook/lab manual and the current citation format works, maybe we should also include a link to the full text online in case people wanted to see the full pdf. La15d (talk) 19:30, 20 April 2017 (UTC)

No you're fine! That's great! I think linking the full text provides more information and easier access than a book citation. Include the reference so we can potentially replace it! Abbystewart (talk) 19:33, 20 April 2017 (UTC)

Okay I updated it! Btw Abby and Res13k, I started to include our citation commentary on the Userpage in the top left. I copy and pasted your recommendations; I sourced y'all but you can go ahead and delete my comment at the end referencing your usernames and replace it with your current sign. La15d (talk) 19:41, 20 April 2017 (UTC)

Another thing I've noticed is this needs to be cited: "Expression of foreign proteins requires the use of specialized expression vectors and often necessitates significant restructuring by foreign coding sequences" (Citation Needed) Does anyone have any format recommendations in terms of section or organizing the paragraphs? La15d (talk) 19:24, 20 April 2017 (UTC)

History

On the main page history and controversy are two different, small sections. They should be spliced because the history of rDNA is heavily shrouded in controversy. The controversy section is too brief, not elaborative enough. It touches on GMOs, but I think the article should go farther into the controversy instead of two hyperlinks. Starting from “Today, recombinant DNA molecules…genetically modified food controversies” should be cut from the article. Instead, this should be added “With new guidelines in place, rDNA has been deemed unhazardous and is used in a plethora of products and organisms, including food. Labeled as genetically modified, common cash crop foods such as corn, cotton, and soybean have foreign DNA inserted into their genome. Usage of foreign DNA in cash crops has led to great controversy on whether modified food should be labeled—or even legal.” ElizaBarrett (talk) 02:52, 20 April 2017 (UTC)

The history section can definitely be improved through a multitude of ways. First, there is no mention of the discovery of restriction endonucleases (restriction enzyme) during the late 1960s by Werner, Arber and Hamilton Smith; the restriction enzymes were later discovered in microorganisms. These enzymes protect the host cell from the bacteriophage. Theres is also no mention of the discovery of the enzyme reverse transcriptase by Temin and Baltimore nor the mention of the successful generation of Recombinant DNA molecules by David Jackson, Robert Symons and Paul Berg. All of these advances in recombinant DNA need to be recognized in the overall history of this page. Dsg14c (talk) 19:46, 20 April 2017 (UTC)

This history section can be improved by including how Robert Pollack first raised concerns about potential biohazards of cloning in 1971. This could be phrased as "Concerns regarding the potential biohazards of cloning were first raised by Robert Pollack in 1971." This occurs prior to the the first publications describing the successful production and intracellular replication of recombinant DNA appeared in 1972 and 1973. There can be further discussion about how there were concerns about this technology prior to its successful completion. This can tie into the controversy section, but limit the detail because it should be thoroughly detailed in the controversy section. Ngrab14 (talk) 01:28, 21 April 2017 (UTC)

Controversy

Recombinant DNA is an exciting topic, however ethic and controversy are to be considered and addressed. Widespread concerns may include:
-possible harmful effects of genetically engineered organisms on the environment and other organisms.
-reduction of genetic diversity naturally with the emergence of genetically engineered organisms.
-is it ethically correct to genetically engineer humans?
-possibility of Recombinant DNA technologies evading individual privacy.
-unnecessary financial expenditure (i.e. funding).
-advances in technology may only be available to those who can afford them.
-does the introduction of Recombinant DNA technologies and genetic engineering to agriculture disrupt natural farming practices.
-will patents inhibit exchange of ideas among scientists?
-when medically applied, does genetic engineering work as well as other treatments? --Austinjak (talk) 05:03, 27 April 2017 (UTC)

The first sentence of the section “Controversy” is not specific enough in addressing the severity of the properties of rDNA which scientists were concerned about. I suggest adding more information in between the first and second sentence about how scientists were apprehensive about the dangerous properties of recombinant DNA because of possible environmental vulnerabilities and the spread of an epidemic that could be associated with developing research in rDNA. It could also be beneficial to add information about Paul Berg and Janet Mertz’s research with lambda and SV40 in 1971 which led to the Conference of Biohazards in Biological Research in 1973. This Conference is also known as the Asilomar 1 Conference which discussed the concerns of the potential for reengineered organisms to spread oncogenes. I think it is important to add this information because the section gives no information about scientific concerns before the Asilomar Conference on Recombinant DNA in 1975. Both the Conference of Biohazards in Biological Research in 1973 (addressing Berg and Mertz research) and the Gordon Conference of Nucleic Acids of 1973 (addressing Boyer and Cohen's research) discussed these potentials 2 years before. ash15d 18:04, 20 April 2017 (UTC)

I agree that the controversy section needs to be revised and expanded. Many topics in science and technology are controversial--it's important to state why. I think adding the part about the Conference of Biohazards in Biological Research is a good idea, too, because it gives the reader some factual information about the extensiveness of the controversy. Good source! Abbystewart (talk) 18:25, 20 April 2017 (UTC)

The "Controversy" section is missing crucial information regarding cloning. I believe that there should be a point emphasizing the public fear of cloning and the debates/conferences that took place during the 1970's. In addition, there should be information regarding the impact these debates had on society. These recombinant DNA debates impacted many different sectors of society. These sectors included the courts, Congress, the executive branch, interagency committees, foreign governments, the National Academy of Sciences, professional societies, the new biotechnology industry, university scientists, local governments and most importantly the media. AlejandroArias (talk) 21:50, 20 April 2017 (UTC)

I also agree that the 'Controversy' section is missing a lot of important information, and also citations. The edit that I made above successfully lists a number of concerns, and my cited material is a valid textbook published in 2010. --Austinjak (talk) 14:02, 27 April 2017 (UTC)

I agree with ash15d about how more information should be included regarding the possible environmental vulnerabilities and risks associated with recombinant DNA. At the end of the sub-section "Insect-Resistant crops" under the section uses, it mentions how "Environmental issues associated with the use of these transgenic crops have not been fully resolved." . This is a very limited and brief reference that should be covered more thoroughly in the controversy section. Ngrab14 (talk) 01:42, 21 April 2017 (UTC)

The controversy section should be named Controversy background. Also, it should talk more why this topic was controversial during early 1970. I will like to add the follow information: After, the discovery of recombination of DNA the debate of how risky this discovery could be. Maxine Singer, who contribute to solving the genetic code was the leader of this debate. Singer’s opinion was well received because of her strong background on the subject. Recombinant DNA is a great tool to amplify the genetics understanding. However, many were scare that the manipulation of DNA will cause malfunction to heredity material of the species of study. If this happened it could put in danger humans and other species. Thanks to Singer and her group the government drew restrictions on the recombinant DNA research.

I think, like someone else said, that the controversy section should be combined with the history section, as the two have many connections with one another. In addition, in my source, I found that there was one other "inventor" in addition to Boyer and Cohen, named Paul Berg. I would also add more information "Berg conducted an experiment in 1971 that was considered the "landmark" gene-splicing experiment. After this, Boyer went on to insert this rDNA into bacteria where foreign DNA could replicate naturally in its new environment." It should also be mentioned that Boyer and his colleague, Itakura, were the scientists who began the Insulin project in 1978. Kellsonp (talk) 02:07, 22 April 2017 (UTC)

This edit section should be moved under "History", not "Controversy". Kellsonp (talk) 02:21, 22 April 2017 (UTC)

Consensus For 2-3 Edits

Hey y'all, we need to come together and decide the 2-3 edits on the main 'User page' we are going to use. I went ahead and decided to put Citations as one of them since we had multipule responses pointing out deadlinks and wrong articles; but if someone thinks there are more important edits we can replace citations and/or leave it in. La15d (talk) 18:34, 20 April 2017 (UTC)

I agree with this because this is a concrete idea that we can definitely all agree on to change in order to clean up the article more! I'll start looking through the links to fix up any of the dead end links.Csf14c (talk) 18:37, 20 April 2017 (UTC)

I think the edits for the citations are most important. I suggest using the edits for the third paragraph of the introduction for Recombinant DNA, too. There was a lot of feedback on this edit, and I think a revision on the introductory section will significantly improve the overall article. Abbystewart (talk) 19:17, 20 April 2017 (UTC)

I completely agree, editing the citations is one of the bigger priorities. I also think that the recombinant DNA section needs to be altered because majority of the information in there provides most of the substance in the article. Also there were lots of responses and edits in both of these sections that could help enhance the article. ash15d 01:33, 21 April 2017 (UTC)

Okay, I wrote a more finalized edit of the first three introductory paragraphs on the User page. I credited those who gave edits and recommendations for this section--feel free to sign your name there! If there was something I missed or left out, you guys can go ahead and fix it. I basically just compiled most of the edits from that section. Abbystewart (talk) 18:44, 21 April 2017 (UTC)

I think that at least one of the other edits should be adding information in either the "History" or "Controversy" sections. These sections are relatively short and everyone agreed that they should contain more in deph information. What specifically should be edited is up for further discussion. Ngrab14 (talk) 01:50, 21 April 2017 (UTC)

The 'Controversy' section could definitely be expanded. This particular topic pertaining to Recombinant DNA is very "trending" or in other words has been in the news often in recent years. Readers should most likely be more extensively informed. I think a current news article from a valid source would be an interesting and informative addition to this section. --Austinjak (talk) 15:10, 27 April 2017 (UTC)

I've mostly added edits containing notable information that I thought was missing from the original wiki page. There were mistakes in the original citations, but they were mostly all picked up on already, and I agree that those are important to correct. Another edit that I think is really important to add to the wiki is the use of Recombinant DNA to produce commercial biopolymers. I added this edit to the 'Uses'/'uses of Recombinant DNA' sections on the talk page.--Austinjak (talk) 15:10, 27 April 2017 (UTC)

Expression

The expression section of the Recombinant DNA article needs revision. It could be expanded upon, too, though there are already existing articles on gene expression on Wikipedia that can be viewed for more information. Currently, the section is one paragraph that quickly summarizes gene expression. I think the paragraph can be split up into three small sections. This is a minor edit, but it will help with clarity. Additionally, it will be easier for editors to add information because the three paragraphs allow for more specificity. I suggest this section read something along the lines of:

"After transplantation into the host organism, the foreign DNA fragment contained within the recombinant DNA construct may or may not be expressed. The DNA may simply be replicated without expression, or it may be transcribed and translated so that a recombinant protein is produced. Generally speaking, expression of a foreign gene requires restructuring the gene to include sequences that are required for producing an mRNA molecule. The mRNA molecule is then used by the host's translational apparatus (e.g. promoter, translational initiation signal, and transcriptional terminator).

Specific changes to the host organism may be made to improve expression of the ectopic gene. Changes to the coding sequences may be needed as well to optimize translation, make the protein soluble, direct the recombinant protein to the proper location, or stabilize the protein from degradation."

I changed some of the in-text Wiki links as well, and added the link for the Ectopic expression article, since I didn't know what "ectopic" meant before searching it myself. Abbystewart (talk) 19:07, 20 April 2017 (UTC)

Functional Annotation

In the annotation paragraph, it should add the following to be more clear on what functional annotation it is. Functional annotation is what gives an organization to genes, therefore the genes are separated by categories based on their function. These categories give a more clear understanding on a physiological scale of is affected by genes and it shows differences between the sequences.

Ana Conesa, Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Manuel Talón, Montserrat Robles; Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005; 21 (18): 3674-3676. doi: 10.1093/bioinformatics/bti610 — Preceding unsigned comment added by Iem14b (talk • contribs) 20:40, 21 April 2017 (UTC)

I agree with the necessary clarification of functional annotation. I have also found it helpful to add a hyperlink to words so that readers can click words that they don't understand and open another wiki page on that topic. You're cited article is really good!--Austinjak (talk) 15:13, 27 April 2017 (UTC)

I agree with both the original tab and the user's advice. (Pco11)

Application of Genomics

I think this section does not contain enough information considering all the potential applications that could be done with genomics. There could definitely be more information on genomic medicine and some examples could be found. The same concept with the next section "synthetic biology and bioengineering". With this section way it is I don't think it is allowing the reader to see the vast advancements made in this field and how beneficial they are. Kristenmarchena (talk) 21:35, 21 April 2017 (UTC)

I agree with this edit. A lot of readers would personally care more about what they were reading and take more away from it if they could see how this could potentially affect them or how it benefits other people. Some sub-categories could be genetic analysis, genotyping, epigenetics, gene expression and transcriptome analysis, and cytogenetics. — Preceding unsigned comment added by Kld15e (talk • contribs) 03:18, 22 April 2017 (UTC)

I agree with both Kristenmarchena and Kld15e. I don't think the short list of genomic medicine, synthetic biology and bioengineering, and conservation genomics does it justice. I think that the "genomic medicine" area is too broad. It might be beneficial to add some specific examples of genomic medicine like they did under "synthetic biology and bioengineering". For example, it might be beneficial to talk about how and why genomic medicine is regarded as the future of medicine. A specific example of this is E-Cell stimulation. According to Chris Sander from the Science magazine, "Arguably the largest impact of genomic technologies on biological research will come from the emerging ability to simulate cells and organisms on the computer. The goal is to simulate the causal and temporal behavior of a cell as a network of genes and gene products and to simulate the behavior of the organism as a network of cells" Mav15f (talk) 03:59, 24 April 2017 (UTC)

Another specific addition/example of genomics and technology is the bioinformatics approach to genomics and next-generation sequencing. I think technology could be a new section under "Applications of Genomics". An article that expands on this is "Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing" from the Briefings in Bioinformatics magazine. Mav15f (talk) 04:15, 24 April 2017 (UTC)

I also thing that this section could benefit from more information. In the "Genomic medicine" section, I would include information about GWAS. "One of the many ongoing medical studies is called the genome wide association study (GWAS). The goal of this study is to focus on a specific disease and sequence the DNA of as many individuals who have this disease. The hope is to find a pattern or common variation in the genome of these individuals. The greater number of patients who have their genome sequenced, the more reliable the data will be in determining the mutation(s) at root for each disease." Jackierodz518 (talk) 01:57, 25 April 2017 (UTC)

Assembly

The Assembly section very briefly mentions EST's which was one of the questions on the critique report. I think we could add a very clear definition or even give it a subsection to add some more explanation about it. Or we could make the assembly section longer just to show the relation between EST's and the Assembly. Kristenmarchena (talk) 21:53, 21 April 2017 (UTC)

Research Areas

Though not completely necessary, I think it might be helpful to introduce the area of genomics research with a broad look at how much it has advanced in the past couple of decades instead of just listing some research areas right off the bat. I think this might help because the research areas related to genomics are endless and keeps growing, as stated under the "history" section of the article. For example, showing a figure such as this one https://www.nature.com/nature/journal/v422/n6934/pdf/timeline_01626.pdf might help better introduce such a broad topic. Also, I think a brief sub-section under "research areas" should be dedicated to possible future research as well as their applications. Some examples can include exploring the interaction between DNA and proteins in in vivo environments, exploring the ethical, legal and social issues associated with genomic research, among others. Mav15f (talk) 05:23, 24 April 2017 (UTC)

Restriction Enzymes Needed in creation section

(copied from original article, first paragraph under creation) Molecular cloning is the laboratory process used to create recombinant DNA.[2][3][4][5] It is one of two widely used methods, along with polymerase chain reaction (PCR), used to direct the replication of any specific DNA sequence chosen by the experimentalist. There are two fundamental differences between the methods. One is that molecular cloning involves replication of the DNA within a living cell, while PCR replicates DNA in the test tube, free of living cells. The other difference is that cloning involves cutting and pasting DNA sequences, while PCR amplifies by copying an existing sequence.

I was working on the edits and I noticed under the “creation” section it did not once mention the usage of restriction endonuclease enzymes to make the specific cuts on the vector and the DNA that contains the gene of interest. I feel like it should be mentioned because making specific cuts to the vector and to the DNA of interest is a key step in making recombinant DNA. Furthermore, in that same section it mentioned that Polymerase Chain Reaction (PCR) is one of the processes used to create recombinant DNA, but doesn’t PCR only amplify DNA. PCR isn’t specifically used to create recombinant DNA, but it can be used to make more of a recombinant DNA.

Uriel-Louken (talk) 19:02, 25 April 2017 (UTC)

Uses

I think biopolymers should be mentioned in the 'Uses' section of the Recombinant DNA wiki page. These polymers have properties that are useful to pharmaceutical, manufacturing, and food-processing industries. Synthetic polymers have been replaced with biological polymers using Recombinant DNA technologies, enhancing their structural and physical characteristics, decreasing manufacturing costs, and increase yields. Xanthan gum, Melanin, rubber, polyhydroxyalkanoates, and hyaluronic acid are examples of biopolymers produced using Recombinant DNA technology. By providing hyperlinks, excessive details about each biopolymer can be avoided - but these are important commercial products that are synthesized by recombinant microorganisms. --Austinjak (talk) 14:45, 27 April 2017 (UTC)

Genetic transformation of prokaryotes - especially E. coli should be described more in depth.
From the original Recombinant DNA wiki:
"Scientists engineered a non-pathogenic strain (K-12) of E. coli bacteria for large-scale laboratory production of the enzyme. This microbiologically produced recombinant enzyme, identical structurally to the calf derived enzyme, costs less and is produced in abundant quantities." "Recombinant insulin is synthesized by inserting the human insulin gene into E. coli, or yeast (saccharomyces cerevisiae)[14] which then produces insulin for human use.[15]"

Elaboration on transferring DNA into E. coli:
E. coli is the main host cell used in research on Recombinant DNA. To undergo transformation, or introduce free DNA into the cell, mid-log-phase cells are treated with arctic temperature calcium chloride and then exposing them to heat for 2 minutes at 42 degrees Celsius to achieve the uptake of plasmid DNA. Transient openings in the cell wall allow the cytoplasm to be penetrated by DNA. The maximum transformation frequency of this process is about 1 in 1000 transformed cells. The drawback of low transformation rate is outweighed by the ability to readily identify plasmid-transformed cells. --Austinjak (talk) 18:24, 27 April 2017 (UTC)

Uses or History Edit

Under the header Uses or History information can be added regarding an experiment that was conducted in 1981 by Franklin Costantini and Elizabeth Lacy of the University of Oxford whom injected rabbit DNA fragments that contained the adult beta globin gene within murine (mouse) sex cells. They utilized recombinant DNA to create one of the first entirely recombinant animals.

“WIKI done - Whitney - please check”  — Preceding unsigned comment added by Srw15e (talk • contribs) 16:19, 27 April 2017 (UTC) 

Biotechnology uses edit

Recombinant DNA is widely used in biotechnology, medicine and research. Today, recombinant proteins and other products that result from the use of DNA technology are found in essentially every western pharmacy, doctor's or veterinarian's office, medical testing laboratory, and biological research laboratory. In addition, organisms that have been manipulated using recombinant DNA technology, as well as products derived from those organisms, have found their way into many farms, supermarkets, home medicine cabinets, and even pet shops, such as those that sell GloFish and other genetically modified animals.

The most common application of recombinant DNA is in basic research, in which the technology is important to most current work in the biological and biomedical sciences.[9] Recombinant DNA is used to identify, map and sequence genes, and to determine their function. rDNA probes are employed in analyzing gene expression within individual cells, and throughout the tissues of whole organisms. Recombinant proteins are widely used as reagents in laboratory experiments and to generate antibody probes for examining protein synthesis within cells and organisms.[3]

Many additional practical applications of recombinant DNA are found in industry, food production, human and veterinary medicine, agriculture, and bioengineering.[3] Some specific examples are identified below.

Recombinant chymosin Found in rennet, chymosin is an enzyme required to manufacture cheese. It was the first genetically engineered food additive used commercially. Traditionally, processors obtained chymosin from rennet, a preparation derived from the fourth stomach of milk-fed calves. Scientists engineered a non-pathogenic strain (K-12) of E. coli bacteria for large-scale laboratory production of the enzyme. This microbiologically produced recombinant enzyme, identical structurally to the calf derived enzyme, costs less and is produced in abundant quantities. Today about 60% of U.S. hard cheese is made with genetically engineered chymosin. In 1990, FDA granted chymosin "generally recognized as safe" (GRAS) status based on data showing that the enzyme was safe.[12] Recombinant human insulin Almost completely replaced insulin obtained from animal sources (e.g. pigs and cattle) for the treatment of insulin-dependent diabetes. A variety of different recombinant insulin preparations are in widespread use.[13] Recombinant insulin is synthesized by inserting the human insulin gene into E. coli, or yeast (saccharomyces cerevisiae)[14] which then produces insulin for human use.[15] Recombinant human growth hormone (HGH, somatotropin) Administered to patients whose pituitary glands generate insufficient quantities to support normal growth and development. Before recombinant HGH became available, HGH for therapeutic use was obtained from pituitary glands of cadavers. This unsafe practice led to some patients developing Creutzfeldt–Jakob disease. Recombinant HGH eliminated this problem, and is now used therapeutically.[16] It has also been misused as a performance-enhancing drug by athletes and others.[17] DrugBank entry Recombinant blood clotting factor VIII A blood-clotting protein that is administered to patients with forms of the bleeding disorder hemophilia, who are unable to produce factor VIII in quantities sufficient to support normal blood coagulation.[18] Before the development of recombinant factor VIII, the protein was obtained by processing large quantities of human blood from multiple donors, which carried a very high risk of transmission of blood borne infectious diseases, for example HIV and hepatitis B. DrugBank entry Recombinant hepatitis B vaccine Hepatitis B infection is controlled through the use of a recombinant hepatitis B vaccine, which contains a form of the hepatitis B virus surface antigen that is produced in yeast cells. The development of the recombinant subunit vaccine was an important and necessary development because hepatitis B virus, unlike other common viruses such as polio virus, cannot be grown in vitro. Vaccine information from Hepatitis B Foundation Diagnosis of infection with HIV Each of the three widely used methods for diagnosing HIV infection has been developed using recombinant DNA. The antibody test (ELISA or western blot) uses a recombinant HIV protein to test for the presence of antibodies that the body has produced in response to an HIV infection. The DNA test looks for the presence of HIV genetic material using reverse transcription polymerase chain reaction (RT-PCR). Development of the RT-PCR test was made possible by the molecular cloning and sequence analysis of HIV genomes. HIV testing page from US Centers for Disease Control (CDC) Golden rice A recombinant variety of rice that has been engineered to express the enzymes responsible for β-carotene biosynthesis.[10] This variety of rice holds substantial promise for reducing the incidence of vitamin A deficiency in the world's population.[19] Golden rice is not currently in use, pending the resolution of regulatory and intellectual property[20] issues. Herbicide-resistant crops Commercial varieties of important agricultural crops (including soy, maize/corn, sorghum, canola, alfalfa and cotton) have been developed that incorporate a recombinant gene that results in resistance to the herbicide glyphosate (trade name Roundup), and simplifies weed control by glyphosate application.[21] These crops are in common commercial use in several countries. Insect-resistant crops Bacillus thuringeiensis is a bacterium that naturally produces a protein (Bt toxin) with insecticidal properties.[19] The bacterium has been applied to crops as an insect-control strategy for many years, and this practice has been widely adopted in agriculture and gardening. Recently, plants have been developed that express a recombinant form of the bacterial protein, which may effectively control some insect predators. Environmental issues associated with the use of these transgenic crops have not been fully resolved.[22]

I would have started off including what one could argue is the main antimicrobial drug used in the treatment and prevention of bacterial infections, a common term called antibiotics. Of all of the terms currently under the "uses" tab, this term would be the most recognizable to the average reader. Streptomyces and penicillium fungi are two modes of fungi that are used for the high-scale production of well-known antibiotics streptomycin and penicillin. Genetically proficient strains of these kinds of fungi have been developed to proliferate the yield of these particular antibiotics. — Preceding unsigned comment added by Pco11 (talk • contribs) 03:27, 28 April 2017 (UTC)

Genome Transplantation

For the fourth paragraph of the introduction, where they talk about the expression of the recombinant DNA, they mention how the "recombinant protein" may or may not be produced:

"Proteins that can result from the expression of recombinant DNA within living cells are termed recombinant proteins. When recombinant DNA encoding a protein is introduced into a host organism, the recombinant protein is not necessarily produced.[1] Expression of foreign proteins requires the use of specialized expression vectors and often necessitates significant restructuring by foreign coding sequences". 

I think that it would be appropriate to mention and talk about Genome Transplantation after this paragraph, as this is the method used as a true test of the functionality of a synthetic genome which ultimately results from recombinant DNA. It would be useful to know the scientific approach of testing the functionality and ability to express these types of genes.

Bd15c (talk) 05:39, 2 May 2017 (UTC)Bobur Baizack