User:Madscientist2007/sandbox

The Five Pillars of Wikipedia

Just as there are the Five Pillars of Civilization, there are the Five Pillars that help to uphold the integrity of Wikipedia (Poster Envy, n.d.). Wikipedia’s Five Pillars are as follows: 1) Wikipedia is an online encyclopedia; 2) Wikipedia has a neutral point of view; 3) Wikipedia is free content; 4) Wikipedians should interact in a respectable and civil manner; and 5) Wikipedia does not have firm rules. Allow me to illustrate.

Wikipedia is an online encyclopedia.

You can think of Wikipedia as a large, interactive, virtual library in which, we, its users (or Wikipedians) are all librarians charged with its upkeep. In this library, one has access to a multitude of reference materials, such as scholarly articles, which have been pared down and brought together to create singular articles which are important in how they each stand alone and in how they are intertwined. In one place, one website, a person needs no library card other than a device with an internet connection to access verified, factual information on a whole host of topics.

Wikipedia has a natural point of view.

Besides being librarians, we are also the authors of the volumes in this library. As such, it is our responsibility to present, as my grandmother would say, “just the facts, ma’am.” We are not here to give our opinions. We are to tell the facts as they are and to provide all sides of the story as they appear in our source material. This is not our own story. This is not our opportunity to weigh in one way or another.

Wikipedia us free content.

We are librarians and authors. We are also editors – all of us and anyone. We can edit our own work and we can edit that of others. As always, nothing should be verbatim and copyrights still apply. We own nothing other than the little red pen we use to make our corrections.

Editors should interact with each other in a respectful and civil manner.

“Shhhh! Someone else is talking.” “Mind your p’s and q’s.” “ If you don’t have anything nice to say, don’t say anything at all.” These rules of etiquette apply to the world of Wikipedia, just as they do to life in general. It is okay to disagree, but not to be disrespectful. Wikipedians, while not seen, have feelings too.

Wikipedia does not have firm rules.

The world of Wikipedia has not set rules or restraints, just guidelines. We are free to explore and try new things. We are free to be adventurous in our own writing and in our editing the work of others. Let the creative juices flow and let your imagination soar. It is okay to make mistakes. They can be fixed, and if you don’t fix them, be sure and secure, in the fact that some else probably will (or will at least point them out.

Other guidelines

While the Five Pillars are key, there are other guidelines that serve to make our library even better.

Verifiability.

Can the information presented be back tracked? Does the trail lead to a source that can be trusted? No hearsay here please – just the cold, hard facts.

Notability.

Does a topic deserve to adorn the hallowed shelves of our library? Is it worth our time to write about it? Is it worth others’ time to read about it? Have there been those that have written about it before in books, journals, etc.? Are they removed from the subject and do they stick to the facts? Or, do they have an agenda. We may not have set rules, but we don’t let just any topic into our library.

No original research.

I don’t care if you are Albert Einstein. You are not allowed to publish your latest theory of relativity on your Wikipedia page. This is not the place.

Now, if you want to write an article on Darwin’s theory of evolution using information from reliable sources, then go right ahead, Mr. Einstein. I just ask that you do not plagiarize and you do not copy from copyrighted sources. In fact, save us both some time, and just avoid such sources all together.

With that said, welcome to our library. Feel free to browse, search, write, and edit. Feel free to comment, and yes, talking is allowed. Enjoy.

                                                     References

5 Pillars of Civilization. (n.d.). PosterEnvy. Retrieved September 15, 2013, from http://www.posterenvy.com/servlet/the-1506/Five-Pillars-of-Civilization/Detail

Wikipedia:Training/For students. (2013, April 24). Wikipedia. Retrieved September 15, 2013, from https://wiki.riteme.site/wiki/Wikipedia:Training/For_students/

Summary of characteristics of target article

According to Dr. Robert A. Giacalone, a business professor at Temple University, “Small things are seeds that often grow into bigger things. Giant trees start as germinating seeds. So, relax. Watch the small things grow." That is our ultimate goal for our WikiProject – to start with a planted seed, nurture it, feed it, water it, and watch it grow and, eventually bloom, into a flower or a tree.

Just what is our seed, you might ask? Our seed is the article as it is initially presented. In our case, the article in its infancy and is what is known on Wikipedia as a stub. A stub tends to be short in length, and in meaningful content or substance. It is in critical need of additional information. Basically, it is bare bones.

We, as a group, want to grow our stub into something much more substantial. On the other hand, like a seed, a stub does contain the starting material, and is of and in itself not insignificant in the broader scope of things. However, we want bigger and better, not just for ourselves, but for our audience at large, which basically is the world.

Our goal is to strive for an article that is between B class and GA class. B class articles are three steps up from a stub. There are 6 criteria that define this class of articles. There needs to be references, both in the article itself (i.e. inline citations) and at the end of the article (i.e. a reference section). In order for the sources to be reliable, they must be fact-checked, subject to peer review, and published by an actual publishing firm, such as a journal article or textbook. The article does a fair job of explaining the topic. However, further information may be needed in some parts. The article should be structured in its format, with headings and subheadings that help the article along in orderly fashion. The writing should be of good quality, with little to no grammatical miscues. If you have pictures, diagrams, charts, graphs, etc. that help explain and/or enhance the text, they should be included if appropriate. Finally, the article, even if the topic is fairly technical in nature, should be written for the layman, and not the expert. Overall, a B class article is a good, well cited article, but it can be better.

The next step up is a GA class article, with the “GA” standing for “good article.” Like the B class article, the GA article subject to 6 criteria. Here the writing is clean and clear. The article is well organized and is structured in such a way that it flows effortlessly from one subtopic or section to another. The information it contains is documented throughout and backed by reliable sources, which do not include original research. It addresses the key aspects of the topic and provides information that is relevant to the topic at hand. The article is written such that all sides are presented without prejudice. While changes are expected, there should not be a need to revise it on a daily basis. As with a B class article, illustrations, etc. should be used if they are appropriate and increase the quality of the article. However, they, too, should be properly captioned and referenced.

The stub is our seed, our beginning. By the end of the semester, we hope to have a tree.

Practicing Citations

Double Strand Break Repair

Double strand breaks (DSBs) are one of the most problematic forms of DNA damage. If they are not properly repaired, DSBs can lead to more severe problems, such as mutations and chromosome rearrangements. DSBs can be caused by stress factors such as radiation and oxidation. There are two options open to cells when it comes to repairing double strand breaks. One option is homologous recombination (HR), while the other is nonhomologous end joining (NHEJ). The phase of the cell cycle is one determinant in deciding which option the cells pursues. For instance, HR can only be employed during two phases of the cell cycle, S and G2; a template is mandatory for this pathway to operate. On the other hand, NHEJ is not restricted to any particular phase and is not encumbered by the template restraint of HR. Another determining factor in this decision is resection, which results in DNA that is single-stranded. The nonhomologous end joining pathway does not act on DNA that has been resected as the heterodimer involved in the initial steps of the pathway does not bind well to single-stranded DNA. Furthermore, homologous recombination uses single-stranded DNA to “to invade a homologous DNA region situated elsewhere in the genome (donor sequence), which is used as a template for DNA synthesis.”

List of References for Article on Molecular-weight size marker

"Chapter 8 A. Recombinant DNA Technology." Kenyon College. N.p., n.d. Web. 18 Oct. 2013. <http://biology.kenyon.edu/courses/biol114/C

-Briefly discusses gel electrophoresis and the role of markers or standards in this technique

-Discusses various molecular biology techniques,such as PCR and blots (i.e. Northern, Western, and Southern)

"Gel Electrophoresis of Proteins." AES Application Focus. AES Electrophoresis Society, n.d. Web. 18 Oct. 2013. <www.aesociety.org/areas/pdfs/Garfin_1DE_WebArticle9-07.pdf>.

-Discusses the various components of immunoblotting, including the role of markers or standards (Section 9: Molecular Mass Estimation)

Madscientist2007 (talk) 04:57, 22 October 2013 (UTC)

“Gel Electrophoresis of DNA." N.p., n.d. Web. 22 Oct. 2013. <http://depts.noctrl.edu/biology/resource/handbook/gel.pdf.>

-Here’s a paper about gel electrophoresis, using DNA markers

-Although not all sections are revelevant, definitely contains useful information about application

Avise, John C. "Molecular Markers, Natural History and Evolution (Google EBook)." Google Books. N.p., n.d. 2013.Web. 22 Oct.<http://books.google.com/books?id=2zYnQfnXNr8C&printsec=frontcover#v=onepage&q&f=false >

-Here is a book that is all about the evolution of molecular markers

-Will contribute greatly to our history section

"Using Molecular Markers." Population Improvement. N.p., n.d. Web. 22 Oct. 2013.<http://www.fao.org/docrep/008/y5843e/y5843e09.htm>

- Provides very useful information in the first few sections; especially discussion about types of markers, and choosing the right one

Jirwin1097 (talk) 19:37, 22 October 2013 (UTC)

Here are a few more references:

Crow, Dr. Emily. "Choosing the Right Molecular Weight Marker for SDS-PAGE." Bitesize Bio. N.p., 26 Mar. 2012. Web. 21 Oct. 2013. <http://bitesizebio.com/articles/choosing-the-right-molecular-weight-marker-for-sds-page/>.

- Discusses 3 main things that should be kept in mind when choosing a marker for SDS-PAGE, and gives examples of actual products to consider.

Blaber, Dr. Michael. "Lecture 20: Gel Electrophoresis." BCH5425 Molecular Biology and Biotechnology. N.p., n.d. Web. 21 Oct. 2013. <http://www.mikeblaber.org/oldwine/bch5425/lect20/lect20.htm>.

- Discusses the necessary components of gel electrophoresis for both proteins and DNA.

- Has several simple, yet informative illustrations, that help to elaborate on the information on the text

- Most notably, for our purpose, it discusses 2 ways in which DNA markers might be constructed. It also gives some examples of proteins that are commonly used in protein markers.

Company websites:

"Protein Molecular Weight Markers Comparison and Selection Guide." Molecular Weight Marker Selection Guide. N.p., n.d. Web. 21 Oct. 2013. <http://www.piercenet.com/guide/molecular-weight-marker-selection-guide>.

- Gives a brief overview of topics such as: what molecular weight (MW)markers are, MW markers vs. protein ladders, and unstained vs. stained MW markers.

- Be careful when reading this page, as the farther you go down the more the article gets into company-specific products.

"Overview of Protein Electrophoresis." ThermoScientific. N.p., n.d. Web. 21 Oct. 2013. <http://www.piercenet.com/method/overview-electrophoresis>.

- Discusses the different types of gels and protein electrophoresis.

- Most notably, for our purpose, the article briefly touches upon protein molecular weight markers.

"Protein Handbook 2013." Life Technologies. N.p., n.d. Web. 21 Oct. 2013. <www2.lubio.ch/uploads/tx.../Novex_ProteinHandbook-Final.pdf‎ >.

- Page 13 discusses protein standards in general

- Page 17 discusses selecting and preparing protein standards

- Pages 19-22 discusses calibrating protein molecular weight. Be careful as this section starts to get into company-specific products.

Madscientist2007 (talk) 23:55, 22 October 2013 (UTC)

Additional References

Beason Abmayr, Beth. "BIOC 111 Day 2". Rice University. Retrieved 22 October 2013.

-Example of application of DNA markers and their relevance to laboratory study

Ramos, Artur (1999). "Dual and Recombinant Infections: An Integral Part of the HIV-1 Epidemic in Brazil". Research. Retrieved 22 October 2013. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)

-Picture of ladders in use, and application to research

--Pozmi (talk) 03:58, 23 October 2013 (UTC)

Singh, Om P (1 January 2009). "PCR-based methods for the detection of L1014 kdr mutation in Anopheles culicifacies sensu lato". Malaria Journal. 8 (1): 154. doi:10.1186/1475-2875-8-154. Retrieved 23 October 2013. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)CS1 maint: unflagged free DOI (link)

-HQ picture of DNA ladder

Jenson, S. D. (2003). "Validation of cDNA microarray gene expression data obtained from linearly amplified RNA". Mol Pathol. 56 (6): 307–312. Retrieved 23 October 2013. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)

-Images of RNA ladders in use

--Pozmi (talk) 04:12, 23 October 2013 (UTC)

Outline for Article on Molecular-weight size marker

I. Introduction Section

II. History

A. Invention

B. Development

III. Classifications

A. DNA markers

B. RNA markers

C. Protein markers

IV. General principle

A. Effect of gel conditions

i. Buffer

ii. Charge

iii. Concentration

iv. Type

V. Applications

A. Gel electrophoresis

B. Western blot

C. Southern blot

D. Northern blot

E. PCR

VI. Problems

VII. Improvements

VIII. Alternatives

IX. Markers currently on the market

Madscientist2007 (talk) 04:26, 22 October 2013 (UTC)

I added RNA markers to the above outline. I found these mentioned on a few websites, albeit company websites. I am not sure as to how much information we will be able to find for this subsection. Still, I thought it prudent to add it to our preliminary outline. Madscientist2007 (talk) 22:49, 22 October 2013 (UTC)

I added some applications that markers are commonly used for--we can mention which type of marker is used for which application. I also wanted a section for the effects of running conditions on markers; I added it under the general principle, but feel free to move it. Regarding that section, my current references are from scientific companies testing their product under different conditions. For this information to be useful for markers as a whole, it would be better to find less biased sources, but if not, we could put that information under section IX then.--Pozmi (talk) 01:19, 23 October 2013 (UTC)

I love the additions that you made to the outline, especially the effects on gel conditions sections. It certainly helps in making this a more complete story, which is the goal. While I am sure that we will make other changes along the way, as it stands, this outline gives us a great foundation upon which to build. Madscientist2007 (talk) 01:39, 23 October 2013 (UTC)

Ideas

-Having trouble finding information in several topics of our outline: problems, improvements, alternatives. May need to eliminate these from our article. Let me know if you guys find anything related to these sections. Jirwin1097 (talk) 21:15, 22 October 2013 (UTC)

I am having difficulty with this as well. However, I don't know if we should necessarily eliminate them. We may want to try and put them as subsections under a broader term like troubleshooting. In terms of problems, I did read that the mobility of protein standards can be affected by different buffering systems. This in turn affects the apparent molecular weight of the bands of the standard. From what I have read so far, this at least seems to be true for SDS-PAGE and SDS-PAGE buffering systems.

Also, care should be taken when choosing the standard itself.For instance, are unstained or pre-stained standards better for your particular application. This is just one example. With that said, we might want to consider a section or subsection dealing with things to keep in mind when selecting a standard. If nothing else, we should keep it in mind for either a troubleshooting section or the applications section.

Just some thoughts. I am certainly open to ideas. Madscientist2007 (talk) 23:09, 22 October 2013 (UTC)

Images

The following images are DNA, protein, and RNA ladders from Wikipedia Commons and should be safe to use.

• 
  DNA Ladder
• 
  DNA Ladder
• 
  DNA Ladder
• 
  DNA Ladder
• 
  DNA Ladder
• 
  Protein Ladder
• 
  DNA Ladder
• 
  DNA Ladder
• 
  RNA Ladder

--Pozmi (talk) 00:13, 23 October 2013 (UTC)

The following images may be acceptable to use under fair use:

• Protein Ladders in Different Buffers
• Protein Ladders Under Different Conditions
• DNA Ladder Necklace

If we decide to use any of them, then we can upload them to Wikipedia and fill in the necessary information.

--Pozmi (talk) 00:31, 23 October 2013 (UTC)

Good pictures. I especially like the second one that you have listed under fair use. It offers a great comparison. There are several possible places where we could insert it. It would be wonderful if we could find something similar for DNA and RNA ladders. However, RNA ladders will undoubtedly be more difficult. Madscientist2007 (talk) 01:09, 23 October 2013 (UTC)

First Contribution for Article

Hi Pinar and James,

The information below was put through Turnitin.com. The only things that it flagged were the actual titles and website urls in my reference list. None of the actual text was flagged as being similar. I am going to go ahead and post this to our actual article page.

I will also start our progress report on our group page.

Effects of Gel Conditions

As with experimental samples, the conditions of the gel can have an impact on the molecular-weight size marker that runs alongside them. Factors such as buffers, charge/voltage, and concentration of gel can affect the mobility and/or appearance of your marker/ladder/standard. These elements need to be taken into consideration when selecting a marker and when analyzing the final results on a gel.

Buffers

DNA Electrophoresis

Buffers act to 1) establish pH, and 2) provide ions to support conductivity. In DNA electrophoresis, the TAE (Tris-acetate-EDTA) and TBE (Tris-borate-EDTA) are the usual buffers of choice. TBE buffer preferred for small DNA pieces, whereas TAE is better suited for fragments greater than 1500 base pairs. In terms of buffering capacity, TAE is lower when compared to TBE; this generally results in slower mobility of the DNA. TBE is also capable of better resolution. However, TAE is the more preferred choice if you plan to gel extract DNA.

It must be noted that water cannot act as a substitute for one of these buffers, as the DNA will not migrate along the gel. Furthermore, using water instead of buffer will result in the gel melting.

Protein Electrophoresis

As with DNA electrophoresis, buffers can affect the mobility of both the marker and the samples. The pH of the buffer varies with the system used and consequently, each buffer system will have a different effect of the charge of a protein or proteins. In addition, in the case of SDS-PAGE, the binding affinity for SDS can be impacted by the buffering system. Even when using the same percentage and type of gel, the same proteins will migrate at different rates depending on the buffer used.

Charge/Voltage

DNA Electrophoresis

In terms of voltage, the recommended range is between 4 and 10 V/cm (i.e., volts/cm). Agarose gels are usually run at a voltage of 5 V/cm. It should be noted that the distance unit, cm, refers to the distance between the electrodes (i.e., the anode and the cathode) and not the length of the gel itself.

Voltages too far below or above this range will affect the mobility and the resolution of the bands. Low voltages will decrease the mobility and will cause the bands to broaden. On the other hand, high voltages will decrease the resolution of the bands. This is largely due to the fact that voltages that are too high can cause the gel to overheat, and even melt.

Protein Electrophoresis

Voltage plays a role in the mobility of proteins on a gel. Proteins will migrate faster at higher voltages. Consequently, the gel running time will be shorter. Conversely, higher voltages can result in greater band diffusion. Also, if the voltage is too high, the temperature in the electrophoresis chamber can become such that the gel begins to melt.

The voltage that a gel should be run at depends on the type of the gel. For some gels, the voltage remains constant throughout the run, whereas, with other gels, the initial voltage is allowed to remain constant for a specified time before it is increased. This second voltage is then used for a specific time frame, after which, it may also be increased.

Concentration

DNA Electrophoresis

Agarose concentration must be taken into account when selecting a marker. The gel percentage effects the migration of the DNA. Generally, the higher the gel concentration, the slower the rate at which the DNA will move through the gel. This is in addition to the role molecular weight plays in the migration of a DNA ladder or sample, that is to say, that the higher the molecular weight, the slower the DNA will migrate. Another issue to consider is the conformation of the DNA (i.e., closed circular (usually supercoiled), nicked circular, linear, etc.) Typically, supercoiled DNA will migrate the fastest whereas linear DNA will have the slowest migration rate when compared on a gel of a particular concentration.

Gel concentration also has an impact on the ability to visualize the bands run out on the gel. Smaller bands are better separated resolved on a higher percentage gel, whereas increased molecular-weight bands are more easily visualized on a lower percentage gel.

Protein Electrophoresis

In terms of percentage, gels used for protein electrophoresis can be broken down into single-percentage gels and gradient gels. Single-percentage gels are also referred to as linear gels. For linear gels, the selected percentage usually falls between 7.5% and 20% Common percentage ranges for gradient gels are 4-15% and 10-20%. Each type of gel has its own advantages. For instance, linear gels are preferred when several proteins have similar molecular weights; better separation between these proteins will be displayed by a linear gel. On the other hand, gradient gels are a better choice when the samples of interest contain proteins of vastly different molecular weights or that cover a large range of molecular weights.

References

Madscientist2007 (talk) 19:46, 29 October 2013 (UTC)

Different Types of Molecular Markers

Many kinds of molecular markers exist, and each possesses unique characteristics. Before selection of molecular marker, it is important to become familiar with these characteristics and properties. In a particular instance one type may be more appropriate than another. Here are some examples of the more commonly used molecular markers.

RFLP

Restriction fragment length polymorphism is a technique used to detect variations in homologous DNA. Specific restriction endonucleases are used to digest DNA. The RFLP molecular marker is specific to a single fragment.

SSR

Simple Sequence Repeats, or microsatellites, are short sequences of DNA base pairs. This molecular marker is most frequently used for population genetic studies.

AFLP

Amplified fragment length polymorphism is a PCR base DNA fingerprinting technique. DNA is first digested with endonucleases. The restriction fragments are then ligated together. A molecular marker is then generated when specific fragments are selected for amplification.

RAPD

Random amplified Polymorphic DNA is a technique that is conducted the same as AFLP. The difference is that the molecular marker is generated at random.

SNP

Single nucleotide polymorphism is a technique used to detect variation in a single nucleotide.

Notes about article contributions

Hi James and Pinar,

As I am sure we all realize by now, there are a lot of websites (albeit, mostly company) to sift through for this topic. Some of the searches for molecular-weight size markers (or similar search terms) do bring up hits for molecular markers as well. We must be careful when picking out which sites to use as the two topics are not the same (Molecular-weight size markers vs. Molecular markers. I know from my own searches that I have come across search hits that look really promising, only to start reading the article/paper and find out that it discusses molecular markers and related topics. I know that I have mentioned this before and I am truly sorry if I sound like a broken record. I just would hate for anyone of us to waste time working on the wrong topic, especially with everything else that we have going on.

Just some thoughts.Madscientist2007 (talk) 00:36, 30 October 2013 (UTC)

Hi Erin,

I agree that the name makes it tricky when researching. For example, I came across another marker that I thought we could add, allelic markers used for AFLP, but it turns out this is a genetic marker rather than the type we're looking for. If they were ubiquitously known as ladders rather than markers, then perhaps we could change the name, but considering that the early patents call them "size markers", "molecular-weight size marker" might then be the best description, although not the best search term. I think I'll add this distinction to the article; if we've come across the issue through research then other users are likely to run into it as well.--Pozmi (talk) 02:12, 30 October 2013 (UTC)

Hi Guys,

I was just checking our information for this week. This is a group entry this week. My understanding is that we are all supposed to contribute some substantial entry/information to our actual article. Am I missing something? Please advise.

Madscientist2007 (talk) 02:59, 30 October 2013 (UTC)

Hi Erin,

Yes, I also understood it as everyone adds in their own write-up. Your contribution has been very substantial and I think the article has already improved. I'll be adding in my own write-up within the hour. --Pozmi (talk) 03:08, 30 October 2013 (UTC)

Notes about Unit 10 Contributions

I am currently working on information to help bolster the DNA and Protein markers sections. I am also trying to compile information on different types of protein markers, i.e. unstained, prestained, natural, and recombinant. Madscientist2007 (talk) 17:25, 12 November 2013 (UTC)

I submitted my contribution to Turnitin.com. Only information in the Reference section was flagged. Now that we have the extension, I am going to hold off adding it to our article until we receive our Unit 8 feedback, which should be either today or tomorrow. I will, however, post a preview of it on this page so that you have an idea of what I am planning on adding. Please feel free to let me know if you have any questions. Thanks,Madscientist2007 (talk) 21:12, 12 November 2013 (UTC)

I went through the article and picked out key terms that have their own pages. I set up links for these terms.Madscientist2007 (talk) 02:47, 15 November 2013 (UTC)

I corrected some of the inline citation problems, i.e. citations at the beginning of sentences. Also, the order of citations when there are two citations for one sentence was adjusted (i.e. [18][6] was changed to [6][18])Madscientist2007 (talk) 04:30, 15 November 2013 (UTC)

I took our reviewers suggestion and changed the formatting of the "Effects of Gel Conditions" section. The section is now broken down into two parts: DNA Electrophoresis and Protein Electrophoresis. Each section has the following subheadings: Buffer, Charge/Voltage, and Concentration. For me, this set up gives the section a more logical flow. I would vote to keep it this way. Let me know what you guys think.Madscientist2007 (talk) 15:36, 15 November 2013 (UTC)

I will start putting together our progress report for this unit. Also, not to be a bug, but just a friendly reminder that this unit wraps up tonight.Madscientist2007 (talk) 15:36, 15 November 2013 (UTC)

Suggestions for article as we move forward

I keep going back to the "Different Types of Molecular Markers" section. I haven't changed anything, but I still can't help wondering if the material included really applies to our topic. Unless I am missing something completely, aren't these molecular or genetic markers and not molecular-weight size markers? If I am correct in my thinking, is there really any reason to include them? Shouldn't "different types of molecular markers" tie in more with some of what I have listed in the DNA and Protein Markers sections, like prestained, unstained, natural, and recombinant. To add to this we can talk about things such common sized markers that are available, types of stains/dyes used (i.e. protein ladders are sometimes all one color, sometimes two or more colors, etc.)Personally, I think that we should make a decision soon as to whether we keep going in the same vein with this section or revamp it to better tie it in with our chosen topic. Let me know what you guys think.Madscientist2007 (talk) 15:36, 15 November 2013 (UTC)

As basically, all of our contributions are prose thus far, we might want to start considering adding pictures. I know that one of our reviewers mentioned changing the current picture. We could start at least adding an example picture for the DNA markers and Protein markers sections.Madscientist2007 (talk) 15:36, 15 November 2013 (UTC)

Hi Erin, Good point about the "Different Types of Molecular Markers" section. If we do include it, each subsection is going to need 1-2 paragraphs, which adds up to a lot of content, considering that most of the subjects have their own pages.

As well, looking again at the definition of "molecular marker" and "molecular-weight marker" it does seem that most of them fall into the former category instead.

However, we still might be able to mention some of the techniques. For example, in RFLP each allele acts as a molecular marker, but often the samples are run alongside a DNA ladder (the type of marker we're talking about). You might not necessarily need to use different ladders for techniques likes blots vs. RFLP, etc. The ladder is chosen for its type (DNA/RNA/Protein) and size range (e.g. 1kb). So maybe we could name it "Different Uses of Molecular-Weight Size Markers" and mention the types of markers used for different techniques (with a brief description of each technique). But, there may also be a variation in the types of ladders used for a particular technique. I'll look into some specific examples to use for that section, and add in some of the pictures from our gallery. --Pozmi (talk) 22:42, 15 November 2013 (UTC)

Since you might have more you wanted to add for that section, James, I'll post my additions in the sandbox. --Pozmi (talk) 22:51, 15 November 2013 (UTC)

Hi Pinar, You raise some good points as well. What you have in mind is an interesting approach. It certainly would show that we are coming at our topic from a variety of angles. This goes for the information that James added as well. As we go forward and add further information, given the distinctions between "molecular marker" and "molecular-weight marker", we will have to continually be conscious of our presentation, especially regarding our terminology.Madscientist2007 (talk) 02:05, 16 November 2013 (UTC)

Edit of "Different Types of Molecular Markers"

Turnitin just flagged references and portions that were already on the original molecular-weight size marker wiki page. --Pozmi (talk) 00:26, 16 November 2013 (UTC)

Different Uses of Molecular-Weight Size Markers

Many kinds of molecular-weight size markers exist, and each possess unique characteristics, lending to their involvement in a number of biological techniques. Selection of a molecular-weight size marker depends upon the marker type (DNA, RNA, or protein) and the length range it offers (e.g. 1kb). Before selecting a molecular-weight size marker, it is important to become familiar with these characteristics and properties. In a particular instance one type may be more appropriate than another. Although specific markers can vary between protocols for a given technique, this section will outline general markers and their roles.

RFLP

Restriction fragment length polymorphism is a technique used to detect variations in homologous DNA. Specific restriction endonucleases are used to digest DNA. The RFLP molecular marker is specific to a single fragment. Along with alleic RFLP markers, a molecular-weight size marker, in this case a DNA ladder , is also included on an electorphoresed agarose gel. The DNA ladder allows for the size of the restriction fragments to be estimated.

AFLP

Amplified fragment length polymorphism is a PCR-based DNA fingerprinting technique. DNA is first digested with endonucleases. The restriction fragments are then ligated together. A molecular marker is then generated when specific fragments are selected for amplification. AFLP markers are run alongside a DNA ladder on a gel. A common AFLP DNA ladder is 30-330bp long. The fragments of this marker lie at 10bp intervals to increase precision.

RAPD

Random amplified polymorphic DNA is a technique that is conducted similar to AFLP. The difference is that the molecular marker is generated at random. The most common molecular-weight size marker for this technique is the 1kb DNA ladder.

PCR

An electrophoresed gel showing PCR products. The leftmost lane represents a DNA ladder with fragments at 100bp intervals.

PCR (polymerase chain reaction) is a DNA amplification technique that can be applied to various types of fragments. These include SNPs (single nucleotide polymorphism), which consist of a single nucleotide, and SSRs (simple sequence repeats), or microsatellites, which are short sequences of DNA base pairs. Both SNPs and SSRs are molecular markers used frequently for population genetic studies. After amplification through PCR, these small fragments can be visualized using gel electrophoresis, and again DNA ladders play a role in determining fragment length.

Looking ahead to Unit 12

Hi James and Pinar, I know that we have a few days before Unit 12 begins and our third contribution comes up. However, we should probably start taking a look at the following:

• sections that still need to be added from the outline
• current sections that still need to be refined (for example, the introduction)
• pictures that we want to add in and where we want to place them

As this current unit is a peer review week, we will also get additional feedback that way. However, as Dr. Safford has given the class an extension on the reviews, we may get this feedback as late as Friday. With that said, we should look ahead towards how we want to handle next week's contribution. Just some thoughts, especially as the semester is beginning to wrap up (after this week, there are only 3 more units (one of which is peer review week))Madscientist2007 (talk) 17:29, 17 November 2013 (UTC)

Unit 12 Contribution Notes

Hi Pinar, Thanks for starting the progress report for this unit. I added two comments to reflect the small changes that I have made to the article so far. By the way, what did you think of our latest review?Madscientist2007 (talk) 22:50, 23 November 2013 (UTC)

Hi Erin, it seems that two main points cropped up again in the latest reviews -- terminology and structure.

I think that both of these issues should be looked at after we've filled in most of our content, since they affect all areas of the article. For the molecular weight-size marker vs. other marker types, I hope we've made a clear distinction. Most people said it was confusing to switch between marker and ladder. However, "ladder" seems to be a prevalent term in most of our reserach, so I do think it should be mentioned somewhat. But, if we are to have one main term throughout the article, what should it be?

-marker

-molecular-weight size marker

-ladder

Also, depending on the section, we'll be describing them by types as DNA markers, protein ladders, etc.

As for the structuring, I'm intrigued by the idea to reorganize everything by marker type, like DNA/RNA/Protein. And then, within each section have subsections like development, use, etc. Some pros for this format are that it's easier for user to distinguish between the marker types, and they can immediately access all the given information for a particular marker type. Also, in some subsection areas we have more information for markers types like DNA/protein than for RNA. This reformatting might clean up the appearance in sections that don't have equal amounts of info.

On the other hand, the format we have now is more helpful to users to understand molecular-weight size markers as a whole. They can learn about different marker developments across all types, different uses across all types, etc. With the alternative format, users can still compare these things, but in our current format, with the similar information being side-by-side, it's much easier.

Since Wikipedia is so easily editable and reversible, after we decide that we've filled in most of our content, we can reformat the sections and compare the two versions. Getting the opinon of our reviewers on the reformatting will also be helpful!

P.S. Do you know a way of indenting the replies without having the put a colon at every paragraph? Sometimes I put in a lot of mini paragraphs and I wanted a bit of a shortcut to indent them. Ah well! --Pozmi (talk) 02:30, 24 November 2013 (UTC)

Hi Pinar, In terms of terminology, we should probably stick with marker. As you mentioned before, this is the term used in our topic heading. While I agree that ladder should be mentioned, we need to be even more careful now that Jim has pointed out in the article that there is a difference between molecular weight markers and molecular ladder markers in the protein section. As such, we may want to limit using the term "ladder" to this section and use marker for the rest of the article (other than the introduction, as many sites do use the term ladder interchangeably with marker).

I have been giving some thought to the formatting and I agree with your stated pros and cons for each style. In the hopes of getting some outside opinions (i.e. non-class mates)I have even had two members of my family (one with a science background and one without) to read over what we have so far and asked them as to which formatting style they think gives the article more flow. Their consensus was that splitting the article in sections by type, i.e DNA, protein, etc., would be a better way to go. After talking to them about it, I also realized that most people reading our article for work or school would probably be interested in information on either DNA markers or protein, and as such, if they should want to compare items, it would more likely be with in the same heading,for example, comparing unstained and prestained protein markers. Unless, of course, it is a very specific project which requires info on both DNA and protein markers. However, I think that it is more likely that they will focus on DNA or protein.

As for timing on these edits, I think that we might want to give these changes at least a trial run during this unit. I agree with your thinking on waiting. However, if we want input from reviewers, we only have one more unit in which reviews are done. After that, there is only one more unit for the semester, in which we make our final contributions. I think we should make the changes by the end of this unit so that reviewers can weigh in these changes, especially the formatting. As you said,things are easily reversible on Wikipedia, and we can always change things back. I just don't think that we should miss an opportunity to get feedback from our classmates while there is still time. I don't mind going in and changing the formatting. Going back to the terminology for a second, we should be careful when editing James additions in the protein section as ladder is the appropriate term there is some instances. Just some thoughts. Let me know what you think.Madscientist2007 (talk) 14:21, 25 November 2013 (UTC)

I changed the format of the article. I think that we should hold onto this general format at least until we get the next set of reviews back.Madscientist2007 (talk) 01:39, 26 November 2013 (UTC)

I started changing "ladder" to "marker" where it seemed appropriate. Please feel free to change a particular instance back to the way it was should you feel that the original term was better the given context, especially if it is in a section that you wrote. James, I didn't touch the sections you wrote about Choosing the correct protein standard (other than in the title). We need to be careful with this section due to the distinction between molecular weight markers and molecular ladder markers. Overall, we need to eliminate confusion in the article as much as possible.Consistency is key.Madscientist2007 (talk) 03:54, 26 November 2013 (UTC)

I have been adding my changes to our progress report as I go along. Please feel free to let me know if you have any questions.Madscientist2007 (talk) 03:57, 26 November 2013 (UTC)

Just a friendly reminder that we need to watch the time in terms of posts/edits/changes/additions as Wikipedia is 5 hours ahead. With that being said, posts/edits/changes/additions for this unit need to be done by 6:59 at the latest if we want them to be marked with today's date. To be on the safe side, we should really shoot for 6:00 at the latest for a deadline. Just a thought.Madscientist2007 (talk) 14:19, 26 November 2013 (UTC)

Here are the comments from the OA about our 2nd contribution:

Content coverage: 5/5 - again, excellent

Wikilinking: 4/5 - decent, but could use more in the latter 2/3rds of the article

References: 4/5 - well referenced, but many citations were minimalistic and should have more fields

Writing: 5/5 Madscientist2007 (talk) 21:12, 26 November 2013 (UTC)

I went through and tried to add more wikilinks. I was able to add some. However, part of the problem is that many of the terms we use later in the article have already been wikilinked in the first portion of our discussion. Another issue is that some terms do not have a wiki page or are considered disambiguation terms and none of the options given quite fit our context. I wonder if we shouldn't consider linking to outside sources for some of the terms, especially in the last 2/3 where wikilink is sparse. Let me know what you think. Thanks, Madscientist2007 (talk) 22:09, 26 November 2013 (UTC)

An Outside Review

Hi James and Pinar,

I hope you do not mind, but I asked a family member to take a look at our article, in the hopes of getting an outsider's perspective. He is a layman in terms of molecular biology. However, he is not a total science layman, as his background is in electrical engineering and he has a great passion for physics and math. He is also a good writer and a perpetual learner. He loves reading over material like this.

Overall, he really liked the article and was very impressed with the amount of work that we have done on it. He did, however, have a few suggestions. I have listed them below:

• His favorite part was the Different Uses section. He found it quite interesting. He remarked that it helped him better understand the whole concept. He did feel that this section might be better suited elsewhere, such as the development sections. He suggested that if we did move it, we might want to consider a completely separate Development section.

• Include a few sentences in the intro between the two current paragraphs giving an overview of what the markers are used for in terms of techniques, purposes, etc. (e.g. running them on an agarose gel with DNA samples used for genotyping)

• Development section under DNA markers: For the 1st sentence of the 2nd paragraph, he felt that we should fine tune the part where it talks about high resolution so that it is more obvious that we mean resolution in terms of clarity of the bands that make up the marker.

• For structural standpoint, he felt that it would be better if we had an intro giving an overview, then broke the body into a developments section, a design section, etc., and then finish with some time of conclusion. As for a conclusion, he mentioned that we could even put the overview uses there (see second suggestion) as a way to wrap it up. He felt that the current structure sort of just lets things hang at the end.

He said to feel free to take or leave these suggestions as we wish. These were just some ideas he had based on how he would approach it if he was writing something like this.

He also wishes us the best of luck as we finish up our paper! Let me know what you think! Again, I hope you don't mind me doing this. Thanks, Madscientist2007 (talk) 04:13, 13 December 2013 (UTC)

Erin, thanks for getting more feedback on the article, and thank you to our reviewer for taking the time to read it and make suggestions. I mentioned this in my reflective essay but I also wanted to say to my group members that it was a pleasure working with you and editing Wikipedia is a great project idea! I would definitely like to see something like this in my other courses (and past courses) because it helped improve my research skills and taught me to be critical when choosing sources -- all while learning about the topic in-depth. I hope the article we worked on will be of help to other users! --Pozmi (talk) 04:58, 15 December 2013 (UTC)