Wikipedia talk:USEP/Courses/JHU MolBio Ogg 2012/Section 83/Group 83A

Hi, This is Amy Hall. I am ready to get started on our Group project. Do either of you have any preferences for the article yet? Aehall47 (talk) 23:11, 9 October 2012 (UTC)

I started investigating some possible articles for selection. I found that quite a few of them that are stub articles that could be expanded. However, how much expansion available would be of question. These ones would be DNA C, H, N or X. FsrA, and Oskar. I also investigate the Homeotic Selector Gene article. It looks like it is also a stub article that could be expanded and referenced. I found the following PubMed book excerpt. http://www.ncbi.nlm.nih.gov/books/NBK26913/#A3874 There were also peer reviewed articles that could be used as references. Our final option would appear to be the DNA Gyrase article that has a fair amount of content without being properly referenced. I am not sure how much work this would be and how that might affect our grades. Can we aim to get our article selected by tomorrow so that we have time to write our justification of our selection? Aehall47 (talk) 20:41, 13 October 2012 (UTC)

Hi, This is Aslaa. Thank you Amy Hall for the early start and the research. Sorry for the late reply. I am also ready to get started. I do not have a preference for any topic; so am willing to work on anything. I do suggest, however, something that we could contribute more to than just proper referencing as with the DNA Gyrase article. The articles on DnaC, DnaH, DnaN, DnaX, and FsrA seem interesting, but their expansion maybe limited. The homeotic selector gene seems to be our best option here. Aahmed25 (talk) 17:25, 14 October 2012 (UTC)

Hi Aslaa, with no input from Amy should we go ahead and choose an article. It looks like 83E might be going to choose Homeotic Selector Gene. What do you want to do? Aehall47 (talk) 23:28, 15 October 2012 (UTC)

This is Amy Benson. I am fine with the Homeotic Selector Gene article. I am with Aslaa that I am afraid to add just citations to an article like Gyrase. However I am up for the challenge in eidting the Mutation article. There are a few missing citations and it is listed as high importance. I also looked at the DNA mismatch repair and found that it was lacking references and details. Abenson9 (talk) 01:38, 16 October 2012 (UTC)

Amy B, DNA mismatch repair is one that interested me as well. We can expand it and add references. But since we need to submit our justification by today, we need to decide on a topic. Are we all okay with the homeotic selector gene article? OR, do either of you prefer something else? Aahmed25 (talk) 13:24, 16 October 2012 (UTC)

I am fine with the Homeotic Selector Gene or the DNA Mismatch. We can go with the Homeotic Selector Gene since you found an interesting article with valuable information to get us started. Abenson9 (talk) 14:25, 16 October 2012 (UTC)

I think that we should go with the DNA mismatch repair or DNA polymerase article. We can leave the Homeotic Selector Gene to the other group who is interested in it. I agree with Amy that there is a considerable amount of information that is lacking from the DNA polymerase article that keeps it from being a great article, including all of the references to date. I also like that there has been a fair amount of input on the talk page and the High importance of the article. If you are both good with it, let's go for it. Who wants to write the justification? Aehall47 (talk) 16:20, 16 October 2012 (UTC)

I can start the write up today at lunch if someone wants to come behind me and edit/update it. Hopefully we can perfect it by this evening. Abenson9 (talk) 16:24, 16 October 2012 (UTC)

Great, I can work on it tonight. Amy, if you will post your write up here then both Aslaa and I can do some edits and we can get it transferred to the project page once we all sign off on it. Aehall47 (talk) 17:00, 16 October 2012 (UTC)

Article assessment from other groups

Kate from Group 83D gave this assessment

Small_nucleolar_RNA_U3

This page is designated a stub article and only has very basic information. It is a low priority article and the last activity on the talk page is from 2009. The writing could flow better and once more information is added it should be broken into sections per the MCB style guide. I think the first paragraph could stand by itself and the rest of the info could be placed into a structure section. The article does have references and some good external links. It is very broad, neutral, and stable. The last edit was made in 2011 and there is only one small image. More background information would be helpful to add such as discovery, U content, and gene structure.

Here is a link to the proteins http://www.uniprot.org/uniprot/O43818 Aehall47 (talk) 00:57, 16 October 2012 (UTC)

Lauren from Group 83D gave this assessment

Segment_polarity_gene

This stub has four sentences that give a brief overview, but it could easily have a lot more information along with some pictures. It has one reference and several links to other pages, but one of the linked pages does not exist. It was last edited last month, but the only changes were italics and two links, and the last edits before that were in February 2011. The segment polarity gene has been extensively studied, so there is a large amount of information available for research and addition to the stub. The importance of the gene in development and the results of mutations could be greatly expanded. Lamcmaho (talk) 18:55, 13 October 2012 (UTC)

I will come back and add some more info when I find it. Aehall47 (talk) 23:56, 15 October 2012 (UTC)

This article is longer than a stub and has a few references, but it is lacking a lot of citations. It is also has a short overview and could use some expansion on the function section. There could also be a lot more references and expansion on the different families citing research articles. Abenson9 (talk) 01:54, 16 October 2012 (UTC)

Centrosome

Again this article has a lot of information but I think it could be ordered differently to provide better flow. There are some concers with one of the research articles referenced according to the talk page. Abenson9 (talk) 02:05, 16 October 2012 (UTC)

Justification of Article for Group 83A

We have chosen to edit and update the DNA Polymerase Wikipedia article due to the “High Importance” placed on this article by the MCB WikiProject. Currently, the status of the article is rated as “Start Class” meaning that it has an overall grade below a C on the quality scale. The DNA Polymerase page has more information than a stub article but it lacks flow, clarity and numerous references. Finding and adding references should be a quick fix that will greatly enhance the article and the article’s credibility.

A good starting point will be to investigate further the suggestions from the talk page and implement those changes where appropriate. At first glance, we have also identified that the article lacks information on the functionality of the various DNA Polymerase subunits. In addition, there is significant information and research that can be added about the holoenzyme complex. We have also just learned about processivity of DNA Polymerase when interacting with clamp proteins and this vital information is missing from the article. The sections outlining the DNA Polymerase families lacks references, flow and connectivity. Additionally, these sections can be expanded to elaborate on the similarities, differences and research performed on the different families. While we do not want to duplicate the sections referencing Prokaryotic DNA polymerase and Eukaryotic DNA polymerase on other Wikipedia pages, we feel that sections could be included that outline any similarities and differences between the two types of polymerases.

We think that the DNA Polymerase page will allow us as a group to not only expand our knowledge on a very important subject in molecular biology, but the different needs of the page allow us to work on various functions within Wikipedia that will expand our overall knowledge of Wikipedia.

Abenson9 (talk) 17:38, 16 October 2012 (UTC)

Made some edits. Looks good Aehall47 (talk) 23:32, 16 October 2012 (UTC)

Updated the links and corrected a typo. Now just waiting to hear from everyone on the finality of this and we can move it to the main page. Abenson9 (talk) 23:58, 16 October 2012 (UTC)

Hi Amy! I'm actually in group 83B but I thought I could help you out with your links; I did them yesterday for my group.

• For MCB, if you look at the title of the page, it says, Wikipedia:WikiProject Molecular and Cellular Biology; that's what you'll need to put in your brackets. If you want different text to show up, put in a | then the text you want. Example from mine: MCB WikiProject (click edit and you can see what this looks like)
• To link to subsections of articles, format it as Page Title#Subsection inside the brackets. For quality scale, that page is under MCB's Worklist, so inside the bracket's would be Wikipedia:WikiProject Molecular and Cellular Biology/Worklist#Quality Scale (final link would be quality scale; you can use spaces or underscores between words, both work for me)
• For your prokaryotic/eukaryotic pol articles, the page title inside the bracket has to match the page title exactly; you have polymerases and the page is just polymerase. You can use Prokaryotic DNA polymerases and Eukaryotic DNA polymerases (same idea above, page title|preferred text inside the brackets )

Hope that helps and saves you some time! Best, Divya Db4an (talk) 18:35, 16 October 2012 (UTC)

Thank you so much Divya, that was very nice of you! Hopefully we can help you out in return at some point during the semester. Amy H. Aehall47 (talk) 23:32, 16 October 2012 (UTC)

Yes! Thank you so much! That definitely saved me some time!Abenson9 (talk) 23:58, 16 October 2012 (UTC)

moving the justification to the project page, hope that is OK. I am pretty sure it can still be edited there. I am getting ready to log out for the night. -AH Aehall47 (talk) 01:16, 17 October 2012 (UTC)

I was watching the clock and giving everyone time to respond. I am fine with it being moved and being done for the night! Thanks! Abenson9 (talk) 01:28, 17 October 2012 (UTC)

This looks great. Looks like all the links are working fine. Thanks Amy B and Amy H. Aahmed25 (talk) 03:47, 17 October 2012 (UTC)

Article rationale assignment feedback

Two small comments. You should have used a header for the rationale section (==Article Justification==) instead of just bold ('''Article Justification'''). Also, you shouldn't sign stuff with four tildes on the project page. Signing posts should only be done on talk pages. Klortho (talk) 20:17, 17 October 2012 (UTC)

Processivity

DNA polymerase’s rapid catalysis is due to its processive nature. Processivity of DNA polymerase refers to the average number of nucleotides added each time the enzyme binds a template. The average DNA polymerase requires about one second locating and binding a primer/template junction. Once it is bound, a nonprocessive DNA polymerase adds nucleotides at a rate of one nucleotide per second. Processive DNA polymerases, however, add multiple nucleotides per second drastically increasing the rate of DNA synthesis. The degree of processivity is directly proportional to the rate of DNA synthesis.

DNA polymerase’s ability to slide along the DNA template allows increased processivity. There is a dramatic increase in processivity at the replication fork. This increase is facilitated by the DNA polymerase’s association with proteins known as the sliding DNA clamp. The clamps are multiple protein subunits associated in the shape of a ring. The sliding clamp loader proteins open up the ring structure of the sliding DNA clamps allowing binding to and/or release from the DNA strand. Protein-protein interaction with the clamp prevents DNA polymerase from diffusing from the DNA template, thereby ensuring that the enzyme binds the same primer/template junction and continues replication. DNA polymerase changes conformation, increasing affinity to the clamp when associated with it and decreasing affinity when it completes the replication of a stretch of DNA to allow release from the clamp.Aahmed25 (talk) 23:44, 4 November 2012 (UTC)

Hi, this is what I gathered regarding DNA polymerase's processivity and clamp association. It still needs some work, for I have yet to add the sources I used or cite it. Feel free to add/edit it. I will continue to work on it. The other section am addressing is still in progress. I can begin to write our progress report; I just need feedback on where you guys stand with your sections. Aahmed25 (talk) 23:53, 4 November 2012 (UTC)

This looks great. I am having trouble figuring out how to add the references. I was also wondering if either of you thought that we should change the Index for the page. DNA families seems like it should be a section header, both in the index and on the page, with the different families listed beneath. This would also indicate that maybe the header that DNA families is currently under should be deleted or expanded in some other way? I reveiwed the talk page and verified that all of the suggested changes have been made or clarified. I am still working on the families and updating them and citing them. Aehall47 (talk) 00:27, 5 November 2012 (UTC)

I agree with your suggestion regarding the families section being a header. I recommend reorganizing the entire article. I worked out different organizational schemes and I emailed both of you what I thought was more appropriate. Let me know what you think. Aahmed25 (talk) 01:05, 5 November 2012 (UTC)

I also agree that it needs to be reorganized, especially given that we want to add and expand on sections. Abenson9 (talk) 02:01, 6 November 2012 (UTC)

Quick question about references and citing sources. If we are referencing a paper that references another paper, but the comment that they make is followed up by 3 different papers, all presumably doing various research and come to the same conclusion, can we just reference the one paper (that references the rest of them)?Abenson9 (talk) 03:04, 6 November 2012 (UTC)

Yes. In fact, it's actually preferred that you reference secondary sources (reviews) rather than primary research articles. Klortho (talk) 04:26, 6 November 2012 (UTC)

Thanks! That was the answer I was hoping for too! Abenson9 (talk) 04:56, 6 November 2012 (UTC)

DNA Polymerase III holoenzyme

DNA polymerase III holoenzyme is the primary enzyme invoved in DNA replication in E. coli. It consists of three assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The core consists of three subunits - α, the polymerase activity hub, ɛ, exonucleolytic proofreader, and θ, which may act as a stabilizer for ɛ. The holoenzyme contains two cores, one for each strand, the lagging and leading. (http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2005.04805.x/full) The beta sliding clamp processivity factor is also present in duplicate, one for each core, to create a clamp that encloses DNA allowing for high processivity. (http://www.jbc.org/content/270/49/29570.long) The third assembly is a seven-subunit (τ2γδδ′χψ) clamp loader complex. (http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2005.04805.x/full) Of the seven subunits of the clamp loader complex, most have a known function - γ binds ATP, δ′ stimulates clamp loading, χ removes DnaG primase from primer, τ acts as an ATPase to activate clamp assembly and dimerizes the two cores, and ψ’s functionality is still unknown (http://oregonstate.edu/instruct/bb492/lectures/DNAII.html and http://www.jbc.org/content/270/49/29570.long). The clamp –loading complex loads the beta sliding clamp onto the DNA at the primer:template junction (http://oregonstate.edu/instruct/bb492/lectures/DNAII.html) Abenson9 (talk) 04:18, 6 November 2012 (UTC)

This is what I have gathered for the holoenzyme. When looking up information, I found that there was already a page for the holoenzyme, but I figured we could still add it to the Pol III section. Abenson9 (talk) 04:18, 6 November 2012 (UTC)

DNA Polymerase family/subunits

http://users.ox.ac.uk/~kearsey/reprints/reviews/kearseyR02.pdf

http://users.ox.ac.uk/~kearsey/reprints/reviews/kearseyR02.pdf http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0000786 http://www.nature.com/nrm/journal/v5/n12/box/nrm1530_BX1.html http://www.ebi.ac.uk/interpro/IEntry?ac=IPR006172 http://www.answers.com/topic/dna-polymerase#DNA_polymerase_families link includes the current Wikipedia page on dna polymerase but also includes oxford dictionary’s write up on dna polymerase

above is a link to a paper that I found which lists out a lot of the functionality of the different polymerases. Abenson9 (talk) 04:42, 6 November 2012 (UTC)

added a few more links Abenson9 (talk) 05:00, 6 November 2012 (UTC)

Unit 9 Progress Report

We have divided the article into six different sections in order to focus on one issue at a time. Each of the group members is responsible for expanding and/or adding a new section. Points we are currently addressing include processivity of DNA polymerase, the different polymerase families and types of polymerases and expanding the functionality of the enzyme. We have started to add missing references and have also reviewed the comments on the talk page for our article to ensure that suggestions have been addressed or will be addressed in the final article.

As far as the remaining weeks, we have a full agenda. Our goal is to change the organizational scheme of the article entirely. Since the article seems to be missing a significant amount of information, we will be adding new headers and sections to the table of contents. We have discussed and designed a new organization system in order to add the missing information. Our plan at this time is to have headers for history, function/action, DNA polymerase families, Prokaryotic DNA polymerases and Eukaryotice DNA polymerases as well as headings for references and external links. Currently, the article completely lacks information on the history of DNA polymerase, so we plan to include a new section regarding the discovery and purification of DNA polymerase.

Furthermore, the section on functionality lacks subsections on the catalytic mechanism of DNA polymerase. One of the group members will be addressing that topic and adding a subsection for processivity and the mechanism of action. In the sections for eukaryotic and prokaryotic DNA polymerases, the article provides links to the prospective pages but does not include any information regarding them. Our plan is to keep the two sections while addressing them in more detail. For the eukaryotic DNA polymerase, subsections will elaborate on the 15 different DNA polymerases including telomerase. As for the prokaryotic DNA polymerase, subsections will be headed with DNA polymerases I-V with at least a brief description of function and possible species information as well. We will be doing this in an effort to provide information that is not found on the Prokaryotic DNA polymerase or Eukaryotic DNA polymerase pages.

We have compiled data and information that has yet to be added to the article. We need to work on referencing and citing. Considering that we are all equally new to Wikipedia, this will be the most challenging part. We hope that interactions with other Wikipedia users and editors will be a source of help. Also, the different articles on our classroom page should be a great way to start. Aahmed25 (talk) 02:16, 6 November 2012 (UTC)

Reviewed and approved. Aehall47 (talk) 02:35, 6 November 2012 (UTC)

It seems like its missing a few words. Thank you Amy H; your review added a few more words. The requirements of the report is to be ~400-500 words. It is approximately 355 words now. I am not sure if that will be an issue. I will postpone posting it to the group page to tomorrow so we can have more time to edit and add more to the report. Aahmed25 (talk) 02:54, 6 November 2012 (UTC)

This version addresses your concern :-) Aehall47 (talk) 03:41, 6 November 2012 (UTC)

This looks good to me other than I added a link to the Eukaryotic DNA polymerase page. Abenson9 (talk) 04:32, 6 November 2012 (UTC)

Article Outline

1. History

1.1 purification

2. Function/Action

2.1 Catalytic Mechanism

2.2 Processivity

3. Variations among species

3.1 Prokaryotic Polymerases

3.1.1 pol I

3.1.2 pol II

3.1.3 pol III

3.1.4 pol IV

3.1.5 pol V

3.2 Eukaryotic polymerases

3.2.1 Polymerase beta and lambda

3.2.2 Polymerases alpha, delta and epsilon

3.2.3 Polymerase eta, iota and kappa

3.2.4 Polymerase Rev1 and polymerase zeta

3.2.5 Polymerase sigma

3.2.6 Telomerase

3.2.7 Polymerase gamma

3.2.8 Polymerase mu

3.2.9 Polymerase theta

4. DNA Polymerase Families

4.1, 4.2, 4.3 etc

Hi guys. I posted a copy of the preliminary outline so we can actively make changes to it and have it available for everyone to access. Lets try and have it finalized within the next few days. Aahmed25 (talk) 21:34, 11 November 2012 (UTC)

Hi, I don't know if you've gotten the feedback that I gave to Dr. Ogg to pass along yet, or not. But I think that you must post this outline and this proposal to the article's talk page, now. This is a major reorganization of an article that already has a good bit of content, and it is very important that you engage the existing editors of this article before commencing. Don't be afraid! Let them know the context, and I'm sure you will get constructive feedback. One thing that I notice already is that Prokaryotic DNA polymerase and Eukaryotic DNA polymerase already have their own main articles, separate from this one. Are you considering merging those two sub-articles into the main DNA polymerase article? I think it would not be a bad idea -- both of those articles are pretty sparse, and the sum total of all the material here doesn't seem too much for a single article. Klortho (talk) 03:05, 12 November 2012 (UTC)

Should we post on the Eukaryote and Prokaryotic polymerase talk pages as well about the possibility of merging them with the DNA polymerase page? Abenson9 (talk) 01:48, 13 November 2012 (UTC)

Yes, see Help:Merging. Here's what I'd suggest:

• Start a new section here titled "Proposed merger of subsections into this article"
• Tag each of those two articles, at the top of the article pages (not the talk pages) with the {{Merge}} template, like this: {{merge|DNA_polymerase|discuss=Talk:DNA_polymerase#Proposed_merger_of_subsections_into_this_article|date=November 2012}}.

It shouldn't be controversial, so you could just wait a couple of days, and if no one objects, go ahead and do it.

Klortho (talk) 03:03, 13 November 2012 (UTC)

Peer-Review

Hey Group 83A, I just wanted to let you know that I have looked over what you have done so far and am impressed by the amount of work that you have taken on. I really think that the merger of Prokaryotic DNA polymerase and Eukaryotic DNA polymerase with your article benefits everything as those two articles were previously lacking and the merger presents all the information on one page. The one thing that the article is really lacking besides a bit of fine tuning is citations. I know from reading your progress report that they are in the works, and i can definitely relate to citing and referencing being challenging since we are new to Wikipedia. One thing that really helped me is the Wikipedia template filling tool. If you have a PubMed ID you can generate a citation easily. If you don't and it is a journal article that is on PubMed, I just search the title to get the ID. I hope this helps with your citing. Keep up the great work! JGLehman3 (talk) 01:50, 21 November 2012 (UTC)

I would like to echo what John said about adding more references to support the content of your article. You also have a link to a page that does not exist concerning Malcolm E. Gefter. I checked to see if maybe an article exists under a variation of the name, but I was not able to find one. You have an excellent amount of information in your article, but if I were to suggest any expansion not yet mentioned, I would say possibly give a little more information about how polymerase is used in experiments. You say that various DNA polymerases are used in experiments and then go on to discuss different types of polymerases; maybe you could list types of experiments for which each type of polymerase is used when you describe each one. Lamcmaho (talk) 04:26, 2 December 2012 (UTC)