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

Units 1-6

Introductions/General

Hi guys,

I actually just wanted to ask you if you have decided on a certain article? I was busy with my projects and midterm for a couple of other classes im concurrently taking but on the 15 of October I will literally complete all aspects of this project, including choosing an article and fullfilling the requirments the professor has asserted.

Stay intouch or communicate so we can do this together and share ideas.

Thanks. Assad071490 (talk) 02:14, 15 October 2012 (UTC)

Hi Assad and Divya,

I'm sure we've all been busy so no problem. I spent a little bit of time looking at the list of potential articles to choose, what criteria we should use, and the other group's discussions (so we don't pick anything already under consideration in another group). My suggestion would be to select nucleotide excision repair. It has a fair amount of content already (so expansion might not be the main way we improve the article) but has relatively few sources, the flow of the test is not extremely easy to read, and the text is so full of acronyms it is difficult to get through. In terms of sources, it has some, but only half are actually cited in the text, which is another weakness. We could add citations to the non-cited sources, and of course, add further sources to what is included and any new test we add. Also, I've found a few cool images that I think would benefit beyond the simple one currently included.

It's getting pretty near the deadline for this assignment, I'm happy to do another article if anyone has another preference - but we should probably get moving pretty quickly. Carl.d.martin (talk) 02:31, 15 October 2012 (UTC)

Assad: Hello d. I think it is a good choice, wonderful. just one more thing I would like to clear, are we just submitting a summary of why we chose this article? or is there any addition to what has to be done? thanks.Assad071490 (talk) 02:38, 15 October 2012 (UTC)

Divya: Carl, I think we have to generate our own figures because of copyright issues and whatnot. You have to have the authors permission and a bunch of other things when you upload the image. (I did this for the ridiculous picture in my sandbox). Feel free to correct me if you know otherwise! -d Db4an (talk) 16:27, 15 October 2012 (UTC)

Sorry about my late reply. I was out of town this past weekend and trying to finish a few assignments due last night for other classes. My thoughts on this are below. I'll be on gchat for most of the day so if you want to talk about this real time/put together a final statement, shoot me a message at any time. I just sent both of you emails! Cheers, d Db4an (talk) 15:30, 15 October 2012 (UTC)

Article Selection Process

hello guys,

Sorry I forgot to mention, but since this is due on the 16, it is better we all share the most of what we can in the chossing and arbitration for the summary for this project, so we can actually be in a position of completing this by 15 october by midnight. I will be working on this project but if time is lapsing and no responses have been posted, I may have to choose an article and initiate the project along with the summary.

So please I advise that we communicate and get this efficiently done.

thanks guys. Assad071490 (talk) 02:33, 15 October 2012 (UTC)

Hello Carl,

I was just wondering if we all can possible post our personal rationales for the choice of this nucleotide excision repair by october 15 after noon, at 1pm or 2pm. Then I can actually accumulate all our rationales and "mix" them, meaning all our rationales from each of us into an accumulative summary and then by the next day hopefully we will be good to go : ) but our last day to actually work deligently is Monday october 15. We have to give it our all, with our utmost efforts too. :)

thanks guys. Assad071490 (talk) 02:53, 15 October 2012 (UTC)

Oskar vs Nucleotide Excision Repair

Article links

• Nucleotide excision repair
• oskar

Assad: hi Carl and Db,

I have posted our group as assigned to topic "nucleotide excision repair". Carl and me decided on this yesterday while we were posting, but is it okay with you db? regarding the acronyms in the text as carl mentioned, Im sure the interpretation would not be that hectic, since we can still figure them out and we have our course textbook "Molecular biology of the Gene"that we can refer to as well as reference in the upcoming tasks(unit 9 & 12) for better understanding of the topic. If expansion is not the best option, the references the author used seem pretty plausible. Im sure assessing them would lead us in the right direction.

So guys, I am creating the page under th specific title the professor mentioned and I am posting the summary of rationale. Is it ok with you guys? Feel free to make changes by editing but let me know if you do by posting on our talk page for the group. I know the more ideas we accumulate from eachother and aggegate them into our rationale, the more quality we have.

Thanks Carl. and Db stay connected. Assad071490 (talk) 15:42, 15 October 2012 (UTC)

Divya: Looks like we're posting at the same time Assad. So I've been looking at nucelotide excision repair a bit more, and I'm not so sure about this article. Picking a less developed article might be the easier way to go. In my experience, editing something poorly written is much harder than writing from scratch. (I'm taking a science writing class right now, and I wish I could write most of those things from scratch.) Nucleotide excision repair is a big topic that can lead to quite a few other things. The article we end up writing will either be A) very long or B) very brief in terms of content. Generating diagrams is also going to be a pain. I'm still game to do it if this is what you two want to do, but it's no where near my first choice.

That being said, I really like the potential for oskar. The article is a stub, but there there is a lot on the subject if you run a search via Entrez. I think we can generate more figures and be much more thorough in our article since it just covers one gene. oskar has been studied extensively (see Entrez search above), so we'll have a lot to work with. I can write up most of the rationale for this since I'm looking at it now. We'll mostly be doing grammar edits with nucleotide excision repair. Assad, the book will not be as helpful as you think; it's an introductory textbook. You'll be looking at primary literature for most of those acronyms. (If I remember correctly, citing primary lit is preferred as well.)

Also, Assad what rationale are you posting? I would like to see/edit it before we move forward. Db4an (talk) 16:03, 15 October 2012 (UTC)

Assad: hey Divya,

the issues that you stated are correct and perhaps the alternative you presented are legitimate. Im just alittle confused on which rationale to work on, because carl emailed me on my jhu outlook and said he was working on the draft, I actually was about to assemble a rationale too but I havent yet, so should I change our topic article?

I actually sent you short messages, we can communicate on your gmail chat if you would like. I am logging onto my yahoo now :)

oskar seems perfect, in the matter that is has information with respect to primary literature, nucleotide excision repair may lead us astray since there might be similarities or differences in respecet to base excision repair and transcriptional repair types. Assad071490 (talk) 16:22, 15 October 2012 (UTC)

Divya: Assad, I haven't gotten anything from you (email, chat, etc). I received that e-mail from him last night as well. Carl is on the west coast (got that from the intro forum, not trying to be creepy!) so it's only ~930 AM his time; I think he hasn't looked at this yet, which is completely understandable considering the time difference. I removed our listing on our course page until we discuss this further. I want to make sure we're all on the same page!

To be clear Assad, what is your preference? I couldn't tell by your post. Thanks! Best, d Db4an (talk) 16:40, 15 October 2012 (UTC)

Assad: Hi Divya,Carl.

I would postulate that oskar would be a more better article to work on. is it okay for you?

PS: hey db, im on yahoo, it states your offline on gmail is that correct? do you think it would make a difference with yahoo,gmail,live..etc? I was about to post my assesment for the article on oskar now and I am thinking about changing our claim from nucleotide excision repari to oskar. is it good for you guys? db and suggestions since we are in the same time zone and geographical track :) Assad071490 (talk) 16:47, 15 October 2012 (UTC)

Divya: Assad, if you don't mind, could you respond to the relevant post/not create a new section for each post you make? To indent your response, just put a colon before the paragraph. We have to both be on the same e-mail client, so chat won't work. I don't have your yahoo address, and I can't send you an e-mail from wikipedia. You need to enable that option (see unit 3 on our class page). Please, please do not claim anything on our class page until we are all in agreement. Send me an e-mail for further correspondence today (search through my.jhu.edu, check your jhu email, or go to my user page). If you want, type up your thoughts on the article, and I'll send you mine. Db4an (talk) 17:06, 15 October 2012 (UTC)

Assad:Divya, sorry for that, I actually am doing my advance cell biology assignment at the same time so couldnt keep track of that. Anyways I have sent you my response regarding the rationale to your JHU email, plus my yahoo account email is as follows: asadhussain_17@yahoo.com :) You can read my response and hopefully youll find everything there. If you would like to send me your email, send it to my JHU email or Yahoo, but since we have different email servers, I prefer the JHU email account :)

thank! Assad071490 (talk) 17:39, 15 October 2012 (UTC)

Oskar Article Assessment

hey guys,

here is my assessment/rationale for the oskar article. the article is specific since it relates to only a single gene that contributes to the development of the embryo in the fruit fly- drosophila. diagrams on the different stages of the embryo development can be added in context of how the gene functions on those numerous stages. It is specific also in a way that it monitors at the posterior pole during embryo development. We can include a technique(how many are possible) that would emphasize the regulation of this gene. Concurrently we can include other factors that explain the genomic expression or pattern of this gene during embryogenesis. In my opinion, the topic is specific and we can cover an excellent amount of detail. alot of contents can be added but as long as we stay on topic, for instance covering aspects of this oskar genes regulatory networks, techniques and how changes or mutations would impose consequences on gene exression and patterns.

Also whatever I said above, we can cover any other aspects too but I know the information we might have to retreive from other journals or primary research literatures, but Duvya is right, alot is out there and its easy to search for too. we can deviate from these contents I stated and incorporate other ones too.

thanks! Assad071490 (talk) 17:56, 15 October 2012 (UTC)

Final Selection: NER

Hi Assad,

Divya and I just spoke and we think the NER is a good idea after all - I think she's going to post text for a rationale. Reading up on Oskar, it didn't seem like there was enough worthwhile content to include, especially in relation to our class. Please let us know what you think! Carl.d.martin (talk) 02:38, 16 October 2012 (UTC)

Assad: hey guys, I have no problem with NER as well : ) also I have low signal here in my ambulance office, our IT system is shut down for some reason, but I logged on to my partners smart phone Galaxy 3S : ) and thanks divya for the final post. I am still not home yet, but ill take a look at the final product since I also have my midterm tomorrow.

you can proceed with anything you would like. its a "yes" from me on everything. thanks Assad071490 (talk) 02:43, 16 October 2012 (UTC)

Divya: Assad, we got your e-mail and contribution earlier; Carl and I went ahead with final edits since you would be busy tonight and had an exam tomorrow! I sent you the link for the googledoc so you should be able to change anything you don't like/see how we edited. Best, d Db4an (talk) 03:08, 16 October 2012 (UTC)

Units 7-9

Useful Papers/Pictures

We're using google drive to keep papers that might be useful in one central place. Here's the link: NER Articles. The articles are labeled in the format 'Journal Year First Author.' Db4an (talk) 19:36, 28 October 2012 (UTC)

Assad

Hey Carl & Div,

I just wanted to ask you guys if we are allowed to use any texts? like the one for our course(Watson,Baker) or any other texts such as my advance cell biology class. I was reading the Amplicon Article that our group is assigned as a reviewer and I think its very beneficial in the context that its related to the repair processes of DNA. The PCR-Polymerase Chain Reaction mechanism that it covers, I have great detail of such in my Advance Cell BIo book. If you would like I like somehow correlate the information further on in this project under our outline of "repair and Ligation".

Also I wanted to mention that since the excision mechanism we are covering deals with using the undamaged DNA strand as a template to replace the damaged one, further on in our project, should we cover somewhere in any of our project segments that how this is related to DSB repair? Double stranded repair, which fall into function when both strands of the DNA are damaged. Let me know guys, I am emailing you both as well to let you know about any updates I am about to do, With your consensus that is :) also about the rough draft of our progress report.

Thanks guys

Assad071490 (talk) 21:17, 4 November 2012 (UTC)

Assad, we can use books but not class notes. Appropriate references need to be verifiable and reliable. One of the things we need to keep in mind whilst editing is what our article should be doing. I honestly don't see a clear/direct relation between the amplicon article and NER; I would not add it. While PCR is great, it has nothing to do with the repair and ligation sections. If you want, you can write it but I have a feeling it will be deleted. I know the amplicon article mentions PCR, but it is related to what they are doing; the amplicon article is also a work in progress by another group in our class. We shouldn't be using that article as our model. (No offense to that group. Their edits are coming along splendidly, but it's not a FA article yet). Take a look at some of the review articles in the google drive (Sancar 2004, Cleaver 2009, etc).and maybe re-read the DNA repair article. That's what we're aiming for. Db4an (talk) 21:42, 4 November 2012 (UTC)

Images

I was pretty confused about image licensing, copyrights, etc., but I think I figured some things out from the figure in NER. I'm going to put the links here just in case they might be helpful in the future.

• List of science sources using CC licenses
• MCB WikiProject requested pictures. This mostly looks like requests for protein figures. I don't think we'll need any but, if we do, I can make my way around Pymol.
• Can I add something to Wikipedia that I got from somewhere else?
• Requesting copyright permission

I think the diagram on the NER page now is helpful, but the Comic Sans is just killing me. If we could just change that ridiculous font, it would be perfect. I think we can edit that under the CC license, but not 100% sure. Db4an (talk) 08:46, 4 November 2012 (UTC)

Assad

Hey Div, I know you were trying to copy or download images but in many instances there is a copy right issued and it wont let you download and what not for reason, as you mentioned, but have you tried clicking on that certain image and trying to open or load the image as a PDF file? because from personal experience and also when I copy images on my discussion threads, I open the images with another program on my computer like adobe, or windows image displayer etc. but I do have to manipulate with it. If you have any problems let me know the link and ill try my best to illustrate that or an alternative.

thanks

Assad071490 (talk) 20:45, 4 November 2012 (UTC)

Assad, I think I understand what you're saying, but I don't think we can go about this the same way we would in class. In class, we're covered by educational use; here, we are not. Most journal articles/books are copyrighted and we cannot use them even if we have the picture. We would need the authors' permission to use their figures. From my understanding, even if we made a new figure that looked like one in a paper, it would still violate copyright rules because it looks like the paper figure. Does that make sense? The general gist of things I've gotten from reading through the above is that Wikipedia errs on the side of caution; if you aren't sure that you have the right license or copyright permissions, do not use it. Db4an (talk) 21:01, 4 November 2012 (UTC)

Assad

hey Div, The DNA article is better. after reading the amplicon and PCR information, I did seem they were comprised of some useful information but also irrelevant briefings. good point. I'll brush up on some other interesting articles that we have in the google drive too.:)

thanks

Assad071490 (talk) 00:31, 6 November 2012 (UTC)

Working on Connection with Cancers

Hi Divya and Assad, I added 5 papers (so far) to the google drive on the relationship between NER and cancer. There is some pretty interesting material connecting DNA polymorphisms in the excision repair genes to eventual cancer states. These seem like a relatively good starting place to beef up this potential section of the wiki article. Carl.d.martin (talk) 20:48, 2 November 2012 (UTC)

Assad::: Hey Carl and Div,

I just checked and I have received the article links on my JHU email. I will review them and email both of you. Also I will add something on our talk page/contribution page as well.

Thanks for clarifying the links Div.

Assad071490 (talk) 17:06, 4 November 2012 (UTC)

Example Article: DNA Repair

Hi Carl and Assad, I know we're supposed to pick an example article to help guide us while we write the NER one. What are your thoughts on our example article being DNA repair? It is highly relevant to our topic, and the article itself is a featured article (FA). The article uses bullets and numbering liberally, which is something we could definitely apply to our article to make it easier to read.The talk page has quite a few contributors, and mentions things that will probably be issues for us (ie diction, image copyrights, etc) Db4an (talk) 03:06, 4 November 2012 (UTC)

NER Article Outline

Original Outline:

1. Uvr Proteins
2. Nucleotide Excision Repair in Eukaryotes
3. Global genomic NER
4. Transcription coupled repair in Eukaryotes

Potential New Outline:

1. NER in Prokaryotes

1.1. Damage Recognition

1.2. Dual Incision

1.3. Repair & Ligation

2. NER in Eukaryotes

2.1. Damage Recognition

2.1.1. Cooperative Binding

2.1.2. Kinetic Proofreading

2.2. Dual Incision

2.3. Repair & Ligation

3. Transcription Coupled Repair (TCR)

3.1 Diseases Associated with TCR

4. Global Genomic Repair (GGR) [currently Global genomic NER]

4.1 Diseases Associated with GGR

5. NER and Cancer

Subsections TBD

5.1 NER Disfunction result of DNA Polymorphism

5.2 Impact on Tumor Growth and Prognosis

5.3 Potential for NER-related Therapeutic Targets

Carl.d.martin (talk) 02:55, 5 November 2012 (UTC)

I've been going through the papers and looking at the DNA Repair article; the above might be something we can use as a rough format. Things will almost definitely change/shift/merge as we start writing, but this may be a starting point for what we want the article to look like. The subsections of prokar/eukar NER are a hybrid of Sancar 1996 (pg 47) and 2004 (pg 51). We'll most likely need to change the headings, but I think that will be easier to do once we actually write the corresponding sections. Cleaver 2009 lists diseases associated with TCR and GCR; I'm a fan of how the DNA repair article deals with this: short list of a few diseases with their corresponding symptoms.

Anyway, that's all I got! Thoughts? Db4an (talk) 07:33, 4 November 2012 (UTC)

Assad::Hi Div & Carl, the example article as you mentioned ( DNA Repair ) seems pretty relevant and up to date. I will review the article thoroughly and add additional correlations with our original NER project, Also I have power back finally at my hourse! so glad :) I will update you guys further.

thanks.

Assad071490 (talk) 17:00, 4 November 2012 (UTC)

Love the Outline

Divya, your outline is great - I'll spend some time tonight to try figure out what potential subsections would make sense for the NER and Cancer portion. Carl.d.martin (talk) 02:16, 5 November 2012 (UTC)

Hi Divya and Assad, I added 3 potential subsection headings in the potential outline above - please modify edit as needed. Carl.d.martin (talk) 02:56, 5 November 2012 (UTC)

Assad

Hey Carl, I really like the additional cancer subsections you added. They right on! :) In essence there pretty much in chronological order and it would be easy for us to cover the aspects of dysfunctions in NER leading to such a state & what caused such discrepancies, the metastasis process and at last treatment options. wonderful additives.

Thanks.

Assad071490 (talk) 00:35, 6 November 2012 (UTC)

Carl, I like the sections you added! We may need to rename the sections later on, but I think that will be much easier to do once we write the sections. No doubt we'll have to edit a lot of the section names. Db4an (talk) 20:43, 6 November 2012 (UTC)

Proposed Merging: TCR to NER

Transcription coupled repair is currently its own article, and labeled as an "other" repair pathway. However, it's an NER subpathway. I'm not sure if TCR should remain its own page with NER crosslinking to TCR, or if we should explain TCR thoroughly in NER. Either way, I added a discussion section on the NER talk page and added a merge tag to TCR. If TCR remains its own page, then I think GGR should have its own page as well. Thoughts? Db4an (talk) 20:43, 6 November 2012 (UTC)

I was going to merge these this morning, but I just realized I didn't place the merge tag in the appropriate place (ie it belongs on the actual article page, not talk page). If we don't have any objections by Thursday, I'll merge the two using a selective paste merger. Db4an (talk) 18:35, 12 November 2012 (UTC)

Progress report for Unit 9

Hi Assad, Divya and I worked up a progress report for where we are and our plans. She's going to post it on the project page - please take a look if you're able tonight, otherwise we can discuss anything tomorrow. Looks like we're making good progress!! Carl.d.martin (talk) 23:07, 6 November 2012 (UTC)

Breakdown of Section Editing Responsibilities

Hi Divya and Assad, Seems like Divya has focused on NER in Eukaryotes and the TCR portions - would you like to be responsible for coming up with drafts for those portions? I'm most interested in the Cancer portion, and can do Prokaryotic NER as well. Assad, would you be interested in focusing on GGR and finding figures and images for the article? That seems like one of the biggest portions we need to improve. Lets decide this asap so we have plenty of time to get drafts and review each other's material. Thanks! Carl.d.martin (talk) 23:25, 6 November 2012 (UTC)

Sounds good to me! Thanks Carl Db4an (talk) 23:32, 6 November 2012 (UTC)

Feedback: Other Groups/Individuals

Aslaa

Hello, Your group seems to be heading on the right direction. Your progress report provides great details on where you stand. It also provided useful links for other groups to use with regards to imaging and copyright issues. It will be of great help to my group as well. I have one suggestion on the article itself. I recommend that you expand more on each of the different Uvr proteins. Breaking down each component of the Uvr protein complex would help readers understand how Nucleotide excision repair works. Overall, your outline looks great. Good luck with the remaining portions of the article. Aahmed25 (talk) 22:45, 11 November 2012 (UTC)

Hi Aslaa! Thank you for your feedback. The Uvr protein section is a bit tricky; there is already an article for UvrABC endonuclease. We need to figure out how much we want to include on our page vs crosslinking vs merging the UvrABC page into ours. We don't want to go into too much detail, as this would make our article unnecessary detailed. We are still grappling with the merge issue; the UVrABC complex only appears in NER. We're looking for article combinations similar to our situation (ie an element only appears in one topic; does that element have its own page?) to help us make a decision. Db4an (talk) 16:00, 12 November 2012 (UTC)

Assad

hello aslaa, thanks for the compliments and the suggestions. you are right about the Uvr proteins and its componential factors that would enable everyone to better comprehend the functioning or application of Our topic of nucleotide excision repair. We will work on the merging issue as Divya has suggested and avoid the extraneous information but definitely incorporate the relevant one. We are seeking out other articles for the UVr protein complex though. It is primarily only in our NER article though.

thanks!

Assad071490 (talk) 16:27, 29 November 2012 (UTC)

Amy B.

I too think you guys have made amazing strides to your wikipedia page. I especially like the breakdown of topics and the cancer sections at the bottom of the article are a great addition! I have a slight typo correction on the NER and Cancer section - you need an 'e' on the end of single-nucleotide in the second sentence. The main question I have is you a layout/content question. It is hard to segregate prokaryotic vs. eukaryotic and GGR vs. TCR without somehow referencing one of them thus putting the cart before the horse. I don't know if you would benefit by going in less detail about GGR process in the Eukaryotic section and saving those specifics for the actual subheading? Just a thought. Also, the heading UvR proteins should that be changed to flow with the rest of the article and be called NER in prokaryotes? These are my major formatting/flow questions. Another question is the table at the end of the article. I like this and really think that it is a smart way to give all of the proteins without overwhelming the reader. My question surrounds the list of the proteins and wondering if you will include a separate table for Uvr proteins? I really like the way you kept the diseases section short and sweet just cross-referencing and giving a few symptoms.

Here are just a few nit-picky and just minor things I noticed becuase I am weird like that :) The GG NER section references a paper but there is no citation for it (there really aren't many citations other than the cancer sections... I don't know if they are in the works like ours or not). NER in Euk has duplicate/replicate links to other wikipedia pages. I know I read somewhere in all of our reading on editing wikipedia that it is best practice to link just the first reference so that the text flows better visually. There is an instance of GGR being used as an abbreviation without it being defined after firs using global genome repair. Again these are small things, but I just happened to notice them when trying to really read the article for feedback. Overall I believe you guys have done a good job so please don't take the above to think that I don't appreciate the amount of effort that has been put into it. Abenson9 (talk) 03:07, 1 December 2012 (UTC)

Hi Amy! Thank you so much for your feedback. We like nitpicky, don't worry! :) The more critiques you have, the more we can improve so don't feel bad about helping us! If you see any sort of grammar/syntax edits you would like to make, feel free to do so. It takes a lot more time for you to have to explain it out here, and then one of us go back and fix it, check if you think it sounds okay, etc. Just mark it a minor change, and we can just see the edit when we're working on our page! No big deal.

Prokary vs eukar / GGR vs TCR: We need to get on our game about this; you are definitely right. There are issues with referring to one thing before introducing it, etc. We haven't gotten to this just yet, which is why it's still a bit jumbled. As of right now, we hope to introduce in the following order: Prokaryotic, Eukaryotic, GGR, TCR. Introducing the topics this way should help introduce ideas in an orderly manner so segregating is not an issue (hopefully). I'm actually working on the Eukaryotic section right now (just haven't saved to the page yet), so it should sound a little better in a few hours!

Uvr proteins heading and Uvr protein table: Definitely need to change the heading. We've been debating merging the UvrABC endonuclease into NER for a while, and finally decided to start the merge process for that. (Aslaa brought this up a little while ago, and we've been going back and forth since then). Carl should be doing that relatively soon, and can give you a bit more information about that. If we end up merging it in, then another table in the Prokaryotic NER section would definitely be a great idea! Thank you for catching that.

Random paper reference: That's weird. The original article had that I think, so whoever is working on that should be updating it soon. deleted

As for the duplicate links, we're hoping to take care of those smaller things to improve flow a little later in the week. Again, feel free to make those small changes if you feel comfortable; we have no problems with it! If you find anything else, just let us know. Db4an (talk) 03:54, 1 December 2012 (UTC)

Edit: Amy, I was thinking about what you said about structuring a bit more this morning, and changed up the layout a little bit. Let us know if that's a bit clearer! GG-NER and TC-NER still need to cleaned up, just FYI.

Units 10-12

Section additions

Hey guys, I had set aside some time today for our article so I put up a few edits on our article page. I know we talked about putting all of these genes into a table earlier, so I made one for the eukaryotic pathway. It's still pretty rough and could use some editing in the function column. I'm pretty sure I checked all of the Wikipedia/GeneCard links, but if one of them is not working, please change it! All of the information regarding orthologs came from the GeneCards entry, and the list of associated genes came from this page and the Friedberg/Hanawalt reviews.. The subpathway/function columns are a combination of a 2001 Friedberg Nature review (pmid: 11900249), a 2008 Hanawalt Nature review (pmid: 19023283), and the function description for the associated GeneCard entry. Not entirely sure how this should be referenced, so I haven't added the Nature review references yet. Feel free to change. Db4an (talk) 02:45, 13 November 2012 (UTC)

Updated content on NER talk page

Hi Divya and Assad, I added a draft for the cancer portion. Its rough and hasn't been linked or formatted much - but its a start. I'm going to work on the prokaryotic NER portion next, and once they're both to this level will begin linking and so on. Please take a look and let me know what you think (edit as you see fit!!). Carl.d.martin (talk) 22:25, 15 November 2012 (UTC)

As I mentioned on the talk page there, you should go ahead and insert all this content right into the article. Don't worry about formatting. For the references, just insert the text that you have now inside <ref>...</ref> tags.

Like this: Instead of:

... the human population [1,2]. If located in ...

Write:

... the human population.<ref>Kwok PY and Gu Z. Single nucleotide ...</ref><ref>Collins FS, Guyer MS and Charkravarti A. Variations on ...</ref> If located in ...

Let me know if you need more help, and I can get you started. Leave a note on my talk page to make sure I see it.

Klortho (talk) 14:14, 16 November 2012 (UTC)

Hi Klortho, thanks for the advice. I did go back an add that content to the actual article page and did the reference formatting like you suggested. Carl.d.martin (talk) 19:49, 30 November 2012 (UTC)

Assad

hey carl and div, As I was reading the objectives for unit 12, it seems we are on the right track so far but the only thing necessary at the moment would be to make suggestions to the groups work that is assigned to us and take other groups suggestions as well :).. if I am correct it is the amplicon paper. Lets get in touch with that group, make suggestions then share them with eachother, by mail or on our group talk page so we can summarize it for the unit 12 section progress report.

thanks

Assad071490 (talk) 02:31, 28 November 2012 (UTC)

Assad

Hey Carl and Divya :), Divya as we interacting via email, which I will do again shortly, I wanted to inform you that we are suppose to generate a new progress report under the topic "unit 12 progress report" in which we have to state what we have done by interacting with the other assigned group work and its members. If you would like, I can generate a report exemplifying the suggestions we have taken and also made to other groups and send it to you via the johns Hopkins email by tonight. you can make any alterations or post it then.

thanks!

Assad071490 (talk) 16:34, 29 November 2012 (UTC)

Unit 12 progress report (draft)

Hello Carl and Divya,

I was a little free in my EMS headquarters miraculously and decided to write a draft for the Unit 12 progress report. I am emailing you this as well so you can make any alterations and post it on our project page. I was reading the objectives for unit 12 and came upon the fact that not only do we have to comment on others work but also write a progressive report! anyways here it is as follows and I will copy/paste and email this to you at the moment as well. Here it goes;

With respect to the progress we have made, there are two aspects in account so far. Suggestions we have made to the assigned group C for their amplicon article and certain proposals we have taken and primarily are working on to enhance our article. First I would like to cover our aspect before I progress on interacting as peer reviewers for Group C. Our current outline is the suggestive path that we are working on. In addition to the DNA polymorphism in excision genes relating to cancerous states, there were an additional of 5 articles added to our google drive where all the material relevant to our article and topic can be accessed. Progressing further with cancer and its connections, there are proposals we have made to crosslink Transcriptional coupled repair with NER, in the repair mechanism since TCR is the subpathway for NER. At last we have been suggesting through the interaction of other group members of group 83A to implement the description of the Uvr protein complex from the UvrABC endonuclease article. We are solving how much relevant information to cover regarding the components of each Uvr protein for the enhancement of the article and NER function. Also we would like to merge the UvrABC complex into NER, but are figuring out merging solutions.

Our interactions with group C, as we were assigned as their peer reviewers was informative as well. certain suggestions they implemented as soon as we have advised them. very impressive. With our group proposal they had expanded their introductory section of the amplicon, the are narrowing down their content section for a "clean up" since at the moments it is extremely broad and would arise hardship for their work. To better understand amplicon functioning they have also described its role in popular technologies. They have eliminated there irrelevant example section and posted a concise, relevant and to the point example of the polymerase reaction assay they have mentioned. For a better understanding up the topic, the group has also been advised to describe the distinguished categories and subtypes of the amplicon included in there sub content section of circular extrachromosomal and linear inverted amplicon.

Assad071490 (talk) 20:07, 29 November 2012 (UTC)

Nice job Assad! Carl and I used your report to write up a final progress report this morning. It's up on the main project page. Feel free to edit if necessary. Db4an (talk) 17:47, 1 December 2012 (UTC)

Update on editing: 11/30

Hi Divya and Assad, I'm still working on content for the prokaryotic NER portion. Divya, it looks like you've been editing the NER page quite a bit - looks great! Assad, have you had any luck finding new figures or images yet? Carl.d.martin (talk) 19:54, 30 November 2012 (UTC)

Not too much! I'm working on Eukar NER right now and will put that up in a few hours. Your Cancer section is looking good too. I went ahead and did the TC-NER merge, so that's done. Assad sent me some pictures he found so I uploaded them onto our page. I think he's going to post a full list of images he found later tonight/tomorrow. Db4an (talk) 04:05, 1 December 2012 (UTC)

That's great! I've gone ahead and suggested the merger of UvrABC endonuclease into our prokaryotic NER portion. We'll see if any discussion occurrs, otherwise I think it makes sense to mover forward with it. Carl.d.martin (talk) 15:38, 1 December 2012 (UTC)

Awesome. Amy B from our reviewer group had some points about our article structuring, and those points became more obvious as I was reading over the article this morning. I tried to reorder things to address her valid point. Feedback on this would definitely be appreciated. I also rewrote the lead section and tried to follow the points in the Wikipedia:Manual_of_Style_(lead_section).

Assad's image list

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195855/ figure 1

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462412/ figure 1

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851970/ figure 1

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201922/ figure 7

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709936/ figure 1,

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915888/ figure 2, figure 3, figure 4

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472782/ figure 4, figure 5

(I'm just posting them because he emailed them to us, and I think he might be busy this weekend; we need the list for our progress report). Db4an (talk) 17:47, 1 December 2012 (UTC)

Assad

Hey divya, so far I think we would be able to go with the images that are provided in the list. I read the other groups critiques and have not read the desire to add an additional image for a certain section because the ones available are pretty much relevant. Just in case if you would like me to do anything else or search information regarding anything, please just let me know :) Also I tried searching for additional images, but I pretty much come up with duplicates of the one we have or about more than 90% similar images with literature illustrations as well. Though I have not checked Science Direct yet, but the NIH website or related articles I have done so. If you would like me to head on to something else, just let me know then. :)

Thanks:)

Assad071490 (talk) 00:23, 4 December 2012 (UTC)

Prokaryotic NER

Hi Divya and Assad, I found a good schematic for Uvr proteins, uploaded to the wikimedia commons and then inserted into our article. It was an open access article, so should be good. I think it adds to the usefulness of the section. Carl.d.martin (talk) 19:40, 12 December 2012 (UTC)

Assad

Hey Carl, I just went over the schematic representation. Its wonderful! just what we needed and this is what we actually aimed to implement in our project article to improve it. Also I remember mentioning this in the unit 12 progress report as well. Divya had mentioned it too. Great collaborative work. I like the illustration because it clearly "draws" out the mechanism behind the UvrABC endonuclease complex and the chronological essential steps that occur by each of the complexes subunit, such as UvA, UvB etc. There obvious function of to cleave the phosphodiester bond to some nucleotides(4 and 8) upstream and downstream was a pertinent information added in regards to specificity.

Best

Assad071490 (talk) 01:16, 15 December 2012 (UTC)

Hi Assad, thanks! Glad you like the addition - I think it helps round out the material in that section pretty effectively. I think the article looks great, and when compared to what was there prior to our starting to work on it the difference is huge! Carl.d.martin (talk) 10:21, 15 December 2012 (UTC)

Looks good to me! Thanks Carl Db4an (talk) 14:34, 15 December 2012 (UTC)

Unit 14: Summary

Hi Divya and Assad, I couldn't sleep much after the news from Connecticut so I thought I'd put together a draft for our end of term summary. Please edit or modify as you see fit - been a real pleasure working with you both, I think the article looks great!Carl.d.martin (talk) 11:22, 15 December 2012 (UTC)

Added a few small edits to the progress report, see below. I also went through this morning and finished up the last few small things down our To-Do list, mainly references for captions, grammar throughout, and links in the NER/Cancer section. Just to recap for anyone reading, we decided not to merge the UvrABC section and left a "further information" at the top of the subsection. Thanks for a great semester guys! Db4an (talk) 15:43, 15 December 2012 (UTC)

Thanks Divya, good additions! I'm going to post this on the project page. If you or Assad have any further edits please feel free to edit it there.

Carl.d.martin (talk) 17:26, 15 December 2012 (UTC)

Unit 14: Summary

During this project, our group made a significant improvement to the nucleotide excision repair (NER) article. We expanded the initial article outline to include more granular subsections, added new sections, merged with another article, included crosslinks and expanded the content in the article.

Nearly double the orignial length, the NER article now contains a glossary of NER asociated proteins, 4 new schematics detailing NER processes, and a new section detailing some of the implications NER has for cancer biology. We also expanded the Further Reading section to include three new sources, and the Reference list now contains a more useful index of relevant NER materials.

We also interacted significantly with other editors; we responded to questions and critiques regarding our work on the NER page, and also posting feedback on other groups’ progress. We received very helpful feedback from Group 83A on our work and attempted to respond to their posts as effectively as possible. We also received some anonymous feedback, and responded to that critique after investigating their concerns. We detailed this in the Unit 12 Progress Report.

In all, our group is satisfied with our work. We believe that we were very successful in accomplishing our initial goals and improving the NER article. Carl.d.martin (talk) 11:22, 15 December 2012 (UTC)