Wikipedia talk:USEP/Courses/JHU MolBio Ogg 2012/Section 81/Group 81B

 Group 81B Wiki Collaboration Page 

Topic Selection Discussion
Hi Giseladelcarmen and Jbaradei! Looks like we'll be selecting a topic for the group assignment this unit! Does anyone have any particular topics they'd like to suggest out of the list? I still need to spend a bit more time reviewing them to assess a list of items that could use improvement, however right away I think the Helicase and Telomeres sections have a lot to offer as a project. Both are topics with a lot of information, and there doesn't seem to be a very good representation on the Wiki pages. For example, There were some topics we touched on in a class discussion on telomeres that I don't see mentioned anywhere in the WIki article. What topics do you guys think could be good? It may be good to decide on a few we're interested in, and a proposal of topics to add to see what the strongest choices for us are? Any other suggestions on how to go through the decision process? Jennifergr (talk) 12:06, 8 October 2012 (UTC)


 * Hi Jennifergr and Jbaradei. Thank you for starting the talk page. I think that Telomeres will be a great article to work on. The telomere shortening part doesn't have any references. I'm sure we can improve this section by adding more information and also the appropriate references. We can also do a good job on making the "Telomere and cancer" sections more readable for non-technical users. That said I would like to claim Telomeres as our article if Jbaradei agrees. Gisela Gonzalez 15:49, 8 October 2012 (UTC) — Preceding unsigned comment added by Giseladelcarmen (talk • contribs)


 * Please, each of you pick two articles "as individuals" to start out with: "As an individual, make an initial assessment of at least two of the articles..."  So if your group has three members, then you'll first compile a list of six articles from which to choose. Klortho (talk) 16:20, 8 October 2012 (UTC)


 * Hey! I looked through the articles up for editing and think that either Telomeres or Cooperative binding would be the best bets for us based on amount of work that still needs to be done on them. That being said I am all for Telomeres if you two are. There is a ton that can be added. In fact two scientists just won the nobel peace prize for converting adult stem cells into enbryonic stem cells and I would bet that telomeres has something to do with it. I would like to get this topic claimed and get started right away. Im not one for letting things go to the last minute, as Im assuming from the discussion frequency you two are maintaining, you dont either so I think this will be a great group to work in. Jbaradei (talk) 17:02, 8 October 2012 (UTC)
 * Hello collegues...the more I look at the options I have the more Im liking other topics like "Segmentation gene" which has like NOTHING written about it, but a lot in some publications and on google. DnaE, I, or S, Micrococcal nuclease, Transversions, and 2'O-methylation also have NOTHING written about them. Telomeres has a ton written already on its page and I am worried about making a good enough contribution to the page to get a good grade. That being said this is a democracy and I am in on Telomeres if you both want it..just wanted to show the other options. Jbaradei (talk) 22:52, 8 October 2012 (UTC)


 * Hello! I think you are right Jbaradei It will be better to work with articles that have nothing written. Since each of us have to pick two articles I will pick "Bacteriophage T12" and "leaky scanning". Even though I found the subject about Telomeres to be interesting I also think it will be better for us to work on a new article. Gisela Gonzalez 13:11, 9 October 2012 (UTC) — Preceding unsigned comment added by Giseladelcarmen (talk • contribs)
 * Thanks Gisela. If I had to pick two from the ones brought up so far Id go with either Segmentation gene or Bacteriophage T12. Im flexible and definately dont want to split hairs about this so what do you say we go with a majority vote?Jbaradei (talk) 14:26, 9 October 2012 (UTC)


 * Segmentation gene has my vote. Gisela Gonzalez 16:29, 9 October 2012 (UTC) — Preceding unsigned comment added by Giseladelcarmen (talk • contribs)
 * Thats my vote tooJbaradei (talk) 17:42, 9 October 2012 (UTC)


 * Hi all - it looks like we first have to make up the assessments to present before deciding. The only thing I worry about on the ones with nothing written about them, is that the reason there may not be a lot written is that there isn't a lot of good, available information to compile something on (but of course this isn't necessarily true, just a possibility in some cases) - so the assessments will help out with this - when assessing, if there is more information needed, we can point out is needed and on the topics without much info, where this information can be found. I'll get some points together for telomeres and helicases. I'll try to have these ready by tonight so we can decide tomorrow on the topic? Jennifergr (talk) 13:23, 10 October 2012 (UTC)


 * I also added an Article Assessments section in the Group Project Page for us to post a little about the 2 articles we evaluate Jennifergr (talk) 13:26, 10 October 2012 (UTC)


 * I've added an assessment of Telomeres and Helicases. After doing my two assessments (and only deciding between those two) I think Helicases may have the most sections we can create to add more substance to the article (such as Activation Barriers, Passive and Active Helicases, and Diseases and Disorders of Helicase Disfunction). This is only my opinion on the two I reviewed, after we have some info on the other ones you guys were looking into, we can see what we think has the most opportunities out of the 6. Jennifergr (talk) 16:01, 10 October 2012 (UTC)
 * Jennifer you are 100 percent right! Doing an assessment on the two items that had nothing on them made me realize why that was! Helicases does seem like the item needing the most work and with your ideas of what to include it should make this a less frustrating experience. We even have an article for the active/passive helicases at our disposal. There is also diagnostic assays that measure helicase activity that we can talk about. We can expand on viral helicases, etc. Jbaradei (talk) 23:10, 10 October 2012 (UTC)


 * I also thought having done an assignment recently on helicases, with the article you mentioned, could be an advantage for us, as we've recently been researching and writing on this specific topic, so may feel more comfortable exploring it, as well as writing a reference for it - thanks for your further suggestions on sections! I added them to the assessment so we have a complete view of what's available for each topic! Jennifergr (talk) 23:21, 10 October 2012 (UTC)
 * Shall we just go ahead and claim helicases?? Others have already started claiming their projects, I dont want to miss out. If you see this and agree go ahead and go to the class page and claim helicases. If you want me to do it I will, just let me knowJbaradei (talk) 23:29, 10 October 2012 (UTC)
 * I emailed Gisela a few hours ago right after your last post to see if she could weigh-in before we claimed something on the class page - I meant to post right away to let you know but forgot after emailing her - sorry!! Jennifergr (talk) 03:04, 11 October 2012 (UTC)

How should we handle the rationale writeup? Should one of us take the first crack at it and the others can add as needed? If so I can start the first draft, then email it to you both for revisions, tie everything up and submit it after all revisions are added and we have an agreement on the rationale contents. Jbaradei (talk) 12:56, 11 October 2012 (UTC)


 * Good morning! thank you for waiting for my input. I just claimed Helicase :-). I think that is a good idea Hanna. I thought about each one of us writing a rationale and then bringing the material together but having a main one to edit is going to be easier to agree on. Gisela Gonzalez (talk) 13:46, 11 October 2012 (UTC)
 * Awesome...Jennifer it was your idea to claim helicases so I wanted to ok it with you that I start the writeup before asking your permission first..if you wanted to start it thats fine, just let me know which you would prefer. I am definaly with Gisela in thinking it will be better to add onto a rough draft than each writing our own...it will save time too. Jbaradei (talk) 14:02, 11 October 2012 (UTC)
 * Yes, definitely OK Hanna! Thanks for claiming this on the Course Page Gisela and thanks for offering to start the write up, Hanna! Jennifergr (talk) 14:09, 11 October 2012 (UTC)
 * Ok the first draft was sent to you two. Please let me know if you didnt get it.Jbaradei (talk) 19:34, 11 October 2012 (UTC)

OK! The rationale has been posted with days to spare. Great job this week and thank you so much for all the easy flowing teamwork in getting all the assessments done, coming up with a article decision, and overall just working togethor. Im sure we all have nightmare stories of group projects going bad due to lack of enthusiasm from a team member, but luckily it doesnt seem like we have the problem! GO TEAM! :)Jbaradei (talk) 15:40, 12 October 2012 (UTC)

Helicase Article: Initial Sections/Research Breakdown
These are the sections that we've identified so far (I've left spaces if you guys feel there are any missing). I would think we could each grab 1/2 topics, and start an initial research phase and creation of the section. After we've finished, we can kind of pass them around to each other, each person taking on other sections, adding more info, clarifying areas, etc. Does this make sense?

Also, the Helicase Groups section above I think is pretty dense - so the person taking this on could try to evaluate if there may be a better way to present/label the information currently containing superfamilies, and evaluate what specific helicases (ie viral, annealing, DNA repair) could be elaborated on and how. My suggestion, if we stick with the 5 topics identified in our rationale, is that one person takes on Helicase Groups and the other two group members can take on 2 topics each, as I think the workload is about the same. I've taken the first two on the list, but this is assuming this method is OK with everyone - please add suggestions if you guys think I'm missing something or you don't agree with taking on the sections this way. Jennifergr (talk) 23:55, 11 October 2012 (UTC)
 * I added RNA helicase because I think we can polish that section a little. I'm assuming that the order in which they are in the table doesn't represent the order they are going to be presented in the article right? Gisela Gonzalez (talk) 13:40, 12 October 2012 (UTC)
 * Thanks Gisela!! And you're right, I think I just went through the rationale and listed them as they were listed in the rationale for the table, but not as they'd appear in the article. We could either decide that after we've gotten the sections together, or if you have any suggestion on the order, feel free to change around the table to reflect it. Jennifergr (talk) 13:51, 12 October 2012 (UTC)
 * Wow!! we have our rationale already!! thanks Hanna for posting it. It looks great! Regarding the content structure I was just thinking of something like this:
 * 1. History (Discovery)
 * 2. Function (passive and active helicases here?)
 * 3. Structural Features
 * 4. Superfamilies
 * 5. Helicase disorders/disease
 * 6. Diagnostic methods
 * 7. RNA helicases
 * What do you guys think? We can also wait to have all the material and then arrange it. Gisela Gonzalez (talk) 18:37, 12 October 2012 (UTC)

No need to sign stuff on project page
Hi, I notice you guys have been signing a lot of the material you put on your project page. There's no need to do that. The talk page is for discussion, where you indent and sign each post, so it's easy to see who authored what. But the project page should be more for finished work. You can always see who authored what through the page's version history. So, no need to sign things there. Cheers! Klortho (talk) 22:34, 10 October 2012 (UTC)


 * Thanks for the info - I thought we were getting graded on our input in the assessments, and wasn't sure if it would be helpful for us to sign so it would be easier to tell who was posting what so I figured it couldn't hurt to add it. From now on I won't worry about it when adding info on the Group page. Jennifergr (talk) 22:48, 10 October 2012 (UTC)
 * The page's version history is more reliable than that -- it can't be forged! (Not that anyone would do that, of course ...   :)  Klortho (talk) 22:59, 10 October 2012 (UTC)
 * Great - thanks!! Jennifergr (talk) 23:09, 10 October 2012 (UTC)

Unit 9 progress report
Hello! I just added a draft for the unit 9 progress report. Please feel free to edit it and add information as necessary. Gisela Gonzalez (talk) 19:21, 31 October 2012 (UTC)


 * Thanks for starting the progress report. How do you two want to go about adding to the progress report. Should we all just right a little blurp about our progress or do you want to make it one combined article that one of us will oversee?? Jbaradei (talk) 22:53, 31 October 2012 (UTC)


 * I was just thinking about each of us adding some info. According the the guidelines we should write about.


 * Any progress made so far on improving the article.
 * Any significant interactions you've had with other Wikipedia editors. Were they helpful? Did any edits you made get reverted?
 * To-do list for improvements that you plan to make in the remaining weeks
 * Any other problems or concerns


 * I basically just copied what we have discussed here in the talk page so far. I thought we were going to write the full article and then paste it on wikipedia but I guess we should start adding our edits?? what do you think? Please feel free to add more info. . Gisela Gonzalez (talk) 15:01, 1 November 2012 (UTC)


 * Through my research I found a fantastic article about helicases that I think has a great amount of referrable data that can be added to this website. The webpage from this article is http://www.jbc.org/content/281/27/18265.full#ref-1 . Reference accordingly. Jbaradei (talk) 17:51, 1 November 2012 (UTC)
 * Hey group, I added my progress so far to the progress report section on the group page. Please let me know if you ok with the way that I added these notes, or if you would like them changed to something you think is more coherent. I hope you are both safe from Sandy...it was brutal here but the loss of electricity definately gave me some "study time". 50.78.48.241 (talk) 18:28, 1 November 2012 (UTC)
 * My appologies, those anonymous posts were from me. I will delete and resubmit them to show progressJbaradei (talk) 20:08, 1 November 2012 (UTC)


 * So sorry for the delay guys - for some reason I wasn't getting notifications about the new messages on Talk, even though I had been in the past - I just saw these. I was a little confused by the Progress Report also, as my understanding was the same as Gisela's, that we wouldn't be adding our edits until the end of the semester, working on our articles offline to ensure their accuracy and appropriateness before publishing anything for others to use as a reference. I figured after we each worked on our assigned sections, we'd have each other look over them for edits and suggestions, and after final approval from everyone, post to the Wikipedia article - it seems the most responsible to me, however maybe some groups are focusing on one topic at a time, instead of breaking them up and working on them concurrently, so maybe some groups have had the time to finalize a section or two. For the progress report I can follow along with the current format, with a general description of what I've researched so far and what I still need to work on. Do we have a tentative deadline we'd like to make for our first section to hand over for group review? Jennifergr (talk) 12:56, 2 November 2012 (UTC)
 * Jennifer, I think we have to start our posts when possible for two reasons...1, it will give us a buffer incase the reviewers find errors or the our moderator doesnt allow certain posts. 2, it will give our reviewer group time to do the edits that are needed for their grade. Lets go with majority rule on this, like we have before, what do you two think...Im for posting when possible. Jbaradei (talk) 14:36, 2 November 2012 (UTC)
 * I don't have an issue posting as soon as possible (my previous post was explaining my previous assumption and why I was confused, not explaining my preference), I was just working on all of these concurrently, so none are close to complete, they're all in the middle of research and are just in notes, but I'll focus on just one for now. So is the idea that they're posted prior to any group input? I wasn't sure if we were being graded as a group on the edits published, so didn't want to post anything without the groups' OK - but I'll do whatever is decided Jennifergr (talk) 15:02, 2 November 2012 (UTC)
 * Why dont we post our "rough draft" in this talk section in the format that you want to display the research in. That way the rest of us have a chance to see what you will add to the article and how you want to display it. Once you do that at the bottom of the post write how long you will leave it in the talk section for revisions/comments before posting on the article itself (try and give a week if possible). That will allow the rest of us time to look over the draft and not only proofread based on its substance, but also based on its presentation. Jbaradei (talk) 01:43, 3 November 2012 (UTC)
 * Perfect - will do. I'm currently focusing on the Disease/Disorders section, and going along "disease/helicase by disease/helicase" - Once I have finished one disorder, I thought posting it may be appropriate, and I can continue to add as I complete the rest of the descriptions. I'll post in the Talk section accordingly. Jennifergr (talk) 12:48, 3 November 2012 (UTC)


 * Going back to the progress report. I think sticking to the bullet points the professor has recommended is the easiest way to go. For progess lets just add comments to the sections as Ive started. For the rest what do you two think of just placing bullet points for each criteria and each adding to it as necessary?Jbaradei (talk) 01:46, 3 November 2012 (UTC)
 * This sounds good to me - Jennifergr (talk) 12:48, 3 November 2012 (UTC)


 * Hello Group. I added what I think should be the last parameters we need to hit for our progress report. Please review/revise and add/change whatever you deem necessary. I will not be able to check this for the rest of this unit (work travel) so dont feel the need to check with me for any revisions to anything I wrote, just go ahead and do it. I trust you both :) Jennifer can you leave the two sections you put up for review until friday?? Jbaradei (talk) 23:47, 4 November 2012 (UTC)
 * Looks good, I'm still working on my update to the Function section (Passive/Active Helicases) for the Progress Report, that will be up today. I'll be away from Friday to Sunday, with very limited internet access, if any, until Sunday evening, so I won't be able to post the sections on Friday - you guys can leave all comments/edits for them and Monday, the 12th, I'll plan on posting. Jennifergr (talk) 08:33, 5 November 2012 (UTC)
 * I think that the progress report looks really good! Just a friendly reminder to add the proper indentations in the talk page and to add Bacteriophage T12 to your watch list. Gisela Gonzalez (talk) 15:14, 5 November 2012 (UTC)
 * Great - I have a little more to add but will soon - I also added our page to review a week ago or so, they've already started to edit it it looks like as I've been getting notifications. Is there a place on our Talk page where the indentations are being used incorrectly? Or is it another Talk page? This one looks OK to me, so if it's this one, let me know what's wrong so I can fix it ;) Thanks! Jennifergr (talk) 15:41, 5 November 2012 (UTC)
 * Progress Report is due today, however it looks like we're still missing the info on the Superfamilies and RNA Helicase progress. Jennifergr (talk) 12:18, 6 November 2012 (UTC)

XPD helicase point mutations
XPD (Xeroderma pigmentosum factor D, also known as protein ERCC2) is a 5'-3' SF2 family ATP-dependent helicase containing iron-sulphur cluster domains [2, 3]. Inherited point mutations in XPD helicase have been shown to be associated with accelerated aging disorders such as Cockayne syndrome (CS) and trichothiodystrophy (TTD) [1]. CS and TTD are both developmental disorders involving sensitivity to UV light and premature aging, and CS exhibits severe mental retardation from the time of birth [1]. The XPD helicase mutation has also been implicated in xeroderma pigmentosa (XP), a disorder characterized by sensitivity to UV light and resulting in a several 1000-fold increase in the development of skin cancer [1].

XPD is an essential component of the TFIIH complex, a transcription and repair factor in the cell [1, 4, 5, 6, 7]. As part of this complex, it facilitates nucleotide excision repair by unwinding DNA [1]. TFIIH assists in repairing damaged DNA such as sun damage [1, 4, 5, 6, 7]. A mutation in the XPD helicase which helps form this complex and contributes to its function causes the sensitivity to sunlight seen in all three diseases, as well as the increased risk of cancer seen in XP and premature aging seen in TTD and CS [1].

XPD helicase mutations leading to TTD are found throughout the protein in various locations involved in protein-protein interactions [1]. This mutation results in an unstable protein due to its inability to form stabilizing interactions with other proteins at the points of mutations [1]. This, in turn, destabilizes the entire TFIIH complex which leads to defects with transcription and repair mechanisms of the cell [1].

It has been suggested that XPD helicase mutations leading to CS could be the result of mutations within XPD causing rigidity of the protein and subsequent inability to switch from repair functions to transcription functions due to a "locking" in repair mode [1]. This could cause the helicase to cut DNA segments meant for transcription [1]. Although current evidence points to a defect in the XPD helicase resulting in a loss of flexibility in the protein in cases of CS, it is still unclear how this protein structure leads to the symptoms described in CS [1].

In XP, the XPD helicase mutation exists at the site of ATP or DNA binding [1]. This results in a structurally functional helicase able to facilitate transcription, however it inhibits its function in unwinding DNA and DNA repair [1]. The lack of cell's ability to repair mutations, such as those caused by sun damage, is the cause of the high cancer rate in XP patients.

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→ ''I'll leave this section, XPD Helicase Mutations, up until the 12th - then if it seems OK I can add it into the Helicase page. From looking at the guide for Mol Bio articles on Wiki, they state that articles should be densely referenced - I was having a bit of difficulty realizing if any of the information should not be referenced, and decided to err on the side of caution. Also, I wasn't sure if the section got confusing with all of the abbreviations of diseases, let me know what you think about that and if anyone thinks it would be better to write them out.'' Jennifergr (talk) 21:32, 3 November 2012 (UTC)

RecQ family mutations
RecQ helicases (3'-5') belong to the Superfamily II group of helicases, which help to maintain stability of the genome and supress inappropriate recombination [2, 6]. Deficiencies and/or mutations in RecQ family helicases display aberrant genetic recombination and/or DNA replication, which leads to chromosomal instability and an overall decreased ability to proliferate [2]. Mutations in RecQ family helicases BLM, RECQL4, and WRN, which play a role in regulating homologous recombination, have been shown to result in the autosomal recessive diseases Bloom syndrome (BS), Rothmund-Thomson syndrome (RTS), and Werner syndrome (WS), respectively [1, 6].

Bloom syndrome is characterized by a predisposition to cancer with early onset, with a mean age-of-onset of 24 years [3, 6]. Cells of BS patients show a high frequency of reciprocal exchange between sister chromatids (SCEs) and excessive chromosomal damage [7]. There is evidence to suggest that BLM plays a role in rescuing disrupted DNA replication at replication forks [7].

Werner syndrome is a disorder of premature aging, with symptoms including early onset of atherosclerosis and osteoporosis and other age related diseases, a high occurance of sarcoma, and death often occurring from myocardial infarction or cancer in the 4th to 6th decade of life [4, 6]. Cells of WS patients exhibit a reduced reproductive lifespan with chromosomal breaks and translocations, as well as large deletions of chromosomal components, causing genomic instability [4].

RTS, also known as poikiloderma congenitale, is characterized by premature aging, skin and skeletal abnormalities, rash, poikiloderma, juvinile cataracts, and a predisposition to cancers such as osteosarcomas [5, 6]. Chromosomal rearrangements causing genomic instability are found in the cells of RTS patients [5].

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→ I'll leave this section, RecQ family mutations, up until the 12th for comments, editing, reviews, etc. - then if it seems OK I can add it into the Helicase page. Jennifergr (talk) 22:38, 4 November 2012 (UTC)


 * I think that both sections look very good. I do not believe that is necessary for us to post the changes here for group review. This is just my opinion. But I thought that the main idea is for us to review other groups and the other groups to review our work. I think we should start editing the main Helicase page so we can start having interaction with editors. Please let me know what you think. Gisela Gonzalez (talk) 15:44, 7 November 2012 (UTC)
 * Ok, I posted these so the other group can begin to review them. From the grading description, I do believe all of us are being graded on all of the sections, not only the sections we produce ourselves - I think it may be a good idea for us to take a look at the other sections we're publishing to see if there are any suggestions we can make on them, so we can post them on the Wikipedia site and then add our comments, if any, here in Talk? Jennifergr (talk) 09:43, 10 November 2012 (UTC)
 * Actually, I guess the discussions about suggested revisions should take place in the Helicase Talk page? As opposed to on our page? Jennifergr (talk) 09:54, 10 November 2012 (UTC)

Group notes/comments about article posts
Per the proposed structure of the article we initially created, should we move the Helicase discovery section above Function? Jennifergr (talk) 00:14, 13 November 2012 (UTC)

Unit 12 Progess Report
Hello Group,

Do to the holiday, and the fact that I wont be able to do anything for this class during it, I am going to get an early start on our progess report for next week and add whatever I need to. Please add to/revise the contents as you see fit. I started a peer review page on the 81E also and began the discussion with them. I hope you all have a great holiday. Jbaradei (talk) 19:42, 16 November 2012 (UTC)

Adding Images
Hello! I need some help adding images please. Do you know how to find out if you can use a specific image from a scientific article please? Gisela Gonzalez (talk)
 * Hi there; I believe in order to use an image from a publication, such as a journal article, you would need to receive permission from the publisher, unless there is a suitable CCBY license (which should be printed on the page with the article if there is I would think, see here). Wikipedia lists some sites for free images here - Jennifergr (talk) 21:11, 20 November 2012 (UTC)
 * Thanks Jennifer. Gisela Gonzalez (talk) 13:59, 21 November 2012 (UTC)
 * Finally!!! got one image to stay in the page. I found it at protopedia. I tried to look for more helicase images but I didn't see any other picture that we could use. I'll keep looking Gisela Gonzalez (talk) 16:58, 11 December 2012 (UTC)

Peer Reviews
Hey GroupB! I'm Michelle, one of the peer reviewers for your group. Looks like you guys have really put a good amount of work into your article. The first thing I noticed was going to recommend is adding some more images. I know I like to have a visual when learning and they are always helpful. I have noticed above this addition is being discussed already. Also, possible expanding the initial intro would be good as well. Another thing, is to possibly reorganize the categories. I think they all flow well except the DNA Helicase Discovery coming after the RNA helicases. Moreover, I really like the addition of the discovery timeline and the superfamilies how it they are broken down. Also, I think you guys did a great job with including references and with linking key terms to other wiki articles. Keep up the good work! Myaworsk (talk) 16:19, 23 November 2012 (UTC)

Final Progress Report
Here we are! I have started our final progress report section on our project page. Please revise as you see fit. Thank you both for all your hard work. Good luck in your studiesJbaradei (talk) 13:24, 10 December 2012 (UTC)
 * Thanks so much for being on top of these Progress Reports and getting them started! I believe we've both added the appropriate sections for our contributions. Thanks to both of you for all your work, it was a pleasure working on the Helicase article with you two this semester, maybe we'll meet again on the Wiki Helicase Talk page as edits are continued on the page :D Have a wonderful winter break! Jennifergr (talk) 22:40, 13 December 2012 (UTC)