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

Hi: BCoss1
Hi BCoss1, How are you doing? I'm just testing this group page. Dgambrah (talk) 14:08, 5 October 2012 (UTC)

Article of Interest -1
Hi Brittany, I have found an article I would like to work on. The article's name is RNA of unknown function. This is a stub article and although it is listed as low importance, I think we can find additional information and contribute by adding value to the article's development. I did a quick search and found this related article on the web, "Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis", which could be very helpful in the process. I will continue to assess other articles of interest from the list. Please let me know your thoughts and your choice of articles. Dgambrah (talk) 00:44, 12 October 2012 (UTC)

Article of Interest -2
Hello Brittany, I have found another article of interest I would like to work on. The article's name is Endonuclease. Again, it's a stub article with mid-importance which needs additional citations and information. We need to pick one of these articles so please let me know your thoughts and choices so we can claim one. Thanks. Dgambrah (talk) 04:59, 13 October 2012 (UTC)

Out of town
Hi! Sorry for the delay. I have been out of town for work but will return tomorrow early afternoon and will get back to you. Thanks! 50.43.141.216 (talk) 20:35, 13 October 2012 (UTC)
 * Hi, Brittany, don't forget to make sure you are logged in whenever you make any edits in Wikipedia! Klortho (talk) 22:03, 13 October 2012 (UTC)
 * Brittany, thanks and please keep me posted. Dgambrah (talk) 00:04, 14 October 2012 (UTC)

Endonuclease
Derrick, I have had a chance to review some of the articles and I also think that we should work on the Endonuclease article. I think there is a lot of information that we can add to this page for improvement. Let me know if you are good with this and we can talk about the next steps moving forward. BCoss1 (talk) 18:56, 14 October 2012 (UTC)


 * Brittany, I agree with you on Endonuclease as our article of interest. In the meantime, I will go ahead and claim it on the course page. The next step is annotating the rationale behind our choice on our group's project page. I have already started a new section on our page entitled "unit 6 article selection rationale", our write-up rationale will go under this section. Please let me know your thoughts thus far. Dgambrah (talk) 00:34, 15 October 2012 (UTC)

Next Steps
Good morning, Now that we have selected an article, please correct me if I am wrong, but we need to write a one page response as to why we chose this article and what we will be changing on it? Is this something we both do, or we each write up some reasons and we can combine them? Let me know your thoughts. BCoss1 (talk) 11:42, 15 October 2012 (UTC)
 * Hi Brittany, you are correct we need to write about a page response (~300-400 words) as to why we chose this article and what we will be changing on it. This summary is a group effort, so our write-up will be combined as one. I will start off on our project page under the heading "unit 6 article selection rationale", please click edit and tweak, change, or add any text where applicable so that we can have one consolidated summary (due 10/16). My understanding is that we do not need to sign off on the project page only on talk pages. Please let me know what you think. Thanks. Dgambrah (talk) 18:00, 15 October 2012 (UTC)
 * Hi Derrick, I will go ahead and add some additional information/thoughts tonight. I will let you know if I come up with any questions along the way and I will also get back to you when I have finished so you can take another look.BCoss1 (talk) 23:46, 15 October 2012 (UTC)
 * Brittany, OK and thanks. Dgambrah (talk) 00:42, 16 October 2012 (UTC)
 * Hi Derrick, I have edited our page to include some additional information. Go ahead and look it over and make any adjustments you see necessary.  I look forward to working with you on this and definitely think we can make some significant contributions together.  BCoss1 (talk) 01:08, 16 October 2012 (UTC)
 * Hi Brittany,thanks for all your input and the summary looks good to me as far as the areas we would like to improve upon. I simply added the word "provide" to this sentence which now reads, "We can provide depth to the article by adding information regarding how endonucleases are affected by mutations in different cell types". Please let me know if that's what you meant and correct me if I misread it. Besides, I also think we can make significant contributions together and I look forward to working with you. Let me know your thoughts and thanks again. Dgambrah (talk) 11:36, 16 October 2012 (UTC)

Unit 9 to-do list for progress report
Hi Brittany,

We have to write a progress report and I would like to know your thoughts thus far. Here are my thoughts moving forward. We enumerated 7 things that we would like to do to improve the article. I think we can break the items down to specifics and possibly share the workload. So that each person would be responsible for information on certain number of items. The items are numbered 1-7.

1.	Functions of the 3 different categories of endonucleases – (i.e., type I, II, & III) 2.	Restriction behavior – how does this restriction allow the enzymes (types I, II, & III) to behave differently in terms of mechanisms? 3.	Endonucleases importance in prokaryotic and eukaryotic organisms. 4.	Its applications in - Recombinant DNA technology and DNA repair. 5.	Endonuleases overall significance toward molecular biology for readers. 6.	Pictures 7.	Mutations

I will research information on some of my proposed items above that could be included in the unit 9 progress report. Please let me know your thoughts. Dgambrah (talk) 01:24, 2 November 2012 (UTC)
 * Good morning Derrick,
 * I definitely think it is a great idea to split the topics among the two of us. Do you want to work on points 1-3, I can work on 4,5,& 7 and then together towards the end we both can contribute to the picture aspect of the article?  I also think it is a good idea to continue to give each other updates on these topics and if one of gets stuck the other person can help look into it as well.  Let's try and add one of the points to the article by sunday night and then we can start our summary on monday and have it edited and updated by both of us on tuesday.  Let me know your thoughts on this and if you are okay with the items or if you have started working on different ones.  BCoss1 (talk) 13:42, 3 November 2012 (UTC)


 * Hi Brittany,


 * I agree with you and yes I can work on points 1-3. I also agree with you that we give each other updates to indicate any progress and especially if one gets stuck on something, well said. This part of the assignment is a progress report (~400-500 words) and your proposed timeline is do-able to get the progress report done by tuesday 11/6. I will work on one of my points and update you via talk accordingly. I also think we can both contribute on the pictures in the end, if we can find them. Besides, please keep me posted on your thoughts.Dgambrah (talk) 19:37, 3 November 2012 (UTC)


 * I have obtain some information that would be helpful in our progress report. This information is in reference to my point number one i.e., Functions of the three different categories of endonucleases – Type I, II, and III. Please see the info in the project page under the heading unit 9 progress report and the source of this info is also under the heading references. In keeping with our timeline, we will be able to incorporate this info in addition to your findings in the summary of the progress report by Monday. And as you rightly stated, have it edited and updated by Tuesday. Please let me know your thoughts. Thanks. Dgambrah (talk) 23:31, 4 November 2012 (UTC)


 * Hi Derrick,


 * I have updated the progress report to include the plan of attack we talked about this weekend. I also included a "struggle" section for each of us to provide feedback as to what obstacles we have encountered so far.  Let me know what you think and feel free to edit/add accordingly.  BCoss1 (talk) 02:32, 6 November 2012 (UTC)


 * Hi Brittany,


 * Thanks for doing that and I have updated my struggles as well. I think it's important for us to write down the obstacles so that we can provide feedback in both directions. The summary for the Unit 9 progress report looks good to me. As always please let me know your thoughts. Dgambrah (talk) 21:19, 6 November 2012 (UTC)

Peer-reviewers checking in!
Hello Group81A,

Group81F is here to check in as your reviewers. From what we see the article already establishes endonuclease background information, categorization, and nomenclature. Your group has already noted that the article can be improved in multiple ways but we’d like to recommend a couple suggestions. Firstly, as stated in your article rationale the inclusion of images would greatly help the article ‘come alive’ since images essentially get the reader’s attention. Is there structural homology between each type of endonuclease? If not, what about within each type? Check out Wikipedia articles like EcoRI and BamHI which include PDB crystallographic structural images. Perhaps there is notable structural homology between these endonucleases that can be represented in an image.

Secondly, this article makes numerous references to restriction enzymes, so by adding restriction enzymes to the ‘See Also’ subheading you will help giving the reader easy access to this article for further understanding. Wiki’s restriction enzyme page would be a good template for your group’s article. This page includes a subheading called ‘Applications’ which gives the reader an understanding of real life roles of such enzymes. The addition of an ‘Applications’ heading to your article may help your group in formulating the roles that endonucleases play in recombinant DNA technology and DNA repair, as you've stated in your article rationale.

Lastly, the references subheading on the article’s page seems disorganized. According to Wikipedia, the use of ‘ibid’ is discouraged because the links are easily broken. Also reference 2 and reference 5 appear to be repetitive.

Please keep in mind that these are merely suggestions. Don’t feel obligated to undertake these points. As far as your group’s struggles, just know that there are plenty of editors on Wikipedia and our OA Klortho will be overlooking majority of our work so don’t sweat it! Keep up the good work and happy editing! ShanSabri (talk) 21:47, 11 November 2012 (UTC)

Unit 12 progress report
Hi Brittany, I have transferred my notes on - Functions of the three different categories of endonucleases – Type I, II, and III to the actual article. As per our discussions with the OA Klortho we were supposed to make our annotations on the actual article in order to interact with external viewers. So with regards to unit 12 progress report due on (sat 12/1), I will continue to gather some content on my second and third points and then share them on the actual article. Please let me know your thoughts? Thanks. Dgambrah (talk) 02:29, 29 November 2012 (UTC)
 * Hi Derrick-I will also go ahead and include my previous updates to the actual article as well. I will also go ahead and work on the second section of content as well. Question, I can't seem to figure out how to make a new section in our article, is this something you can help me with?  I will do a lot of work tomorrow and Saturday morning.  Work is killing me, lol.  Anyways, in regards to the progress report I think we can do something similar to what we did the last time and include the new content that we added as well as new struggles.  Let me know your thoughts!  BCoss1 (talk) 00:48, 30 November 2012 (UTC)
 * Hi Brittany,
 * I hope all is well. Sure! I can absolutely help in making a new section. To make a new section just click edit on top of the article and on the article itself find a suitable location that you want to insert your contribution. Then type a suitable heading for your contributions and attach "==" at both ends of the heading (for example, ==heading== or ===subheading===). When you click "save page" it will create a "new section" that you can add your contributions/contents underneath. I hope this helps.
 * I received some feedback from our reviewers with regards to the initial contents that I added on the actual article. I have made some minor editing based on their recommendations besides the references section. I will be working on it on Friday and Saturday to figure out how to properly cite book references that will reflect information added. So no worries, I am still getting use to how this wiki works and I am sure we will get there.
 * I have added a new section called "Categories of Endonucleases" and have edited the contents that I added under there including the citation as per the reviewers feedback comments. So check it out, the contents have footnote (2) citation attached. As always please let me know your thoughts. Thanks. Dgambrah (talk) 12:00, 30 November 2012 (UTC)
 * I have gone ahead and added the following contents to the article - The restriction enzymes used in molecular biology usually recognize short target sequences of about 4 – 8 base pairs. For instance, the EcoRI enzyme recognizes and cleaves the sequence 5’ – GAATTC – 3'. This is information regarding the restrictive behavior of the enzyme under my point #2. I also rearranged some of the sentences on the article so it can flow better from a reader's perspective. Thoughts? Dgambrah (talk) 17:09, 1 December 2012 (UTC)
 * So I am having a really hard time getting my citations to work correctly on our progress report. I want to make sure I do them correctly here before I actually update our article.  I have all the material done I just cannot figure out the citation part.  I put the ISBN number and pubmed number into the guide our prof gave us but cannot figure out to add the footnotes in and then add the corresponding citation at the bottom.  I will keep trying.  Please let me know if you have any advise. BCoss1 (talk) 21:06, 1 December 2012 (UTC)
 * Never mind, I figured it out. I have added both subjects I was responsible for to the article.  I will now take a look and peer review the other article and also add to the progress report.  Please take a look at the article and let me know what you think.  I hope you enjoy the rest of your weekend!  Thanks for all your help.BCoss1 (talk) 21:34, 1 December 2012 (UTC)
 * Hi Brittany,
 * I took a look at your additions to the article and they look good. Enjoy the rest of your weekend, I am sure we will get there. Thanks. Dgambrah (talk) 01:16, 2 December 2012 (UTC)

Endonuclease mini-review
Hi, group 81A, I hate to say it, but I think your article still needs a fair amount of work. I've done a little mini-review on the article talk page. I think, especially important is to disambiguate it from the "restriction enzyme" article. If endonucleases are, in general, different from restriction enzymes, then you need to make that clear. You also could definitely use more content, some figures, and maybe a little better organization. Klortho (talk) 16:34, 9 December 2012 (UTC)

Last Edits
Hi Derrick! I have done a lot of editing on our article. I tried to improve upon some of the suggestions and also some of the areas I originally contributed. If you read the final progress report for our group I explain everything that I have done. Please let me know what you think and I look forward to see what final contributions you make and what the article looks like in the end. BCoss1 (talk) 18:14, 14 December 2012 (UTC)


 * Hi Brittany,
 * Here are my final contributions as per the suggestions from our reviewers:
 * Introduced restriction endonucleases as being the most important nucleases in biotechnology with the following statement: There are a small amount of significant classes of endonucleases that cleave only at the specific nucleotide sequences (such as the restriction endonucleases which are so vital in biotechnology).
 * Removed ambiguous statement that may have been inserted by previous editors of the article: “A given sample of DNA is likely to contain a recognition sequence for any restriction endonuclease”.
 * Inserted a brief definition of Recombinant DNA with the following statement: DNA formed by the joining of genes into new combinations.
 * Refined the introductory sentence under the categories section.
 * Linked DNA ligase and Recombinant DNA
 * Inserted the heading for Notations and Further discussions: This was done to separate some pertinent contents from the categories section.
 * Let me know your thoughts. Thanks. Dgambrah (talk) 02:38, 15 December 2012 (UTC)


 * Here are my final contributions as a peer-reviewer to the nucleic acid structure article.
 * I also agree that the group has done a great job! That said, here are some suggestions that I thought the group could consider to further improve the article. I thought the group could insert a table to include contents for the following areas:
 * Secondary Structures and Properties of Fibrous Proteins
 * Structure
 * Characteristics
 * Examples
 * Thanks. Dgambrah (talk) 02:38, 15 December 2012 (UTC)