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

Intro

Hey there, Rachael & Shivani!

I thought I'd just say hello as we start our journey on this Wiki project! I'm a bit nervous for it haha! Just wondering, have y'all looked through the topics yet? Do you have preferences? Rashaalam (talk) 19:00, 5 October 2012 (UTC)

Hey Rasha & Shivani! Sorry I haven't been on here in a few days! Where did we find out our groups? Do you know if there is a specific list of topics? I noticed earlier when reading about Topoisomerases the Topoisomerase page looks like it could use dome work. Some citations are needed and "Discovery" section consists of: "Discovery: The first topoisomerase, E. coli topo I, was discovered by James C. Wang.[2]" Hope this helps Rmeskowitz22 (talk) 21:24, 8 October 2012 (UTC)

No worries, Rachael! It's all on our main course page, where we have our assignments listed for each Unit. If you keep scrolling down past the Units, there's a list of our groups and group members, and there is also a list of topics we can choose from below that. And I've seen the Topo article too haha! I don't remember if that's in the list, but if you want to add on, sometime, you can :) Rashaalam (talk) 21:47, 8 October 2012 (UTC)

I just took a peek at the this Topoisomerase is not on there. Bummer :-( Rmeskowitz22 (talk) 22:36, 8 October 2012 (UTC)

What about the Bacteriophage T12 topic? It is a very short article and I would love to learn more about its mechanisms. We deal with bacteriophage at work a lot :-) Rmeskowitz22 (talk) 22:44, 8 October 2012 (UTC)

If you find an article you want to work on, and it's not on the list, you could suggest it to Dr. Ogg. Here's what she wrote on the course page: "However, if you locate an article that you feel needs improvement, you can propose to work on this article. An article that is not on the list below, must be approved by myself and the OA." Klortho (talk) 23:43, 8 October 2012 (UTC)

Oh thanks for that, Chris! I missed that. So we CAN do one of the many topoisomerase articles, if we decide on that. I was also looking at the Helicase topic. And I just looked at Bacteriophage T12 as well, and that's definitely up for changing too. I guess the good thing is that at least now we have a smaller range of topics to decide on :) Rashaalam (talk) 00:27, 9 October 2012 (UTC)

Hi Rasha and Rachael! Sorry for joining in late. I looked at the articles that you guys are talking about. I would like to work on them though I saw some more articles that don't have much in them such as dnaI, dnaE, dnaS and transversion. Don't want to add up on your shortlist but just trying to suggest some more topics.Shivani (talk) 18:13, 9 October 2012 (UTC)

No worries about being late OR adding to the list, Shivani! =) I'll just start a new section to reorganize and list out the topics we've all mentioned now. — Preceding unsigned comment added by Rashaalam (talk • contribs) 19:40, 9 October 2012 (UTC)

Topics Discussion

I thought we'd discuss the topics in a new section with a fresh look/mind. I am a little bit OCD about things looking neat too ;) Shivani, I'll say it again, don't worry about adding topics, we should all go through topics we like/want to work on and we can discuss it to narrow down on one for the project. I'm listing the topics we've mentioned below, and you guys can both add on if you find another article that interests you & needs work :)

1. Topoisomerase
2. Bacteriophage T12
3. Helicase
4. DnaI/DnaE/DnaS
5. Transversion

Personally (and this is just an opinion/option I'm mentioning to put it out there), I think it might be better to work on an article that has LESS information on it, because then we can write it ourselves and the references and everything will be from scratch, so we'll be more sure of our own work. Rashaalam (talk) 19:53, 9 October 2012 (UTC)

It's definitely easier to get started on an article that is less developed. Klortho (talk) 11:47, 10 October 2012 (UTC)

Thanks Rasha for the neat list and I'm also in favor of choosing a topic with less information so that we can have a lot to add to it. I'll look through these topics and get back to you soon.Shivani (talk) 16:16, 10 October 2012 (UTC)

Hey guys! First off - thanks, Shivani, it's no problem at all! :) I also wanted to say that - as much as I don't want to rush - we should get our article decided soon, because we'll be choosing them on a first-come, first-serve basis and we also have to write about a page to say why we've chosen that particular topic article. It would be a lot better for all of us if we could at least choose a topic in the next day or two and lock it down for ourselves :) Rashaalam (talk) 05:00, 11 October 2012 (UTC)

Hey Guys! Sorry I've come into this conversation late! I agree, it would be much easier to work from an article with less on it. I'd say that knocks out Topoisomerase, Helicase is taken. The rest of the articles are stubs. It's not a big deal what we choose other than that. Although I am partial to the Bacteriophage haha. Wanna try to shoot for a topic by the end of today so we can get the assignments cranking. Rmeskowitz22 (talk) 15:39, 11 October 2012 (UTC)

End of day today sounds great! Although y'all might hear from very late because of the time difference, so sorry if I DO get very late! I saw helicase was taken, that's what prompted my message hahaha! The more I think about it, the more I'm with you on Phage T12, Rachael. That article has practically nothing on it, and since we'll be talking about a phage, rather that something more specific, we can get all sorts of information and build the article. DnaI/E/S are very specific and we might really have to go through a lot of papers to get information on them. As far as Transversion goes, I'm not sure. We'll have to include how it happens, why it happens, and what effects it has... which, actually, makes it a good topic too. HAHA can you guys see I'm typing as I think? So I would say that for me, the topic choice is between transversion and T12. Rachael can you lay out what kinds of sections we might have for T12? That would help. THANKS :) Rashaalam (talk) 19:03, 11 October 2012 (UTC)

Sure! I will! No worries about being late. I will be at work till about Midnight Eastern time so I will be checking here in between sampling. Science never stops haha! That's how I feel on the Bacteriophage. Maybe....

Introduction on bacteriophage

Mechanism

How or where from it can be contracted

How it effects organisms and which organisms it is most prevelent in

Testing and assays

How to kill/ deactivate

Maybe even, but we'd have to look more into it but how it could effect industry as well. I know the bacteriophage that effects E. coli is very important in fermentation of recombinate E. coli. Rmeskowitz22 (talk) 21:41, 11 October 2012 (UTC)

Hi Guys! So now three groups have already chosen their topic. That puts some pressure on us.I was searching for some information on bacteriophage T12 and came across some information.T12 is a temperate bacteriophage of S.pyogenes, the bacteria responsible for a number of diseases in humans. We can look through some more articles and see how this phage affects the pathogenicity of S.pyogenes. We can include the physical map of the T12 genome. I came across this article:The gene for type A streptococcal exotoxin (erythrogenic toxin) is located in bacteriophage T12. http://www.ncbi.nlm.nih.gov/pubmed/6389348 which shows that the gene for the toxin is present on the bacteriophage.

Though I could not find any information on its industrial use such as in fermentation. But we can sure study more about its role in the production of the erythrogenic toxin A and in scarlet fever.Shivani (talk) 03:17, 12 October 2012 (UTC)

Hey Guys! I looked for some more information about T12 but I couldn't find much about it's role other than it's role in the pathogenicity of S.pyogenes. But I guess it's a nice topic and we can work on it. So, I'm in for T12. Let me know so we can start working on it.Shivani (talk) 03:48, 12 October 2012 (UTC)

Thanks Shivani! Athough I don't want to make the decision for the team it looks like Bacteriophate T12 will be our best bet! The industry thing was just a suggestion- since most places use E. coli for their recombinant proteins, but you never know haha! I'm going to put us on the map for Bacteriophage and we can take it down if either of you object. it looks like we are off to a good start though Rmeskowitz22 (talk) 03:51, 12 October 2012 (UTC)

Awesome! Yeah I'm fine with Bacteriophage =) Thanks, Rachael! I would honestly rather choose a topic and "reserve" it rather than lose the ones we were narrowing down on! Great, I'll start working on information too. Also, we do have to write a rationale on choosing this article. Let's discuss that - I'll start a new section - and we can hopefully have that done in a couple of days and have it on our project page earlier than the 16th :) Rashaalam (talk) 06:52, 12 October 2012 (UTC)

Drafting the Rationale Assignment

So here's our section to brainstorm and/or come up with a rough draft of our rationale. How do we start? I suppose we'll include the fact that it's an "orphaned" article with very very little information. Also, Rachael, I think it would be interesting to mention T12's usage in industry! Maybe not in a whole section, but at least mention it. It will all depend on the information we find. And actually that could be a reason too - it is an important phage with usage in industry. Rashaalam (talk) 06:56, 12 October 2012 (UTC)

Hi guys! I started this. Please feel free to add on and change anything!

Bacteriophage T12 is considered a "stub" of an article, or as we like to call it "orphaned." The current article is only a few sentences long with very basic information. This is unfortunate because organisms like phage, in this even Bacteriophage T12 are very interesting and vital organisms to understand when studying microbiology and molecular biology. Bacteriophages are very unique and their mechanisms can cause much destruction with little effort.

Bacteriophate T12 has a hand in scarlet fever. In cases like this the virulence of the bacteriophage may have assisted in the development of a toxin, streptococcal pyrogenic exotoxin type A or SPE A. This toxin is a main player in the contraction of scarlet fever (1). In this article we could expand more on how this phage actually does this and how it has effected medical developments today such as vaccines.

(1) L P Johnson, M A Tomai and P., "Bacteriophage involvement in group A streptococcal pyrogenic exotoxin A production." J. Bacteriol. 1986, 166(2):623.

Rmeskowitz22 (talk) 13:01, 12 October 2012 (UTC)

Hi, I'd actually suggest that you do your drafting, revising, and editing right on your group's wiki page. That's actually the whole point of a wiki! Plus, it will give you good practice. Klortho (talk) 15:49, 12 October 2012 (UTC)

Thanks Chrisl! Will do! I wasn't sure if that was just for the final drafts or what :) I'll copy and paste onto that page and we can continue from there. Rashaalam (talk) 18:13, 12 October 2012 (UTC)

Thanks guys! Nice start. I will see you on the group wikipedia page with some more information on this topic.Shivani (talk) 10:26, 13 October 2012 (UTC)

Thanks Rachael, I just saw your edit. I'm planning to add to it later today. We have to have ~300-400 words, and it's going to be formal on the Group page, so I'm going to take off our little comments :) Just a warning so it's not a shock the next time you look at it :) And you and Shivani can both go ahead and edit the rationale freely as you find information/reasons. If you want, leave a note here, but you don't have to :) Rashaalam (talk) 23:41, 14 October 2012 (UTC)

I just finished up the editing. We are at just about 200 words. If we can add on to the rationale and get it to 300 words it'd be nice, but I honestly don't know what else to add! I'm looking around for more articles and papers but that'll be useful for the actual Wiki article, not the rationale. :/ Rashaalam (talk) 01:24, 15 October 2012 (UTC)

Thanks Rasha! I know what you mean. There is a lot of information but we don't want to use that as the rationale per say. 155.91.45.231 (talk) 13:21, 15 October 2012 (UTC)

Ok folks! I added a little bit more to the last pargraph... that puts us at about 280 words. I know we should be going for content more than word count but that at least gives us an idea of where we are at. Rmeskowitz22 (talk) 11:35, 16 October 2012 (UTC)

Thanks Rachael! I think we're close enough at this point, and I can't think of any other reason to add for rationale. I mean, it's an important phage and the article DEFINITELY needs more information because there is more information about it out there. *sigh* But I think we're good right now :) Rashaalam (talk) 18:31, 16 October 2012 (UTC)

Thanks Rasha for fixing the second reference. I noticed I made a mistake there.Shivani (talk) 19:51, 22 October 2012 (UTC)

Sharing Data/Information

Hey girls!

I wanted to at least get something in place for us to share any papers we may find, and maybe split up the sections so there's no confusion about who's writing what. I have looked up a couple of papers, and I thought there must be a way to share them... then I thought that we could use DropBox. DropBox is actually a cloud storage service, and there's a certain amount of space you get for free. I thought while we're working on this project and finding information, we could all use a shared folder on DropBox to let each other see the papers we've found. What do you think? And I suppose we can talk about sections once we have all found some information and know how to begin :) Rashaalam (talk) 01:34, 21 October 2012 (UTC)

Hi Rasha!

Thanks for starting the discussion. Even I looked up some of the articles on T12 though I think there is not a lot many articles on this bacteriophage. But I am sharing the links to the one I found. I think dropbox is a good idea. I searched a little bit about it as I have never used it. But if we are allowed to do so then I will download the application. For now, I am sharing links to some of the articles that I found:

Bacteriophage T12 of Streptococcus pyogenes integrates into the gene encoding a serine tRNA. McShan WM, Tang YF, Ferretti JJ. http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.1997.2591616.x/pdf

Group A streptococcal phage T12 carries the structural gene for pyrogenic exotoxin type A.Lane P. Johnson and Patrick M. Schlievert http://www.springerlink.com/content/x8k7t1757vt275p8/

The fundamental contribution of phages to GAS evolution, genome diversification and strain emergence. David J Banks, Stephen B Beres, James M Musser.http://www.sciencedirect.com.proxy1.library.jhu.edu/science/article/pii/S0966842X02024617

Bacteriophage involvement in group A streptococcal pyrogenic exotoxin A production.L P Johnson, M A Tomai, and P M Schlievert https://www-ncbi-nlm-nih-gov.proxy1.library.jhu.edu/pmc/articles/PMC214650/ Full paper: http://jb.asm.org/content/166/2/623.full.pdf — Preceding unsigned comment added by Sgarg9 (talk • contribs) 21:17, 22 October 2012 (UTC)

Shivani (talk) 21:20, 22 October 2012 (UTC)

Drop Box sounds great! I feel like I've used it before for my undergraduate work- if its free I'm in! I think a good idea might be to break up who will work on certain sections and then we could enhance the sections of one another. That way we are not all working on the same section without knowing it. Rmeskowitz22 (talk) 14:41, 23 October 2012 (UTC)

Great, I've already added Shivani's pdfs to my folder. Let's do this - you girls email me an email address that you would use to open the dropbox account. I'll share the folder using your emails. I *think* you might be able to see the folder before you make an account, but either way, I can at least start the sharing process. Email me at rashaalam@gmail.com :) As for the article itself. I was just looking through one of the papers. I wouldn't mind sprucing up the introduction and go through as much of mechanism I can find. Rachael, would you mind talking about how T12 relates to industry? You said you've worked with it, right? Shivani, what do you think about T12 relating to disease(s)? Of course, these are just options - y'all have to write the sections so you pick, but I thought I'd throw those topics out there :) And we can all work on each others' sections to edit/enhance anyway. Rashaalam (talk) 18:18, 23 October 2012 (UTC)

Thanks Rasha- I have been doing research and this Bacteriophage really doesn't has an affect on the industy like T7 does since it is more specific to Strep pyagonese....I think we should get an Outline going too...

1. Indroduction **Rasha

2. Mechanisms **Rasha

3. Involvement in Scarlet Fever (and Other diseases if it works) **Shivani

4. Testing and assays **Rachael

4. Deactivation and Prevention **Rachael

These are just some ideas of how we might set up the article PLEASE feel free to change it up, add stuff or change what you do... I tried to go off of Rasha's suggestions! — Preceding unsigned comment added by Rmeskowitz22 (talk • contribs) 15:06, 26 October 2012 (UTC)

Hey, sorry for the late response! It's a religious holiday for me, so we've been and will be a bit busy this weekend :) Rachael this sounds perfect to me :) Rashaalam (talk) 03:30, 27 October 2012 (UTC)

Hey Guys, Sorry to respond this late. I created my dropbox account and saved some of the articles in there. My emailid is sgarg01@gmail.com. I was looking at other phage articles and also on some papers relating to Bacteriophage T12 and I think in the introduction section we can include some information about the discovery of T12.And we can also include a section about the virion structure and its genome. I am trying to search for some papers from where we can get this information and will get back to you with the information. The other section I was thinking of is about the life cycle of T12 which can include subsections like Infection of the host bacteria and the Lytic and Lysogenic cycle. I think Rasha this is what you must be thinking to include in the Mechanism section alnogwith how T12 is responsible for turning the nonvirulent bacterial strain into a virulent one. Just trying to clear things for me:). So I will work on Section 3(Involvement in Scarlet fever) and will also try to work on virion structure and genome if I could gather some information.And will also help with the other sections.Shivani (talk) 20:17, 4 November 2012 (UTC)

No worries, Shivani! Your message is helping me clarify things too :) Good idea about the discovery of T12! And I'm so annoyed because I HAD come across an article, but I've lost it now >_< I hope I can find it again... it didn't have THAT much information I could use, but maybe with fresh eyes and a new purpose I could find something! Rashaalam (talk) 22:36, 4 November 2012 (UTC)

Drafting the Article

I believe we might be able to do this on the talk page of the actual article- but I wanted to capture this work real quick!

You're right, we should now shift to the talk page of the article. And thanks for including the next section. We'll try and figure out that citation and incorporate it :) Rashaalam (talk) 23:23, 28 October 2012 (UTC)

Guys I'm having a really hard time finding information. Where are you guys getting info from? I've found a few papers, but nothing specific to mechanism. Also, Rachael, if you want to put in your section from below into the article, please do, so that we can see that it was YOUR work in the editing history :) AND I wanted to mention - please watch the talk page of the article so when one of us edits the others get a notification! Thanks! Rashaalam (talk) 07:05, 30 October 2012 (UTC)

I found this website, and it has nothing specific about T12, but there's a section on "applications" which might be helpful, as well as one on evolution. Maybe y'all want to check it out: http://www.thebacteriophages.org Rashaalam (talk) 05:59, 31 October 2012 (UTC)

Killing Bacteriopphage T12 and Prevention of Scarlet Fever

Bacteriophages are very robust organisms and are very hard to kill and very easily spread (need citation). UV light can enhance phage T12 production along with the production of streptococcal pyrogenic exotoxin A, also knows as the scarlatinal toxin . However, this is only to a point. The UV light stresses lysogenic bateria causing them to propagate and burst the host bacterial cells (need citation). In the case of T12 exposure to UV lights increases the propagation of bacteriophage T12 at 20 seconds of exposure. After 20 seconds of exposure the UV light starts to kill the bacteriophage .

Peer Review from Group 81B

Hello Group 81E! First off, my compliments on picking the article you did. In my experiences having to start a wikipedia article from scratch has always been a tiring process due to the extra attention to initial formatting and the necessity of establishing "integrity" for the article, but I must say that you have done a commendable job so far, the article is clear, concise, and already has an established scientific integrity to it. Below are just a few topics I thought you might want to look into:

• An explanation or delving into the erythrogenic toxin characteristics.
• Is there a diagnostic test to detect bacteriophage T12? If so implementing that data into the article could prove useful.
• Our group implemented the history of discovery of our subject into the artile. That could be a topic that coule be added to your article (i.e. who discovered it, when, how, any interesting extenuating circumstances in the discovery)
• Is there a mode of action that switches the phage from lysogenic to lytic?
• Is there any sigma factors that are incorporated in the growth of this phage once it infects a cell?

Just a couple of suggestions. I hope they help. I will be reviewing the article from time to time so if there is anything I can do to help you or if you need any elaboration on my comments feel free to leave them here or on my group's (81B) page.Jbaradei (talk) 16:05, 16 November 2012 (UTC)

Thank you, Hanna! We'll keep al this in mind as we continue! Good topics :) Rashaalam (talk) 19:51, 16 November 2012 (UTC)

Hello everybody. I'm also from group 81B and I just wanted to add a few comments. According to wikipedia guidelines the references should be placed after punctuations.I know this only because I did the same thing and someone else in our group pointed it out. I also noticed an error with a reference in the Genome section. The article looks like it's shaping very well. :-) Gisela Gonzalez (talk) 14:39, 20 November 2012 (UTC)

Thanks Gisela for pointing out about the references. We'll fix the references.Shivani (talk) 17:03, 20 November 2012 (UTC)

Thanks, guys! And thanks, Shivani, for fixing that up :) I hope everyone's having a great Thanksgiving weekend! Rashaalam (talk) 22:26, 24 November 2012 (UTC)

Thank you for your input! I am actually working right now on the ways to detect the phage :-) Rmeskowitz22 (talk) 18:27, 28 November 2012 (UTC)

Peer Review of Group 81C

Hey guys, I'm starting the discussion on the review of Group 81C's RT-PCR article on the Group's talk page. When you guys get around to looking through the difference in the articles you can join me there :) Hope you're having a great Thanksgiving break! Rashaalam (talk) 22:23, 24 November 2012 (UTC)

Hey guys Sorry I have been MIA! I hosted Thanksgiving this year so I was caught up with all that! Hope your Thanksgiving was amazing! I am going to try to get to updated our article, the peer review and the update tonight and tomorrow! Rmeskowitz22 (talk) 12:54, 28 November 2012 (UTC)