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

Introduction

- Check One! Jpark623 (talk) 03:25, 6 October 2012 (UTC)

- Hello Group 81c Kkotani1 (talk) 15:28, 6 October 2012 (UTC)

- Hey, Kes. Are you receiving an email notification regarding changes to the page? Jpark623 (talk) 19:26, 8 October 2012 (UTC)

- Hey Jea. Yes, I am getting email notifications on this page. Looks like we need to select an article for our group by the end of next unit. It's on first-come, first-serve basis, so we should start thinking about our approach and criteria now, huh? Kkotani1 (talk) 22:34, 8 October 2012 (UTC)

- Sounds good. Any subject in mind? Jpark623 (talk) 22:47, 8 October 2012 (UTC)

- Looking through the instructions, sounds like we need to do an individual assessment on at least two articles first. I'll scan through them to see if any may be good candidates. Why don't we regroup here afterwards? If we both come up with similar suggestions, it makes the selection easier... if not, we'll have more to select from. Kkotani1 (talk) 22:54, 8 October 2012 (UTC)

- Ok, I'll work on my portion of the assessment later tonight. Jpark623 (talk) 23:08, 8 October 2012 (UTC)

-Hi Jea and Kes. Sorry it has taken me so long to contribute. Keeping up with three courses this semester plus a full time job is proving to be quite the challenge. I will take a look at the articles you have assessed and leave my comments MHN2785 (talk) 13:58, 10 October 2012 (UTC)

Feedback on indentation on talk pages.

When having a discussion on a talk page, it's conventional to indent each subsequent reply by putting a colon at the beginning of the line. It helps make the who-replied-to-whom thread a little bit easier to follow. It's a good habit to get into, especially because you should anticipate participating in talk-page discussions on the article that you eventually decide to work on. Like this:

Here's the first reply to the main topic of this discussion. -- User B

Here's a reply to the reply -- User C

And now a reply to the reply to the reply -- User B

Here's a second reply to the main topic -- User D

I hope that helps. Click the "edit" button to see what the colons at the beginning of the lines look like. Cheers! Klortho (talk) 23:52, 8 October 2012 (UTC)

This is helpful. Thanks. Kkotani1 (talk) 00:00, 9 October 2012 (UTC)

Initial Assessment: Gal Operon

Quality Scale: Stub Importance Scale: Low Other Group Assessment: As of now, no other groups have proposed the expansion of the article.

Although the article importance is rated as low, gal operon is an important example of negative regulation involved in the utilization of the sugar galactose. Due to the popularity of using lac operon in undergraduate courses for learning, the expansion of the gal operon article seems to have been overshadowed by the information contributed to the lac operon article. Because there are numerous sources available regarding the subject, the article should be relatively easier to expand on and our contribution should benefit anyone wishing to learn about the encoding of enzymes used in galactose metabolism as well as those looking for other sources to negative operon regulation alternative to lac operon. -Jpark623 (talk) 00:00, 9 October 2012 (UTC)

I agree that there is a lot of room for expansion in this article. I like how the article for lac operon is broken down into structure, regulation, development, and use in molecular biology sections. Since there is a lot of information about the gal operon, it would be easy to expand this article and maybe structure it similar to the lac operon. However, it is a low priority. MHN2785 (talk) 14:22, 10 October 2012 (UTC)

Yes, the expansion of this article should be a walk in the park. If another group chooses this article, should we peer review it? Hehe! -- Jpark623 (talk) 05:21, 11 October 2012 (UTC)

Unit 5: Initial Assessment (Kkotani1)

I took an approach of scanning through the articles using simple criteria vs. doing deeper dives on each topic. I would suggest taking a look at following articles:

Consensus sequence

Helicase

Retrotransposon

Reverse transcription polymerase chain reaction

They all have Start quality scale and leave sufficient room for our team to expand on. They are also rated as High on importance scale, so each topic is deemed sufficiently relevant. Running quick article searches through JHU library engine, fair number of hits also come up for each. Kkotani1 (talk) 00:34, 9 October 2012 (UTC)

Initial Assessment: 2'-O-methylation

Quality Scale: Stub Importance Scale: Low Other Group Assessment: As of now, no other groups have proposed the expansion of the article.

2'-O-methylation is another under-appreciated article with a low importance scale. However, 2'-O-methylation is used by various RNA molecules for RNA biogenesis and functionality and is considered to be an essential process for cellular viability. It's surprising that this article has not been expanded since the 2'-O-methylation of the backbone ribose is the most common modification seen among RNA modifications. Due to the modification being conserved by numerous RNAs, I believe the difficulty in writing this article will lie in the sorting, grouping, and summarizing the abundant sources of literature involving the 2'-O-methylation. -Jpark623 (talk) 01:00, 9 October 2012 (UTC)

Initial Assessment Discussion

Let's start a new discussion on our initial assessment of the topics here... with correct indentation. :p -- Jpark623 (talk) 01:04, 9 October 2012 (UTC)

Sounds good. Using this platform/environment is going to take a little getting use to... By the way, have you heard from MHN2785 at all? Kkotani1 (talk) 01:19, 9 October 2012 (UTC)

No, I have not. She hasn't checked in yet. Tomorrow is technically the last day of the unit week so perhaps we'll hear from her tomorrow? Juggling between work, school, and life can be so demanding *sigh* -- Jpark623 (talk) 01:37, 9 October 2012 (UTC)

Kes, I've just browsed through your suggested topics and I like the RT-PCR article due to the following reasons:

(1) The article is less developed and I could see us expanding on history, procedure, and application at the least.

(2) There seems to be plenty of sources out there that we can reference.

(3) The article is of high importance and it would be a greater contribution to the Wiki community compared to one of a low importance.

Regarding your other three suggestions, I do like the subjects and wouldn't mind researching them but wouldn't it be less time consuming for us if we picked a stub article rather than a start? XD -- Jpark623 (talk) 01:37, 9 October 2012 (UTC)

This does sound like a good candidate. I agree that under-developed article would be desirable - we can experience building it from the ground up and develop appreciation for providing a comprehensive, holistic picture on the topic. Also agree that availability of sources and relevance to wiki community are important. I think other three and the two you suggested are also viable as well... but I would support moving forward with RT-PCR. Let's get input from MHN2785 and decide on the path forward. We'll want to claim whichever article we decide on quickly and start building the case in unit 6. Cheers. Kkotani1 (talk) 02:15, 9 October 2012 (UTC)

I agree that this is a good candidate. Since it is a first come first serve basis for "claiming" articles, I think we should go ahead and grab it. It is surprising to me that this article is so under developed considering how important RT-PCR has been to molecular biology research. I was took a look at the talk page for this article and noticed that someone in 2008 said that they wanted to do a complete overhaul of this article. I don't think that ever happened so it looks like it is up to us. I will wait for you all to agree and then I will go ahead and change Group X to our group number in the table on the project page. MHN2785 (talk) 14:40, 10 October 2012 (UTC)

Let's claim it. Kkotani1 (talk) 03:33, 11 October 2012 (UTC)

K, sounds good to me. -- Jpark623 (talk) 05:05, 11 October 2012 (UTC)

Claimed it on the class page. Kkotani1 (talk) 02:32, 12 October 2012 (UTC)

Confounding talk page and group page

Hi, guys, I just realized that you have a lot of discussion going on on the group project page which really belongs on this talk page. Generally speaking, the talk pages are for discussions (where you sign your posts, and indent them, etc.) and the group project pages are for finished pieces of work, where authorship of specific pieces is not so important. Klortho (talk) 10:27, 9 October 2012 (UTC)

Ah, I see. Thanks, Chris. I'll move the threads. Jpark623 (talk) 12:03, 9 October 2012 (UTC)

Great! One more minor bit of feedback -- try to remember to use an edit summary when you make a change on anything other than a talk page. I see here, when you moved the threads, that you deleted a whole bunch of stuff (see "-2642") but there's no summary, so I'd have to dig to find out what happened (if I didn't already know it). You should write something like "moving threads to talk page". Klortho (talk) 13:49, 9 October 2012 (UTC)

Will do! -- Jpark623 (talk) 17:23, 9 October 2012 (UTC)

Thanks, Jea, for moving the treads. Chris, I didn't realize you didn't have to use an edit summary when changing this talk page - so thanks for that as well. Kkotani1 (talk) 01:07, 10 October 2012 (UTC)

Alternative to RT PCR Article

Hi group. I just wanted to propose an alternative to the RT-PCR article in case someone else snags it. I think the Cooperative binding article might also be a good choice. As it currently is this article mostly outlines the biochemistry of the cooperative binding. I think we can add a lot of information about the molecular biology application/ importance of cooperative binding. MHN2785 (talk) 15:13, 10 October 2012 (UTC)

Hello, Meredith! I'd be ok with expanding the article, but either you or Kes would have to take charge in explaining the kinetics. Explaining functions has never been my strong suit... :) Cooperative Binding to Linear Biopolymers -- Jpark623 (talk) 16:58, 10 October 2012 (UTC)

Discussion on Unit 6 Report

Hey guys. Now that we've got the article selected, thought I'd start a new discussion here as we work toward the report due for Unit 6 around the rationale for our selection. We've already touched on main reasons:

• Limited content on current page (as measured by "Start" quality)
• Importance to wiki/science community (as measured by "High" relevance rating)
• Availability of reference sources

I think we can start building our case by expanding on these three main areas. We can also add additional dimensions if you have other suggestions as well. Let me know your thoughts.

Also, as a side note, I'm out of the country (US) most of next 3 weeks starting tomorrow. Will likely be able to check in once most of days, but just get me on email if you need immediate input as I'll at least have access to that through my phone. Kkotani1 (talk) 02:56, 12 October 2012 (UTC)

Hey Kes. Thanks for changing the status of our article to claimed. Using the 3 points above as the basis for our rationale of choosing the article is a good idea. I've been trying to do some background reading on RT-PCR and it's proven difficult to distinguish papers written on Reverse Transcriptase PCR and Real Time PCR due to their acronyms being the same. I'll draft up our initial rationale sometime tonight and email you and Meredith with an attachment later. Let touch base then. Have a safe trip. -- Jpark623 (talk) 11:30, 12 October 2012 (UTC)

Hi Kes and Jea. I'm going to try to create a sandbox for our rationale, so that we can work on using the Wikipedia syntax and incorporating it into our rationale for choosing the RT-PCR article. Feel free to make edits on this page. I also sent my comments/additions/changes as an email to you both.

/Rationale. — Preceding unsigned comment added by MHN2785 (talk • contribs) 17:21, 14 October 2012 (UTC)

Looks like I forgot to sign my last entry. I added the draft of our article to the sandbox link above. I still haven't figured out how the source citing works yet, but I think this is a good start. MHN2785 (talk) 17:33, 14 October 2012 (UTC)

Hey Meredith. I've just finished reading your revision and I think it's a good addition highlighting another importance of RT-PCR. If it's okay with you, I'd like to combine it in the second paragraph for fluidity. Also, I'd advise against using sandbox for tracking changes since it clears itself every few hours (twice a day, I believe). Cloud document editing/storage sites like google drive and skydrive keeps revisions to changes so if you'd like, we can upload it to one of those servers. -- Jpark623 (talk) 18:04, 14 October 2012 (UTC)

Is it feasible just to use the project page even as we work through our revisions? It keeps track of changes and the report won't be evaluated until the end of the unit - so as long as we get it to the final draft shape by the, it should be ok. I'll start making my notes offline and will add to the document once we align on where to hold the working draft. Thanks. Kkotani1 (talk) 19:03, 14 October 2012 (UTC)

We can do that too but do you mind holding off on your revision for a few minutes? I'm almost finished tweaking what Meredith has sent us and I would appreciate your input on both of our revisions combined. Also, your writing samples tell me that you're probably the more eloquent writer in our group and it would be nice to have your tone for our post. -- Jpark623 (talk) 20:33, 14 October 2012 (UTC)

Sounds good. Will load up the current draft in its entirety to the project page fist, then I'll start the new round of revisions. Thanks. Kkotani1 (talk) 00:11, 15 October 2012 (UTC)

Draft is up on the project page. Took a first stab at reorganizing the contents around our key reasons for selecting this article. There was significant amount of really good background material in the draft - they will be certainly be useful for the actual article. Ended up taking fair amount of it out in this version to more or less balance the content and focus around actual reasons for selecting the article... and fitting it within 300-400 word limit guidance. My apologies for being quite liberal with this edit. If you feel they should be added back, feel free to do so. Kkotani1 (talk) 00:49, 15 October 2012 (UTC)

Wow, nicely edited and organized! I feel that the latest revision you've made should be our final draft or very close to being one at the least. I'm fairly impressed with the results. What do you think, Meredith? -- Jpark623 (talk) 04:32, 15 October 2012 (UTC)

I agree. I did make one minor edit to one of the sentences in the last paragraph and added a link, but other thank that I think it has come together nicely. Thanks for adding that to the project page Kes. I didn't realize that the sandbox would clear tracked changes every few hours. MHN2785 (talk) 04:40, 15 October 2012 (UTC)

No worries. We're all new to wikipedia here. I'm still trying to find our way around just like you. -- Jpark623 (talk) 05:25, 15 October 2012 (UTC)

Added few links as well. Other minor things for us to consider. In the second paragraph, we touch on timing of Northern blot but not on the intro of RT-PCR - Jea, if you have this handy from all your reference materials, I think it'll be nice to include (but not a "must" so don't go digging for it if you don't have it). We also discussed that there is significant confusion around the acronym RT-PCR... some using it to refer to "real time-". Being able to clear this up adds to the appeal and rationale for selecting this article. But again, it's a nice-to-have. I don't have the bandwidth to work on this myself before Wed and suspect you guys are in a similar situation, so I'll only raise it as an option. I think we're in good shape overall. Thanks for good communication and collaboration on this. Kkotani1 (talk) 07:13, 15 October 2012 (UTC)

Added section on nomenclature inconsistencies but decided not to expand further on the introduction to RT-PCR. As I was typing, I ended up getting into the concept of reverse transcription and PCR procedure, which would have resulted in the overall length of the summary being longer than it should. The paper that Meredith introduced in our 2nd revision has really good background on the history and use of qPCR/RT-PCR which we can use on our actual article. Thanks for your continued participation despite being out of town and let me know if you'd like anything else added/revised. -- Jpark623 (talk) 23:44, 15 October 2012 (UTC)

Jea, thanks for working on it. Looks great. Kkotani1 (talk) 00:06, 17 October 2012 (UTC)

Thanks Jea for adding the part about the nomenclature. I think this will be important for the article as it does get confusing. Overall I think the rationale looks great. MHN2785 (talk) 16:17, 17 October 2012 (UTC)

Drafting on Wikipedia

Of course it is up to you guys, but I would recommend just editing your rationale in place on your project page, rather than using this custom subpage. Wikipedia was designed for collaborative editing, so it would make sense, and give you good practice.

The suggestion to use Google docs or some other site like that makes me cringe, I have to say. I think Wikipedia, for collaboration, is superior! Also, I noticed that you're actually editing in a subpage's talk page, which really doesn't make sense. Talk pages are for discussions. I'm just trying to steer you a little bit into the Wikipedia mindset -- it will be more important when you start interacting with outside editors. Klortho (talk) 22:15, 14 October 2012 (UTC)

Summary of References

Hey group. Although it's only been a week, it feels as if we haven't spoken in ages! How are you two doing?

I just wanted to post a summary of the sources that we've gathered so far organized by subject. I doubt we'll use all of them due to redundancies, but they should provide us with a good starting point for writing our article. Please feel free to make corrections and addition that you find necessary. Also, don't forget to utilize the Wiki template filler. -- Jpark623 (talk) 12:59, 24 October 2012 (UTC)

Hey Jea. Thanks for adding these. Very helpful. Kkotani1 (talk) 07:08, 26 October 2012 (UTC)

This is very helpful. Should we start assigning work based on the different sections outlined here?MHN2785 (talk) 21:09, 30 October 2012 (UTC)

Introduction

• "Real-Time Quantitative Reverse Transcription PCR".
• "RT-PCR Methodology".
• "QRT-PCR - OpenWetWare".
  • Note: Reference only.
• "PCR techniques - OpenWetWare".
  • Note: Reference only.

History

• "The Biotechnology Revolution: PCR and Cloning Expressed Genes | Learn Science at Scitable".
• Alwine JC, Kemp DJ, Stark GR (December 1977). "Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes". Proc. Natl. Acad. Sci. U.S.A. 74 (12): 5350–4. Bibcode:1977PNAS...74.5350A. doi:10.1073/pnas.74.12.5350. PMC 431715. PMID 414220.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
• Streit S, Michalski CW, Erkan M, Kleeff J, Friess H (2009). "Northern blot analysis for detection and quantification of RNA in pancreatic cancer cells and tissues". Nat Protoc. 4 (1): 37–43. doi:10.1038/nprot.2008.216. PMID 19131955. S2CID 24980302.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• "History of polymerase chain reaction - Wikipedia, the free encyclopedia".
  • Note: Reference only.

Principles

• Bustin SA, Benes V, Nolan T, Pfaffl MW (June 2005). "Quantitative real-time RT-PCR--a perspective". J. Mol. Endocrinol. 34 (3): 597–601. doi:10.1677/jme.1.01755. PMID 15956331.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
• "Molecular - PCR - Reverse Transcriptase PCR and Real-Time Reverse Transcriptase PCR".
• Bustin SA (October 2000). "Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays". J. Mol. Endocrinol. 25 (2): 169–93. doi:10.1677/jme.0.0250169. PMID 11013345.{{cite journal}}: CS1 maint: date and year (link)
• Ståhlberg A, Rusnakova V, Forootan A, Anderova M, Kubista M (September 2012). "RT-qPCR work-flow for single-cell data analysis". Methods. 59: 80–88. doi:10.1016/j.ymeth.2012.09.007. PMID 23021995.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  • Topic: Naming inconsistency
• "Sample Preparation for PCR, Real time PCR & RT-PCR | Life Technologies".
  • Note: Additional Sources

Protocol

• "Biotools Products: Labs Biotools - Reverse Transcription PCR".
• "RT-PCR".
• "MasterAmp™ RT-PCR Kit for High Sensitivity, Epicentre® (an Illumina® company)".
• "QIAGEN - Sample & Assay Technologies".
• Shiao YH (December 2003). "A new reverse transcription-polymerase chain reaction method for accurate quantification". BMC Biotechnol. 3: 22. doi:10.1186/1472-6750-3-22. PMC 317330. PMID 14664723.{{cite journal}}: CS1 maint: date and year (link)

Challenges

• "QIAGEN - Sample & Assay Technologies".
• Freeman WM, Walker SJ, Vrana KE (January 1999). "Quantitative RT-PCR: pitfalls and potential". BioTechniques. 26 (1): 112–22, 124–5. doi:10.2144/99261rv01. PMID 9894600.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
• Souazé F, Ntodou-Thomé A, Tran CY, Rostène W, Forgez P (August 1996). "Quantitative RT-PCR: limits and accuracy". BioTechniques. 21 (2): 280–5. doi:10.2144/96212rr01. PMID 8862813.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)

Application

• Hierro N, Esteve-Zarzoso B, González A, Mas A, Guillamón JM (November 2006). "Real-time quantitative PCR (QPCR) and reverse transcription-QPCR for detection and enumeration of total yeasts in wine". Appl. Environ. Microbiol. 72 (11): 7148–55. Bibcode:2006ApEnM..72.7148H. doi:10.1128/AEM.00388-06. PMC 1636171. PMID 17088381.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
• Techathuvanan C, Draughon FA, D'Souza DH (February 2011). "Comparison of reverse transcriptase PCR, reverse transcriptase loop-mediated isothermal amplification, and culture-based assays for Salmonella detection from pork processing environments". J. Food Prot. 74 (2): 294–301. doi:10.4315/0362-028X.JFP-10-306. PMID 21333152.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
• Slomka MJ, Pavlidis T, Coward VJ; et al. (July 2009). "Validated RealTime reverse transcriptase PCR methods for the diagnosis and pathotyping of Eurasian H7 avian influenza viruses". Influenza Other Respi Viruses. 3 (4): 151–64. doi:10.1111/j.1750-2659.2009.00083.x. PMID 19627372. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
• Emery SL, Erdman DD, Bowen MD; et al. (February 2004). "Real-time reverse transcription-polymerase chain reaction assay for SARS-associated coronavirus". Emerging Infect. Dis. 10 (2): 311–6. doi:10.3201/eid1002.030759. PMC 3322901. PMID 15030703. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
• Urbach A, Schuldiner M, Benvenisty N (2004). "Modeling for Lesch-Nyhan disease by gene targeting in human embryonic stem cells". Stem Cells. 22 (4): 635–41. doi:10.1634/stemcells.22-4-635. PMID 15277709. S2CID 23231597.{{cite journal}}: CS1 maint: multiple names: authors list (link)
• "QIAGEN - Sample & Assay Technologies".
  • Note: Additional sources

Publication Guidelines

• Bustin SA, Benes V, Garson JA; et al. (April 2009). "The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments". Clin. Chem. 55 (4): 611–22. doi:10.1373/clinchem.2008.112797. PMID 19246619. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
• Bustin SA (April 2010). "Why the need for qPCR publication guidelines?--The case for MIQE". Methods. 50 (4): 217–26. doi:10.1016/j.ymeth.2009.12.006. PMID 20025972.{{cite journal}}: CS1 maint: date and year (link)
• "www.vetmed.ucdavis.edu" (PDF).
  • Note: Not a good source. Reference only.
• "www.microarrays.ca" (PDF).

Initial list added. -- Jpark623 (talk) 12:59, 24 October 2012 (UTC)

Merged method section into protocol. -- Jpark623 (talk) 13:03, 24 October 2012 (UTC)

Working on our article toward Unit 8

Looks like the next milestone is Unit 8. We'll need to start working on the actual article between now and then. Suggest we first lay out a brief plan - how we might organize various sections, rough estimate of when we may want to accomplish certain tasks, etc. A vision for our end-game, if you will. I have a long flight to catch tomorrow so will give it some thought. Let's reconnect when we have some ideas and we can start dividing up some work.

Also noticed that we've been assigned as reviewers on stable nucleic acid lipid particle being edited by Group 81F. We'll need to start getting up to speed on that topic as well. Cheers. Kkotani1 (talk) 07:20, 26 October 2012 (UTC)

Sounds good. Let's touch base this weekend. -- Jpark623 (talk) 09:52, 26 October 2012 (UTC)

Sorry for the delay. Been out of power and internet. Amazing how dependent we are on electricity... couldn't get anything done. On the upside, I had to cancel my business trip this week so I'm at least in the US and able to work on this. I meant the milestone was Unit 9. I think we still need to take the same approach - not sure how much work we can get done on the actual article with delays this week, but at a minimum, we should lay out our plan and document it for our progress report. Kkotani1 (talk) 23:18, 1 November 2012 (UTC)

Glad to hear that you're safe! Hopefully Meredith is doing okay too. I'm in the west coast so the only exposure to the hurricane (storm?) I've received was from the news. The damage and destruction left by Sandy looks devastating... Although I'd like to do more to help, all I can realistically do is donate to the Red Cross from here... Regarding the unit 9 agenda, we have the weekend to finish up so we should have plenty of time to complete the bare minimum at the least. :) -- Jpark623 (talk) 06:06, 2 November 2012 (UTC)

Kes, Sorry to hear you were affected by Sandy. I am in Utah, so I wasn't affected either, but my parents live in Upstate NY. They went through all the preparations in case they were hit by the storm but it miraculously went around them. Glad to hear you have power again!MHN2785 (talk) 03:13, 6 November 2012 (UTC)

Unit 9 Progress Report

Here is the list of specifics we have to address in the progress report for this units.

• 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

Maybe we could start to generate the progress report by adding information to each of these bulleted points. Once all of the information is there we can draft the progress report in prose. Let me know what you think!MHN2785 (talk) 21:24, 30 October 2012 (UTC)

Suggestion: you could draft it in-place, right on your project page. Or create another page specifically for that purpose, like a subpage of your group page, for example, Wikipedia:USEP/Courses/JHU_MolBio_Ogg_2012/Section_81/Group_81C/Progress_report. Klortho (talk) 00:06, 31 October 2012 (UTC)

Thanks, Chris. We might do just that! -- Jpark623 (talk) 14:45, 31 October 2012 (UTC)

Hey Meredith. That sounds like a good plan. I really liked the dynamic that we had on our previous write up. Since it seemed to have worked quite well, shall we pursue the unit 9 write up in a similar manner? -- Jpark623 (talk) 14:45, 31 October 2012 (UTC)

Thanks for getting this started. Agree on the approach, and we did work it out quite well last time as a team. An obvious caveat is that we need to do some of the groundwork outlined in above section and make some actual progress. As it stands now, we don't have much to add under any bullet. Kkotani1 (talk) 23:24, 1 November 2012 (UTC)

Judging from my calendar, we'll have 5 weeks to complete our wiki article. I've started writing out an introduction (recycling what we've written for our proposal), which means we'll have 6 sections to complete after this week. Assuming we don't add anymore sections, I propose we complete a section for each of the next 4 weeks and two sections on the final week. Since the protocol and publication guideline sections should simply involve copying and pasting, I'm wondering if we could group those two together for the fifth week write up.

I think we should aim to complete the introduction this week, so we can include that in the progress report. Also in the porgress report we should include a list of the sections and the dates we aim to complete them. I like the idea of combining the prodocol and publication guidline sections into one week. MHN2785 (talk) 14:27, 2 November 2012 (UTC)

Regarding interactions with other editors, I doubt we'll have any responses but we could try posting a question on the talk page to gather information on what others would like to see included in the article. For problems, I don't know about you guys but I'm slightly concerned that the our sources include both RT-PCR and qRT-PCR (or RT-qPCR) without differentiation. We could treat those as separate entities and just write on RT-PCR, but since most of scientific work is currently being done with qRT-PCR, not only will the separation significantly limit our sources, our article would be drastically shortened due to not having much to talk about. I guess a remedy would be to explain in the introduction that RT-PCR involves two approaches (amplification and quantification) and treat them as two leaves of the same branch. Any ideas? -- Jpark623 (talk) 06:06, 2 November 2012 (UTC)

I did a quick google search for quantitative reverse transcriptase PCR and I didn't find any Wikipedia pages, so I think it would be ok to treat amplification and quantification as two leaves of the same branch.MHN2785 (talk) 14:27, 2 November 2012 (UTC)

Ok, I'll try to have the first revision to the introduction finished tonight. However, due to work obligations, I may not be able to get it to you until tomorrow morning. Shall we do what we did last time around and perform a few revisions before handing it over to Kes? -- 66.87.113.48 (talk) 14:51, 2 November 2012 (UTC)

Sounds good - it'll be great to get the intro done this week. Once we start making edits to the article, we could also see if natural interaction occur with other editors on this. I'm a bit behind with few things but will try getting caught up. Thanks. Kkotani1 (talk) 19:12, 3 November 2012 (UTC)

Added a draft progress report for Unit 9. I know we're working on Intro section off-line. If we end up finalizing and publishing it by Tue, we can update the report accordingly. Also shuffled the order of sections slightly - let me know if it makes sense or if we should revert. Thanks. Kkotani1 (talk) 04:53, 5 November 2012 (UTC)

Wow, what an improvement from the initial bullet points! Draft you say? It's perfect if you ask me. I must admit that your style of writing is an inspiration. I'm out of town at the moment but I'll add the supplement sources for the intro as soon as I return later tonight. Thanks, Kes! -- `Jpark623 (talk) 05:18, 5 November 2012 (UTC)

You're being entirely too generous with your feedback... Anyway, looking at the timeline, I think we're in good shape overall but let's see how far we can get on the Intro in this unit. Cheers. Kkotani1 (talk) 06:16, 5 November 2012 (UTC)

I made some very, very minor edits to clarify the time line, but other than that I think the progress report looks great. Are we still aiming to publish the introduction by the end of Unit 9? I apologize, I know I said I would take a look at the draft we have been emailing about this weekend, but I too am a little behind and playing catch up. For some reason I decided that in addition to work and 3 grad classes it would be a good idea to take and ASQ certification exam in December.MHN2785 (talk) 03:22, 6 November 2012 (UTC)

Since we all seem to be quite busy with our lives, perhaps email is not the best way to exchange revisions. I've created a subpage at Wikipedia:USEP/Courses/JHU_MolBio_Ogg_2012/Section_81/Group_81C/WIP to store our article revisions until they are polished for prime time. -- Jpark623 (talk) 15:34, 6 November 2012 (UTC)

Yay -- nice to see that you've seen the light! Email is a terrible way to communicate revisions. That's what wikis are for, after all! Klortho (talk) 21:42, 6 November 2012 (UTC)

Thanks Jea! I will continue my edits on this page. MHN2785 (talk) 03:40, 7 November 2012 (UTC)

Unit 10/11 Progress

Thought I'd start a new section to organize our progress. We've all reviewed/edited the Intro section at this point - let's do final checks on contents, grammer, etc. and make sure we're all comfortable. Thanks. Kkotani1 (talk) 04:58, 11 November 2012 (UTC)

Hey Kes. It looked good to me. I'll be adding a few more things to the history section before starting the next section. Will send you and Meredith a draft by tomorrow morning. Per Dr. Ogg's guidelines under her email heading, Wiki project comments U9, I've moved our draft to the actual article page. I hope that's ok. Jpark623 (talk) 15:00, 12 November 2012 (UTC)

The intro looked good to me as well. Thanks Jea for moving the draft to the actual article page. I have to apologize for not getting back to you two about the history section yet. Work has been a little chaotic lately, but I am taking all next week off and I have blocked off time in my schedule Monday and Tuesday to dedicate specifically to working on the article. I want to make sure I'm pulling my weight on this project. Thanks for all of your hard work! MHN2785 (talk) 04:08, 15 November 2012 (UTC)

Hi. History section has gone through few round of revisions, but it'll be great if you can review/edit as well. I've also posted our plan on the talk page of the article to give folks a heads-up on where we're headed. Doesn't seem like there's much activity there, but let's see if we start getting some input from other editors as well. Cheers. Kkotani1 (talk) 05:53, 15 November 2012 (UTC)

I think we're all in the same boat, Meredith. We've only got 4.5 more weeks to go so hang in there! Thanks for taking the initiative to get a conversation going in the Talk section, Kes. We should be receiving feedback from the group that's reviewing us pretty soon. By the way, the "Principles" section draft is getting quite long. Should we split it up? - Jpark623 (talk) 23:06, 16 November 2012 (UTC)

Hey Jea. It's great that you've got tons of contents already. Agree on splitting it up - if you can load the portion you've already drafted to WIP page, we can get the review process started in parallel. Thanks. Kkotani1 (talk) 07:30, 17 November 2012 (UTC)

Uploaded what we've got so far. The content hierarchy was not arranged based on any logic. Feel free to change it. - Jpark623 (talk) 15:07, 17 November 2012 (UTC)

Copyright Rules

Any one know what the copyright rules are on using images from brochures? I'd like to use a few images from here:

http://www.sigmaaldrich.com/etc/medialib/docs/Sigma-Aldrich/Brochure/fluorescent_dna_probes.Par.0001.File.tmp/fluorescent%20dna%20probes.pdf

Although it doesn't look open source, it doesn't look copyrighted either... -- Jpark623 (talk) 19:21, 21 November 2012 (UTC)

Sorry, that's a no-go. Look at the bottom of the brosure, in the fine print. It says copyright 2008, all rights reserved. You could contact the company and ask if they'd be willing to release the figures with CC-BY license, but you'd probably have more luck trying to find a similar figure in Wikimedia Commons, or failing that, make your own with Inkscape. User:ShanSabri did this for an image for Stable nucleic acid lipid particle, and he might be willing to help you. Klortho (talk) 01:28, 22 November 2012 (UTC)

Hey Chris. Thanks for pointing out the copyright sign. I completely failed to see the logo on the last page as I was skimming through the contents. Over the weekend, I played around with making my own images in vector format and I had a question for ya. When creating vector images based on copyrighted material, do you know how much resemblance to the original content is possible? For instance, what if I converted the original image to a vector format and simply changed all of the colors. Would the image still be copyrighted? -- Jpark623 (talk) 12:17, 27 November 2012 (UTC)

I am not sure. I think some resemblance would be okay, but I don't think automatic conversion of the format (bitmap to vector, as you suggest) would by okay. I think you should probably redraw it by hand, at the very least -- but I am not a lawyer. Klortho (talk) 12:41, 27 November 2012 (UTC)

Alrighty. Thanks! -- Jpark623 (talk) 13:03, 27 November 2012 (UTC)

Unit 12 Status

Jea, thanks for loading up all the Principles contents - really nice work. I've done some minor edits, rearranged the contents a bit, and loaded the section to the actual article page. Figured we can continue to refine there moving forward. Unit 12 doesn't close until next Sat with Thanksgiving in between, so we have some time to make progress on the Application section and stay on track with our plan. I'll start working on the Unit 12 progress report in the meantime as well. Thanks. Kkotani1 (talk) 17:59, 23 November 2012 (UTC)

Hope you had a great Thanksgiving, Kes. I just got around to reading the edits that you've made to the principles sections and it looks really good! I know we had originally planned on adding another paragraph or so to expand on the quantification methods but if it's okay with you, would you mind if we moved onto the next item on our to-do list? Rereading the principles section, I'm quite pleased with the amount and depth of the content that we currently have. Also, thanks for starting on the progress report. Please let me know what I can do to contribute. Thanks again! -- Jpark623 (talk) 11:55, 27 November 2012 (UTC)

Hope you enjoyed your Thanksgiving as well. Agree, we certainly have a good deal of contents. Let's move on to the next section. Thanks. Kkotani1 (talk) 02:54, 3 December 2012 (UTC)

Peer Review from Group 81E

Hi guys!

I just wanted to get in touch with you all about your article. You guys are doing a REALLY good job! There's a lot added, and the reference list is huge, so kudos on getting all of that sorted and done! One change I would suggest is to move the Introduction section above the Contents box. You wouldn't need to title a section "Introduction" if you set it that way. Also, I see that the original "Uses" section is still remaining on the bottom of the page. You could incorporate it into your article or split the current Introduction and add Uses as the first section after the Contents box. One last thing I've noticed is that you need to edit the formatting of the "Real Time RT-PCR" heading. It's just a little smaller than the earlier headings. Other than that, I would say great job, so far! I'd like to add that I tend to be a very nit-picky and specific editor, but everything I've mentioned is just a suggestion :) You guys have your research and have your plan for the article, and I look forward to seeing how it shapes up at the end :) Rashaalam (talk) 23:27, 24 November 2012 (UTC)

Hey Rasha. Thanks for your invaluable suggestions. They are very much welcome and appreciated! I'm sure my group mates would agree that we'd prefer your thorough suggestions over those that are apathetic and deficient. Working backwards through your suggestions:

(1) the "Real-Time RT-PCR" section is a subsection of "End-Point RT-PCR vs. Real-Time RT-PCR" so the heading seems correctly sized. I think the spacing before the heading misled you into thinking that it belonged to a upper tier section.

(2) your keen observation is correct in noticing that the "Uses" section should be concatenated with another section. I believe the "Applications" section that will soon be added is a good candidate.

(3) regarding your placement of the introduction, I've created a temporary page here. I'd like Kes and Meredith's input on which version looks better. Personally, I'm fine with either.

Thanks for the suggestions, Group 81E. Please keep them coming! :) -- Jpark623 (talk) 13:00, 27 November 2012 (UTC)

I've moved the page with the temporary layout to my sandbox. -- Jpark623 (talk) 00:57, 28 November 2012 (UTC)

Looking through bunch of other articles, it does seem more common to have intro-like descriptions right at the top. So I'm ok with moving the intro section. Agree with your other comments as well. Thanks. Kkotani1 (talk) 02:56, 3 December 2012 (UTC)01:26, 28 November 2012 (UTC)

Thanks for the input, Kes. Due to our introduction being longer than other articles, placing the contents box under the intro looked out of place. Instead, I've placed the box on the right side. Also, I've deleted the table outlining the acronyms used for the article. It seemed unnecessary since we only use RT-PCR throughout the article. -- Jpark623 (talk) 02:38, 28 November 2012 (UTC)

Looks good. Suggest we make the change "live" unless we hear from Meredith otherwise by tomorrow so we can continue editing/refining the article there. Thanks. Kkotani1 (talk) 05:12, 28 November 2012 (UTC)

Well, I actually went ahead and changed the article earlier but Reo On reverted it back to the older version. I'm not sure how he fits into this project but he didn't like the changes that I had made. He looks to be a major contributor to the wiki community so I'm not sure if we should change it again... -- Jpark623 (talk) 05:30, 28 November 2012 (UTC)

Oh, yeah, I see that now. Had just looked at the article without peeking at the history, so assumed that you hadn't made the change. Looks like placement of the table wasn't in line with what's typically done... and he was in favor of keeping the table. If we moved the intro without these changes, I think it becomes difficult to read. I think it's ok if intro resided in either place, so let's keep it as is, if you agree? Kkotani1 (talk) 05:43, 28 November 2012 (UTC)

Sounds good to me. -- Jpark623 (talk) 05:47, 28 November 2012 (UTC)

Great, guys! I believe the Contents box has to stay on the left where it is. And as far as I saw, there is a bit of the current Introduction section you could include (or even start off with) in the upcoming "Applications", as you mentioned, Jea, and have a decent sized Introduction above the Contents box. But that might affect continuity too. Like I said, that was all I saw as far as improvements go for now :) On another note, as I look at it again, I think the Intro wouldn't be so bad as it is above the box! If you want to keep the Table, you can include that later. In fact, you don't need it, I think, because you've clarified during the article with parentheses and linking. For example, including - "polymerase chain reaction (PCR)" and qPCR is good! Also, Jea, thanks for explaining about the sections. Yes, it was the spacing that was throwing me off. Maybe if we could reduce that it would be clearer. Is that possible? I feel like if the spacing was more like the smaller space right before "End-point RT-PCR" it would be perfect. That's about it! Rashaalam (talk) 06:22, 28 November 2012 (UTC)

Hi Guys! I just wanted to chime in with Rasha. I and super impressed with the article! I will take a little more time to read it with a fine toothcomb but it looks great! I started reading and thought "it would be nice if this was in there" and bam! In there it was in the next paragraph. Other thoughts I had were already in other sections. You did an amazing job at organizing this article. Thanks for making it a very easy read :-) Rmeskowitz22 (talk) 22:26, 29 November 2012 (UTC)

Ok I'm back. Only two small suggestions. One - Maybe link SYBR Green to its Wiki article. Another in two different sections it is stated something like "RT_PCR is great, but it still has some issues." Both things you mention in each section are different but it sounds slightly repetitive. Maybe try putting both issues into one of the sections? Other than that awesome work! Rmeskowitz22 (talk) 00:10, 30 November 2012 (UTC)

Hi Guys! I truly agree with my group mates Rasha and Rachael. You have done an amazing job on this article. Everything looks completely organized, clear and quite impressive. I notice a lot of information that has been added to this article. I just took a brief look at the article for now but will definitely get back with some suggestions if I find any necessary .Shivani (talk) 06:14, 30 November 2012 (UTC)

Hey Guys! The overall article looks good but would like to point out some minor things. I know these are quite small things but I think we should make the article as perfect as it can be. First, may be we can connect some of the terms in this article to their Wikipedia article such as northern blot in the introduction section which I noticed has been connected in the later sections but I think it would be a good idea to connect whenever the term is used in the article. The other terms that we can connect are gene expression in the Principle section, TaqMan, amplicon, introns and exon. I would also like to point out two minor grammar mistakes: In End-Point RT-PCR vs. Real-Time RT-PCR section, the line “Quantification of RT-PCR products can largely divided into two categories” should be “Quantification of RT-PCR products can largely be divided into two categories”. Then in Relative RT-PCR section, the line “Once normalized, a direct comparisons of relative transcript” should be “Once normalized, a direct comparison of relative transcript”. One more thing I would like to suggest regarding the End Point RT-PCR section: The last few lines in the subsection Comparative RT-PCR which compares the three methods of achieving End Point RT-PCR can be placed in a separate paragraph at the end of the three methods. It’s just a suggestion. Other than that everything looks awesome.Shivani (talk) 07:40, 30 November 2012 (UTC)

Unit 12 Progress Report

Hi Kes and Jea! For some reason I stopped getting emails about changes being made to all of the pages on my watch list. I didn't realize until today that Group 81E had given us so much great feedback on our article so far. I made a few minor changes to the article itself today and I started a section for our progress report on our group project page. Feel free to add to it as we go along. So far we are on track with our timeline. As you have interactions with group 81F about their article Stable nucleic acid lipid particle, you can add a summary of those interactions to the progress report as well. By the close of the unit I will be adding more information to the "Applications" section of our article. Specifically, I would like to add examples of how RT-PCR is used in research and examples of how it is used to diagnose disease. MHN2785 (talk) 03:02, 29 November 2012 (UTC)

Final Week!

Hey guys. So we're down to a final week. We have 3 sections left - Challenges (I moved some existing contents there), Protocol, and Publication Guidelines. I think we should put at least some high-level contents there to finish up the article? Kkotani1 (talk) 01:59, 11 December 2012 (UTC)

Hi Kes and Jea. I will work on the Protocol portion and have it finished tonight. Does someone want to take responsibility for the Publication Guidlines section? Also I think we should address some of the things Klortho brought up on the talk page for our article. Such as including figures and maybe restructuring a little bit. I have started a section on our group page for our final progress report. I just wanted to say, great job on the article! It has been great working with you two on this group project.MHN2785 (talk) 16:34, 12 December 2012 (UTC)

Kes I see that you already made some of the changes that Klortho suggested. Thank you!MHN2785 (talk) 16:40, 12 December 2012 (UTC)

Hey Meredith, been great working with you as well. Put a few lines in the article on publication guideline. Feel free to revise. Also added a draft final report to close out the project. Looked around a bit for suitable graphic without much success... any thoughts on what we can do there? Kkotani1 (talk) 02:35, 13 December 2012 (UTC)

Jea, I just saw that you put some contents for pubs on WIP page. Go ahead and replace the brief contents I put in the article with what you've got. Thanks. Kkotani1 (talk) 02:38, 13 December 2012 (UTC)

Hi Kes I did find a graphic that I would really like to use but I'm not sure if its licensed or how to find out. Thoughts? I'll email you and Jea the image. MHN2785 (talk) 05:13, 13 December 2012 (UTC)

Hi Kes, I haven't had much sucess finding a suitable graphic either. All of the ones I liked are protected by copywrite. I might try making my own (just a schematic of the general process). But don't feel obligated to use what I come up with. I can't guarantee it will be good.MHN2785 (talk) 17:38, 13 December 2012 (UTC)

Hi Beth. Jea was able to develop a couple of graphics but feel free to add if you come up with additional ones. I've incorporated Jea's contents into the Publication Guideline section. Final report has also been updated. I think we're all set. Thanks. Kkotani1 (talk) 04:59, 14 December 2012 (UTC)

Thanks for tying up all of the loose ends, Kes. I'm not sure where we'd be without you. It's been great working with you. -- Jpark623 (talk) 05:57, 14 December 2012 (UTC)

Everything looks great. I think we are all set too! Thanks for developing thos graphics Jea. MHN2785 (talk) 15:44, 14 December 2012 (UTC)

Guys I had to come and tell you, the article looks AMAZING now! Good job! =) Rashaalam (talk) 00:34, 15 December 2012 (UTC)