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

Hello Robert,

Can you please verify that you can seem this message on our group talk page?

ShanSabri (talk) 19:05, 5 October 2012 (UTC)

Group 81F - Verified
Shan,

I apologize for my late response, but I am now tracking updates to our group page. I look forward to working together on our project!

Rob — Preceding unsigned comment added by Uplifted1 (talk • contribs) 18:04, 8 October 2012 (UTC)


 * Great! ShanSabri (talk) 19:39, 8 October 2012 (UTC)

Re: Articles of Interest
Shan,

I'm in favor of working on a page that has little or no substance at the moment so that we can start with a "fresh slate," so to speak. Take a look at the page entitled "Stable nucleic acid lipid particle." These particles, apparently, are a relatively new delivery system for siRNA, which eliminate nonspecific binding to RNA and degradation caused by RNAses. I've attached an article for your review explaining these SNALPs, as they're referred to. While the article is designated as "Low-importance," reading over the attached article makes me think the current designation improper. Let me know what you think.

Robert

Underwood, L.(2010). siRNA gene silencing for therapeutic purposes. MMG 445 Basic Biotechnology 6:59-64 — Preceding unsigned comment added by Uplifted1 (talk • contribs) 19:03, 8 October 2012 (UTC)


 * Great find Rob! I'm actually quite familiar with the RNAi pathway so this topic is of interest to me. I used to use this pathway to perform tissue specific gene knockout on Drosophila melanogaster. I liked how the author gave multiple therapeutic applications for SNALPs and that the wiki article only has one virus-specific application. The wiki article also has no mention of Aptamers so I feel like we could somehow incorporate this information into the article. ShanSabri (talk) 19:37, 8 October 2012 (UTC)

Re: SNALPs selection
Shan,

I went ahead and reserved this article for us to work on, but if you want to work on another article, let me know so that we can reserve it before another group does.

Uplifted1 (talk) 12:52, 10 October 2012 (UTC)


 * Thank you for reserving that article. I'm looking into the wiki article on 'Consensus Sequence' (http://en.wikipedia.org/wiki/Consensus_sequence). I feel like we can improve and expand on this topic. From a bioinformatics standpoint, a consensus sequence is important to identify conserved residues among different species. We can link the consensus sequence specifically to phylogeny, evolution, and other biological topics. We can also link to different programs which create sequence alignments and consensus sequences. A wiki user in the article's talk page even suggested to add an example for clarification. I think we may even be able to link to the Kozak sequence for further information. This article is labeled as High-importance and Start-class on the quality scale. There are only two references on the article. Let me know what you think about it. If you find interest in any other article feel free to let me know. ShanSabri (talk) 19:43, 10 October 2012 (UTC)


 * Disregard my previous post. I thought we had to pick two articles. Turns out we only need to pick one. ShanSabri (talk) 20:21, 10 October 2012 (UTC)

Confounding group project page and talk page
Hi, Shan, This is just a little bit of feedback on your changes to your group's project page. You wrote in the first person ("I found ...") and signed your edit. That's more the style for a talk page, like this one. Keep in mind that your group's project page is more for finished write-ups of things, where tracking individual authorship is not so important. Think of the talk page as a discussion forum, and the project page as the final report(s) that you'll work on collaboratively and turn in. Klortho (talk) 13:27, 10 October 2012 (UTC)


 * Okay sorry about that. I'll edit it so it's more of a formal style. Thanks for the heads up. ShanSabri (talk) 19:24, 10 October 2012 (UTC)

Units 7 + 8
Hello Rob,

During the next unit or so we should begin to work on our assigned article. Below are a couple key points that Professor Ogg laid out for us to think about. I've listed my suggestions, feel free to do the same.
 * Will you be expanding existing section, adding new sections, or completely reorganizing the article?
 * We can expand the application section showing SNALP's interactions with heptoma and carcinoma cells to reduce tumor growth. Perhaps we can somehow add a section explaining the mechanism behind the delivery system.


 * Can you find other articles on similar topics, that are more developed, that you can use as a guide?
 * Perhaps the wiki article on siRNAs. This article also explains the challenges faced when using siRNAs as knockout tools.


 * Begin to gather and organize reliable sources
 * I've added some sources to our group page under the article rationale heading. What do you think of these references? Also, I apologize for posting that rationale before running it by you. I was under the impression that we each had to write separate rationales.


 * Any suitably-licensed images that you can add?
 * I found the figure 1 from the Rossi article (reference 1 on SNALPs wiki page) to be quite informative. It shows the in vivo delivery system of siRNAs using SNALPs to achieve gene silencing. Perhaps we can integrate this image into the Wiki article.

Once we can confirm what would be beneficial to the article, I saw we should split up the points and start writing up drafts. ShanSabri (talk) 19:31, 25 October 2012 (UTC)
 * Shan, I think you've provided a good outline of things we can address with this article. Of course, addressing all of them is outside of the scope of this assignment, but I think picking those most important will improve the article substantially.  With that in mind, the mechanism behind the delivery system is a must so that readers have some foundation from which to understand all that follows.  I'm not sure if you noticed, but I went ahead and added a "References" section as there were references just "floating" at the bottom.  Prior to doing that, I compiled a proposed format for our article from reading various wiki guidance documents.


 * Lead - while the article has a "lead" section, it's not a good one. In fact, it does nothing to inform a reader what the article is about aside from stating a specific point about SNALPs.  A good deal of work can be done here.


 * Background - like you mentioned, I agree that this is a necessary section that would obviously cover the mechanics of the delivery system, but also cover how it's been used in the past, when it was discovered, etc.


 * Milestones - I found an interesting write-up on a blog discussing SNALPs and, while it may not be suitable for citing purposes, it outlines some of the milestones in SNALPs research. It would be an interesting section that we could present in bullet format, naming the milestone and its importance.


 * Applications/Research - this section is well-suited for a discussion on SNALPs and their potential involvement in reducing tumor growth with various cancers. We may be able to break this down so that there's a "Research" section outlining various research on SNALPs that may not highlight a potential for direct therapeutic benefit(e.g. I found an article discussing ways of increasing potency in general.)  An "Applications" section could be used to discuss therapeutic uses for SNALPs, like you've mentioned with certain cancers and tumor growth.


 * See Also, Further Reading, External Links - we can populate these sections as we do work on the above, more substantive sections. If we find an interesting website dedicated to SNALPs(e.g. The blog I found focused exclusively on RNAi) or other resource not suited for citing, we can quickly include it here.


 * So, I'll start compiling references for inclusion into the article. If it's alright with you, I'd like to tackle the background section, which would include the mechanics of the drug delivery system.  Let me know if that works.Uplifted1 (talk) 20:01, 25 October 2012 (UTC)


 * This sounds good Rob. I'll begin to contribute to the Applications section with the citations that I've mentioned in the Unit 6 Rationale post. I'll be sure to add any additional citations that I use to the References section. Also, I've added Figure 1 of the Rossi article to the the wiki page to help readers understand how SNALPs function and I've also linked to the RNA Interference and Small Interfering RNA Wikipedia articles to give the readers a more broader understanding of why SNALPs are being used. I hope to get more posted by the end of this week so that we can begin on the unit 9 report. ShanSabri (talk) 19:08, 30 October 2012 (UTC)
 * I guess the image I've added to the article will be taken down because it fails the first non-free content criterion under Wikipedia's fair use claim. There is a more extensive explanation found on my user talk page. I've made a simple diagram using Inkscape to illustrate the structure components of these lipid nanoparticles. Check it out and let me know what you think. I still have the file to edit so it shouldn't be a problem to add or remove components. It's very basic but I feel like it may aid in the readers understanding. File: SNALP ShanSabri (talk) 16:57, 2 November 2012 (UTC)

Unit 9 Progress Report Draft
Hey Rob, I've typed up a short and quick draft for our unit 9 progress report. I figure this would give us a decent building block for when we have to post our report on our group page at the end of this unit. This is in no means a final draft so please disregard any grammatical errors. Feel free to restructure, add, or edit the draft below at your convenience. You made some great points of improvement in your previous post (under the unit 7+8 section) which I think we should integrate into our progress report. I'm still a little confused about the narrative we should be using so I put everything in third person.

Group 81F has improved Wikipedia’s article on Stable Nucleic Acid Lipid Particles (SNALPs) in a number of ways. Firstly, the addition of a References section was made to categorize the listed references accordingly to Wikipedia’s standards. Secondly, figure one of J.J. Rossi’s article (ref: 1) was added to the introductory section to help readers understand and visualize the in vivo delivery system of siRNAs using SNALPs. However the addition of this figure got the attention of Fut.Perf. who stated that the image was in violation of Wikipedia’s “first non-free content criterion in that it illustrates a subject for which a freely licensed media item could be found or created that provides substantially the same information or which could be adequately covered with text alone.” Therefore Group 81F has decided to sketch the structural components for which a SNALP is made using InkScape, an open sourced graphics editor. is intended to aid in the readers visualization of the structural components for which a lipid nanoparticle is made. Group 81F has also linked SNALPs to the RNAi pathway and siRNA Wikipedia articles to provide the readers with a broader understanding of this particular topic. ShanSabri (talk) 16:53, 2 November 2012 (UTC)
 * Just a suggestion, but a lot of groups are drafting and editing their progress reports in-place, right on the project page. It kind-of makes more sense than posting it here on the talk page, where it's not clear if you want people to edit it in-place, or to comment on it.  Another alternative is to create a sub-page of your project page to draft and work on it, something like USEP/Courses/JHU_MolBio_Ogg_2012/Section_81/Group_81F/Progress_report. Klortho (talk) 00:44, 3 November 2012 (UTC)
 * I think it's fairly clear that what has been posted by Shan serves to initiate discussion. Moving forward, we'll consider creating an alternative page as you suggested because to post on the Project Page seems to contradict previous instruction that "final" work be posted there.  In any event, thanks for the advice.Uplifted1 (talk) 19:02, 6 November 2012 (UTC)
 * Oh, I guess you're referring to my comment above, "the final report(s) that you'll work on collaboratively and turn in". Sorry if that was confusing.  I was just trying to draw a distinction between discussion threads (which you can think of as similar to the discussion forums in Blackboard) which belong on talk pages, and (let's call them) "work products".  I didn't mean to imply that you should wait until the work product is final before putting it on your project page.  By all means, draft it and edit it there, in place, if you find that useful.  Facilitating that kind of collaborative editing is the main thing that wikis are good for. Klortho (talk) 22:02, 6 November 2012 (UTC)

Draft Report Subpage
Shan,

I've created a subpage for posting drafts for upcoming progress reports. It can be found here: http://en.wikipedia.org/wiki/Wikipedia:USEP/Courses/JHU_MolBio_Ogg_2012/Section_81/Group_81F/Progress_report

Let me know if you have any questions.

Uplifted1 (talk) 19:16, 6 November 2012 (UTC)


 * It looks good Rob. I've made a couple edits to fix the broken Wikipedia links and posted the report to our group project page. If you feel the need to edit the report more go right ahead. I've added siRNA and RNAi Wiki links to the See Also section on the SNALP Wiki page. Should we also add some of the keyword which you've listed in the background section such as the RISC complex and mRNA? ShanSabri (talk) 16:10, 7 November 2012 (UTC)

Hello from Group 81C
Hi guys. Group 81C has been assigned to peer review your article. Looks like you’ve already made good progress and given some thoughts to additional sections to be added. One thing our group has done from a planning perspective is to take a bit more structured approach – we’ve map out what we wanted the article to look like by the time we’re done and put some target timelines to prioritize our activities on a week-to-week basis. We’ve also defined some roles within the team based on our capabilities. May or may not fit your group’s working style, but some potential suggestions to consider. Looking forward to following your progress on this article. Cheers. Kkotani1 (talk) 01:56, 14 November 2012 (UTC)