Talk:Trans-acting siRNA

Article Updates
Hi, As part of our Molecular Biology class project we are planning to update this article by adding some additional information. We plant to post the following sections soon and hope to add some images as well.

Mechanism

Discovery

Biosynthesis

Examples of plants in which this is found

Feedback or suggestions will always be very welcome.Katesee (talk) 21:17, 15 November 2012 (UTC)


 * I added the headers for the sections and the information for the discovery section. I still need to go back and make sure i have formatting and linking right withing the new section.  I was wondering if you think it would make sense to have subsections for each of the four families?  It might make things easier to follow. JGLehman3 (talk) 03:48, 21 November 2012 (UTC)
 * Do you mean in just the biosynthesis section or others? We could separate the two types of synthetic pathways but I'm not sure there will be enough content for each to have it's own section. I'm open to it though. Do you think we should reorder the sections, maybe make discovery first then biosynthesis, then mechanism? Katesee (talk) 21:52, 27 November 2012 (UTC)
 * I was referring to just under the biosynthesis section as small subsections. I was thinking it might be more visually pleasing especially for people who are not familiar with the subject.  If there is not enough information for each though, i think we can just leave it how is.  I agree with the reordering and am going to do that right now.  We have definately added a lot of information to this article.  I think in the last few weeks we need to focus on:
 * 1. finding a picture for the biosynthesis/mechanism


 * 2. making sure we have citations for everything where they need to be


 * 3. making sure the article is well linked to the rest of wiki


 * 4. editing to make sure everything is clear and concise
 * Anything else i missed? JGLehman3 (talk) 17:29, 1 December 2012 (UTC)
 * The different families have slightly different mechanisms, so the mechanism section is another place to potentially separate the information on the families. Like I put in the progress report, I have one image uploaded and in the works, but I'm figuring out the proper copyright details to continue with it. I can look for other images as alternatives. Lamcmaho (talk) 04:43, 2 December 2012 (UTC)

Peer Review
Hi Group 83D, while this seems like a difficult topic to discuss. However, my suggestions are as follows: Under the mechanism section, it will be helpful to link si-RNA to other wiki sites to allow the reader gain a better understanding of si-RNA. Under the biosynthesis section, it will be helpful to include a figure that describes the details of the biosynthesis pathway. It may also be helpful to place your discovery section before the mechanism section because the details seem like a history section. It will also be helpful to add a little more detail to the possible uses of a trans-acting RNA in today's world of medicine. Other helpful suggestions is to include more description of the importance of trans-acting pathway.Seguncha (talk) 14:57, 28 November 2012 (UTC)

I think you guys have done a wonderful job in organizing the article and making it easy to read. The only suggestion I have is adding some figures, as Seguncha has stated. Skhan58 (talk) 18:09, 2 December 2012 (UTC)

Peer Review 2
The article looks really good and very "wikipedia like"! Here are more detailed suggestions (sorry my last post was not in depth).
 * 1) " It was discovered that suppressor of gene silencing 3 (SGS3) and RNA-dependant RNA polymerase 6 (RDR6) are involved in the same pathway as ZIP." --You may want to mention SGS3 is a protein and RDR6 is an enzyme.
 * 2) Add a wikilink for "Argonaute"
 * 3) "TAS1, TAS2, and TAS4 families require..." Can you tell us what these abbreviations stand for and what is TAS1,2 and 4? They re brought up without background.
 * 4) "Endogenous trans-acting siRNAs (ta-siRNAs)" Since this is found towards the end of the article, you probably can use either trans-acting siRNA or ta-siRNA, the parentheses seem unnecessary.

Otherwise, great job!

Skhan58 (talk) 06:19, 6 December 2012 (UTC)

Final week mini-review
Hi, guys. Here's a final-week mini-review of your page. It is just a few random notes, that I jotted down while skimming the page, and is not intended as a comprehensive review.


 * The introduction could be expanded a little, I would think. For example, what is the difference between a trans-acting siRNA and a regular siRNA?
 * Also, try to introduce technical terms before you use them. For example, "precursor".  Someone without a biology background, or even somebody with one, but unschooled in RNAi, would not know what this is.
 * Under "Discovery", you are giving a little bit of the history of the discovery of this, but you neglect to mention any dates, or who did the work.
 * You are going to have to replace the figure. It is not too complicated, and I'd suggest that you could probably redraw it pretty easily yourselves, either with Inkscape or Visio.  Then you could upload that to Wikimedia Commons.
 * You could also try to add other figures. Please see some suggestions here, under "Figures and Images".
 * Your sections are a bit too technical. Try to imagine that you are writing to a bright high-school or freshman undergrad student.  Go slowly, and introduce concepts before you use them.  Try to avoid jargony sounding words like "elucidate".  For example, under "Biosynthesis", you have a sentence that begins, "TAS1, TAS2, ...".  What are TAS1 and TAS2?  I guess they are families of ta-siRNAs, but you have not introduced them anywhere.  (I see that Skhan58 already mentioned this problem in his review.)
 * It seems that the article is too short, but I think that a lot of that has to do with the fact that it is too dense. If you were to write things out as I described in the previous bullet, I think the article would at least double in size.  Nevertheless, check your references to see if there is more important content that you could add.

Klortho (talk) 03:31, 10 December 2012 (UTC)
 * I expanded my sections a bit and tried to add to the intro. Maybe if we each come up with a sentence or two we can strengthen it. 198.176.188.201 (talk) 19:49, 11 December 2012 (UTC)
 * Sorry, browser crashing all day. I added this comment. Katesee (talk) 22:57, 11 December 2012 (UTC)

Suggested improvements re: sequence complementarity and conservation in land plants
I don't agree with this statement in the introductory paragraph: 'ta-siRNAs differ from other siRNAs in that they bind with less sequence specificity to their targets.[2]' Complementarity of several tasiRNAs to their targets is quite good, and there hasn't been enough mechanistic analysis to say much beyond that. The next sentence ('They function more like microRNAs because they do not require full sequence complementarity in order to direct cleavage of the target RNA.[4]') sounds like it is comparing plant tasiRNA to animal miRNA, which often only match targets in their 'seed' region.

The 'Presence in Plants' section could be improved to emphasize that the TAS3 gene family is conserved in almost all land plants, while other families studied so far are lineage-specific. I just made a quick edit about Arabidopsis-specific gene family numbering.

It might be worth citing Rui et al., and/or Xia et al., and/or Cho et al. and/or Banks et al.

JS Hoyer (talk) 18:05, 20 July 2014 (UTC)