Talk:CH391L/S14/SmallRNAs


 * --Dennis Mishler (talk) 08:13, 9 April 2014 (CDT) Jorge, there are a few grammar/typos located throughout the article. In particular, the introduction and the "sRNAs in metabolic engineering" were sections where the errors interfered with my understanding of the section.
 * Jorge Vazquez (talk) 13:04, 14 April 2014 (CDT)I corrected most of them I think and now the wiki should be in a much better shape.


 * --Dennis Mishler (talk) 08:13, 9 April 2014 (CDT) Also, since you have written a review on this topic (ref #4), make sure you are not "self-plagiarizing" anywhere in the article. Make any quotes from that article very obvious, and keep them to a minimum.  Remember, this includes verbatim copying as well as copying with minor changes.
 * Jorge Vazquez (talk) 13:07, 14 April 2014 (CDT)anywhere I mentioned and idea that I had already mentioned in my review has been properly cited. There are no written fragments with high similarity to my review but still the ideas and concepts have been properly cited. Figures and legends are identical to the review and other papers but have been properly cited as well.


 * --Dennis Mishler (talk) 08:13, 9 April 2014 (CDT) I would like to see a future directions sections that expands on current work and possible future work. From your wiki article, I don't have a full appreciation of how commonly this methodology is being currently used...  are there other current examples?
 * Jorge Vazquez (talk) 13:07, 14 April 2014 (CDT)I added a new section and I hope I was able to answer your questions. In general, this methodology has been used not in a wide manner except for a few examples and much less when talking about metabolic engineering.


 * You provide a nice table, but you don't really describe these works. At least a couple of them should be addressed in either the "current research" or "future directions" sections.
 * Jorge Vazquez (talk) 13:16, 14 April 2014 (CDT)Sorry, I did not mention in the wiki that at least three works out of the list have been addressed in different sections. I added a note to refer to the table whenever I addressed a work listed in it. Sorry I did not format the table to be presented in a more friendly format but it was just going to take me long time to do that and I just wanted to give a grasp of how many works have addressed this specific topic in the last 10 years.


 * --Ella Watkins (talk) 11:59, 10 April 2014 (CDT) "In addition, sRNA capacity to simultaneously multiple genes has enabled the vision of sRNAs as a powerful tool for metabolic engineering applications. Hereby I will focus on a specific type of sRNA and its presence in synthetic biology." The bolded part, I am not sure if it is supposed to say multiply? Also, I understand that sRNAs bind to mRNAs and can affect what happens to the mRNA (inhibiting, leading to degredation, etc.) but can one sRNA have multiple effects? For example one sRNA activates one mRNA and inhibits a different one? Or is that not how they work? Do they all have one specific action (i.e. activation, inhibition...) and act on different mRNA with the same action?
 * Jorge Vazquez (talk) 13:16, 14 April 2014 (CDT)Thanks Ella, yeah there is examples of sRNAs that have this dual ability e.g. DsrA. I added this to the section Future directions. They usually have two different binding regions in the same sRNA.


 * --Gabriel Suarez (talk) 04:20, 11 April 2014 (CDT) I really liked the overall structure and comprehensive coverage of sRNAs in your wiki report. Writing is clear and very easy to follow. I also liked that figures are very well described. Maybe it shocked me a little bit that the article is written in first person "In this article I will...", but I guess that's ok. It might be good give a brief description of what is meant by "metabolic engineering", that way it should transition better into that subject in the section of "sRNAs in metabolic engineering". BTW, great presentation!
 * Jorge Vazquez (talk) 13:16, 14 April 2014 (CDT)Thanks Gabriel, just corrected that of the first person. I added the definition of metabolic engineering.


 * --Liz (talk) 07:17, 11 April 2014 (CDT)Agreed with comments above about grammar in the Introduction, not really sure what part Ella has in bold means. (Orthogonally= orthogonality?) Also, I think something more like "This article will focus on..." could get the point across in a better way. I think you should reword later uses of first person in a similar (or not) way. Figures should be larger- especially given such descriptive captions. Small typos and word choice (berak, synthetize, diversity to variety or "diverse mechanism" kind of thing, so =to, ) issues to be fixed. Overall, you do a great job explaining the terms and important concepts associated with this field. As far as any missing information, what I would like to see a little more of is maybe how this technology developed, and like Dennis said kind of where it is going now.  You do mention the work of Sharma et al but I guess my question would be - was this a huge breakthrough? How did their progress fit in the history of general progress on knowledge/ synthesis of sRNA? And of course you include the table and Hao, but maybe a highlight of one or two more especially interesting papers would emphasize how interesting this is. Great job overall- obviously you're really knowledgeable on the subject!
 * Jorge Vazquez (talk) 13:19, 14 April 2014 (CDT)Thanks Liz, I corrected most of the grammar mistakes to the best of my knowledge. I added a future directions section and I hope I am able to answer most of your questions.

--drewtack (talk) 07:49, 11 April 2014 (CDT)Disclosure: i have not read comments above, sorry if I'm repeating. This is as I go through. I think you mean orthogonality in the intro, not orthogonally? and what type of specific sRNAs are you talking about at the end of the intro? The next section I feel should at least mention miRNAs, or whatever the eukaryote equivalent is. Additionally, maybe some mention in their role in evolution? I don't know, this could be way off, but I feel like I've heard these are highly susceptible to mutation, and have a less significant impact when mutated, so they are a driver of evolution. Or I might be completely wrong here. Your table is blurry no matter what, making it very difficult to read. Everything else looks pretty good. One thing I might mention sylistically is that your captions are long, especially in comparison to the size of your images. It looks silly, if you just made your images bigger, it would appear that they justify such large captions, and I think your captions are appropriate, just the images are a little undersized.
 * Jorge Vazquez (talk) 13:25, 14 April 2014 (CDT)Thanks Drew, very good feedback. I corrected grammar mistakes but did not have time to address the evolutionary issue, sorry. I know there is at least one publication regarding that that I came across and in general the binding regions are highly conserved and bear some evolutionary plasticity. I am unsure as to what the implications in synthetic biology would be though and that's also why I do not feel confident to include this in the wiki. As for miRNAs I have added that mention in the introduction.

--Chen-Hsun Tsai (talk) 11:20, 14 April 2014 (CDT) I think this is a very well written wikipage, with many well described examples of sRNAs mechanisms. I only have two things: first I think there are too many words in the figure captions, maybe you can describe the figures in the main text instead. Second is the first-person style, it connects the paragraphs well but it also makes the article more like a presentation, not a wiki.
 * Jorge Vazquez (talk) 13:25, 14 April 2014 (CDT)Thanks Chen. I corrected that of the first person style but I did not remove words from the figure captions since some of them are very complicated. What I did in contrast is to increase the size of the figures to make them more appropriate to the same of the captions.

--Dennis Mishler (talk) 07:54, 11 April 2014 (CDT) Ashley's critique

Overall Format and structure:  Very well formatted and structured. The introduction is simple yet encapsulates the basic idea of some of the functions of sRNAs. Maybe it would help to expand the figures, specifically in the first section, as I think they are very helpful.

Introduction and background material: I like the introduction as it gives a good, brief overview of what sRNAs are and why they’re important. There are a few grammatical errrors that I would recommend fixing though: “These RNAs are in… genes and thus are essential for an organism’s survival under different extreme environmental conditions” I would also suggest rewording the sentence starting with “Their high modularity and orthogonally” “In addition, the capacity of sRNA molecules” I would also recommend trying to find a different word for “enabled” It may be helpful to bold the statement “Hereafter, I will refer to them simply as sRNAs” as it is a very important sentence in terms of the reader taking away correct information from the rest of the article. Also, if you have this sentence in the article, then perhaps it may help the flow of the article to take away the last sentence of the introduction “Hereby I will… biology.” Towards the middle of the paper, there is a lot of nomenclature being used that, perhaps, a non-expert would have trouble understanding without looking the terms up. Methods and main body/concepts: The article was very easy to follow and explained concepts clearly. There were a few grammar mistakes though, some of which I have listed below: “sRNAs can be classified as cis…” “This property, in turn, …” “Trans-encoded… addition to mRNAs; an example…” “…a diversity diverse array of mechanisms…” Under “Designing a synthetic sRNA”: “They were able so successfully able to identify sRNA…” “…Correlation between structure and function…” Under “sRNAs in metabolic engineering”: “…developing an alternative methodology…”

Relation to iGEM and future directions: Very interesting and it seems pretty thorough. One thing I would recommend is that although the iGEM projects are cited in the bibliography, it may be good to include citations in the paragraph itself.

Figures, Figure legends, and citations: The figures were very helpful throughout the article, and the captions were all very well worded and helped explain the topics at hand. A diverse array of citations is found throughout the article, though I believe there are citations missing regarding the Ocean and Uppsala Universities’ iGEM project (though, granted, the two projects were mentioned very briefly).


 * Jorge Vazquez (talk) 13:52, 14 April 2014 (CDT)Thanks Ashley, I appreciate your feedback. I went over most of your comments and modify the wiki accordingly.