Wikipedia:Featured article candidates/RNA interference
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- The following is an archived discussion of a featured article nomination. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article review. No further edits should be made to this page.
The article was promoted 18:32, 22 February 2007.
RNA interference[edit]
This article, on the subject of the 2006 Nobel Prize in Physiology or Medicine, was the MCB collaboration from December. It was brought to GA status by TimVickers a couple of weeks ago, and has since been substantively expanded by me. It's had a very productive peer review here. Incidentally, this was also the first article I edited with my then-shiny-new account last spring ;) Comments appreciated as always. Opabinia regalis 06:03, 14 February 2007 (UTC)[reply]
*Oppose copyright status of Image:Adult worm.jpg is unclear, at best. Most likley it is speedable. Hipocrite - «Talk» 15:01, 14 February 2007 (UTC) Corrected Hipocrite - «Talk» 15:47, 15 February 2007 (UTC)[reply]
- Comment The website it was obtained from states: "Images or text created by Wormatlas may be used by individuals or organizations for non-profit educational and scientific purposes with proper acknowledgement of Wormatlas (http://www.wormatlas.org)", which would make it fair use AFAICT. Still not good, but perhaps acceptable. Any tagging ideas? Fvasconcellos 23:49, 14 February 2007 (UTC)[reply]
- I replaced it with a freely-licensed image from PLoS Genetics. It's not quite as pretty, but it's also an example of an RNAi experiment, which is nice. I'm not sure fair-use of a worm image would fly; it's not really any different from a fair-use image of a living person in terms of replaceability. Opabinia regalis 01:15, 15 February 2007 (UTC)[reply]
- Comment The website it was obtained from states: "Images or text created by Wormatlas may be used by individuals or organizations for non-profit educational and scientific purposes with proper acknowledgement of Wormatlas (http://www.wormatlas.org)", which would make it fair use AFAICT. Still not good, but perhaps acceptable. Any tagging ideas? Fvasconcellos 23:49, 14 February 2007 (UTC)[reply]
- Comment. Perhaps a Wikipedia:External peer review would be useful? If we can get an academic review or two, it would be quite useful. One style comment: either reference all facts in lead or none. Currently with only last sentence of lead referenced it looks somewhat strange.-- Piotr Konieczny aka Prokonsul Piotrus | talk 17:59, 17 February 2007 (UTC)[reply]
- Comment There has been some discussion about improvements to this article on the talk page, despite the unusual dearth of participation here. I'm not sure that any RNAi expert is going to approve of the balance of topics or choice of emphasis in a review he or she didn't write ;) (Note: I'm not an RNAi expert.) I'd certainly be curious about what an external reviewer thinks, but wouldn't know where to find such a person, as I'm not interested in associating my real-life identity with my wikipedia work, and 'some fossil from the Internet wants you to take a look at this' is unlikely to generate much interest. Opabinia regalis 02:22, 18 February 2007 (UTC)[reply]
- Oh, and - the citations in the last sentence are mostly there to give a pointer to the original 1998 paper, which seems more useful than making someone read/scroll to the very last section to find it. Does it look that weird? Opabinia regalis 18:13, 18 February 2007 (UTC)[reply]
Comments
The sentence "In Drosophila, miRNA and siRNA are differentially processed by distinct argonaute proteins and dicer enzymes." tells us there is a difference, but doesn't say what this is. If this difference is important you need to say what it is, but if it is only a curiosity, it would best to remove it.
- Really? As far as I understand, we don't know the reason for the specificity yet, although I guess that sentence should point out that it's true in plants as well as Drosophila. There's a paper from 2002 claiming that miRNA and siRNA are not processed differently in mammals, pointed out by both of the Drosophila studies, but it's old enough and contains enough outdated assumptions that I'm hesitant to include it. At any rate, I think the point is important in the sense that the endogenous-regulatory and exogenous-immune pathways are more divergent than they might appear at first look. Opabinia regalis 23:26, 18 February 2007 (UTC)[reply]
- I tried just cutting the word "differentially" does this change what you were trying to say? I was reading this to say that the processing was different, not similar processing by different isoforms. TimVickers 23:33, 18 February 2007 (UTC)[reply]
- Really? As far as I understand, we don't know the reason for the specificity yet, although I guess that sentence should point out that it's true in plants as well as Drosophila. There's a paper from 2002 claiming that miRNA and siRNA are not processed differently in mammals, pointed out by both of the Drosophila studies, but it's old enough and contains enough outdated assumptions that I'm hesitant to include it. At any rate, I think the point is important in the sense that the endogenous-regulatory and exogenous-immune pathways are more divergent than they might appear at first look. Opabinia regalis 23:26, 18 February 2007 (UTC)[reply]
:*The image of the argonaute proteins needs to be bigger.- Done. Opabinia regalis 23:26, 18 February 2007 (UTC)[reply]
The sentence "In animals, these nucleases are known as argonaute proteins." needs to add what these proteins are called when they are not called argonaute - add plants, bacteria or protozoa?
- That's old; they're all argonautes. Thanks for pointing this out. See the additions to the evolution section; there are even argonautes in bacteria. Opabinia regalis 23:26, 18 February 2007 (UTC)[reply]
The sentence "The miRNA activity, which is a major means of regulation of cell cycle progression and cell proliferation, is also clustered in P-bodies. would be best to move the function of miRNAs to the later section on biological functions and keep the material on localisation together.
- I must not have my thinking cap on straight, because I'm not sure what you're suggesting here - the localization stuff already is together? I moved the function stuff for miRNA to the functions section, which is rather short because we do have a somewhat decent article on miRNA (though it needs some ref-formatting work). Opabinia regalis 23:26, 18 February 2007 (UTC)[reply]
I'm unsure what this means "Plants such as the Arabidopsis thaliana express multiple dicer homologs that show differential specificity to infection by different common viruses." it sounds like the dicer homologues are being infected by viruses!
- Ah, we can't have that! Does the rewritten version make more sense now? Opabinia regalis 23:26, 18 February 2007 (UTC)[reply]
The first paragraph of the "Evolution" section needs more references.
- Expanded a bit with another, older but larger genomics study. It's surprising how little investigation of this has happened so far. Opabinia regalis 23:26, 18 February 2007 (UTC)[reply]
Nowhere is the distinction between antisense and RNAi explained clearly. I have never been very sure about this myself, so it would be good to have it laid out somewhere, perhaps in the lead? TimVickers 18:26, 18 February 2007 (UTC)[reply]
- I think the current usage of 'antisense' mostly involves the introduction of single-stranded fragments, expected to physically bind mRNA and block translation (ie, stoichiometrically), whereas RNAi explicitly refers to exploitation of the dicer/RISC pathway. Some of the early antisense applications are now thought to have worked through the RNAi pathway, which I suspect is going to be generally true in an organism that expresses RdRP. The one antisense drug that I know of (fomivirsen) is a modified oligo, so it likely wouldn't be recognized by the RNAi machinery anyway. I'm not sure how much of this belongs in the lead, since antisense isn't really mentioned except a brief note in the technology section, and a lot of the excitement for antisense drugs has transferred to siRNA. Maybe this is best placed with the biotech stuff then? Opabinia regalis 23:26, 18 February 2007 (UTC)[reply]
- I suggested the lead since it is sometimes important in introducing a subject to clarify the difference between the area you are going to discuss and related but frequently-confused areas. What about something in the last lead section like "Historically, RNA interference was known by other names, including post transcriptional gene silencing, transgene silencing, and quelling. It was also frequently confused with antisense suppression of gene expression, which does not act catalytically to degrade mRNA but instead involves single-stranded RNA fragments physically binding to mRNA and blocking translation." TimVickers 23:45, 18 February 2007 (UTC)[reply]
- Thanks for reviewing this article, I was starting to think I'd tripped a few TLDR triggers ;) As always, your edits much improved the prose. Opabinia regalis 23:27, 18 February 2007 (UTC)[reply]
Support all my concerns have been addressed. TimVickers 00:43, 19 February 2007 (UTC)[reply]
- Edit-conflicted thanks for the review! Opabinia regalis 00:45, 19 February 2007 (UTC)[reply]
- Comment Ref 59 is empty.
It's a named ref, so I guess its first instance was removed and the ref text not moved to the second instance. Mind if I check the history and re-instate it, or was it on purpose?Was that a typo—"Samuet" supposed to be "Saumet"? (Saumet A, Lecellier CH (2006). "Anti-viral RNA silencing: do we look like plants?". Retrovirology 3 (3). PMID 16409629) Fvasconcellos 00:03, 19 February 2007 (UTC)[reply]
- Yep, just a typo - fixed now. Thanks!
- Support, article provides an "encyclopedia appropriate" overview of the topic. --Peta 04:04, 19 February 2007 (UTC)[reply]
- Comment - Good balance of plants and animals but I feel some more fungi stuff is needed. I've read ref 35 myself, and though yes some pathways are missing in fungi, they are still present in many of them. Maybe put some theories in as to why the fungi have lost these pathways. Also, RNAi was noticed in fungi at around the same time as plants - where it was called quelling. (Million_Moments 23:23, 19 February 2007 (UTC))[reply]
- Added a brief reference in the history section, though as far as I understand, work in fungus wasn't part of the main trajectory. I'm not sure about theories related to the loss of RNAi components - I know loss of RdRP is supposed to be correlated with greater genomic transposon load, but I'm not aware of any theories relating to specific lineages. If you know of any, do tell ;) I can't actually access ref 35 from here and originally read the paper quite a while ago now, so if there's anything pertinent in there, feel free to add it; I won't be able to look till tomorrow at the earliest. Opabinia regalis 02:27, 20 February 2007 (UTC)[reply]
- Hope you don't mind but since I am working on dsRNAs in rust at the moment I added a few sentances about RNA silencing proteins in fungi. You might wanna check them over, they might also be better suited to the evolution section. One other thing: fungi also have an RNA interferance pathway that is in my knowledge is unquie to fungi: MSDU. I think since you've mentioned RITS that should be in there as well. (Million_Moments 17:29, 20 February 2007 (UTC))[reply]
- Shouldn’t this go in the evolution section? Maybe the entire section on the variation among organisms be a subsection of Evolution, or Evolution being a subsection of variation. They’re much too linked with each other to separate them. Fad (ix) 17:47, 20 February 2007 (UTC)[reply]
- I think that's a good idea.(Million_Moments 18:37, 20 February 2007 (UTC))[reply]
- I think we have to be careful here with how much detail can fit in one article. This article could be three times its current size and still omit or gloss over fruitful areas of research. If anyone wants to create a subarticle specifically about unique features of RNAi in fungus, that's great. (I was thinking of eventually creating an article on plant innate immunity, since there's an enormous amount of work out there on the plant/virus arms race.) I truncated the fungus addition just a bit, to keep it consistent in length with the other organisms and to remove some speculation on why unicellular organisms might lose the pathway. (I doubt 'unicellular = less complex life cycle = less need for RNAi' works, at least in that simplified form, because the pathway was well elaborated in the ancestral eukaryote.) MSUD sounds like a phenomenon that needs its own article more than it needs much elaboration in this one. There is actually a lot of somewhat related work on miRNA-induced meiotic events in Drosophila that is touched on in the piwi article, but not at all in the RNAi article itself. I do think RITS might have gotten a little overbilled in my desire to equitably cover 'classic' mRNA-degradation RNAi and the more recent work that has broadened the definition.
- Correspondingly, I'm somewhat indifferent to moving the variations section; I'd rather see that material quite brief and earlier in the article than the evolution section, because the goal in the evolution section itself was to discuss the pathway as a whole rather than loss or modification of individual proteins in individual species (which, again, could be a whole article in itself). I thought of moving just the second paragraph so that the general plant/animal distinction remains early in the article. Opabinia regalis 02:36, 21 February 2007 (UTC)[reply]
- I think that's a good idea.(Million_Moments 18:37, 20 February 2007 (UTC))[reply]
- Shouldn’t this go in the evolution section? Maybe the entire section on the variation among organisms be a subsection of Evolution, or Evolution being a subsection of variation. They’re much too linked with each other to separate them. Fad (ix) 17:47, 20 February 2007 (UTC)[reply]
- Hope you don't mind but since I am working on dsRNAs in rust at the moment I added a few sentances about RNA silencing proteins in fungi. You might wanna check them over, they might also be better suited to the evolution section. One other thing: fungi also have an RNA interferance pathway that is in my knowledge is unquie to fungi: MSDU. I think since you've mentioned RITS that should be in there as well. (Million_Moments 17:29, 20 February 2007 (UTC))[reply]
- The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article review. No further edits should be made to this page.