Wikipedia:Peer review/RNA interference/archive1

RNA interference

This article, on the subject of the 2006 Nobel Prize in Physiology or Medicine, was the MCB collaboration from December. It was recently elevated to GA status by TimVickers and is undergoing expansion by yours truly. I have two specific review requests in mind, in addition to general comments -

How's the balance between plants and animals? (NB: as of this writing, the history section still needs a bit of work.) A long-standing observation about this article, and many published RNAi reviews, is the relative lack of acknowledgement of work in plants.
While the article's subject is unlikely to be easily understood by anyone without a background in biology, RNAi is largely at the alphabet-soupy stage in the literature, making it easy to lapse into alphabet-soupiness in the article. Is it readable?

Opabinia regalis 02:17, 7 February 2007 (UTC)[reply]

I don't have time to check it all yet and will try and edit the aticle as well as give comments. Three things that jump out are the following from the history section:

"When the scientists had a closer look they discovered that both types of genes, the endogenous and the newly introduced transgenes, had been turned off"

The problem here is that turned off is quite a sloppy term and, for me at least, more descriptive of the transcriptional state. As written it sounds more like an example of TGS.

This section has been rewritten, with a bit more specifics on these papers. Opabinia regalis 05:53, 8 February 2007 (UTC)[reply]

"After these initial observations in plants, many laboratories around the world searched for the occurrence of this phenomenon in other organisms."

Here Kemphues and Birchler should be cited with respect to their work in C. elegans and drosophila.

Do you have specific papers in mind? Opabinia regalis 05:53, 8 February 2007 (UTC)[reply]

The ones i was thinking of are Pal-Bhadra M et al. (1997) Cosuppression in Drosophila: gene silencing of Alcohol dehydrogenase by white-Adh transgenes is Polycomb dependent. Cell 90:479-90 PMID 9267028 and Guo S, and Kemphues KJ. (1995) par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell. 81:611-20 PMID 7758115 The latter one is recognised as the first paper to note the cosuppression phenomena in C. elegans although it was no the topic of the paper. David D. (Talk) 02:31, 11 February 2007 (UTC)[reply]

Ah, the famous Bhadras ;) Added. Opabinia regalis 05:16, 12 February 2007 (UTC)[reply]

Yes them ;) David D. (Talk) 06:03, 12 February 2007 (UTC)[reply]

"at the Carnegie Institution of Washington and the University of Massachusetts"

Do their institutions need to be cited? I think this could be found by clicking their links. Currently it breaks the flow of the sentence causing it to lose some of its impact. David D. (Talk) 03:03, 7 February 2007 (UTC)[reply]

Did I already remove this last night, or am I just blind? I don't see citations to the institutions anywhere. Opabinia regalis 05:53, 8 February 2007 (UTC)[reply]

The example I am looking at is in the very last paragraph of the article. The sentence that ontroduces the work of the Fire and Mello. David D. (Talk) 06:03, 12 February 2007 (UTC)[reply]

Ah, you said 'citation' and I was looking for footnotes. (As if there aren't enough of those already.) You're right, the institutions aren't important. Opabinia regalis 03:49, 13 February 2007 (UTC)[reply]

After a brief look, a key thing to balance plants and animals would be a diagram that compares the process in plants and animals - probably to replace the lead image; any recent review that compared the two will have a diagram showing the similarities and differences in the two kingdoms. The lead I doesn't give a good sense of when and why organisms use RNAi (during development and defense?). Gene knockdown and functional genomics talks exclusively about animal examples, the techniques are widely used in plants - the cyanide free cassava and gyssopol free cotton are good examples of biotech, there are heaps of basic plant science examples too - maybe the use in medicine could be expanded to use in biotech + medicine? The image stack syntax the article is using isn't working for me, Dicer is covering up everything. --Peta 05:45, 7 February 2007 (UTC)[reply]

In response to the above: I cleaned up the writing in the history section (no new content) and added a short description of the function of the RNAi pathway to the lead. I think the current "role in medicine" section may be demoted to a subsection of "applications" or somesuch, with biotechnology as the second subsection. The images are de-stacked - Peta, does that bunch the edit links for you? Opabinia regalis 06:29, 7 February 2007 (UTC)[reply]

Edit links are bunched and argonaute is floating oddly and covering the text, since its a space issue I'd probably just give the ago/DNA complex image the chop - its pretty, but not that informative for the general reader. For other images, there's a pretty good fair use argument for a pic of the original petunias, and PLoS might have some good images too. I like the applications idea.--Peta 08:10, 7 February 2007 (UTC)[reply]

Added a section on plant engineering, and some brief discussion of genomics work in plants. Can you think of any other major plant engineering projects?

I always like protein structures anyway, but I think the complex is a useful image (though maybe less so in thumbnail). I couldn't get the two argonautes to sit next to each other in a table, so I think I'll just re-render them and make a single composite image with both. I'll dig through PLoS to see if there are any variegated flowers - even if there is a fair-use claim for the petunias, they're not of very high quality in the online PDF. It would be nice to have an image for the lower half of the article besides "RNAi is used in fruit flies. Here's a fruit fly." Opabinia regalis 05:53, 8 February 2007 (UTC)[reply]

I think the plant additions cover a good scope of the work that is being done. Biotech isn't just plants, wasn't the BSE free cow produced with RNAi? I could scan the petunias at higher res if you want, I'll also have a poke around for other images, the fly and worm are a bit dull.--Peta 06:11, 8 February 2007 (UTC)[reply]

Not sure offhand about the cow, but I'll flesh out the biotech stuff tomorrow - I wanted to hit the plant stuff in one go while I had some time. If you think the petunias are fair-use here, a better scan would be great, thanks - I'm not sure if they're "irreplaceable" though? Yes, they're first, but do they convey anything to the reader that a newer, free image wouldn't? (Big fat grain of salt: I don't like fair use, so I haven't become well-versed in the ins and outs of it here, and I could be talking nonsense.) Opabinia regalis 07:12, 8 February 2007 (UTC)[reply]

The BSE cow uses a different technique. FU of the petunias has the historic thing on their side; and the advantage that the phenotype is visibly obvious and that they are already discussed in the article. Any kind of before and after phenotype shot would probably work.--Peta 07:57, 8 February 2007 (UTC)[reply]

This pic from PLoS gives an idea of how rnai would work for medicine. --Peta 08:12, 8 February 2007 (UTC)[reply]

On a different note, should RNA Silencing (lowercase doesn't) really redirect to RNAi the term seems to be used to cover a wide variety of processes in plants - basically it seem to be used to describe any knockdown from a endogenous or external nucleic acid template (see Mol Cell. 2005 Aug 5;19(3):421-8 for a review). My main point is that RNAi is one of may RNA silencing processes.--Peta 01:31, 9 February 2007 (UTC)[reply]

So you saw the new PLoS images, I figure - there may be a derivative of the new top figure that's less busy and more colorful. Also, thanks for the pointer to the Flickr image; would be nice for Mello's article too. I also replaced the uncooperative argonaute images; does the new one fit? I'm thinking the RNA silencing redirect should be converted to a proper stub in the proper case; I'll put it on my mental list of supporting stubs to create.

I may be dense - I didn't get much time for poking around today - but I haven't found anything notable that is neither plant biotech nor preclinical application. It seems that there isn't yet substantial work on animal applications outside of models, which is perhaps not too surprising since it's such a pain in mammals. Do you know of any work in that area that I might've missed? I'll look more thoroughly tomorrow; it's been kind of busy with work this week. Opabinia regalis 04:46, 9 February 2007 (UTC)[reply]

The images are looking really good. This company seems to have one "RNAi drug" in clinical trials, so does this one. There are no commercially available plants that were specifically engineered to express hairpins to induce RNAi, however the ringspot resistant papaya (commercially available; there are probably other examples too -Flavr Sarv was also an antisense construct) was developed using antisense to the viral coat protein, resistance is mediated via RNAi.--Peta 23:57, 11 February 2007 (UTC)[reply]

Added a quick mention, as you already noticed by now; thanks for the virus article ;) I don't want to go into too much detail, since they weren't explicitly developed with RNAi. The clinical trials were mentioned in the medicine section, but I linked the companies also. Opabinia regalis 05:16, 12 February 2007 (UTC)[reply]

Please see automated peer review suggestions here. Thanks, APR _t 21:46, 10 February 2007 (UTC)[reply]
This is moving on to FAC, so please continue any criticisms there ;) Thanks! Opabinia regalis 05:54, 14 February 2007 (UTC)[reply]