Talk:RNA interference/Archive 1

Aims

The current intent of this article is to be reasonably novice friendly, but even then the topic is intrinsically technical. Wikipedia has some real experts writing theirs now, and its heading towards highly advanceed and detailed molecular technical discussions that are completely out of reach for beginners, and I suggest we don't go there David Tribe 19:15, 4 February 2007 (CST)

Citation style

See Help:Citation style David Tribe 21:33, 6 February 2007 (CST)

Three editor Approval

(Tribe, Leng, Sculerati) After further editing that has occurred subsequent to conversations between Tribe and Leng, Tribe and Schulerati

I think its time to place this template with a one week period before the deadline. I see the whole process as a system of checks and balances with trade offs between our goals . I will update the URL pointer as various copy edits come in David Tribe 23:48, 6 February 2007 (CST)

David Tribe has nominated this version of this article for approval. Other editors may also sign to support approval. The Biology Workgroup is overseeing this approval. Unless this notice is removed, the article will be approved on February 16, 2007.

• Melded in bypassed Chris day edit suggestions in response to his talk comment. My reference change in seen in his diff link was deliberate, omitting a dead link and citing Ann Reviews more consistently ( I hope ). I will return to his comments to ensure none are ignored (Ci speriamo, il mio amico) David Tribe 01:39, 10 February 2007 (CST)

• Extended approval period to 16 Feb 2007 to allow time for Chris day's edits already discussed David Tribe 20:34, 11 February 2007 (CST)

All substantive issue raised in approval period are addressDavid Tribe 18:59, 18 February 2007 (CST)

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RNAi is ridiculously amazing. -Tom Kelly (Talk) 17:30, 16 December 2006 (CST)

Before approval, I think the role of suppressors of gene silencing - especially viral ones - should at least be mentioned in the article. And I would like to point out that nowadays, even we plant people do not longer use the term PTGS, but mostly RNAi, as essentially this is the same across kingdoms. In addition, I think the antiviral role of RNAi should be pointed out in the introduction. And I will remove the "so-called" before PCR. That sounds like it is normally called otherwise or should be. --Mathias Klode 09:51, 16 February 2007 (CST)

Jargon

I think there's too much Jargon in this article. I can't find anywhere what RNA stands for or what RNA is. The article needs to be introduced in a more accessible manor. It should be understandable to someone who is form outside the Biology field. The reader is thrown in the deep end here. The most technical section, "Cellular and molecular mechanisms." is the first. The topic could be more gently ramped by giving the history and background information first and dealing with the technical descriptions nearer the end after the use has learned the background.

Also, what's with all the bold text. Words seem to be bold at random. Derek Harkness 05:04, 26 December 2006 (CST)

Thanks so much

David Tribe 17:20, 26 December 2006 (CST)

I think this is a wonderful article, I found it extremely clear and interesting. Of course it's not aimed at a lay reader, but I think not all aticles can or should try to be. I think perhaps the opening paragraph could be worked on a bit, I juggled it perhaps not very successfully, but I'm happy to nominate this for approval when you want. I've copy edited the article but not otherwise contributedGareth Leng 07:05, 31 December 2006 (CST)

Further text relating to miRNAs added. Content finished; need to now focus on clarity and typo consistency. WP is far more advanced scientifically and way out of reach for beginners. David Tribe 18:58, 4 February 2007 (CST) May need to re-draw complicated PLos Flow chart figure David Tribe 19:17, 4 February 2007 (CST)

transcriptional gene silencing

Hi David, i've been reading through this is little more now and I notice that there is an ommission. In plants PTGS and TGS (as used in the figure) were used to distinguish between silencing that degraded the mRNA compared to silencing that shut off transcription. There is a very brief mention of the TGS phenomena with respect to centromere function but that is it. Was this an intentional omission? Certainly it is more well studied in plants and the animal studies all focus on the RNA stability/interference. It is probably true for animals too, given the key role in centromere function but I'm not aware of anyone looking that hard for it. Chris Day (Talk) 00:01, 9 February 2007 (CST)

Adding to this, i also see there is a section titled Multi-protein transcriptional silencing complexes generate the guide strand RNA that does not seems to address transcriptional silencing. The other Matzke figure, to the left of that section does show TGS as one of the potential outcomes. So should we add TGS into the article or do you want to focus more on the RNA stability/interference issues? If the latter, we may want to reconsider the two Matzke figures. Chris Day (Talk) 00:51, 9 February 2007 (CST)

These issues need to be sorted out. Probably not tonight as Ill have to do real work to fix them and I'm tired. I might wait a few hours till mourning in Boston before I deprotect (to help you wade in where you want to) 'cos the wee hours are when the goulies fly around. The short answer is that I was mentally glossing over the gaps you mentioned and perhaps was lazily avoiding the effort needed to fix them. If need be Ill extend the approval deadline to make sure we do it right. Thanks so much for your attention to the issues.David Tribe 01:50, 10 February 2007 (CST)

I'd say don't worry about unprotection. I can set up a sandbox in my usersapce to work on some stuff. I have some ideas but will need to research for accuracy. Chris Day (Talk) 02:02, 10 February 2007 (CST)

Hi David after the vandalism spree and the confusing jan 2nd dates in the edit history I'm a little unsure of which is the current version. When i compare my last version to the current protected version it appears some of my edits have been changed back. This may have been intentional on your behalf or maybe not? Its hard to tell. This is a mix of edits. Some of them reduce the redundancy in the text, removed one paragraph redundant with previous section and reference to natural miRNA's in one title. One is a typo (or to of), another I think is too vague, regulatory rather than coordinating. The ref change is not mine. Chris Day (Talk) 10:46, 9 February 2007 (CST)

Linked to WP RNAi

The WP RNAi effort is now converging on this one a bit. Great. Lets hope that interwiki rivalry is working for the best outcomes everywhere David Tribe 20:46, 11 February 2007 (CST)

Suggested novice-targeted Intro to RNA interference

• David: To answer some critiques, and make the Intro more 'introductory', I swapped 1st and 2nd pgraphs, and edited with try for more clarity. Check it out, below. If you don't like it, ignore it.

Messenger RNA (ribonucleic acid) (mRNA) is a single-stranded polymer whose sequence of nucleotide bases transports information, present as the double-stranded deoxyribonucleic acid (DNA) code of genes, to regions of the cell where that genetic information is used for synthesizing proteins. Understanding the flow of information from DNA to mRNA to proteins - a process known as gene expression (see figure) - is necessary for understanding the process of RNA interference (RNAi), as RNAi potently inhibits that information flow, thus effectively silencing gene expression. Hundreds of human genes are affected by natural regulatory circuits that involve RNAi mediated processes.

Specifically, RNA interference (RNAi) is a mechanism in eukaryotic cells that is triggered when such cells are exposed to certain double-stranded ribonucleic acid (dsRNA) molecules. The process has been detected in many organisms, including animal, plant and protist cells. The distinguishing characteristic of RNAi is destruction of mRNA molecules that share at least some of the sequence characteristics of dsRNA trigger molecules to which the cells have been exposed.

The discovery of RNAi is a major technological breakthrough in biological research, perhaps as important as the development of the so-called polymerase chain reaction (PCR), an in vitro technique that enables even tiny amounts of specific mRNAs to be measured easily. In experiments using RNAi in the fly Drosophila or in the worm Caenorhabditis elegans, the effect of the loss of function of every known gene on a molecular pathway, cellular structure, or organism phenotype can now be determined rapidly and easily.

--Anthony.Sebastian (Talk) 15:58, 13 February 2007 (CST)

First figure

Seems too much. I'd revert to David's original. http://pilot.citizendium.org/wiki/User_talk:Anthony.Sebastian