Talk:SmY RNA

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This article has been mentioned by multiple media organizations:

Declan Butler (December 16 2008). "Publish in Wikipedia or perish". Nature. {{cite news}}: Check date values in: |date= (help)
Torsten Kleinz (December 17 2008). "Molekularbiologen schreiben für Wikipedia (Molecular biologists write for Wikipedia)". heise online. {{cite news}}: Check date values in: |date= (help)

Jargon and context[edit]

The intro to this article is esoteric and full of jargon (in bold): "They are thought to be involved in mRNA trans-splicing because they copurify with spliceosomes and with some of the same proteins that associate with small ribonucleoprotein particles containing SL1 and SL2 trans-spliced leader RNAs." Even someone like me who has university level knowledge of what things like spliceosomes are, this article lacks context. --Steven Fruitsmaak (Reply) 19:02, 17 December 2008 (UTC)[reply]

is "university level knowledge" a description for "watching a tv-show about that particular topic"? http://www.nature.com/news/2008/081216/full/news.2008.1312.html —Preceding unsigned comment added by 153.97.93.25 (talk) 21:21, 17 December 2008 (UTC)[reply]
Steven, almost all the things you note in bold are crossreferenced to other Wiki pages that define the terms. The intro is certainly telegraphic at the moment and could be improved, but at the same time, it seems to me that we wouldn't want to define "spliceosomes" redundantly, for example; surely there's going to have to be a balance, especially on a page that's a small part of a larger RNA project. Seaneddy (talk) 21:43, 17 December 2008 (UTC)[reply]
- Well, we don't currently have an article for copurification, so someone either needs to write that article, or different wording should be used here. Could you say "...they have an affinity for binding with spliceosomes..." instead of "...they copurify with spliceosomes..."? Keep in mind I know nothing about molecular biology :P Kaldari (talk) 23:30, 17 December 2008 (UTC)[reply]
- "copurify" isn't supertechnical, it just means that if you purify spliceosomes, SmY RNAs come with them: SmY copurifies with spliceosomes. This would tend to imply that SmY RNAs probably bind to (have an affinity for) spliceosomes, but there's other interpretations. It's generally preferable to state an observable result ("SmY copurifies") rather than an inference ("SmY has an affinity for"). For example, it'd be possible that SmY RNAs bind to something else that's binding to spliceosomes; a phenomenon sometimes called "piggybacking". Seaneddy (talk) 02:16, 18 December 2008 (UTC)[reply]
  - Ooh, "co-purify". I read it as something like the DNA equivalent of "copulate". --77.75.161.35 (talk) 23:18, 20 December 2008 (UTC)[reply]
- I would admit that I don't understand the larger part of the article, but given the crossreferences I'd guess that I could do better. »Jargon« is not synonymic to »technical term«. mkluwe (talk) 17:16, 19 December 2008 (UTC)[reply]
  - It looks like someone was nice enough to create a copurification article, so nevermind :) Kaldari (talk) 16:28, 18 December 2008 (UTC)[reply]

We should be aware of the RNA Biology "policy" [1] that all their journal articles now require Wikipedia pages. This may result in a proliferation of articles like this. Superm401 - Talk 15:56, 19 December 2008 (UTC)[reply]

Looks like the article requires(?) jargon. However, there really needs to be a 2nd paragraph in the lead, either before or after the present paragraph, which covers the notability of /use for/ the subject matter in very Simple English^TM. Pretty please? - Hordaland (talk) 19:25, 18 December 2008 (UTC)[reply]

Ambiguity[edit]

Does the sentence fragment "found in nematode species" mean that all nematodes possess this, or that of all species, only some nematodes possess it? For the former, I'd propose we use "found in nematodes" or "found in all nematodes", and for the latter "found in some species of nematode". Mind matrix 00:01, 20 December 2008 (UTC)[reply]

Uh, I should have read ahead. The answer is in the Phylogenetic range section. I'll update the intro accordingly. Mind matrix 00:02, 20 December 2008 (UTC)[reply]

Phylogenetic range[edit]

Maybe we should add an infobox for phylogenetic ranges which can be implemented on other bio-molecular articles as well. Lord Metroid (talk) 02:56, 20 December 2008 (UTC)[reply]

Kohs additions?[edit]

I deleted material that was earlier added by Ribo specialist (talk · contribs):

However, it is important to note that there is some evidence that introns in specific sequence elements are not copurified by SmY, so there is ongoing debate about their role in protein association.

The user has since been blocked as a confirmed sockpuppet of Thekohser (talk · contribs), long-time Wikipedia critic Gregory Kohs who also commented on this project at the Nature site. [2]. I also just realised that the same user changed some numbers

with most Rhabditid species having 8-32 related paralogous copies, while other nematodes have 1-6.

which used to be

with most Rhabditid species having 10-30 related paralogous copies, while other nematodes have 1-5.

I changed that back now to the original numbers.

Please add this material back in if a reliable reference can be found. AxelBoldt (talk) 19:06, 22 December 2008 (UTC)[reply]

The orginal wording in the pre-print article is: "The SmY family has undergone a large paralogous expansion in Caenorhabditis and Pristionchus species, with copy numbers of 10-26, compared to 1-4 copies in other nematode genomes." Kaldari (talk) 20:21, 22 December 2008 (UTC)[reply]

Strangely, though, one of the other species in the chart has 5 copies, so it seems that 1–5 would be more accurate. Kaldari (talk) 20:23, 22 December 2008 (UTC)[reply]

I was trying to clean up the tags on User:Ribo specialist and User talk:Ribo specialist, but I can't find where the evidence is. I tried to look for both a WP:RFCU subpage and a WP:SSP subpage, but didn't find them. —AySz88 \^-^ 22:54, 23 December 2008 (UTC)[reply]

Legend needed[edit]

I started Template:RNA structure key to use as a common legend for RNA structures like File:SmY-structure.png in this article, but I could not determine for certain what the "n", "r", "R", "Y", "Δ", and "<", and ">" stand for.

The charts on either side of this structure are very confusing; if they do not describe the structure, they should be presented separately. -- Beland (talk) 19:39, 24 December 2008 (UTC)[reply]

Have a look at the table at DNA sequence. Narayanese (talk) 20:03, 27 December 2008 (UTC)[reply]

The tables describe differences between species for each base pair on the same same line. There you can also see that the < > in this particular structure refers to 2 pyrimidines that don't basepair (not always there?). Narayanese (talk) 20:12, 27 December 2008 (UTC)[reply]