Talk:RNA thermometer

Proposed changes to improve article
I was asked to discuss my recent major edits here (one of which was partially reverted). Although the article was recently awarded GA status, I feel that there are a few issues that need to be resolved, so I will also list my additional concerns before going ahead and performing any more edits. CatPath (talk) 18:23, 2 September 2011 (UTC)
 * Neither the eukaryotic Hsp90 nor HSR1 (heat shock RNA-1) elements have been shown to be RNA thermometers, so I deleted all sentences that mentioned those RNA molecules. However, as pointed out to me on my talk page, the cited articles do state that both are potential RNA thermometers. Perhaps I was too aggressive in deleting the passages; I'm fine with the current version that describes HSR1 as a potential RNA thermometer, and I would be ok with restoration of the Hsp90 passage as long as it's made clear Hsp90 is only a potential RNA thermometer.
 * The effects of magnesium ion concentration on the RNA structures are mentioned when describing the λ cIII and FourU RNA thermometers. This level of detail is not needed since it's not something that's mentioned in the secondary sources that I've read.
 * The following sentence is not quite correct: "More recently, bioinformatics searches have been employed to uncover several novel RNA thermometers."  None of the candidates were tested experimentally, except for the upstream region of pspD, which turned out not to be an RNA thermometer. It should be made clear that the other sequences that were identified are candidate RNA thermometers.
 * There's no description of the ROSE image in the text and in its current form is not helpful. An important point that needs to be made is that nonstandard base pairing stabilizes the structure. Is there a way to highlight the nonstandard base interactions in the image? It's also difficult to figure out which bases are paired and which are not.  Without an explanation of the novel structure in the text and/or modification of the image, the structure will look like a run-of-the-mill stem-loop structure to the reader.
 * The following passage needs to be modified: "...a lone example of a trans-acting RNA thermometer has been found in RpoS mRNA where it is thought to be involved in the starvation response." DsrA RNA is the potential RNA thermometer, not RpoS RNA. The RpoS mRNA is the target of the DsrA RNA. Again, DsrA RNA should be described as a "potential" RNA thermometer.
 * I was going to remove the experimental details demonstrating prfA to be an RNA thermometer and replace it with a short description of the thermometer itself.
 * I was planning to remove the last section, "Other Examples," and incorporate those examples into the Mechanism section.
 * Thanks for bringing these up for discussion.
 * Re 2: I suppose it's really the opposite of overly-detailed, as all RNA structure is affected by metal ion concentration, so perhaps it could be removed as a given.
 * Re 4: I agree, highlighting such bases would be really useful. But while such bases are easy to represent with 2D diagrams, in 3D representations it becomes clear they don't actually have the 'sticking out a mile' conformation that 2D diagrams show for simplicity. I still think a 3D structure is valuable and of interest, even if it's not the best way of highlighting key structural features. The image could perhaps be edited to contain a 2D representation of the same element above it.
 * Re 5: Fair comment, the experimental details are not ultimately relevant to the article. I think I just included them for variety and interest, as I didn't want a list-like section giving example after example. Which brings me to your last point, I entirely support this move, integrating the list into prose was always the intention.
 * Any points I haven't specifically addressed I fully agree with. I do have a tendency to hold back on the uncertain qualifiers, so where they are required, please do add them  Jebus989 ✰ 19:10, 2 September 2011 (UTC)

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