New genome article added to 'PLoS ONE prokaryotic genome collection'

A new PLoS ONE article describing whole genome sequence of a contaminating mycobacterial species, Mycobacterium abscessus is the most recent addition to the 'PLoS ONE Prokaryotic Genome Collection'.

 

The article presents most important observations such as those related to the presence of several novel virulence determinants of non-mycobacterial origins and that these were perhaps acquired from other environmental organisms and pathogens including Rhodococcus sp., Streptomyces sp., pseudomonads and Burkholderia cepacia.

Standards for genome data reporting: should we go about it?

Within my overview article that accompanies the PLoS ONE Prokaryotic Genome Collection, one thing that I did not touch base with was the standards for genome data reporting. The Genome Standards Consortium (GSC) is now already in place (and I am one proud member of the same!) and they strongly advocate that certain standards be introduced (at the least) at the level of genome meta data. The consortium has recently published aims and objectives, prospective guidelines and envisaged benefits of such 'would be' mandatory standards (http://www.pubmedcentral....).

As a next critical step, the GSC are now starting to ask journals to require that new genome/metagenome publications be accompanied by completed 'Minumum Information about a Genome Sequence (MIGS/MIMS)' reports.

This sounds a wonderful proposition and I guess PLoS journals in this connection could lead headway as they already insist for adherence to certain other standards such as MIAME for reporting microarray data). Until this point, it is all OK. But some people feel that 'monopolizing' standards could be a kind of 'suffocation'. However, I am sure this will not lead to the kind of 'suffocating monopoly' created by certain 'nomenclature commissions' and their 'mouthpiece journals' in the area of taxonomy and systematics.

I discussed this with one of my friend, a genomic/bioinformatics expert and he says ".. my problem with standards is also not only the monopoly, but that it is also really hard to set a minimal role of meta data that need to be entered per genome. I suffer from the lack of organized meta data; but once the entry is enforced, people will just start putting anything to fill the tables and get their data out, which will lead to the opposite of what standards are supposed to achieve".

Given above, it is clear that some discussion and brainstorming is nevertheless required before journals start insisting for the MIGS/MIMS reports. I can not find a better place than PLoS ONE (sandbox) to discuss and resolve such issues.

New F1000 Evaluation of a PLoS ONE article

Yet another PLoS ONE article was evaluated by F1000 Biology, making the total number of evaluated articles to 180. At any given time, about 3-4% of PLoS ONE articles are evaluated at F1000. Below is a simplified version of the evaluation of the article by Myers et al. The article was evaluated by Felix Viana of the UMH Instituto de Neurociencias, Spain.

Evolution of thermal response properties in a cold-activated TRP channel.
Myers BR, Sigal YM, Julius D
PLoS ONE 2009 4(5):e5741 [abstract on PubMed] [citations on Google Scholar] [related articles] [FREE full text]

"This is an interesting study, comparing functional properties of ortholog thermosensitive TRPM8 channels in frogs and rats. It suggests that intrinsic thermosensitivity is tuned to the normal operating range of body temperature. Animals populate different ecological niches. Survival in these environments is strongly dependent on properly tuned sensory systems that allow the rapid detection of food and the avoidance of dangerous situations, like predators or exposure to extreme temperatures. TRPM8 is a transient receptor potential activated by cold temperatures and cooling compounds like menthol {1, 2}. In mice, TRPM8 is critical for the detection of mild cold temperatures, and perhaps for unpleasant or noxious cold. In this paper, the authors cloned and characterized the functional properties of frog, specifically Xenopus laevis and Xenopus tropicalis, TRPM8. These aquatic frogs are poikilotherms, their core body temperature fluctuates with environmental temperature, in a range clearly below the core body temperature of mammals and birds. While various properties (i.e. menthol sensitivity and voltage-dependence) of frog TRPM8 were similar to those described for rat and mice, there was a clear shift in the thermal response of the channel towards temperatures below their "normal" core temperature. The amino acid sequence of Xenopus TRPM8 displays 75% identity to the rat sequence. This result suggests that this thermo TRP is under strong evolutionary pressure, likely reflecting an important role in temperature sensing in species other than mammals. Besides the intrinsic interest of this novel information for thermosensory biology in general, a careful analysis of the differences in sequence between different species, and the construction of chimeras, may provide additional insights into the mechanism of temperature gating of TRPs, an important unsolved question".

References: {1} McKemy et al. Nature 2002, 416:52-8 [PMID:11882888]. {2} Peier et al. Cell 2002, 108:705-15 [PMID:11893340].