Sunday, December 27, 2009

“Filling the gaps in the tree of life” and “Stochasticity in gene expression” in my Picks of the Week from RB.

Another week has gone by and some very interesting molbio blog posts have been aggregated to Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.

Note that I'm only taking into consideration the molbio-related blog posts aggregated under "Biology".

Congratulations to everyone who got their post selected.

This will be the last "Picks of the Week" of 2009 and I want to take the opportunity to thank everyone for their support. This has been a great experience and "Picks of the Week" has been a tremendous success.

Now, the Picks....

1) The GEBA (Genomic Encyclopedia for Bacteria and Archaea) project is “aimed at systematically filling in the gaps in sequencing along the bacterial and archaeal branches of the tree of life”.

The prokaryotic genome sequences that have been obtained (currently, there are more than 1,000 complete or nearly complete genome sequences of microorganisms available) reflect a selection based on “clinical or functional importance (to us), ease, biotechnological or pharmaceutical potential, etc”, and have covered a wide range of biological and functional diversity, but not a phylogenetic one. It represents a biased view of the tree of life and limits our understanding of the evolution, physiology, and metabolic capacity of these fascinating groups.

So, what is GEBA?

In a nutshell, it’s a large-scale systematic (and phylogeny-driven) effort to sequence bacterial and archeal genomes from across the tree.

This project represents the first systematic attempt to use the tree of life itself as a guide to sequencing target selection.

Iddo Friedberg at Byte Size Bio discusses the first paper derived from this project, reporting the genome sequences of 56 culturable species of Bacteria and Archaea, which were selected to maximize phylogenetic coverage.

Also, you will find a video from Jonathan Eisen, one of the project leaders, talking about GEBA.

2) The different steps in gene expression are stochastic biochemical events and this randomness can lead to substantial cell-to-cell variability in RNA and protein levels and have phenotypic consequences even within a clonal population of cells. Notably, just last week a friend of mine (who is a grad student at Ben Lehner’s Lab at CRG and was visiting for a few days) and I, were discussing the impact single-cell studies can have on our understanding of the mechanisms of gene expression, so the selected post comes at a perfect time!

Tim Sampson at "The Times Microbial" @ Phagehunter.Org (Formerly known at "Blogging for Bacteriophages") discusses an article which was published in Science a few years ago addressing the impact these variations can have on a process as important as cell fate in bacteria.
This will be the first of a two-part series of posts on this fascinating subject.

That's it for this week. Stay tuned for more MolBio Research Highlights!

ResearchBlogging.orgSome of the articles discussed in this week's selected posts:

Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B., Hooper, S., Pati, A., Lykidis, A., Spring, S., Anderson, I., D’haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E., Kyrpides, N., Klenk, H., & Eisen, J. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, 462 (7276), 1056-1060 DOI: 10.1038/nature08656

Maamar H, Raj A, & Dubnau D (2007). Noise in gene expression determines cell fate in Bacillus subtilis. Science (New York, N.Y.), 317 (5837), 526-9 PMID: 17569828

ScienceBlips: vote it up!