Monday, October 12, 2009

Omics-dominated issue! Genomics, metagenomics, reactomics and more, 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".

As previously stated (see here), "Picks of the week" will now be posted on Mondays, so here we are, and with a fascinating "Omics-dominated" issue.

Congratulations to everyone who got their posts selected.

This week, 4 (actually 5) blog posts are highlighted:

1) Iddo Friedberg brings us a fantastically written post on microbial diversity. The driving force behind his post? A recent article reporting that due to sequencing errors, metagenomics studies may be overestimating the number of reported operational taxonomic units, by as much as two orders of magnitude! Although he doesn’t get into the paper’s details, I considered this article to be so enticing, that I had to highlight it for you to check out.

2) Thoughtomics blogs about a recent article which reports a fascinating finding: it appears that there is a striking negative correlation of genomically encoded tyrosine content and biological complexity (as measured by the number of cell types in each organism). That is, the more complex the organism, the less tyrosines in its proteins.

Further, a correlation was also found regarding tyrosine kinases in the metazoan lineage, although of a reverse nature: the more tyrosine kinases you have, the less tyrosine your proteins have! A provocative explanation to all this, in the context of the evolution of signaling networks in multicellular animals, is presented, as discussed by the authors.

3) Keith Robison from Omics! Omics! discusses an interesting new article published in Science describing “a sensitive metabolite array for genome sequence–independent functional analysis of metabolic phenotypes and networks, the reactomes, of cell populations and communities.”

The authors synthesized an array consisting of over a thousand substrate compounds ("collectively representing central metabolic pathways of all forms of life") immobilized to a glass slide. By applying cell extracts to this array, the authors effectively performed a high-throughput screening of enzyme activities: "Productive catalytic action of an enzyme on a substrate of the array, gave a fluorescent signal". Further, the protein remained linked to the nanoparticle, from which it could then be cleaved, trypsinized and identified by mass spectrometry.
"Proof of principle was shown by reconstruction of the metabolic maps of model bacteria. Utility of the array for unsequenced organisms was demonstrated by reconstruction of the global metabolisms of three microbial communities derived from acidic volcanic pool, deep-sea brine lake, and hydrocarbon-polluted seawater".
4) Finally, Dan Koboldt and Keith Robison at MassGenomics and Omics! Omics! respectively, both discuss a recent article on the topic of cancer genomics. Through the use of Illumina technology, a Canadian group sequenced both the genome and transcriptome of an oestrogen-receptor-alpha-positive metastatic lobular breast cancer and compared it to a primary tumor sample from the same patient, from 9 years earlier.

The authors found 32 somatic non-synonymous coding mutations in the metastasis and measured the frequency of these somatic mutations in DNA from the primary tumour sample: most of these mutations were absent from the primary tumor. Interesting questions arising from this result are discussed on these posts.

Also, as the authors performed mRNA-Seq to assess the transcriptome, they were able to validate two instances of high-frequency, protein-altering RNA editing events, and they found that the “ADAR RNA-editing enzyme was one of the most highly expressed genes in the metastasis”.

From the article:
Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression.

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:

Quince, C., Lanzén, A., Curtis, T., Davenport, R., Hall, N., Head, I., Read, L., & Sloan, W. (2009). Accurate determination of microbial diversity from 454 pyrosequencing data Nature Methods, 6 (9), 639-641 DOI: 10.1038/nmeth.1361

Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, & Linding R (2009). Positive selection of tyrosine loss in metazoan evolution. Science (New York, N.Y.), 325 (5948), 1686-8 PMID: 19589966

Beloqui, A., Guazzaroni, M., Pazos, F., Vieites, J., Godoy, M., Golyshina, O., Chernikova, T., Waliczek, A., Silva-Rocha, R., Al-ramahi, Y., La Cono, V., Mendez, C., Salas, J., Solano, R., Yakimov, M., Timmis, K., Golyshin, P., & Ferrer, M. (2009). Reactome Array: Forging a Link Between Metabolome and Genome Science, 326 (5950), 252-257 DOI: 10.1126/science.1174094

Shah, S., Morin, R., Khattra, J., Prentice, L., Pugh, T., Burleigh, A., Delaney, A., Gelmon, K., Guliany, R., Senz, J., Steidl, C., Holt, R., Jones, S., Sun, M., Leung, G., Moore, R., Severson, T., Taylor, G., Teschendorff, A., Tse, K., Turashvili, G., Varhol, R., Warren, R., Watson, P., Zhao, Y., Caldas, C., Huntsman, D., Hirst, M., Marra, M., & Aparicio, S. (2009). Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution Nature, 461 (7265), 809-813 DOI: 10.1038/nature08489

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