Monday, October 19, 2009

Houdini viruses and probing the 3D architecture of the human genome, 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 posts selected.

This week, two blog posts made the cut:

1) Lab safety procedures are of utmost importance, particularly in labs that work with human pathogens. A few cases of “lab escapees” have been reported in the virus literature: the last case of smallpox and the 2007 outbreak of foot and mouth disease in the UK where probably the result of escaped lab strains. Ian York from Mystery Rays from Outer Space discusses a recent article reporting a Brazilian isolate of a particular Dengue virus strain, which appears to be closely related to one isolated in Asia more than two decades ago.

(As) dengue viruses mutate and evolve fairly rapidly, this kind of stability (35-fold lower than expected) would be extraordinary in a virus that’s been circulating for two decades.
One possible explanation (among others) for this is that the reported strain is a lab escapee.

2. For the past 40 years, chromatin structure has been the matter of intensive research. With the development of new methodologies, we’ve been able to study beyond the structure of the nucleosome filament into the fascinating, yet still incompletely understood, world of higher-order chromatin folding.
Techniques like the widely applied chromosome conformation capture technology (3C, and its derivations) have allowed us to “analyze the folding of chromatin in the native cellular state at a resolution beyond that provided by current microscopy techniques”a.

Greg Fish from Weird Things discusses a recent article in Science reporting the development of a new of such techniques called Hi-C which “adapts the above approach (that is, 3C) to enable purification of ligation products followed by massively parallel sequencing”.

Simply put, by using their method, the authors probed the “three-dimensional architecture of the human genome by coupling proximity-based ligation with massively parallel sequencing”.

The thing which sets this technique apart, is that Hi-C allows unbiased identification of chromatin interactions across an entire genome.
Greg comments on two fascinating discoveries arising from this study concerning chromatin conformation and genome organization. You should definitely check both this post and the article out!

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:

Aquino, V., Amarilla, A., Alfonso, H., Batista, W., & Figueiredo, L. (2009). New Genotype of Dengue Type 3 Virus Circulating in Brazil and Colombia Showed a Close Relationship to Old Asian Viruses PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007299

Lieberman-Aiden, E., van Berkum, N., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B., Sabo, P., Dorschner, M., Sandstrom, R., Bernstein, B., Bender, M., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L., Lander, E., & Dekker, J. (2009). Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Science, 326 (5950), 289-293 DOI: 10.1126/science.1181369

References used in post:
a Nature Methods - 4, 895 - 901 (2007)

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