Brandeis at the APS March Meeting: Biological Physics

1 05 2012

Biological Physics
by Matt Perkett and Sandeep Choubey

More than a quarter of this year’s March meeting covered various aspects of soft matter research with more than 170 sessions and 2,000 contributed talks. Brandeis faculty, postdocs, and graduate students contributed more than 20 of these talks. These speakers presented a diverse range of soft matter research interests.

Matt Perkett, a fourth year Physics graduate student, presented his work on virus capsid assembly. MS2 is a small bacteriophage that forms a spherical capsid with a diameter of about 27.5nm. The completed capsid is made of protein dimers that adopt one of two different conformations depending on their position in the completed capsid. The goal of his research was to determine the mechanism by which these dimers are placed into the correct conformation during assembly. Since the kinetics of virus assembly is difficult to determine experimentally, all atom simulations and enhanced sampling techniques were used. The free energy difference between the two different protein dimer conformations was found to be in agreement with experiments and future measurements with bound RNA will determine the selection mechanism during assembly.

Sandeep Choubey, a third year Physics graduate student, presented his work on the regulation of ribosomal genes. Upon adding more ribosomal genes to the E. coli cell, it adjusts the overall transcription of these genes by reducing the average transcription rate per gene, so as to keep constant the level of ribosomal RNA in the cell. It was observed that this reduction in the average transcription level per gene is accompanied by the generation of transcriptional bursts. The goal of his work was to understand the mechanistic basis of these bursts. He considers three possible mechanisms suggested in literature: Promoter proximal pausing by RNA polymerase, cooperative recruitment of RNA polymerase by DNA supercoiling, and competition between RNA polymerase and a transcription factor for binding regulatory DNA associated with ribosomal genes. The statistical properties of transcription initiation were computed and were compared with the distribution of distances between the polymerases transcribing the ribosomal genes, obtained from electron micrographs. It was shown that the three mechanisms can be discriminated by comparing the predictions for the mean and variance of interpolymerase distances with experimental data and further experiments were suggested.

Numerous Brandeis alumni were also present at this year’s meeting. Alvaro Sanchez, (PhD ’10) of MIT presented his work on population dynamics. Evolution has traditionally been viewed as a very slow process that happens over geological timescales. In contrast, changes in the size of a population are typically much faster, occurring in timescales of a few generations time. Therefore, it has been commonplace to assume that both evolution and population dynamics are independent processes. Recently, this view has been challenged, and examples where either population dynamics affect evolutionary change, or the other way around, have been documented. Using cooperatively growing yeast as a model system, we have showed that population dynamics and evolutionary dynamics are linked together through a feedback loop, which dominates both the outcome of the evolutionary competition between cooperators and cheaters, and the demographic fate of the population. This feedback loop saves the population from extinction when a population of cooperatively growing cells gets invaded by a cheater phenotype emerging from random mutation. While the population does not go extinct as a result of invasion by cheaters, it becomes less resilient to environmental changes, and has a higher chance of going extinct as a result of environmental deterioration. Our results were reproduced by simple model, which suggest that this type of coupling could be common in communities that rely on cooperation for their survival.

In addition to the presentations showcased here, a variety of exciting experimental soft matter work was also presented, some of which has already been discussed in greater detail on this blog (Sanchez, Zakhary).




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