Oregon State University Genome Research and Biocomputing 2010 Conference Recap

This will be a quick post of some impressions from yesterday and today’s Center for Genome Research and Biocomputing (CGRB) Fall Conference at Oregon State University.  The speakers were uniformly high quality, with Peter and Rosemary Grant’s talk the consensus of highlight of the program.

Jay Dunlap, “Genetic and Molecular Dissection of a Simple Circadian System”

Dunlap works on the circadian clock in Neurospora, a filamentous fungi. Like the circadian clock in mammals and insects, the basis of the Neurospora clock is a heterodimer that autoregulates the transcription of its own genes.  This autoregulation gives rise to the daily rhythmic expression characteristic of a circadian clock.

Dunlap’s lab has done some hard-core molecular work to dissect the basis of this autoregulation.  This includes chromatin immunoprecipitation assays to demonstrate that methylation at the locus of a key circadian clock regulator is necessary to its proper function, a mutant screen that eventually demonstrated phosphorylation of a protein heterodimer was necessary for proper autoregulation and finally expression microarrays to look for peripheral elements of the circadian clock.  This is one of the better understood molecular genetic pathways, but Dunlap reminded us how much work remains.

My only criticism, which is really more of a difference in philosophies, is Dunlap’s reliance on mutagenesis.  There is natural variation in at least one Neurospora circadian phenotype; such genetic variation has an advantage over lab-induced mutations in that it is maintained by natural selection, whereas mutagenesis studies mostly produce phenotypes of large effect that would never survive in nature.  Natural variation, in a genetically tractable context, can thus be used to understand the molecular genetic basis of a phenotype and the environmental context which maintains it.

Richard Spinrad, “OSU Research Now, Next, and After Next.”

Spinrad discussed the present and future of academic research, with a focus on the need to better communicate science to the general public and to secure future sources of funding.  Most funding (about two thirds of OSU’s research budget by the look of his pie chart) comes from the federal government, while industry and non-profits made up another two percent each.  He discussed the need to make up for the expected federal research budget reductions.  One opportunity Spinrad mentioned is better partnerships with industry.  As corporations reduce in-house R & D, they may outsource it to universities.  There are significant issues with academic-corporate relationships that I won’t get into, but he’s basically right; basic research will need to find other sources of support and corporations will be one of those sources.

My take on his talk:  We’re all aware of the need to communicate our work more broadly and the likelihood of shrinking federal research budgets, but Spinrad didn’t have suggestions for how to address these problems besides attempting to give talks geared to a general audience when we’re traveling and finding ways to increase funding from industry and non-profit sources.  These ideas are both obvious enough to be useless without more detail.  I’m sure he’s been working on such ideas, I would like to have seen his talk include some.

Daniel Schafer, “Some Lessons from the Biometry of Evolution and the Evolution of Biometry.”

This was a, dare I say, entertaining talk about the history of statistics within evolutionary biology.  I only mention it for two points.  The first is that the speaker briefly mentioned the negative binomial-P distribution as a method for RNA-seq data analysis.  Who wants to host him for a potentially dry and very valuable seminar, such as this one?  Secondly, he and the moderator kept on referencing this video.

Peter and Rosemary Grant, “Evolution of Darwin’s Finches” The Roles of Genetics, Ecology and Behavior.”
The Grant’s long term (and ongoing!) data set of darwin finch evolution on Daphne Major is one of the most valuable scientific studies ever conducted.  They have documented evolution of beak size in response to environmental changes for several decades now (more detail available via Google, but a good source is here) and have recently described some of the genes responsible for this variation.  Data sets linking genetic changes to specific ecological changes are nearly impossible to produce.  This is one of the best.

The second part of the talk described incipient speciation driven by a stochastic event (the original PNAS paper is here).  The descendants of a hybrid male immigrant and a hybrid female bred exclusively with each other, producing a lineage with unique beak and body morphology.  The mechanism of this reproductive isolation was a new song, which appears to be the result of imperfect copying of the local species song by the initial hybrid male.  The reproductive isolation is maintained by his descendant’s learning this unique song from their father.  This accident of imperfect imitation leading to reproductive isolation illustrates how important such stochastic events can be to speciation.

As with the last time I saw them, the Grants ended with their thesis:  “To understand the diversity of species we see around us we need to understand the dynamic interactions between genetics, ecology and behavior.”  Their life’s work is the best evidence for this.

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