Category Archives: Uncategorized

Trying to get the website re-started

…but not there yet.  Thanks for your patience.


Update 2017-07-07: We’re now actually getting the website restarted and up-to-date to reflect current people, projects, and publications here at UI. Cheers.


New PLoS Genetics paper; Harvard Crimson article; Mary Lidstrom wins Procter & Gamble Award; Will’s future job

The last two weeks have seen much good news. First, Sean’s PLoS Genetics paper came out which describes analyses of global gene expression that occurred immediately after metabolic engineering of formaldehyde metabolism in Methylobacterium (i.e., acclimation to the new pathway) and after eight populations evolved to grow on methanol using a new pathway (i.e., adaptation). Remarkably, although there were massive transcriptional changes that were highly parallel across the evolved populations, nearly all of these simply reversed the immediate perturbations caused by swapping out the methanopterin pathway for a glutathione one. Second, in addition to the other kind press Miki’s Genetics paper on clonal interference that I mentioned before, undergraduate Lauren Claus wrote a very nice piece about it for the Harvard Crimson. Third, I am very thrilled to pass on that my graduate advisor, Mary Lidstrom (U. Washington), was named the laureate for the 2013 Procter & Gamble Award in Applied and Environmental Microbiology by ASM. Extremely well-earned! Fourth, I am extremely excited to say that our lab’s own Will Harcombe has had a successful job search, ending in an excruciating decision. He will be starting off 2014 as an Assistant Professor in the BioTechnology Institute at the University of Minnesota as a member of the Department of Ecology, Evolution and Behavior.

Some Good News to Start the Year

With two weeks remaining in winter, the season about to end has been actually been pretty good to us with the exception of the record-breaking 28″ dump last month.  I can start by congratulating Josh Michener for landing an NRSA postdoctoral fellowship (and for his PNAS paper that emerged from his graduate work with Christina Smolke).  It has also been quite nice to see four more papers surface from the lab in the last two months.  The first one came out in  Molecular Biology and Evolution and describes work by my former postdoc, Deepa Agashe (now running her own lab at the National Centre for Biological Sciences in Bangalore, India), who looked at the selective pressures acting upon codon bias.  She systematically varied codon throughout a highly-expressed methylotrophy gene in Methylobacterium extorquens AM1, generating seven synonymous variants to compare to the wild-type coding sequence.  Remarkably, the selective effects we report were massive, including that the “perfect gene” comprised of exclusively the most frequently-used codons expressed very little protein and led to extremely low fitness.  Thanks to our collaborators Allan Drummond (now at University of Chicago) and Ceci Martinez-Gomez (Lidstrom lab, U. Washington) for their great help.  The second was a project from the lab of Chuck Davis (Harvard) in PLoS Genetics that I contributed to in terms of thinking about the parallels between horizontal gene transfer in bacteria and what they have observed between the mitochondrial DNA of a parasitic plant and its host.  The third is a Primer I wrote for PLoS Biology that discusses just how much of ecology or evolution can be detected from metagenomic sequencing.  A major goal of the paper was to frame an excellent paper in the same issue from Matt Herron and Michael Doebeli that examined adaptive diversification in a two resource environment.  Finally, the fourth just came out today as a Highlighted Paper in this month’s issue of Genetics.  This describes work by my former graduate student, Miki Lee (now a postdoc in the lab of Jiandong Huang at the University of Hong Kong).  Early in her thesis she discovered that a surprising kind of beneficial mutation – the integration of an introduced plasmid into the host genome – occurred many times in each of eight evolving populations.  During a five month post-defense mini-postdoc, one of the things she did (besides co-develop FREQ-Seq) was to follow-up on her old results and put together a fascinating story of clonal interference between simultaneous versions of this type of mutation (not to mention everything else going on).  She detected waves of up to 17 similar (but distinguishable) alleles all rising and falling in the same population, only sometimes ( 3 of 8 ) being fortunate enough to give rise to the eventual winning lineage.  Adaptation is not simple, but it is undoubtedly amazing in the outcome and the process.