First test of FBA’s ability to predict evolution published; a third F1000 recommendation and Addgene.com article; mentoring nomination; lab comings and goings

The past month and a half have seen several pieces of good news: 1. Will Harcombe’s paper just came out in PLoS Computational Biology.  We are both extremely relieved and proud to have gotten this out, as it represents the first direct test ever as to whether central metabolic fluxes actually evolve to become optimal,Continue reading “First test of FBA’s ability to predict evolution published; a third F1000 recommendation and Addgene.com article; mentoring nomination; lab comings and goings”

New paper; another Faculty of 1000 recommendation; and Mary Lidstrom elected to the National Academy of Sciences

Less than two weeks after the last post, there is more happy news to report. 1. Nigel Delaney‘s PLoS One paper came out yesterday that describes the end result of an extended effort to push Methylobacterium culturing as far as possible. It reports a new optimized medium, new strain lacking cellulose synthesis that caused clumping, and conditions and methods for high-throuput,Continue reading “New paper; another Faculty of 1000 recommendation; and Mary Lidstrom elected to the National Academy of Sciences”

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

Praise for Miki’s paper; TV show; ASM Distinguished Lectureship

1. In the past three weeks we’ve been fortunate to have received some additional press for Miki’s recent paper mentioned in the prior post.  Beyond being a ‘Highlighted Paper‘ in the March issue of Genetics, we were kindly recommended by Deborah Charlesworth of the Faculty of 1000, and the Harvard Gazette ran an article about it, too. 2. Back on Darwin’s birthday (12 February)Continue reading “Praise for Miki’s paper; TV show; ASM Distinguished Lectureship”

Latest News:

Remarkably, three more months have gone by since my last post.  We have crowned a new Ph.D. from the lab, Dr. Nigel Delaney, back on 30 October.  He gave a fantastic presentation concentrating on his new work estimating the distribution of fitness effects of successful mutations for one of our strains of Methylobacterium.  He has now gottenContinue reading “Latest News:”

End of Summer Update.

In the past month and a half we’ve had four new papers come out. First is one led by myself and Stephane Vuilleumier in Journal of Bacteriology announcing the genome sequences of six strains of Methylobacterium. Second, Hsuan-Chao Chiu, his then-mentor Daniel Segre and I have a follow-up to last year’s Science paper in Proceedings of the Royal Society B that extends some general theory that considers how epistasisContinue reading “End of Summer Update.”

Publication: “Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation.”

 3 June, 2011 – Our paper uncovering a generic trend for diminishing returns between beneficial mutations was published in today’s issue of Science.  Besides an excellent perspective in the same issue by Kryazhimskiy et al. on our paper and that of our colleague, Tim Cooper (U. Houston), reporting the same finding in E. coli, stories were alsoContinue reading “Publication: “Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation.””

New Website, New Publications.

At long last, we have done a make-over of our website.  In terms of scientific output, since the Science paper last mentioned as news nearly a year ago, we’ve had publications in Cell (a Preview about a great paper from the group of Sander Tans), Cell Reports (David Chou uncovered a remarkable diversity of genetic pathways to parallel optimization of geneContinue reading “New Website, New Publications.”