Category Archives: Uncategorized

Jessica and I enjoyed writing Perspective for new Science paper on evolvability

None of us are looking for extra work to do, but when invited to write a Perspective for this great paper out of the lab of Andreas Wagner, Jessica Lee (now at Global Viral) and I made time to make it happen. The Research Article from Zheng et al. – “Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks” (Science, 2019. 365:347-353) – took advantage of the ability to select upon fluorescent proteins in a FACS machine to impose various selective pressures. They permitted cryptic variation to accumulate by imposing purifying selection upon yellow fluorescence for yfp variants. They then used this pool to begin selecting upon the upper range of green fluorescence. These diverse pools adapted faster and through a wider variety of paths than if they just began with the single ancestral yfp variant.

In our Perspective – “Tales from the cryp(ic)” (Science, 2019. 365:318-319) – we enjoyed pointing out comparisons to some awesome work of friends and colleagues that touched upon these questions: Jeremey Draghi‘s exploration of robustness, Eric Hayden‘s similar work with ribozymes, and Joe Thornton and Mike Harm‘s use of ancestral reconstruction to look at epistasis from a historical perspective.

Great commentary by Jennifer Farrell and Sam Brown on our new PNAS paper

Screen Shot 2018-11-28 at 12.55.42 PMWhat a wonderful surprise! I had no idea PNAS was doing a commentary on our paper, and then I found this excellent piece written by Jennifer Farrell and Sam Brown (Georgia Tech). They end their piece hoping that Will Harcombe (now at U. Minnesota) continued to evolve the two-species system described in this paper. Thankfully I know the answer is yes, and there will be more good stuff to come that he has carried forward in his own lab.

Review published on role of sequencing in revolutionizing studies of experimental evolution.

Screen Shot 2018-11-16 at 5.43.20 PMEric Bruger and I penned a review (Bruger and Marx, 2018. Current Opinion in Microbiology) that seeks to address the manner in which sequencing technologies have opened the door to whole new questions in experimental evolution. It was a joy to highlight the incredible work our field has accomplished in such a short time. I knew sequencing would be coming when I started my lab in 2005, but the magnitude of change has been incredible.

Two papers led by Will Harcombe – one in PNAS – on cooperation in synthetic communities

In the past months we have had two papers on the E. coliS. enterica system that Will Harcombe developed, and worked on when he was a postdoc in the lab.

One of these (Hynes et al., 2018. Biomedical Physics and Engineering Express) reports the ability to examine communities via bioprinting, and also represented a collaboration with two of my best friends Daniel Segrè and Nate Cady.

The second of these (Harcombe et al., 2018. PNAS) just came out a few weeks ago online in PNAS. It describes Will’s amazing finding of bidirectional costly mutualism evolving between species in the lab. Repeatedly E. coli evolved to break its own metabolism to excrete galactose to S. enterica during growth together on lactose (which S. enterica can’t use) in order to obtain methionine, which S. enterica had previously evolved to produce in return. I was excited to discover that, just a couple days ago, PNAS published a commentary on our paper penned by Jennifer Farrell and Sam Brown.

Papers stemming from KnipBio

Screen Shot 2018-11-16 at 5.13.21 PMBack in 2013, I co-founded KnipBio with Larry Feinberg. KnipBio’s goal is to develop Methylobacterium as an aquaculture feed ingredient that can simultaneously reduce the need for fishmeal-derived protein and provide high-value components and properties. In the past two years, our first publications have come out describing the successful use of this single-cell protein with a variety of aquaculture species (Tlusty et al., 2017. PeerJ, Hardy et al., 2018. Aquaculture Research). It has been very exciting to see work move from the lab and translate to practical outcomes.

Congrats to Siavash for a successful PhD defense

IMG_3898This past Tuesday, 11/13, Siavash Riazi presented his defense for a PhD in BCB entitled “Mathematical modeling and analysis of gene expression to understand phenotypic heterogeneity and the response of Methylobacterium extorquens to formaldehyde toxicity.” His work was co-advised by Chris Remien (Mathematics) and me, and represents his first PhD student, and my first to finish here at Idaho. Many thanks to committee members, Holly Wichman, Steve Krone, and Craig Miller. And most of all congrats to Dr. Riazi!

Not a BoRE at all

Not nearly as exciting as the news from current and former lab members, but as of the last nearly two years I have been serving as a member of the Board of Reviewing Editors at Science. Although nobody needs more work to do, this has been a really neat opportunity to see just emerging work from many disciplines come streaming by. And it has been quite rewarding to see some of those that I expressed great excitement for make it to review and successfully out the other end, now appearing in print.

Tenure news!

Besides new jobs, the lab now has the first alumni to be granted tenure. Alex Bradley is now an Associate Professor in Earth and Planetary Sciences at Washington University, St. Louis. Deepa Agashe is now tenured in Ecology and Evolution at the National Centre for Biological Sciences (NCBS) in Bangalore. Many congrats to you both!!!


Very excitingly, two postdocs landed PI-level jobs this year. Jannell Bazurto has landed an Assistant Professor position in Plant and Microbial Biology at the University of Minnesota, and will start her own lab in January, 2019. Jessica Lee has landed a job as a Fellow with the non-profit, GlobalViral, and also has an Adjunct Assistant Professor position at San Francisco State University. They bring the total number fo PIs to emerge from the lab to nine!

Welcome to the new students in the lab

This past year has seen some big turnover in the lab with many new positions, etc. In terms of undergrads, we are excited to have Olivia Speare and Mete Yuksel on the team. They are working on protein biochemistry and phenotypic heterogeneity, respectively. Furthermore, it is exciting to have Isaiah Jordan now having started graduate school in the lab as part of the BCB graduate program. He is also working on phenotypic heterogeneity, building upon the exciting results of former postdoc Jessica Lee and others.