People and Contact Information
University of Idaho | Department of Biological Sciences
*Photo is with Rasmus and Solvei in Jasper National Park.
Research Associate Professor
Sergey Stolyar | sstolyar (at) uidaho.edu
I knew Chris from our time together in Mary Lidstrom’s lab at UW. Since then, I have had a series of research positions at the Institute for Systems Biology, UW, and PNNL. I have been happy to join the team, and have focused my efforts on our DOE project studying synthetic microbial communities, and upon using a combination of engineering and evolution to bring novel metabolic capacities to Methylobacterium.
Jessica A Lee | jessicalee (at) uidaho.edu
I’m currently studying microbes as a postdoctoral researcher in the Marx Lab at the University of Idaho; you can find out more about what I’m up to on my Research page. Our lab works on Methylobacterium extorquens, but I’ve also had experience researching bacteriophages, mycelial fungi, bacteria that eat fungi, synthetic microbial consortia, and super-diverse bacterial and archaeal communities in soils and sediments.
Jannell Bazurto | jbazurto (at) uidaho.edu
Tomislav Ticak | tticak (at) uidaho.edu
Eric Bruger | elbruger (at) uidaho.edu
Siavash Riazi | riaz5408 (at) vandals.uidaho.edu
I did my undergrad in University of Tehran in Cell and Molecular Biology. Currently I’m a PhD candidate in Bioinformatics and Computational Biology. My project is co-advised between Marx lab and Chris Remien’s group (in Math dept.) I’m working on modeling phenotypic heterogeneity and in particular how a population of M. extorquens responds to formaldehyde stress. The work includes ODE, PDE models and probability theory. The project is interdisciplinary and involves working on growth data so I do both simulations and inferring/estimation of parameters from data using different statistical approaches.
Alyssa Baugh | baug7691 (at) vandals.uidaho.edu
Caleb J Renshaw | rens0687 (at) vandals.uidaho.edu
I’m a third generation UI undergrad studying biochemistry and mathematics. My research in the Marx Lab focuses on the molecular work of designing and building a genetic dual-regulator system to simultaneously and independently control expression of two separate genes in M. extorquens with the goal of producing and analyzing fitness landscapes.
Sam Howell | howe6231 (at) vandals.uidaho.edu
Nick Renn | renn4062 (at) vandals.uidaho.edu
Leah Lambert | lamb7228 (at) vandals.uidaho.edu
I’m an undergraduate studying biochemistry at the University of Idaho, and I’m from Coeur d’Alene, Idaho. I am investigating bacterial stress response mechanisms due to antibiotics and non-antibiotic toxins along with mechanisms of formaldehyde resistance in Methylobacterium extorquens.
Eliott Marsden | mars2123 (at) vandals.uidaho.edu
Joshua Helbing | helb1448 (at) vandals.uidaho.edu
As a research technician and lab manager, I worked with postdoc Alex Bradley and graduate student Nigel Delaney to answer questions about Methylobacterium populations that were evolved experimentally in our lab. I am a transplant from Colorado, where I studied Evolutionary Biology at the University of Colorado at Boulder. When not in the lab, you’ll typically find me in the kitchen. I am now a Director at Finch Therapeutics in Somerville, MA.
Chris Engles – former lab assistant
My focus in the Marx Lab is in understanding the genetic and physiological basis underlying adaption. Particularly, how does underlying pleiotropy and epistasis constrain the adaptive trajectories available to an organism challenged with a new environment? Cellular metabolism provides an ideal framework to address this question. Using the aerobic methylotrophMethylobacterium extorquens as model system allows this question to be approached from the perspective of metabolic specialization. By understanding the mechanistic basis for observed phenotypes in evolved populations, I believe answering this question is possible.
My work explores how various mechanisms of adaptation lead to improved growth in Methylobacterium extorquens AM1, a model microbe for studies of one-carbon (C1) metabolism and microbial evolution. I study at a systems-level the mechanisms by which strains acclimate and adapt to an engineered C1 metabolism: using whole-genome sequencing, microarray analyses, and quantification of metabolites to connect genotypes to higher-order properties such as growth rate and fitness. In a complementary approach, I use a regulated promoter system to directly modulate the activity of key C1 enzymes and measure the effect of these “idealized mutations” on growth rate and fitness. And with the help of students from this year’s OEB100 (2012) class, I am documenting the genomic and phenotypic changes that our model microbe has undergone during fifty years of life in the lab. Together, I hope to help illuminate how factors such as epistasis, pleiotropy, and clonal interference influence adaptive trajectories and shape microbial functions in the lab, in the wild, or in human health and disease.
Microbes are capable of incredible metabolic feats, acquiring energy from a diverse array of compounds. I am interested in how evolution shapes these metabolic capabilities. At the single species level I study how bacteria adapt to acquisition of a novel metabolic pathway. At the multi-species level I study how adaptation alters the productivity of model consortia. Metabolism of various compounds often depends on a complex network of interacting bacteria. I use model microbial assemblages (combinations of E. coli,Salmonella, and Methylobacterium) to test how ecological and evolutionary processes influence community composition and function.
I study adaptation following horizontal gene transfer, seeking to understand the co-evolutionary process as a pathway adapts to its new host and a host to its new pathway. Specifically, I’m looking at the growth of Methylobacterium extorquens on a toxic pollutant, dichloromethane. A pathway for dichloromethane utilization exists in one strain of M. extorquens, but does not function when transferred to a closely related strain. I’m using experimental evolution to evolve the pathway in its new host, exploring the adaptive mechanisms and trajectories.
Alexander S. Bradley (2008-12, now Assistant Professor, Earth and Planetary Sciences, Washington U., MO) http://bradleylab.wustl.edu
Jessica Purswani (2011-12, now postdoctoral fellow, U. Granada, Spain)
Deepa Agashe (2008-11, now Fellow (PI), Ecology and Evolution, National Centre for Biological Sciences, Bangalore, India) http://ncbs.res.in/dagashe
Former Graduate Students
Dipti Nayak | dnayak (at) oeb.harvard.edu
My research focuses on using experimental evolution to understand microbial physiology. For my PhD I am trying to understand the physiological basis of formaldehyde stress response as well as the genetics of the N-methyl glutamate pathway for methylamine utilization in Methylobacterium extorquens using experimental evolution.
I’m interested in the possible forms that the organisms in a population can take on as they evolve. Conceptually we organize these forms according to their fitness and mutational distance from one another on a fitness landscape. I’m working towards an understanding of the physiological traits and interactions that make up a model fitness landscape: the central carbon metabolism of Methylobacterium extorquens.
“Costly cooperation between unrelated organisms presents a Darwinian dilemma: if natural selection favors individuals with the highest relative fitness, why should an organism increase the fitness of its neighbors? Using a unique bacterial system that allows the de novo evolution of cooperation, I am characterizing the ecological dynamics and molecular mechanisms underlying the rise of this social behavior. I also study how selection sorts variations in cooperative strategies within a population, and how this variation affects resistance to cheater invasion. Knowing how mutational diversity impacts cooperative phenotypes, and how selection acts upon phenotypic variety, will lead to a more accurate understanding of dynamic, ecologically complex systems of cooperation.”
I’m a PhD student in Systems Biology. I study E. coli evolving over long periods in laboratory conditions, and the tradeoffs that occur in metabolic flexibility in order to optimize for the present environment.
Completed Ph.D. theses:
Nigel F. Delaney (2012, now postdoctoral fellow, Broad Institute, Cambridge, MA)
Ming-Chun “Miki” Lee (2010, now postdoctoral fellow, Biochemistry, U. Hong Kong)
Hsin-Hung “David” Chou (2009, now an EMBO postdoctoral fellow, Inst. Of Molecular Systems Biology, ETH, Zürich)
Visiting Erasmus Mundus M.S. thesis:
Alex Betts (2012-2013, future Ph.D. student, Oxford University)
Özden Baltekin (2011-12, now Ph.D. student, Uppsala U., Sweden)
Completed B.A. theses:
Lewis M. Ward (2010, future Ph.D. student, Geological and Planetary Sciences, CalTech, CA)
David G. Robinson (2009, now Ph.D. student, Quantitative and Computational Biology, Princeton, NJ)
Other former rotation/collaborating graduate students:
Zain Ali, Anthony Blair, Hsiao-Han Chang, Delbert “Andre” Green, Arnon Levy, Tami Lieberman, Niall Mangan, Jue Wang
Other former undergraduates:
Earl “Alex” Pickett, Chris Ding, Dan Lorenzana, Sherif Gerges, David Guernsey, Ed Kogan, Jessica Berger, Julia Berthet, Kiahana Brooks, Lela Sims, Lucy Liu, Roxana Tarnita, Samantha Parker, Vicky Wu, Will Polachek
Former high school student:
Anthony Blair, Maggie Chen, Melissa Derby, Maryska Kaczmarek(now Ph.D. student, Integrative Biology, U. Texas, Austin)