University of Idaho | Department of Biological Sciences
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 Methylorubrum.
Monica Pedroni | mpedroni (at) uidaho.edu
I am a research scientist and lab manager for the Marx lab, with my research work currently focused on generating barcoded natural isolates of Methylobacterium to study their phenotypes and ecological interactions.
Eric Bruger | elbruger (at) uidaho.edu
My interests encompass patterns of microbial evolution and diversity, as seen both within and outside of the lab, as well as interactions between genes, networks, and within populations of bacteria. After first delving into the world of microbial metabolism by studying thiamine biosynthesis in Salmonella as an undergraduate researcher at the University of Wisconsin-Madison, I pursued doctoral work on the evolution and physiology of cooperative traits regulated by quorum sensing in the aquatic bacterium Vibrio harveyi at Michigan State University. I am uniting these experiences through my work in the Marx laboratory, which focuses primarily on applying sequencing-based approaches to detect epistatic interactions between variants of formaldehyde oxidation pathways in the model methylotroph Methylorubrum extorquens.
Nkrumah Grant | ngrant (at) uidaho.edu
My research interests, writ large, lie in understanding how flexible biological networks are, including their stability over long evolutionary timescales. My current research efforts here in the Marx lab examine the physiological and morphological consequences that arise when organisms are engineered with new metabolic pathways. To this end, I employ several techniques – including fluorescence and time-lapse microscopy using microfluidics and flow cytometry – to study phenotypic heterogeneity at single-cell resolution using the microbial chassis organism, Methylorubrum extorquens. I believe that understanding the features of biological networks that make them more prone to retaining ancient and novel traits will enable synthetic biologists to engineer more efficient organisms in biomanufacturing contexts, while also shedding light on how biologists can predict, and potentially stall, evolution.
Akorede Seriki | seri5256 (at) vandals.uidaho.edu
I am a Biology PhD student with a project looks to understand the physiological basis of phenotypic heterogeneity and inheritance of formaldehyde tolerance in Methylorubrum, as well as how selection has acted to change these phenotypes.
Drew Simpson | simp5363 (at) vandals.uidaho.edu
I am a biology PhD student here at the University of Idaho. I graduated with my undergraduate degree in Biology from Lewis-Clark State College in Lewiston, Idaho. My research focuses around using TnSeq methodology to understand how functional traits relate to genome content, bridging the gap between sequence data and functional trait data in Methylobacterium. Much of this work plays into multiple projects within the lab that builds better genetic pictures for bioengineering applications, as well as contributing to better understandings of bacterial community assemblages and phylogenetic hypotheses.
Hannah Ringel | ring1329 (at) vandals.uidaho.edu
I am an undergraduate student studying microbiology and psychology. In the lab, I have been working alongside Eric Bruger researching the evolution of the ribulose monophosphate pathway in M. extorquens and the effect on carbon conversion and growth.
Tomislav Ticak | now at Proctor & Gamble
I did my graduate work at Miami University of Ohio on biochemical pathways and enzymes of anaerobic microbes. Here at Idaho I have turned to working on the aerobe, Methylobacterium extorquens, and have a variety of projects on pathways of aromatic utilization, formaldehyde sensing, and phenotypic heterogeneity.
Jessica Lee now at NASA Ames Research Center
Jannell Bazurto now at U. Minnesota
Lon Chubiz now at U. Missouri, St. Louis
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 methylotroph Methylobacterium 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.
Sean Michael Carroll now at Axcella Health
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.
Will Harcombe now at U. Minnesota
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.
Josh Michener now at Oak Ridge National Labs
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 Bradley (2008-12, now Associate Professor, Earth and Planetary Sciences, Washington U., MO)
Jessica Purswani (2011-12, now postdoctoral fellow, U. Granada, Spain)
Deepa Agashe (2008-11, now tenured faculty, Ecology and Evolution, National Centre for Biological Sciences, Bangalore, India)
Former Graduate Students
Isaiah Jordan moving to work at Virginia Tech
I was a Biochemistry undergraduate at University of Idaho, and have recently joined the lab as a BCB graduate student. My Masters project uncovered that E. coli also exhibits phenotypic heterogeneity for formaldehyde tolerance, although the phenomenon is different in several key ways.
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 was co-advised between Marx lab and Chris Remien’s group (in Math dept.) I worked 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.
Dipti Nayak now at UC Berkeley
My research focused on using experimental evolution to understand microbial physiology. For my PhD I tried to understand the physiological basis of formaldehyde stress response as well as the genetics of the N-methylglutamate pathway for methylamine utilization in Methylobacterium extorquens using experimental evolution.
José Rojas Echenique now postdoc at U. Toronto
I am 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 worked 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 characterized the ecological dynamics and molecular mechanisms underlying the rise of this social behavior. I also studied 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 was a PhD student in Systems Biology. I studied 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.
Nigel Delaney (2012, then postdoctoral fellow, Broad Institute, Cambridge, MA)
Ming-Chun “Miki” Lee (2010, then postdoctoral fellow, Biochemistry, U. Hong Kong)
Hsin-Hung “David” Chou (2009, now Assistant Professor, National Taiwan U., Taipei, Taiwan)
Former Undergraduate Students
Giovanna Girolami | giro2145 (at) vandals.uidaho.edu
I have been working in the lab with Monica Pedroni looking at negative, toxic interactions between natural isolates of Methylobacterium.
Garrett Woelfl | woel2689 (at) vandals.uidaho.edu
Cole Garrett | garr4677 (at) vandals.uidaho.edu
My project, working with Sergey, is to examine PHB levels and heterogeneity in Methylobacterium strains as a function of strain background, growth substrate and concentration, nitrogen levels, and phase of growth.
Drew Johnson | andr8808 (at) vandals.uidaho.edu
I have been working with Tomislav to evolve Methylobacterium extorquens PA1 to utilize methoxylated aromatic compounds that would derive from hydrolyzed lignin.
Alyssa Baugh | baug7691 (at) vandals.uidaho.edu
I’m studying Microbiology, Biochemistry, and Molecular Biology & Biotechnology at UI. My research involves genetically engineering, assaying, and improving strains of the model methylotroph M. extorquens to metabolize aromatic, lignin-derived compounds by inserting the vanAB(K) and pca gene clusters.
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.
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.
Brad Emery, Brandi Strand, Drew Forlini, Elliott Marsden, Gavin Esser, Hannah Ringel, Josh Helbling, Maria Elizarraras, Mete Yuksel, Nick Shevalier, Sam Howell, Tobias Flores-Wentz, Viky Espericueta
Visiting Erasmus Mundus M.S. thesis:
Alex Betts (2012-2013, then Ph.D. student, Oxford University)
Özden Baltekin (2011-12, then Ph.D. student, Uppsala U., Sweden)
Completed B.A. theses:
Lewis Ward (2010, now postdoc, Earth and Planetary Sciences, Harvard, MA)
Dave Robinson (2009, then Ph.D. student, Quantitative and Computational Biology, Princeton, NJ)
Other former rotation/collaborating/visiting graduate students:
Zain Ali, Anthony Blair, Aline Camargo-Neves, Hsiao-Han Chang, Delbert “Andre” Green, Arnon Levy, Tami Lieberman, Niall Mangan, Jue Wang, Ying Zhang
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, Tim Scott, Vicky Wu, Will Polachek
Former high school student:
Olivia Benski| obenski (at) uidaho.edu
I was an undergraduate Biochemistry major at University of Idaho and have been working as a technician on a protein biochemistry project to understand the function of the formaldehyde-sensing protein, EfgA.
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
Maryska Kaczmarek (now Ph.D. student, Sara Sawyer lab, U. Colorado, Boulder)