People

Principal Investigator

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With Rasmus and Solvei on the first day of ice on our rink           (9 December, 2018)

Christopher Marx

Professor
University of Idaho | Department of Biological Sciences
Institute for Bioinformatics and Evolutionary Studies
Institute for Modeling Collaboration and Innovation
Gibb 134 | 875 Perimeter Drive MS 3051 | Moscow, ID 83844-3051 cmarx (at) uidaho.edu

 Research Associate Professor

 

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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

 


Postdoctoral Fellows

hp photosmart 720Tomislav Ticak | tticak (at) uidaho.edu

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.

 

 

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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 Methylobacterium extorquens.


Graduate Students

Isaiah Jordan | jord2663 (at) vandals.uidaho.edu

I was a Biochemistry undergraduate at University of Idaho, and have recently joined the lab as a BCB graduate student. My project has uncovered that E. coli also exhibits phenotypic heterogeneity for formaldehyde tolerance, although the phenomenon is different in several key ways.

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Akorede Seriki | 
seri5256 (at) vandals.uidaho.edu

I am a new Biology PhD student this fall after having just moved from Lagos, Nigeria. My project looks to understand the physiological basis of phenotypic heterogeneity and inheritance of formaldehyde tolerance in Methylobacterium, as well as how selection has acted to change these phenotypes.


Technicians

Monica Pedroni| mpedroni (at) uidaho.edu

My work as a technician is split across two grants: the NSF Dimensions of Biodiversity project, where I am working to develop a high-throughput manner to generate trait data for natural isolates of Methylobacterium, and our DOE Biosystems project, where I am working to develop microscopy techniques for assaying growth and PHB levels across individual cells.

 

_private_var_mobile_Containers_Data_Application_2C302D0B-93D6-40CF-BB81-C5C07B01C4BC_tmp_32AAFECB-2DEB-46C0-BCD5-3DF35E84C0DB_ImageOlivia 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.

 


 

Undergraduate Students

 

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 mug 191203Drew 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.

 

 

 

Giovanna Girolami mug 191202Giovanna Girolami | giro2145 (at) vandals.uidaho.edu

I have been working in the lab doing media prep and dishwashing.

 

 

 


Group photos

 

Marx lab photo 080822

08.08.22 – Taken outside Biolabs at Harvard, Daniel Segrè photographed us after asking us to jump. Note Nigel took the effort to lift a foot. Left to right: me, Alex Pickett (UG), David Chou (grad), Alex Bradley (postdoc), Deepa Agashe (postdoc), Miki Lee (grad), Nigel Delaney (grad), Kiahana Brooks (UG), Tony Blair (lab manager & MS student), David Robinson (UG)

 

Marx lab photo 091014

09.10.14 – Outside Biolabs in front of the other rhino. On Rhino: Tami Lieberman (grad rotation), Lewis Ward (UG); L to R: Roxana Tarnita (UG), Miki Lee, Dipti Nayak (grad), Tony Blair, Alex Bradley, me, Nigel Delaney, Deepa Agashe, Will Harcombe (postdoc), David Chou, Sean Carroll (postdoc)

 

Marx lab photo 091207 David's defense

09.12.07 – Taken in the lunch room we shared with the Girguis and Pringle labs where we celebrated David’s defense. L to R: Sean Carroll, Lewis Ward, David Chou, Nigel Delaney, Tony Blair (seated), Dipti Nayak, me, Will Harcombe, Sarah Douglas (grad)

 

Marx lab photo 111102

11.11.02 – This one in the fall had the rhino dressed as a bacterium (note the plasmid, phage, and flagella). L to R: me, José Rojas Echenique (grad), Paige Swanson (lab manager then just starting), Lon Chubiz (postdoc), Maryska Kaczmarek (lab manager then just leaving), Nigel Delaney, Nick Leiby (grad), Sarah Douglas, Dipti Nayak, Ozzy Baltekin (visiting grad), Will Harcombe, Deepa Agashe, Alex Bradley, Jessica Purswani (visiting postdoc), Sean Carroll

 

12.10.29 – Yet another in front of the rhino… L to R: Josh Michener (postdoc), Lon Chubiz, Sean Carroll, Nick Leiby, Sarah Douglas, Nigel Delaney, Will Harcombe, me, José Rojas Echenique, Dipti Nayak, Ying Zhang (visiting grad), Paige Swanson

 

Marx lab photo 131114 Will party

13.11.14 – Will’s going away party (and just a month before I left). Note the three fabulous moustaches. Standing L to R: Sarah Douglas, me, Lon Chubiz, Will Harcombe, José Rojas Echenique, Paige Swanson; Kneeling L to R: Dipti Nayak, Josh Michener, Nick Leiby, Sean Carroll

 

Marx lab photo 150911

15.09.11 – In Idaho and enjoying the deck at Patty’s. Left side front to back: me, Tomislav Ticak (postdoc), Nick Shevalier (UG), Siavash Riazi (grad); right side front to back: Josh Wirtz (tech), Alyssa Baugh (UG), Brad Emery (UG, standing), Jessica Lee (postdoc), Jannell Bazurto (postdoc), Gavin Esser (UG)

 

Marx lab photo 151002 Brady Bunch

15.10.02 – Brady Brunch styled photo for me to use at my promotion talk the next week, and thus take advantage of the 3×3 grid of TVs in LSS 277.

 

Marx lab photo 170510

17.05.10 – Going away party for Drew at the Alehouse. Left side front to back: me, Alyssa Baugh, Caleb Renshaw (UG), Jannell Bazurto (postdoc) holding Sora; right side front to back: Drew Forlini (UG), Sergey Stolyar (Research Associate Professor), Tomislav Ticak, Leah Lambert (UG), Jessica Lee, Siavash Riazi

 


Former Postdocs:

Jessica Lee now at Global Viral/San Francisco State

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

IMG_3116Siavash 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 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.

Sarah Douglas 

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.

Nick Leiby 

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)

 

Undergraduate Students

ACB photo 171113Alyssa 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.

 

 

FB_IMG_1499368792460Caleb 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.

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Nick Renn | renn4062 (at) vandals.uidaho.edu

 

 

 

 

 

Leah LambertLeah 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:

Jaya Gandhi


Former technicians:

Josh Wirtz

Paige Swanson – former lab manager

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 on Rumble Seat pin up shoot

Chris Engles – former lab assistant

When I wasn’t sterilizing glassware, ordering lab supplies or updating WordPress sites, I’m taking pictures or shooting movies.  On weekends I can typically be found at my satellite office.

 

Maryska Kaczmarek (now Ph.D. student, Sara Sawyer lab, U. Colorado, Boulder)

Anthony Blair

Maggie Chen

Melissa Derby

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