People

Principal Investigator

IMG_9144

With Solvei and Rasmus in Black Canyon of the Gunnison National Park.

Christopher J. Marx

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

 Research Associate Professor

 

screen-shot-2016-11-28-at-4-36-53-pm

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 720Jessica 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.

 

JVB photo 171113Jannell Bazurto | jbazurto (at) uidaho.edu

I hail from South Florida where I received my B.S. in Molecular Biology and Microbiology at Florida Atlantic University. I performed my thesis work with Dr. Diana Downs at the University of Wisconsin-Madison where I used suppressor mutation analysis to study metabolic integration and plasticity in the purine-histidine-thiamine biosynthetic network of Salmonella enterica and Escherichia coli. After completing my PhD in 2013, I moved with the Downs laboratory to the University of Georgia to pursue postdoctoral studies where I incorporated metabolomic analyses to investigate the pleotropic effects of metabolite accumulation on the metabolic network. In the Marx lab, I am combining my expertise in traditional bacteriology approaches with experimental evolution and systems-level analyses to characterize stress response systems that counteract formaldehyde toxicity in Methylobacterium extorquens.

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

 

 

 

 

 

Eric Bruger photo 171106Eric Bruger | elbruger (at) uidaho.edu

 

 

 

 


Graduate Student

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 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.


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.

IMG_20170706_115205136Nick 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.

 

 


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:

Lon Chubiz 

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.

 Sean Michael Carroll 

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.

William Harcombe 

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.

Joshua Michener 

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)

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)


Former Graduate Students

Dipti Nayak 

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 

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.

Nicholas 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 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:

Jaya Gandhi


Former technicians:

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

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s