Brian Bothner

   

Photo of Brian Bothner.

Department:
Chemistry & Biochemistry

Email:
bbothner@chemistry.montana.edu

Lab Website:
https://www.montana.edu/bothnerlab/

Research in the Bothner lab has two main focuses:
(1) Investigation of cellular response to stress using chemical biology, proteomics, and metabolomics.
(2) Assembly, stability, and dynamics of multi-subunit enzymes and nucleoprotein complexes.

This research takes us from the atomic scale provided by high resolution structural models of viruses and enzymes to complex interaction networks of nucleic acids, metabolites, and proteins that make up a living system.  Methanogens and extremophiles from Yellowstone National Park are at the center of a number of exciting research projects. 

Potential Projects:

Assimilation and trafficking of iron and sulfur in methanogens 

Elucidating the catalytic mechanism behind aerobic methane synthesis 

Metabolics changes associated with aerobic to anaerobic transitions. 

 

 Ross Carlson

   
Photo of Ross Carlson.Department:

Chemical & Biological Engineering

Email:
rossc@montana.edu

Lab Website:
https://chbe.montana.edu/biochemenglab/ 

  

The Carlson group is an biochemical engineering group studying a range of microbial systems including medical infections, biofuels production, and environmental nutrient cycling.  The research combines classic engineering concepts with applied microbiology. 

Potential Projects:

Substrate preference of medical isolates as a function of antibiotic treatments. 

Crossfeeding of metabolites in engineered consortia. 

Fungal biofilms for food production. 

 

Connie Chang

 

 

Photo of Connie Chang.

Department:
Chemical & Biological Engineering

Email:
connie.chang@montana.edu 

Website:
https://www.montana.edu/changlab/ 

Connie’s research interests are drop-based microfluidics, which is the creation and manipulation of tiny drops of fluid that range from picoliters to nanoliters in volume. These drops are created at rates of thousands per second and can be used in applications such as biomaterials, ultra high-throughput screening of bacterial biofilms and viruses, single cell genomics, and directed evolution in biology. Connie's research is funded by the Department of Defense, National Institutes of Health, and National Science Foundation.

Potential Projects:

Single cell sequencing of viral infection

Antibiotic resistance of bacterial cells

Organoid-on-chip and tissue engineering

Synergistic interactions between bacterial species in chronic wounds

Diagnostics on microfluidic chips

Valerie Copie

 

 

Photo of Valerie Copie.

Department:
Chemistry & Biochemistry

Email:
vcopie@montana.edu

Website:
https://chemistry.montana.edu/directory/1524007/val%c3%a9rie-copi%c3%a9

The research taking place in the Copié lab focuses on better understanding and identifying the metabolic pathways and cellular networks that control organisms’ responses to their environments. The biochemical approach includes application of state-of-the-art solution nuclear magnetic resonance (NMR) spectroscopy together with complementary techniques such as liquid chromatography-coupled mass spectrometry (LC-MS) to characterize the metabolomes of diverse systems in an effort to understand how metabolic changes enable different organisms to adapt to environmental stress or report on disease states. 

We welcome students to join our group in the summer and to provide an opportunity for them to learn about NMR metabolomics, how we identify metabolites from spectral patterns observed in one-dimensional 1H NMR spectra, and from these data, how we start characterizing which metabolic pathways are impacted. The lab research is highly collaborative and we welcome students who aspire to conduct interdisciplinary research bridging biochemistry, microbiology, bioengineering, and environmental sciences. 

 Potential Projects:

Identifying metabolic regulatory networks and adaptations necessary for microorganisms’ abilities to thrive in extreme environments. 

Livestock metabolomics research aimed at identifying key biomarkers of Mannheimia haemolytica infections of beef cattle, a microorganism responsible for bovine respiratory disease.  

Determining the cellular networks of gut microbiome dysfunction 

Matthew Fields

 

 

Photo of Matthew Fields.

Department:
Microbiology & Immunology

Email:
matthew.fields@montana.edu

Website:
http://www.biofilm.montana.edu/people/faculty/fields-matthew.html

The laboratory of Dr. Fields uses a combination of physiology, biochemistry, genetics, and molecular biology to better understand structure/function relationships that scale in microbiology, from cells to populations to communities and ecosystems. Ultimately, improved insight of structure/function relationships in microbial systems will allow predictive modeling as well as an understanding of design/function relationships for a variety of natural and engineered systems in different environments.  As Director of the CBE, Dr. Fields works with CBE faculty and staff to support biofilm and biosystem research, education, and outreach important to medical, environmental, and industrial systems.  To date, he has authored or co-authored 113 scientific publications, and his areas of expertise include bacterial physiology, microbial ecology, bacterial genomics, and environmental microbiology.

Potential Projects:

Low-pH, nitrate-reducing biofilms

3D printing biofilms

Phycosome biofilms

Christine Foreman

 

 

Photo of Christine Foreman.

Department:
Chemical & Biological Engineering

Email:
cforeman@montana.edu 

Website:
https://foremanresearch.com/ 

Our research group is interdisciplinary in nature, including biologists, chemists, and engineers with the common goal of exploring microbial survival and material transformations. We use a combination of field and laboratory studies, as well as approaches ranging from the single-cell to the community level to investigate ecological, physiological, and evolutionary studies of extremophiles in icy systems. Additionally, we are interested in physiological adaptations to life in extreme environments, as extremophiles are natural resources for the discovery of pigments, biosurfactants, novel enzymes and other bioactive compounds of industrial relevance.  

Potential Projects:

Image analysis using BiofilmQ 

Environmental biosurfactants 

Epigentic modifications in cold temperature microbes 

 

Robin Gerlach

 

 

Photo of Robin Gerlach.

Department:
Chemical & Biological Engineering

Email:
robin_g@montana.edu 

Website:
http://www.biofilm.montana.edu/people/faculty/gerlach-robin.html 

 

By tapping into the seemingly endless potential of microbes and biofilms to promote chemical reactions, we create solutions for societal problems, including global carbon emissions, sustainable energy production, novel biomaterial development and environmental cleanup. Our current foci are the development of biology- and geology-inspired approaches for construction, material development, environmental remediation and medicine, as well as the development of technologies for producing algal biofuels and bioproducts through the use of extremophilic algae.  

Potential Projects:

Enrichment and characterization of calcium carbonate precipitating biofilms to create novel materials and biocement.  

Screen biofilm samples from Yellowstone National Park and elsewhere for urease genes to expand the pH and temperature range of biocement production. 

Enrichment and characterization of algal-bacterial-archaeal co-cultures with high biomass productivity.  

Screen biofilm samples from Yellowstone National Park and elsewhere for communities, compounds and interactions that lead to increased biomass productivity 

Roland Hatzenpichler

 

 

Photo of Roland Hatzenpichler.

Department:
Chemistry & Biochemistry

Email:
roland.hatzenpichler@montana.edu

Website:
http://www.environmental-microbiology.com/ 

Our research activities focus on microbial ecophysiology: the study of the physiology of microorganisms with respect to their habitat. We are interested in how the activity of the “uncultured majority” – the large number of microbes that evades cultivation under laboratory conditions – impacts humans and the environment on a micron to global scale. We are convinced that only by gaining an understanding of microbes directly in their habitat researchers will be able to elucidate the mechanisms of microbial interactions with the biotic and abiotic world. To accomplish these goals, we apply an integrative approach that bridges the two extremes of the microbial scale bar: the individual cell and the whole community. We focus on understanding microorganisms directly where they live, in their natural environment (in our case, Yellowstone hot springs and deep-sea hydrothermal sediment), rather than in a beaker in the laboratory. Key approaches that students will utilize are to visualize microbes using cutting-edge microscopy techniques and study how environmental change affects microbial metabolic activity.

Potential Projects:

Metabolic activity of a hot spring microbial streamer community 

Effects of temperature extremes on the activity of hot spring archaea 

Linking taxonomic identity and anabolic activity of uncultured microbes in hot spring microbial mats. 

Brent Peyton 

 

 

Photo of Brent Peyton.

Department: 
Chemical & Biological Engineering

Email:
bpeyton@montana.edu 

Website:
https://bpeyton7.wixsite.com/website

As a chemical and biological engineer, my research is focused on characterizing microorganisms and biofilm processes in natural and engineered systems, including the discovery and growth of extremophilic microorganisms and the understanding of biofilms for NASA and space related biofilms. Some REU students that work in my lab group will characterize and grow thermophilic (heat loving) biofilms on plastics that may lead to potential strategies for renewable plastics from current wastes. My group is also interested in biofilms in space, such as biofilms in the international space station or the potential for biofilms on Mars.  RUE students have the opportunity to grow biofilms in a simulated Mars saline seep that has potential to harbor life in the short Mars “summer”.

Potential Projects:

Use biofilm microbes from Yellowstone hot springs to screen for thermophiles capable of growing on plastic wastes. Track promising cultures using microscopy, spectroscopy, and/or chromatography techniques.

Create a simulated Mars saline seep and characterize the development of psychrophilic (cold loving) and halophilic (salt loving) biofilms on and below the surface. 

Adrienne Phillips

 

 

Photo of Adrienne Phillips.

Department: 
Civil Engineering

Email:
adrienne.phillips@montana.edu 

Website:

http://www.biofilm.montana.edu/people/faculty/phillips-adrienne.html 

http://www.montana.edu/ce/directory/1524476/adrienne-phillips 

 

My research focuses on the use of bacterial biofilms for beneficial environmental engineering applications. I am inspired by nature’s ability to adapt to and thrive in extreme environments. My current interests involve the use of biofilms for development of novel materials that can be used for construction and sustainable infrastructure development (such as biological composites as alternatives to traditional cement and concrete) and environmental remediation in extreme environments such as the deep subsurface.  

Potential Projects:

Exploring the use of biofilms in subsurface applications to mitigate GHG emissions from leaking oil and gas or carbon sequestration wells  

Investigating the use of alternate biological grouting materials in cold temperature environments for frost heave mitigation 

Exploring the potential for development of biofilm-based multifunctional building or infrastructure materials  

 

Dana Skorupa

 

 

Photo of Dana Skorupa.Department:
Chemical & Biological Engineering

Email:
dana.skorupa@montana.edu

Website:
http://www.biofilm.montana.edu/people/faculty/skorupa-dana.html

My research focuses on understanding microorganisms in extreme environments and developing microbiological solutions for environmental pollutants. A focal research goal aims to grow heat-loving microorganisms (called thermophiles) capable of degrading problematic plastic wastes. Current recycling practices (if available), often involve the use of high-temperatures and harsh chemicals. The use of thermostable enzymes resistant to commonly used detergents and solvents would enhance the range of biological enzymes in industrial recycling. To this end, my work focuses on culturing thermophiles with desired functions and characterize their novel thermostable enzymes.  

Potential Projects:

Use biofilm sediment microbes from Yellowstone hot springs to screen for thermophiles capable of growing on plastic wastes. Track promising cultures using microscopy, spectroscopy, and/or chromatography techniques. 

Identify physiologically active thermophiles stimulated by plastic wastes using a novel heavy water labeling method.  

Jim Wilking

 

 

Photo of Jim Wilking.

Department:
Chemical & Biological Engineering

Email:
james.wilking@montana.edu 

Website:
https://wilkinglab.com/ 

 

We explore a diverse range of projects, most involving soft materials like hydrogels, microbial biofilms, and biological tissues. These are interdisciplinary efforts that combine engineering, physics, chemistry and biology. Lab members enjoy access to state-of-the art microscopy, 3D printing, high-speed photography and varied collaborations. 

 

Potential Projects:

3D printing of microbial biofilms for cultivating novel microbes 

High-speed imaging of noxious weed seed dispersal 

Using laser cutting to cultivate a thermophile-based microbial mat contained in a milli-fluidic device