Faculty Mentors and Projects

Dr. Brian Ackley

Physiological resistance to pathogens

C. elegans are natural bacterivores, and often encounter and ingest pathogens during feeding. We have been working to understand the physiological mechanisms that the C. elegans host engage when infected, and working to understand how genetic variation in C. elegans and related nematodes alters resistance. We do this with a combination of phenotyping and genomic/transcriptomic analysis. I have developed a work-flow for visiting undergraduate researchers to participate in this project. The goal is to engage them in understanding pathogen resistance and genetic diversity. Students will learn to work with C. elegans, do genetic crosses, test survival in response to pathogens and also work on analyzing DNA and RNA using Next Generation Sequencing approaches. 

Dr. Emily Beck

Evolutionary models of mitochondrial variation

Mitochondria are essential for the maintenance of many cellular processes including energy production and regulation of the cell cycle, cell death, and the inflammatory response. When mitochondria don’t function properly this can lead to neurodegenerative diseases like Parkinson’s Disease, ALS, or MS or age-related cognitive decline like that found in Alzheimer’s Disease. My laboratory develops evolutionary mutant models (EMMs) to overcome technological hurdles associated with the study of mitochondria. EMMs are animals that have evolved something advantageous that in a humans would cause disease. These animals have essentially evolved their own therapies to mitochondrial disorders. In the lab, we use them to ask “What are these animals doing right that humans are doing wrong?” & “Can we copy them to develop therapeutics for disease?” My lab focuses on two EMMs. Threespine stickleback fish which have evolved extreme levels of variation in their mitochondrial genomes and Antarctic icefish which have structurally modified their mitochondrial genomes to survive in extreme conditions. Existing projects focus on the role genetic variation among individuals plays in mitochondrial function and disease, the environmental drivers of mitochondrial stress, and searching the genomes of these unique animals to find gene therapy targets for Alzheimer’s Disease.

Dr. Josephine Chandler

Communication and cooperation in bacteria

Bacterial quorum sensing systems are important for group activities and activated when the population reaches a critical cell density or “quorum.” Our lab is focused on understanding how bacteria use quorum sensing to compete with other microbes in multispecies communities.  Competition often involves control of toxin production or toxin resistance factors that defend against toxins to permit growth under toxin stress. Students in our lab will gain skills in bacterial genetics, antibiotic discovery and mechanisms of antibiotic resistance. Students will also learn about the process of hypothesis development, scientific discovery, communicating science and how to read and interpret scientific literature.
 

Dr. Jae Young Choi

Telomere and stress in plants

How does the chromosome respond to stressful environment? My group uses the plant species Monkeyflower (Mimulus) to answer this question and specifically we are interested in understanding how the telomeres respond to environmental stress. Telomeres have a crucial role of protecting chromosome ends from damage. In this project the student will conduct an experiment on different Mimulus species under environmental stress and test the changes occurring the telomere. Student will investigate how the stress can could influence the length of the telomere (i.e. whether it deteriorates the telomere) and if telomere maintenance pathway genes are mis-regulated under stress. Results will determine the biological link between the telomere and stress response in plants.

Dr. Jennifer Gleason

Developmental stress and behavior

The environment experienced early in life can affect behavior as an adult. Both food availability and temperature affect how large Drosophila are as adults. Size affects both mating success and fighting ability.  The REU student will have a choice of projects examining the interaction between developmental conditions (food availability or temperature) and behavior (courtship or aggression) in a Drosophila species.

Dr. Allie Graham

Odorant/olfactory receptors and high-altitude environments

The Graham Lab is interested in how various organisms respond to low-oxygen stress (i.e. hypoxia), especially in high-altitude locations like mountains. We use large sequencing datasets (transcriptomic, genomic) and physiological measurements to understand which mechanisms are in use, and whether there are common features between them. Recent work from our lab has shown a surprising link between organisms invading mountain locations, and changes to their odorant/olfactory receptors. In this project, using Drosophila, a student will get experience using bioinformatics to process large-scale genomic sequence, and measuring hypoxia-tolerance using micro-respirometry.

Dr. Lynn Hancock

Carbon catabolism in Enterococcus faecalis

As a successful pathogen, Enterococcus faecalis must adapt to the stress of residing in a mammalian host.  The host physiology creates a restrictive environment for bacterial cell growth, as nutrients, including preferential carbon sources (glucose) are rate-limiting for growth.  We identified the central pathway by which glucose enters E. faecalis.  Blocking this pathway results in hyperactivation of the carbon catabolite response—a response dependent on CcpA, a transcriptional regulator.  We identified the E. faecalis CcpA regulon through transcriptomic profiling, as well as carbon responsive elements bound by CcpA.  Over 100 genes are differentially expressed in response to glucose limitation.  After performing bioinformatics on candidate genes to predict function and discussing/reading various papers on the topic of carbon source utilization, the REU student and I will develop a testable hypothesis related to a chosen gene to elucidate its contribution to adapting to host nutrients, including glycoproteins and glycosaminoglycans. The student will develop critical thinking skills and hands-on technical skills in genetic analysis of a bacterial pathogen.
 

Dr. Scott Lovell

Structural biology of proteins from pathogenic organisms

X-ray crystallography is a technique used to provide essential high-resolution structural information for researchers studying various proteins. Details that can be obtained from an experimental protein structure determination include metal binding characteristics, protein-protein interactions, protein-ligand interactions and inhibitor binding modes. Our laboratory uses structural biology methods to obtain mechanistic/functional insight of proteins and to support projects focused on drug development. Students will learn the techniques utilized in protein expression/purification, protein crystallization, X-ray diffraction data collection, structure solution/refinement and structure analysis. These methods will be applied to projects that include select proteins from bacterial pathogens to the development of inhibitors targeting the main proteases of the MERS-CoV and SARS-CoV-2 coronaviruses

Dr. Lisa Timmons

Stress and transposon silencing

In addition to well-characterized genes, most organisms harbor transposons within their genomes. Transposons are DNA sequences that are reminiscent of viruses in their capacity to act as invasive genomic elements persisting within host cells. When transposon mRNA is expressed, the encoded transposase protein enables the mobilization of transposon sequences through “cut-and-paste” or “copy-and-paste” mechanisms. This mobility can lead to DNA damage and can generate new mutations, particularly when transposons integrate into functional genes. As a result, transposon activity imposes genomic stress that can culminate in cellular dysfunction or death.  Transposon activation is notably associated with highly aggressive cancer phenotypes, often characterized by extensive genomic rearrangements.  To counteract these threats, organisms have evolved robust epigenetic silencing mechanisms that suppress transposon expression. While many aspects of these pathways are well-characterized, our research investigates how dietary and environmental conditions influence epigenetic mechanisms regulating transposon activity and how such regulation can be disrupted under unfavorable conditions.  We utilize Caenorhabditiselegans as our primary tool for exploring environmental and dietary influences on transposon activity due to its suitability for environmental and dietary manipulation and its genetic tractability. Student projects may involve molecular biology, genetic, or computational approaches to explore transposon silencing mechanisms or phenotypic analyses of C. elegans strains cultured under diverse environmental and dietary conditions.

Dr. Rob Unckless

The evolution of stress from inside the cell

One of the fundamental tenets of genetics is Mendel’s Law of Equal Segregation, which assures that different alleles have an equal chance of making it into gametes. This is easy to see when the alleles determine biological sex: a male with an X and Y chromosome usually produces sperm that are 50% X and 50% Y and therefore has 50% daughters and 50% sons. Surprisingly, however, this law is broken again and again across a diverse set of organisms. Some chromosomes (usually the X) are able to kill sperm bearing the opposite chromosome (usually the Y) leading to biased sex-ratios that are as much as 100% daughters. We use genomic, genetic and cytological approaches to study how “sex-ratio meiotic drive” evolves and its genetic basis. REU students could be involved in genomic analysis, cytological analysis, or field collections.