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. Caetano Antunes

Microbiome-host-pathogen interactions

In the Antunes Laboratory, we are broadly interested in the roles played by small molecules during host-microbiome-pathogen interactions. To date, we have focused on the impact of microbiome-derived small molecules on enteric pathogen behavior. We have previously shown that the human gut harbors thousands of small molecules, most of which are yet to be identified. Organic extracts of human feces have been used to determine pathogen responses to the chemical milieu of the human gut. Our results show that multiple enteric pathogens, such as Salmonella enterica, Vibrio cholerae, and Clostridioides difficile display marked transcriptional responses to the human gut metabolome, and that genes required for host interactions are modulated. Bioactive microbiome members and compounds can be identified, and our ongoing work is focused on identifying novel compounds and revealing the molecular mechanisms behind bioactivity.

Dr. Justin Blumenstiel

How the genome responds to genomic shock

A key challenge of the cell is to maintain genome integrity across generations. However, selfish DNA elements known as transposable elements can thwart genome stability by causing damage. In the 1940's Barbara McClintock showed that DNA damage had the capacity to trigger genomic shock and the mobilization of transposable elements. However, to this day, we do not understand how this occurs. We are currently investigating how the genome responds to rampant transposable element mobilization and how epigenetic mechanisms based on small RNA regulate genome stability.  The REU student will have a choice of projects examining epigenetic silencing by piRNAs, the influence of DNA damage on transposable element activity and the evolution of mechanisms that ensure the stability of the genome.

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

Temperature stress and mating success

Temperature affects the ability of cold-blooded animals to perform behaviors. Temperature also affects developmental pathways, thus the environment experienced early in life can affect behavior as an adult. If an animal is unable to perform a courtship behavior correctly, this can result in diminished reproductive success. The REU student will have a choice of projects examining the interactions among development temperature, performance temperature, and mating success in a Drosophila species.

Dr. Roberto De Guzman

Structural studies of bacterial virulence proteins 

Many bacteria assemble a protein delivery nanomachinery known as the type III secretion system (T3SS) needle apparatus to inject bacterial virulence proteins into host cells, causing modulations in host cell biology, alterations in developmental profiles, and stress to the organism. Our overall goal is to determine in atomic detail the protein-protein interactions involved in the assembly of the needle apparatus. REU students will test hypotheses on the structure/function of protein interaction sites that are critical for virulence. Typical REU projects involve addressing questions about how the different proteins that assemble into the needle apparatus fit together and how they can be disrupted with small molecules. Projects therefore involve protein expression, mutagenesis, and characterization of proteins by biophysical methods such as NMR, fluorescence and CD spectroscopies. REU students learn how to express and purify recombinant proteins, characterize their structures, and investigate how they interact with other proteins or small molecule ligands.

Dr. Tony Fehr

Role of ADP ribosylation in viral infections

ADP-ribosylation is a stress-related post-translational modification that acts as a host defense mechanism in mammals by restricting virus replication, for example. ADP-ribosylation leads to stress granule formation, correlating with a block in viral translation. All coronaviruses, including SARS-CoV-2 and MERS-CoV, encode a macrodomain enzyme that can erase ADP-ribosylation. The macrodomain is essential for CoV-associated disease in animal models, yet how the enzyme impacts virus replication and the precise residues that contribute to enzymatic activity are unknown. After discussing/ reading about the structure of CoV macrodomains, the REU student and I will identify potentially functional residues and develop a set of mutations for hypothesis testing. This work will help us better understand macrodomain biochemistry and ADP-ribose removal from proteins, and how this biochemistry relates to virus replication and cellular stress responses. The student will learn methods pertaining to biochemistry, molecular biology, and virology, including cell culture, plaque assays, and bacterial genetics. They will also use state-of-the-art software to analyze protein

Dr. Rosana Barreto Rocha Ferreira

Microbiome functions

My laboratory focuses on understanding how the skin microbiome protects humans and animals against skin infections and how different species interact in the microbiome. Specifically, we investigate both antagonistic and beneficial bacterial interactions to better understand how microbiome composition is established in different hosts and how it protects us against infections. REU students in my lab will gain experience in microbiology and molecular biology techniques, biofilm formation, adhesion and invasion assays, and characterization of new bioactive molecules.

Dr. Scott Hefty

Host pathogen interactions

Chlamydia are obligate intracellular bacteria phylogenetically distant from other model system bacteria. We focus on understanding the developmental processes that maintain their unique bi-phasic developmental cycle.  How the organism interacts and manipulates a eukaryotic host cell and triggers or avoids stress responses is still poorly described. Students are taught the theory and techniques for working with Chlamydia as more specific research questions are presented to them. They are provided with supporting literature and discussions to enable us to develop a testable hypothesis for their project. Together, experiments are then designed as we discuss the most robust and rigorous approaches and considerations. These projects often involve molecular biology and genetics approaches that are amenable to shorter term (summer) efforts, and can include reporter gene expression analyses, protein interactions and site-directed mutagenesis, and protein functional analyses.

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 recognizable genes, most organisms have transposons in their genomes.  Transposons are DNA-encoded sequences that are reminiscent of viruses in that they are both invasive genomes  that occupy our cells.  When transposon mRNA is expressed, the corresponding transposase protein catalyzes the ability of transposon sequences to “jump” (cut/paste, or copy/paste) around the genome.  This can cause DNA breakage and new mutations, as when transposon DNA inserts into existing genes.  Transposon gene expression is thus a form of genomic stress that can result in cell death.  Transposon gene activation is also associated with highly aggressive cancer cells, which often have grossly rearranged genome sequences.  Fortunately, epigenetic silencing mechanisms have evolved to silence transposon sequences .  Many details of these silencing mechanisms have been described, but we are particularly interested those epigenetic that silence transposons  during unfavorable dietary or environmental conditions.  We use Caenorhabditis elegans  because we can easily manipulate the environment and diet, as well as explore the effects of mutations in specific genes.    Students may select projects that employ molecular biology or genetics during their analysis of gene silencing mechanisms or projects that involve phenotypic analysis of C. elegans tester strains reared under different environmental/dietary conditions.

Dr. Jamie Walters

Sex chromosomes and sex-specific aging in moths

Research in the Walters lab focuses on evolutionary genomics of Lepidoptera (moths and butterflies). In particular, we research how sex chromosomes evolve, and how they contribute to differences between sexes. One current area of focus is sex-differences aging: in many animals, one sex lives longer than the other, but whether – and why – males or females are longer-lived is highly variable across species. Walters lab REU students will join this research effort and participate in a “bonus” virtual REU program organized by the IISAGE consortium, alongside the KU programming. In lab, students may run lifespan experiments with live moths and also work to analyze genomic data (e.g. RNA-seq or ATAC-seq) addressing sex-differences in longevity and/or sex-chromosome content and evolution. Students with bioinformatics & programming experience (e.g. Unix, R, Python) are particularly encouraged to apply.