Summer Research Program Mentors & Projects

Laura Hernandez, Professor of Animal and Dairy Science

The overall goal of the Hernandez lab is to understand how autocrine/paracrine factors in the mammary gland regulate mammary gland development as well as milk synthesis and secretion. They utilize a combination of in vitro and in vivo models with a variety of mammalian species (mice, cattle, humans) to understand how the mammary gland and the mother adapt to lactation. They also utilize a combination of molecular and whole animal physiological techniques to understand mammary gland physiology.

Projects
Students will investigate the determination of the effects of SSRIs on mammary gland and placental development using immunohistochemistry and quantitative PCR.

Hernandez Lab

Briana Burton, Associate Professor of Bacteriology

The Burton lab is interested in the mechanisms that bacterial cells use to transport biological macromolecules such as nucleic acid and protein across membrane barriers. Under stress conditions such as high cell density or limited nutrient availability, many bacterial species become "naturally competent," or capable of importing DNA from their surrounding environment.

Projects
Students will compare the responses of wild type and mutant strains of competent bacteria under different nutrient limitations and cell densities where resource competition is increased. Students will learn how to (1) prepare donor DNA and perform standard microbiology techniques including transformations and culture plating to study efficiency of DNA transfer; (2) isolate colonies and purify genomic DNA to submit for whole genome sequencing; (3) analyze genomes of their transformed cells to learn about the molecular mechanisms that drive genome changes during this natural cellular transformation.

Burton Lab

Jade Wang, Professor of Bacteriology

Bacterial stress responses allow cells to survive fluctuating environments, antibiotic treatments, and host defenses. While the transcriptional and post-transcriptional networks governing stress responses have been characterized extensively, there are major gaps in our knowledge beyond transcription regulation. The Wang lab seeks to answer the following fundamental questions: How do bacteria utilize stress-induced small molecules to adapt to their specific environmental niches? How do bacteria enter a metabolically dormant persister state that is intrinsically tolerant to a broad array of antibiotic treatments? How do stressed bacteria mitigate potential conflicts between their DNA replication and transcription machineries to ensure survival? What are the molecular mechanisms of bacterial evolution to fit their specific niches?

Projects
The student will investigate how the stress signaling nucleotide ppGpp allows bacterial stress adaptation using bacterial genetics and biochemical approaches.

Wang Lab

Erica Majumder, Assistant Professor of Bacteriology

The Majumder lab employs ‘omics’-guided biochemistry to study the mechanisms and consequences of microbial inorganic metabolisms on environmental and human health. They achieve this by investigating organismal response to perturbations in its environment, gene and metabolite function in situ, and environmental applications of novel microbial chemistries.

Projects
Students will work to identify a community of landfill-derived microorganisms (fungi and bacteria) that can consume stressful carbon sources such as plastics and determine how metabolism is carried out across species. The student will isolate genomic DNA and perform whole genome sequencing to identify the organisms; (2) perform a time series growth experiment comparing a plastic-metabolizing community to a sugar-metabolizing community; and (3) conduct meta-transcriptomics and metabolomics to assess community changes and differential utilization of metabolic pathways.

Majumder Lab

Megan McClean, Associate Professor of Biomedical Engineering

Cells must sense and process diverse stimuli in order to survive and thrive. The McClean research group takes a bioengineering approach to answering fundamental and medical questions about biological signal processing with an emphasis on model and pathogenic yeasts.

Projects
Students will identify stressors and nutrient signals that regulate dispersion from Candida albicans fungal biofilms by using light microscopy, sterile technique, ImageJ image processing, underoil microfluidic device creation, and gene expression analysis.

McClean Lab

Katherine Henzler-Wildman, Professor of Biochemistry

The Henzler-Wildman lab investigates how bacteria respond to external toxins, including antibiotics. The lab is especially interested in how multidrug efflux pumps work in different ways in response to different small molecule toxins and how the toxin and the drug pump activity affects bacterial metabolism.

Projects
Students will work with E. coli and in vitro liposomal assays to test specific mechanistic hypotheses related to multidrug efflux pumps including microbiology drug resistance and susceptibility, NMR and/or mass spec metabolomics, functional assays to monitor the proton motive force, ATP production and NADH production in response to toxin exposure.

Henzler-Wildman Lab

Melissa Harrison, Professor of Biomolecular Chemistry

During development, the single-celled zygote divides and differentiates into all the cells of the adult organisms. All of these resulting cells have distinct forms and functions, but possess nearly identical DNA genomes. In the Harrison Lab, we are interested in understanding how this common genome is differentially interpreted over development to give rise to the numerous distinct cell types of the adult and how dysregulation leads to disease.

Projects
Students will leverage the powerful toolbox available for studies in the fruit fly, Drosophila melanogaster, including molecular, genetic, genomic and imaging strategies, to determine how specialized transcription factors regulate conserved developmental transitions.

Harrison Lab

Robert Kirchdoerfer, Assistant Professor of Biochemistry

The Kirchdoerfer lab studies how coronaviruses enter cells and how they replicate their genomes once inside. During infections of cats with feline coronavirus, the virus coevolves with the host because of stresses due to the antibody response. This coevolution may result in altered pathogenicity of the virus infection, leading to fatal outcomes. The lab uses a multipronged approach to analyze both evolution of the virus and host antibody response using next-generation sequencing, antibody binding, and structural biology.

Projects
Students will compare sequences from closely related viruses sampled from different sites and between cats and map antibody epitopes in cat sera to establish a molecular basis for the evolution of pathogenicity for feline coronaviruses.

Kirchdoerfer Lab

Aaron Hoskins, Associate Professor of Biochemistry

From gene expression to cell division to moving a cell from here to there, biological life has evolved to depend on macromolecular machines made of many biomolecules working together to fulfill specific functions. The Hoskins lab seeks to understand how these machines assemble from their individual components in vitro and in vivo. The Hoskins lab primarily studies the eukaryotic spliceosome—a highly conserved machine composed of 5 snRNAs and about 100 proteins found everywhere from S. cerevisiae to H. sapiens.

Projects
Students will explore how mutations in a yeast protein change gene expression in response to oxidative stress using a variety of techniques including yeast molecular genetics, phenotyping, growth assays, CRISPR, and redox chemistry.

Hoskins Lab

Christina Hull, Professor of Biomolecular Chemistry

Spores of the human fungal pathogen Cryptococcus neoformans must resist extreme stressors to survive in the environment and in mammalian hosts. During the sexual cycle, C. neoformans grows as a unicellular budding yeast and switches to multicellular hyphal growth, which is important because spores resulting from sexual development are more resistant to stress than yeast. To identify potential fungal responses to increasing global temperatures, the Hull lab is adapting attenuated laboratory strains (wild type and selected gene knockout strains) to increasing temperatures during vegetative growth.

Projects
Students will evaluate the resulting temperature adapted strains and their spore progeny for fitness in an array of phenotypic, cellular, and molecular assays to determine the effects of adaptation to temperature stress on cellular responses, including pathogenesis.

Hull Lab

Marisa Otegui, Professor of Botany

The Otegui lab studies membrane trafficking pathways that regulate protein degradation and stress responses. Plants are exposed to drastic changes in their environment that require continuous adjustment of the composition of their cell surface as well as the number and type of organelles. More specifically, endosomal trafficking and autophagic recycling control many aspects of stress responses, development, and nutrient utilization in plants. In addition, the Otegui lab studies cellular adaptation and membrane protection mechanisms in cells undergoing extreme desiccation, such as seeds and pollen grains. The lab seeks to understand how membrane remodeling and trafficking affect plant development and stress responses, using a combination of light and electron microscopy 3D imaging, genetics, biochemistry, and molecular biology.

Projects
Students will explore a) cellular mechanisms that confer membrane and organelle protection during desiccation and drought, and b) endosomal proteins that control fundamental developmental and stress response processes.

Otegui Lab

Silvia Cavagnero, Professor of Chemistry

The Cavagnero Lab studies protein folding and aggregation in the cell, and their implications for bacterial mechanisms and population control, large-scale production of low-cost protein-based pharmaceuticals, and human health. The lab focuses on events related to protein birth, including interactions of nascent chains with the ribosome and molecular chaperones.

Projects
The available summer project focuses on reprogramming the bacterial ribosome via genetic recombineering and chaperone engineering for the production of soluble proteins devoid of inclusion-body formation upon release from the ribosome. The research involves learning recombineering, protein expression/purification, and biophysical methods including fluorescence imaging/spectroscopy and dynamic light scattering.

Cavagnero Lab

Fei Zhao, Assistant Professor of Comparative Biosciences

The Zhao Lab aims to understand cellular and molecular mechanisms underlying sexual differentiation of reproductive tracts. Disruptions in reproductive tract differentiation can lead to disorders of sex development and jeopardize an individual’s future reproductive potential. Our research will provide fundamental knowledge for the development of better strategies for prevention, diagnosis, and treatment of related disorders of sex development and reproductive diseases.

Projects
Students will explore how male steroid hormones regulate male reproductive tract development and functions using transgenic mouse models.

Zhou Lab

Kavi Mehta, Assistant Professor of Comparative Biosciences

The Mehta lab is interested in undertaking how the replication stress response and mutagenic potential are regulated in the presence of both endogenous and environmental genotoxins, including industrial chemicals and viruses. The lab uses large-scale unbiased proteomics, longitudinal whole genome sequencing, basic microbiology, and single-molecule assays to answer these questions.

Projects
We are interested in knowing how specialized and mutagenic polymerases are regulated. A potential summer project would be investigating how putative regulatory motifs within TLS polymerases regulate them.

Mehta Lab

Andrea Galmozzi, Assistant Professor of Endocrinology, Diabetes & Metabolism

Research in the Galmozzi Lab aims to identify functional pathways in adipocytes amenable to pharmacological modulation. This work may lead to the development of novel and safer interventions to treat metabolic disorders, including obesity, type 2 diabetes and cachexia.

Projects
Current projects ongoing in the lab focus on understanding the contribution of heme biosynthesis to brown adipose tissue function, determining the role of lipid cycle on systemic energy homeostasis, and dissecting the crosstalk between cancer cells and adipose tissue.

Galmozzi Lab

Sean Schoville, Associate Professor of Entomology

The Schoville lab focuses on species diversity, determining the role of ecological and evolutionary processes in generating this diversity, and developing management and conservation strategies that incorporate these processes. The lab develops and applies genetic approaches to address research questions, often integrating spatial environmental data, ecological studies, physiological experiments, and morphological variation.

Projects
Students will investigate how alpine beetles respond to short-term stress and evolve in response to long-term environmental change through physiology experiments, protein assays, RNA extraction, and gene expression analysis.

Schoville Lab

Jessica Hua, Associate Professor of Forest and Wildlife Ecology

Natural ecosystems encounter a diversity of challenges in the face of global change, from pollutants to habitat change to shifting climates. Studies evaluating general mechanisms for how organisms across taxa adapt to these diverse local changes have broad implications for developing a theoretical understanding of how organisms respond to global change. The Hua lab investigates the costs to organisms associated with adapting (i.e., pollutant tolerance may lead to tradeoffs with other stressors, such as disease).

Projects
Students will (1) conduct an ecotoxicological assay to identify populations of amphibians that vary in tolerance to a pollutant (e.g., sensory or chemical pollutants), (2) conduct a disease assay to determine if tolerance to the pollutant influences tolerance to the diseases, and (3) conduct high-throughput RNA sequencing to identify mechanisms by which tolerance to pollutants influences tolerance to disease.

Hua Lab

Jacob Brunkard, Assistant Professor of Genetics

Plants dynamically adjust their development to devote resources to support new growth or to defend existing tissues from environmental stress. The Brunkard lab studies the target of rapamycin (TOR), a conserved eukaryotic serine/threonine kinase that monitors conditions, including nutrient availability and environmental stress, to coordinate growth and metabolism.

Projects
Students will test how mutants defective in TOR signaling respond to environmental stresses, such as nutrient deprivation and/or toxicity. Students will grow maize seedlings supplemented with defined “fertilizer” media with a range of nitrogen concentrations and then analyze for TOR signaling outputs, such as changes in phosphorylation of TOR substrates (by Western blot), mRNA levels of TOR-regulated genes (by RT-qPCR), growth rates (using time-lapse imaging), and chlorophyll concentrations (by spectrophotometry). Additional students might test other stresses, such as low/high light, drought/flooding, chilling/heat, etc., and then measure the same outputs.

Brunkard Lab

Christopher Hittinger, Professor of Genetics

The Hittinger lab studies the evolutionary genomics of yeast carbon metabolism, including in stressful environments encountered during the production of sustainable biofuels, bioproducts, and fermented food and beverages.

Projects
Students will compare how diverse yeast species respond to ecologically relevant stresses, especially in the context of temperature, carbon source, or reactive oxygen species. They will use microbiological, molecular genetics, and bioinformatic research methods.

Hittinger Lab

Nathaniel Sharp, Assistant Professor of Genetics

Mutation is the source of all genetic variation, and is critical for evolution. Despite its importance, we still have a lot to learn about mutation. Why does the rate of mutation vary among species, genotypes, and genome architectures? What makes some sites in a genome more susceptible to mutation than others? How do the rate and fitness consequences of mutations vary across environments? What drives the evolution of the mutation process itself? The Sharp lab studies both single-nucleotide changes and the wide spectrum of structural alterations that can dramatically alter genetic structure, promote adaptation, or lead to disease.

Projects
Students will investigate the impact of oxidative stress on the mutation rate and structural alterations in the yeast genome. Students will learn aseptic technique, basic microbiology, and yeast genetics.

Sharp Lab

Audrey Gasch, Professor of Genetics

The Gasch lab uses genomics and systems biology to understand principles of stress-resistance, genetic variation in environmental responses, and evolution of stress defense systems. The lab’s analyses of salt-induced stress in yeast (S. cerevisiae) indicate that fast growing cells tend to be more susceptible to stress than slow growing or quiescent cells and that transcription networks are central to adaptation to salt stress.

Projects
Students will compare stress tolerance across natural strains of budding yeast S. cerevisiae. Their projects will compare growth rates and/or viability in yeast responding to stresses including sodium chloride, heat shock, reductive stress, and other compounds different yeast lineages may see in nature. After characterizing natural variation in stress tolerance, students will use RNA sequencing transcriptomics and genetic mapping to understand the genetic basis of those differences.

Gasch Lab

Claire Richardson, Assistant Professor of Genetics

Aging is the principal risk factor for cognitive decline and neurodegenerative disease. From worms to humans, neuronal aging is associated with decay in cellular function and increased risk for disease pathologies. The Richardson lab aims to understand the fundamental cell biology underlying neuronal aging, which will lead to strategies for intervention.

Projects
Students will investigate how C. elegans cells regulate the rate of protein degradation during adult homeostasis by using genetic crosses, confocal microscopy image acquisition and analysis.

Richardson Lab

David Wassarman, Professor of Medical Genetics

The Wassarman lab developed a Drosophila melanogaster model to study mechanical injury stress to the brain (i.e., traumatic brain injury (TBI)). Their studies suggest that lipid droplet metabolic pathways protect neurons from degeneration following TBI. Lipid droplets are organelles that compartmentalize cytosolic lipids for storage of energy and protection from toxic effects of excessive and damaged lipids.

Projects
Students will use confocal microscopy and metabolite detection assays in flies carrying loss-of-function and gain-of-function mutations in mitochondrial electron transport chain (mETC) genes to assess the necessity and sufficiency of mETC inhibition for lipid droplet formation and neuroprotection following TBI.

Wassarman Lab

Paul Hanson, Distinguished Research Professor of Freshwater Science

The Hanson team studies how climate change, land use, and human activity impact our lakes, as well as the ways in which big data and team science are shaping freshwater research. By measuring lake water quality and running computer simulations of lakes, they seek to understand the changes needed to improve the quality of freshwater, and they use artificial intelligence (AI) techniques to apply their insights to lakes around the world.

Projects
Students will measure water quality on Madison-area lakes, using standard limnological techniques. Measurements will be combined with computer simulations and images from airborne cameras to understand how water quality changes through the summer. Students will learn how their predictions of water quality might be improved through the application of artificial intelligence.

Hanson Lab

Randy Kimple, Associate Professor of Human Oncology

Projects
Students will use cell culture, clonogenic survival, and organoid models of cancerwork to investigate questions such as: 1) how do mesenchymal stromal cells repair radiation induced damage to the salivary gland; and 2) does inhibition of the MET receptor synergize with a novel targeted radionuclide therapy in treatment of lung cancer?

Kimple Lab

Aussie Suzuki, Assistant Professor of Oncology

The Suzuki Lab is at the forefront of biomedical research, focusing on three critical areas: (1) unraveling how cells prevent chromosomal instability to avert cancer development; (2) elucidating the mechanisms by which Human Immunodeficiency Virus 1 (HIV-1) manipulates the host cell cycle; and (3) dissecting the processes involved in the production of Epstein-Barr Virus (EBV) virions during the lytic phase. Despite the diversity of these research area, the Lab's advanced expertise in fluorescence microscopy serves as a unifying foundation, enabling deep insights and significant advancements in understanding complex biological systems.

Projects
Students will explore the mechanisms underlying chromosomal instability, a driving factor in carcinogenesis and developmental disorders. They will gain proficiency in (1) fundamental cell biology techniques; (2) advanced imaging methods, including super-resolution microscopy; and (3) quantitative image analysis, laying a strong foundation for careers as cell biologists.

Suzuki Lab

Kinjal Majumder, Assistant Professor of Oncology

The Majumder Lab studies how small DNA viruses navigate the nuclear environment, establishing themselves for long-term persistence or inducing host genome instability. These infection outcomes are important for engineering oncolytic virotherapies, gene therapy vectors, and understanding how oncogenic viruses cause cancer.

Projects
Students will investigate how viral infection induces cellular DNA breaks on the host genome using comet assays and confocal imaging. They will build skills in performing tissue culture, molecular virology, CRISPR-mediated genome editing, imaging, and data analysis.

Majumder Lab

Jason Peters, Assistant Professor of Pharmaceutical Sciences

The Peters lab uses the power of bacterial genetics and CRISPR-based functional genomics approaches to define the roles of gene networks important in the process of using microbes to convert plant material into valuable biofuels and bioproducts as well as in antibiotic targeting and resistance. We are currently developing innovative CRISPR tools for exploration of gene function in bioenergy-relevant alpha-Proteobacteria (e.g., Zymomonas mobilis) and antibiotic resistant ESKAPE pathogens (e.g., Acinetobacter baumannii).

Projects
Students will use CRISPR-based genetic analysis in alphaproteobacteria to improve biofuel and byproduct yields.

Peters Lab

Emile Gluck-Thaler, Assistant Professor of Plant Pathology

The Gluck-Thaler Lab investigates the genetic bases of fungal pathogenesis by integrating computational biology with molecular genetics and evolutionary data science. Our research is centered on answering two main questions: when do “good” fungi turn “bad,” and how do fungi learn new tricks for causing disease? We answer these questions by looking not only at how fungi interact with their hosts, but how fungi interact with giant transposons called Starships that are hidden within their genomes and have outsized impacts on adaptation. 

Projects
Students will explore how the activity of Starship transposons impacts important fungal phenotypes related to stress, antifungal resistance, and pathogenicity by coupling genetic transformations, competition assays, and bioinformatic analyses of DNA and RNA sequencing data. 

Emile Gluck-Thaler

Aurélie Rakotondrafara, Associate Professor of Plant Pathology

The Rakotondrafara lab studies Sclerotinia sclerotiorum, a pathogen that infects a broad range of economically important crops and is notable for its persistency in the environment. This fungus is necrotrophic, that is, it needs to kill the plant to consume nutrients from the dead tissues. With the limited number of genetically resistant cultivars, disease management strategy relies heavily on fungicide use. The lab aims to identify alternative strategies to combat this devastating disease using mycoviruses for sustainable fungal disease control. One focus it identifying the mechanism underlying the viral encoded replication-associated protein (REP) interference of the normal growth of the fungus and its pathogenicity.

Projects
Students will study the cellular stress responses at the transcription level in the fungus upon exposure to REP and dissect whether the function of REP in viral replication is necessary for the hypovirulence effect.

Rakotondrafara Lab