Mentors and Projects Available

Mentors and Projects Available to Choose From Summer 2018

J. Lucas Argueso, Department of Environmental and Radiological Health Sciences 

Research Profile Webpage Link

Project Title: Gene Copy Number Variation (CNV) Mechanism of Formation

Project Description: Our research program is aimed at exploring the mutational mechanisms that cause the structure of chromosomes to change, leading to CNV formation. We use the chromosomes of yeast cells as a model system to ask questions about the fundamental mechanisms of CNV formation. We are particularly interested in investigating how mutagens present in the environment may increase the normal rate of CNV formation. Students participating in summer research will use these sensor yeast strains to test candidate environmental exposures to determine if they have CNV mutagenic activity. In cases of exposures that test positive, the students will then apply whole genome analysis methods to investigate the specific molecular mechanism through which the CNVs formed.

Learning Outcomes: Participants will gain hands on experience with the yeast model organism, whole genome analysis methods, measurement of environmental mutagenesis.

 Adam Chicco, Department of Biomedical Sciences

Research Profile Webpage Link

Project Title: Role of lipid metabolism and mitochondria in cardiometabolic disease

Project Description: Delta-6 desaturase (D6D; encoded by the FADS2 gene) is a microsomal enzyme that catalyzes rate-limiting steps in the conversion of the essential polyunsaturated fatty acids (PUFAs). Recent studies in our lab have linked D6D hyperactivity to a redistribution of PUFAs in hepatic and cardiac phospholipids in rodent models of obesity/diabetes, aging and hypertensive heart failure. REU program participants will examine the influence of D6D activity and its long-chain PUFA products on cardiovascular and metabolic function using mouse and sheep model systems.

Learning Outcomes: Participants will obtain experience working with mouse and sheep experimental systems and using multiple investigative approaches in basic and translational endocrinology and metabolism research from the subcellular to the organismal level.

Michelle T. Foster, Department of Food Science and Human Nutrition

Research Profile Webpage Link

Project Title: The Connection Between Obesity and Disease Risk

Project Description: The Foster lab currently investigates how adipose tissue distribution, the way we carry our fat, determines our metabolic outcomes using a basic research model, rodents, or cell culture. REU participants will conduct studies that look into the role of estrogen on adipose tissue function. With these studies, we will microscopically look at changes in adipose tissue morphology.

Learning Outcomes: The student will get training in current techniques relevant to obesity and rodent research. The internship will start with a relevant broad review of the literature pertinent to our area research. This will allow the student to advance knowing the purpose of their proposed research.  The participant will gain experience in handling and feeding mice, anatomy and tissue collection and adipose tissue fixation and preparation for histology.

Deborah Garrity, Department of Biology

Research Description Webpage Link

Project Title:  The Role of Cardiac Jelly in Normal Development of the Embryonic Heart

Project Description: The Garrity lab investigates the factors required for normal development of the heart in embryos using zebrafish as a model to understand genetic and biomechanical contributions to the forming heart.  The summer REU participant’s project will focus on the role that cardiac jelly (CJ) plays in cell division.  The participant will use mutants that either increase, decrease, or affect the quality of the CJ in an embryonic heart to determine if cardiac jelly promotes heart development by helping myocardial cells to divide normally. The project will compare wildtype and mutant embryos to determine if the number of myocardial cells is altered in hearts when CJ is abnormal.

Learning Outcomes: A summer REU participant will learn to breed and stage zebrafish embryos, and will be trained in confocal and dissecting microscopy, assays for cell counting, and statistical comparisons.

Shane B. Kanatous, Department of Biology

Research Description Webpage Link

Project Title: The mechanism of diving mammal skeletal muscles support of aerobic metabolism without breathing

Project Description: The overarching question in my research asks: what are the molecular pathways that regulate the specific adaptations that allow diving mammals to sustain aerobic metabolism during breath-hold exercise? An REU participant will test those compounds in terrestrial animals, to determine the appropriate combination of lipids and exercise that will improve both mitochondrial functions, oxygen stores and exercise capacity especially under hypoxic and ischemic conditions.

Learning Outcomes: The participant will develop expertise in physiological and biochemical techniques, including primary cell culture, immunocytochemical analysis, enzymatic assays, SDS-PAGE, and Western blotting. Their mentor will work with the participant to design an individual development plan describing their research, training, and career goals as well as the approaches they will take to achieve those goals and will review and revisit this plan on a regular basis.

Tai Montgomery, Department of Biology

Research Description Webpage Link

Project Title: Identification of factors that modulate small RNA activity in C. elegans

Project Description: Small RNAs are master regulators of gene expression with important roles throughout development and in disease resistance and pathogen defense. To identify factors that modulate small RNA activity, a student will do a genome-wide genetic screen for gene inactivations that affect small RNA stability. The screen will center around a strain of the nematode Caenorhabditis elegans that contains a fluorescent reporter construct for small RNA activity.

Learning Outcomes: The REU participant will gain experience in basic genetics and molecular biology laboratory methods. Additionally, the participant will gain experience doing genome-wide screens using C. elegans as a model. The student will be primarily mentored by the lab PI and will receive additional training and guidance from the lab manager and graduate students in the lab. The student will learn to keep a detailed lab notebook and report on their work during regular lab meetings.

Erin Osborne Nishimura, Department of Biochemistry and Molecular Biology

Research Description Webpage Link

Project Title: Identification of the mRNA transcripts that reside in the ribonucleoproteins (RNPs) in progenitor germline cells (that go on to produce gametes)

Project Description: The undergraduate summer research project in our lab will contribute to addressing the larger question of how progenitor germline cells (that go on to produce gametes) are distinct from other cells in the embryo. The REU participant will seek to identify mRNA transcripts that reside in the RNPs. Specifically, they will screen through a candidate list and identify those mRNAs that exhibit a clumped arrangement within germline cells of the embryo and co-localize with known RNP proteins.

Learning Outcomes: The REU participant will learn basic lab safety, lab etiquette, and best practices; worm husbandry, smFISH to visualize individual mRNAs and their locations within fixed embryos; computationally analyze their results and graphically display their findings.

Kenneth Reardon, Department of Chemical and Biological Engineering

Research Description Webpage Link

Project Title: Optimization of Carbon Conversion Efficiency through Fermentation by Yeast Cells for Biofuel Production

Project Description: We are developing an advanced fermentation process for the conversion of algal hydrolysates to two biofuel products, ethanol and 2,3-butanediol. The goal is to increase the productivity and carbon conversion efficiency of the fermentation process.  The summer REU participant will culture the yeast used for the bioconversion, and perform fermentation experiments to determine the rates of biofuel production, the influence of temperature and pH, and the amount of solid material in the hydrolysate that can be tolerated.

Learning Outcomes: The participant will learn basic lab safety, lab etiquette, and best practices; learn to cultivate baker’s yeast, Saccharomyces cerevisiae; become trained in the use of fermenters; learn to use a liquid chromatograph and other analytical equipment; learn conduct fermentation experiments, analyze data and draw conclusions.

Tom Santangelo, Department of Biochemistry and Molecular Biology

Research Description Webpage Link

Project Title: Identification and Characterization of the Enzymes Involved in Archaeal Lipid Biosynthesis

Project Description: In contrast to the fatty acid-based lipids used by bacteria and eukaryotes, all archaeal membranes are composed exclusively of isoprenoid-based lipids. The project involves a combination of genetic and biochemical approaches. You will generate strains of our model archaeon, Thermococcus kodakarensis, wherein genes proposed to be involved in the mevalonate pathway are targeted for deletion. You will also clone, recombinantly express, purify, and then characterize enzymes predicted to be responsible for production of isopentyl-diphosphate (the end product of the mevalonate pathway).

Learning Outcomes: You will be trained in aerobic and anaerobic microbiological techniques, proper handling of hyperthermophiles, complete in-lab training regarding safe practices with anaerobic chambers, complete hazardous waste and radioisotope training, and master many modern molecular biology techniques. You will directly participate in cloning, sequencing, and protein purifications, and use spectrophotometric and TLC-based assay to characterize purified enzymes.

Christopher Snow, Department of Chemical and Biological Engineering

Research Description Webpage Link

Project Title: Designing and testing self-assembling crystals composed of both protein and DNA building blocks

Project Description: This project aims to realize one of the most transformative goals of nanotechnology – the ability to engineer complex macroscopic materials in which the constituent atoms are nonetheless positioned precisely. Precise control of the 3-D position of functional molecules will open the door for materials with unprecedented performance for diverse applications. The REU program participant will produce and analyze new self-assembling protein/DNA crystals. For more details, check out the project explanation video at csubiomod.com.

Learning Outcomes: The REU participant will gain skills include cloning, expression, chromatographic purification, and crystallization. Additionally, the participant will learn how to computationally model DNA assembly using the coarse-grained simulation software oxDNA.  Science communication skills and teamwork skills will also be developed.