Design2Data
Ashley Vater, University of California-Davis
The D2D program is centered around an undergraduate-friendly protocol workflow that follows the design-build-test-learn engineering framework. This protocol has served as the scaffold for a successful undergraduate training program and has been further developed into courses that range from a 10-week freshman seminar to a year-long, upper-division molecular biology course. The overarching research goal of this CURE probes the current predictive limitations of protein-modeling software by functionally characterizing single amino acid mutants in a robust model system. The most interesting outcomes of this project are dependent on large datasets, and, as such, the project is optimal for multi-institutional collaborations.

Random gene mutagenesis for gene identification linked to prodigiosin production in Serratia marcescens
Verena Carvalho, University of Massachusetts-Amherst
This lab course is designed to provide course-based undergraduate research experiences. You will learn how to prepare, execute, and interpret your own experiments. While all of you will conduct the same techniques in the course, each of you will create their own sets of mutant strains and study different features of your bacterium. We will study Serratia marcescens, an opportunistic, nosocomial pathogen, and is particularly linked to catheter-associated bacteremia, urinary tract infections, and wound infections. It is responsible for 1.4% of hospital-acquired infection cases in the United States. These bacteria are commonly found in the respiratory and urinary tracts of hospitalized adults, and in the gastrointestinal systems of children. Many strains of S. marcescens have a bright red colony color (a tripyrrole pigment called prodigiosin), while pigment production is often temperature-dependent. Prodigiosin is a secondary metabolite, and its expression is thought to be related to phosphate limitation. It was also identified as a natural bioactive substance with high potential for antibiotic and anti-cancer applications. It currently receives renewed attention for its wide range of potential applications, including activities as antimalarial, antifungal, immunosuppressant, and antibiotic agents. It is also prominently known for its capacity to trigger apoptosis of malignant cancer cells, and high activity against stationary phase Borrelia burgdorferi, the causative agent of Lyme disease, has been demonstrated. Given its diverse effects, the exact mechanisms are currently not elucidated, and may be highly complex, including phosphatase inhibition, copper mediated cleavage of double stranded DNA, or disrupting the pH gradient through transmembrane transport of H+ and Cl- ions. Clearly, prodigiosin is a highly promising drug candidate, and is currently in preclinical phase study for pancreatic cancer treatment. In this course, we will use the transposon Tn5 to generate random mutations in the chromosome of Serratia marcescens. The transposon will be provided by a plasmid hosted in a donor E. coli strain, and transferred into your test bacterium via conjugation. We will then first select for successfully transposed mutants by testing for antibiotic resistance, and screen for your mutants that are altered in their pigment production. To identify the gene where the mutation has happened, we will remove the chromosomal DNA from the mutant strains, perform restriction enzyme digest, and generate self-circulating DNA. These plasmids are transformed into an E. coli strain that can replicate the fragment of genomic DNA that contains the transposon, and we can sequence the insertion site with the transposon DNA as anchor. In summary, in this course you will gain hands-on experience with modern genetic and biotechnological techniques, you will gain insights into bioinformatics and into working with public databases, which are all essential skills in modern microbiological research.

BIOL 189T Fungal Biology
Alija Mujic, California State University-Fresno
The diversity, community structure, and functional diversity of fungi in the high Sierra is understudied and is largely unknown from the Sierra Nevada foothills. Through use of direct field sampling I will engage BIOL189T students in sampling efforts to elucidate the fungal biology of these understudied habitats. Students will sample fungal sporocarps (mushrooms) from existing field plots established by the National Environmental Observation Network (NEON) and use morphological identification techniques and DNA barcoding methods to identify the fungal diversity in these habitats. Future iterations of the course will likely focus upon selected fungal taxa identified in previous iterations of the course to investigate the phenology and ecological interactions of the fungal community in these habitats in NEON plots.

Designing Authentic Undergraduate Experiences in Research (DAUER)
Joseph Ross, California State University-Fresno
In this research experience, students will learn about how inheritance of diverse genetic material from their parents can impact the health (fecundity) of offspring. Students will design experiments to mate pairs of populations from a diverse global collection of microscopic worms and measure and compare the fecundities of their hybrid offspring.

Brain Mapping of Psychiatric Disorders
Chris Miller, California State University-Fresno
This course will introduce students to the neuroscience of psychiatric disorders by guiding them through the process of conducting a meta-analysis of fMRI studies of a particular psychiatric disorder of their choice.

The Amazing World of Chemicals - Biosynthesis of natural products
Sibongile Mafu, University of Massachusetts-Amherst
Students have the opportunity to discover or engineer novel compounds through enzyme discovery or modifications of known enzymes. This includes molecular biology encompassing cloning DNA minipreps and transformations in bacteria or plants and analytical analysis of the "novel" compound. This process allows the student to emulate a process used by many biotech companies that manufacture natural products. More importantly the CURE integrates, applies and develops the techniques they have learnt throughout the BMB curriculum with an emphasis of experimental design, data analysis and critical thinking.

Kinetics of bioorthogonal reactions
Jen Heemstra, Emory University
Bioorthogonal reactions such as strain-promoted azide-alkyne cycloaddition (SPAAC) and inverse electron demand Diels–Alder (IEDDA) are widely used for labeling of biomolecules, which in turn enables numerous applications in basic science and biotechnology. The key characteristic of these reactions is the ability of the functional groups involved to react with each other while remaining inert to the other functional groups found in nature. Despite the wide use of these chemistries, relatively few studies have evaluated the effect of reaction conditions on the kinetics of the reaction, and it would be of value to the scientific community to know how factors such as buffer identity, pH, ionic strength, and temperature impact reaction rate. In this CURE, students synthesize reagents or biomolecules and utilize UV spectrophotometry to measure the reaction rate under varying conditions. Students communicate their results in a final report written in the format of a peer-reviewed publication, and this CURE has yielded peer-reviewed research publications to share the data with the scientific community.

Genetic Engineering of Zebrafish to Investigate Tumorigenicity of Cancer Mutations
Terry Shackleford, St. Marys University

Going from big genomics data, to useful data, to experiments in diabetes
Talitha Van der Meulen, University of California-Davis
In diabetes, blood glucose levels are too high and people with diabetes suffer from severe side-effects that include cardiovascular disease, renal failure and blindness. Our lab is interested in studying the different cell types in the pancreatic islet that together regulate blood glucose levels. Our ultimate goal is to understand how human islet cells function and change in health and diabetes and then use this knowledge to contribute to a cure for or treatment of diabetes. In this CURE, students will become familiar with using so-called "omics" data and translating the data into a testable experiment that they will perform. The experiments will be done in the context of diabetes research that is ongoing in the Huising lab at UC Davis. Currently, we have large sets of information about gene expression at the mRNA level in healthy alpha, beta, and delta cells of the mouse pancreatic islet. Students will use bioinformatics techniques to process these sets and compare expression among these cell types during the first half of the course. For the second half, they will use this comparison to select a gene whose expression they will verify at the protein level in mouse pancreatic islets using fluorescent staining of tissue slices, followed by imaging and image-quantification. This process is a first step towards our ultimate goal of studying human islet cells. Once we have tools verified in mouse tissue, we can then apply these to human tissues. Therefore, we ask students to present their validation to the Huising lab.

Introducing hands on concepts of Mammalian Cell Culture and in vitro drug studies in Undergraduate course shells.
HIRENDRA BANERJEE, Elizabeth City State University
The process of learning is both visual and auditory and in the STEM fields, hands on and practicums enhances student learning, retention and understanding of the complex scientific concepts than just memorizing facts from class room lectures. Thus we plan to implement short hands on research modules in our Cell Biology and Human Physiology courses involving projects teaching students with mammalian cell culture techniques and in vitro drug testing skills. Students will learn to culture mammalian cancer cell lines with culture mediums and maintain the cultures in carbon dioxide incubators at ideal temperature, they will then treat them with novel anti cancer compounds to test the efficacy of these drugs and the IC50 doses(dose at which 50% cells dies).The data obtained will be statistically analyzed and results reviewed to study whether it aligns with the hypothesis and specific aims; students will then present their findings in a small research paper and short seminars in class along with their peers, they will be graded according to a rubric that will be provided to them in the beginning of the research experience process. Thus this process will align with CURE objectives of REU incorporation in undergraduate courses.