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.

Yeast, metabolism and suicide: a brewing introduction to biochemical research
Laurent Dejean, California State University-Fresno
This course provides the student with a range of techniques and methodology appropriate to the study or phenomena at the biochemical, cellular, and organismic levels. In the spirit of genuine undergraduate research (CURE), the students will be involved directly in research that is ongoing in the Dejean's lab, i.e. the study of the mechanisms used by Bcl-2 family proteins to cross-regulate cell death and energy metabolism. The students' involvement in this type of research will be following a set of preliminary experiments which are aimed at familiarizing the students with common biochemistry lab skills; and with the manipulation of the yeast Saccharomyces cerevisiae which is to be used as the main model system in their research. Finally, the students will also engage directly with primary literature sources in preparation of their lab reports and an eventual presentation of their research at the Fresno State CURE symposium at the end of the semester.

A short medicinal-chemistry inspired laboratory sequence aimed at understanding and controlling bacterial communication.
Laura Brown, Indiana University-Bloomington
Medicinal chemists are organic chemists (often employed by pharmaceutical companies) who synthesize and develop new organic molecules with favorable biological properties. As an illustrative example, penicillin was discovered in 1928 and developed into a drug in 1942. Resistance quickly arose and continues to be a problem, and penicillin is not effective against all types of bacteria. In the decades that followed, medicinal chemists synthesized a variety of molecules that were similar in structure to penicillin, but that either demonstrated enhanced antibiotic activity or did not exhibit the same resistance profile. A new approach to controlling the pathogenicity of bacteria is to simply "trick" the bacteria into remaining in their "normal" non-pathogenic state by controlling the ability of bacteria to communicate with one another by a mechanism termed "Quorum Sensing." Quorum sensing is a form of chemical communication by which bacteria sense each other's presence via concentration gradients of small molecules. I have a collaborator in the biology department who has developed a biochemical assay to identify inhibitors of this process, and the students who sign up for this course will synthesize a small library of molecules to test in this assay.

The effects of grazing of water coliforms and antibiotic resistant microbes
Kristy Duran, Adams State University; Benita Brink, Adams State University

TRANSFER STUDENT CURE: Multi-organismal genomic analysis of molecular determinants of protein assembly.
Dylan Murray, University of California-Davis

Does grazing influence the structure of aquatic and riparian communities?
Tim Armstrong, Adams State University; Megan Dudley, Adams State University; Dan Gibson-Reinemer, Adams State University
This CURE will examine the effects of grazing using a natural experiment in the mountains surrounding the San Luis Valley, Colorado. The eastern Sangre de Cristo Mountains have not been grazed for at least 50 years, and the western San Juan Mountains continue to be grazed. We will test if grazing affects the structure of aquatic and riparian communities as part of a larger interdisciplinary project.

Mutant Frogs, Hormones, & Genes: Using gene editing to investigate the molecular basis for hormone regulated development
Carla Fresquez, University of California-Davis
Students will investigate a most remarkable example of hormone action in nature: amphibian metamorphosis. They'll observe development of our model, Xenopus laevis, from fertilized egg to swimming tadpole, at which point they can simply add thyroid hormone to induced early metamorphosis. In this iteration of the CURE, students will characterize TALEN induced thyroid hormone receptor mutant lines, including the development of simple and reproducible PCR screening methods for genotyping the large numbers of embryos that result from mating in Xenopus, an advantage of the system if rapid genotyping can be developed. At the conclusion of the CURE, students will appreciate the amphibian life cycle and how the same hormone can cause drastically different cellular, tissue, and organ changes. They will also contribute directly to research on the role of different receptors in mediating those changes, specifically developing rapid PCR screening methods to identify tadpoles with genome editing induced mutations in specific receptor types.