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.

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

Chemical Analysis of Coffee Beans in Collaboration with a Local Roaster
Susan Oxley, St. Marys University
This CURE will take place in an Analytical Chemistry course. Students in the CURE course will collaborate with a local coffee roaster to develop a research question related to quantifying components of coffee beans. Using standard methods of analysis, students will work in groups to perform the analysis and validate their results. The outcome of the research will be a report to the coffee roaster.

Understanding Noncovalent Interactions and Binding through PRRSM
Amanda Hargrove, Duke University
This CURE was designed to increase instruction on noncovalent interactions and intermolecular forces, provide laboratory experiences in biochemistry and chemical biology, and deliver a more consistent chemistry research experience to undergraduates at Duke University while staying within the existing curriculum. First, the concept of noncovalent interactions is visualized in an applied setting by examining 3D structures of small molecule:RNA interactions through a portable virtual reality (VR) environment. Next, using knowledge gained in the Hargrove lab regarding small molecule:RNA interactions along with the literature examples, teams of students evaluate known small molecule:RNA interactions, pose original scientific questions, and design a hypothesis-driven experiment that can be readily tested with commercially available materials using a standard fluorimeter or plate reader. These experiments directly contribute to research that examines patterns in the recognition of RNA structure by small molecules, and the students are able to assess their contribution to this ongoing interdisciplinary project.

Polymer/Materials Structure-Property Relationship Investigations for General Chemistry Students
Zuleikha Kurji, Saint Marys College of California

Synthesis and Analysis of Carbohydrate-based hydrogels
Rebecca Connor, Dickinson College
This CURE has been developed for first-year general chemistry students with a strong background in chemistry who have elected to take an accelerated one-semester general chemistry course. In this CURE, students will have the opportunity to study controlled drug release from carbohydrate-based hydrogels or protein purification using carbohydrate based hydrogels. After learning some basic lab skills and developing their ability to read the primary literature, the students will use what they have learned to design a new synthesis of a carbohydrate-based hydrogel. They will evaluate their hydrogels for mechanical properties and ability to absorb and release model drugs. After their first set of experiments, the class will meet in a "group-meeting" and they will present and discuss their in-progress data. The students will then propose their next set of experiments and perform them. They will write a formal report at the end of the semester detailing their methods used, results generated, and a comparison of their results to the published literature.

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.