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Beyond the acronym: Employing data science to improve engagement in STEM
Pamela Reynolds, University of California-Davis
Forbes magazine ranked UC Davis as the "best value college for women in STEM." Let's investigate why, together! In this hands-on Course-based Undergraduate Research Experience (CURE), you will leverage computational tools and methodologies to explore, analyze and design solutions to maximize discoverability and engagement with STEM offerings right here at UC Davis. Community-based tools like the UC Davis STEM portal help students and members of the broader community discover and connect with opportunities in science, technology, engineering and math. How do we define STEM, and how do people interface with the diversity of offerings at our university? Through this seminar you will learn about web scraping, text mining, natural language processing, and user interface design as you work on projects to optimize search functionality and increase content management automation for the Portal, which serves as a single point of entry for catalogued information related to STEM initiatives, clubs, programs and events on campus. This research will be used to improve the discoverability and accessibility of our university's resources, and identify new opportunities for multidisciplinary research and engagement with STEM. The data we collect and workflows designed in this class will contribute to research in the digital humanities and philosophy of science regarding the shape of the discourse surrounding STEM in academia. It will also have a direct application in helping our students and broader community discover new resources and opportunities. Students will be required to work both individually and collaboratively in groups, and to share their learning with each other. This class is open to first-year freshman and transfer students from all majors. You do not need to be a computer scientist to be successful in this course, but you should be comfortable using a computer and have prior exposure to programming (R, Python, etc.). Your instructor team is looking forward to supporting your learning and engagement with research in this class!

Discipline: Social Sciences:Sociology, Statistics, Computer Science
Core Competencies: Using mathematics and computational thinking, Analyzing and interpreting data, Planning and carrying out investigations, Asking questions (for science) and defining problems (for engineering)
Nature of Research: Informatics/Computational Research, Applied Research
State: California
Target Audience: Non-major, Introductory, Major
CURE Duration: A full term

Genome Hunters (Salty Chips)
Robert Furrow, University of California-Davis

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.

Discipline: Life Sciences, Cell Biology, Health Sciences
Core Competencies: Analyzing and interpreting data, Using mathematics and computational thinking
Nature of Research: Wet Lab/Bench Research, Basic Research, Informatics/Computational Research
State: California
CURE Duration: A full term

Visualizing protein aggregates involved in human disease
Whitney Duim, University of California-Davis

Discipline: Chemistry, Life Sciences:Cell Biology, Physics:Optics, Chemistry:Physical Chemistry, Biochemistry
Core Competencies: Analyzing and interpreting data, Constructing explanations (for science) and designing solutions (for engineering), Planning and carrying out investigations, Using mathematics and computational thinking, Asking questions (for science) and defining problems (for engineering)
Nature of Research: Basic Research, Wet Lab/Bench Research
State: California
Target Audience: Introductory
CURE Duration: A full term

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

Discipline: Life Sciences:Cell Biology, Chemistry, Life Sciences:Genetics, Molecular Biology, Life Sciences, Plant Biology, Chemistry:Physical Chemistry, Biochemistry
Core Competencies: Analyzing and interpreting data, Planning and carrying out investigations
Nature of Research: Basic Research
State: California
Target Audience: Introductory
CURE Duration: Multiple terms

Genes to Ecosystems
Laci Gerhart-Barley, University of California-Davis

Discipline: Environmental Science:Ecosystems, Soils and Agriculture, Geoscience:Soils, Life Sciences:Genetics, Ecology, Environmental Science:Land Use and Planning
Core Competencies: Asking questions (for science) and defining problems (for engineering), Analyzing and interpreting data
Nature of Research: Basic Research, Field Research, Wet Lab/Bench Research
State: California
Target Audience: Introductory, Major, Non-major
CURE Duration: A full term

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.

Discipline: Life Sciences:Anatomy and Physiology, Evolution, Molecular Biology, Cell Biology, Genetics, Zoology
Nature of Research: Basic Research, Wet Lab/Bench Research
State: California
Target Audience: Introductory
CURE Duration: A full term

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.

Discipline: Chemistry
Core Competencies: Analyzing and interpreting data, Planning and carrying out investigations, Asking questions (for science) and defining problems (for engineering)
Nature of Research: Basic Research, Wet Lab/Bench Research
State: Pennsylvania
Target Audience: Introductory
CURE Duration: A full term

Probe the Effect of Physical Graphene Hole Morphology on its Acidity
Michael Groves, California State University-Fullerton
The purpose of this activity is to create and submit a job to a scheduler on a high-performance computing resource and conclude if the job relaxed to below a given threshold. We will also test how changing the requested resources affects the time to complete the job.

Discipline: Chemistry:Physical Chemistry, Chemistry
Core Competencies: Using mathematics and computational thinking
Nature of Research: Basic Research
State: California
Target Audience: Major

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.

Discipline: Chemistry:Organic Chemistry, Analytical Chemistry, Physical Chemistry, Biochemistry
Core Competencies: Using mathematics and computational thinking, Analyzing and interpreting data, Constructing explanations (for science) and designing solutions (for engineering), Planning and carrying out investigations, Asking questions (for science) and defining problems (for engineering)
Nature of Research: Wet Lab/Bench Research, Basic Research
State: North Carolina
Target Audience: Upper Division, Major
CURE Duration: Half a term


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