CURE Examples


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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.

Discipline: Life Sciences:Molecular Biology, Chemistry, Biochemistry
Core Competencies: Analyzing and interpreting data, Planning and carrying out investigations, Using mathematics and computational thinking, Constructing explanations (for science) and designing solutions (for engineering), Asking questions (for science) and defining problems (for engineering), Developing and using models
Nature of Research: Basic Research, Wet Lab/Bench Research, Applied Research
Target Audience: Major, Upper Division, Introductory, Non-major
CURE Duration: Multiple terms, A full term

Laser spectroscopy of atmospherically relevant molecules and clusters in helium nanodroplets
Paul Raston, James Madison University
Superfluid helium nanodroplets present an ideal medium for the study of chemical dynamics at the molecular level. Their low temperature, enormous heat conductivity, and weakly interacting nature allow for the investigation of various things, such as how molecular rotation is effected by a solvent, and how molecules interact with each other. These two topics will be addressed in the lab by (1) measuring the spectra of unexplored molecules in helium nanodroplets and determining their rotational constants; this data will then be used to test known models describing the interaction between the molecule and helium solvent, and (2) synthesizing and characterizing unexplored molecular clusters in an effort to better understand molecular solvation; students will solvate the "unexplored molecule" with an atmospherically relevant species (O2, N2, H2O), and investigate the resulting clusters with laser Stark spectroscopy.

Discipline: Chemistry:Physical Chemistry
Core Competencies: Analyzing and interpreting data, Using mathematics and computational thinking, Constructing explanations (for science) and designing solutions (for engineering), Planning and carrying out investigations, Asking questions (for science) and defining problems (for engineering), Developing and using models
Nature of Research: Basic Research
State: Virginia
Target Audience: Non-major, Major, Upper Division
CURE Duration: Multiple terms, A few class periods

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

Discipline: Life Sciences, Cell Biology
Core Competencies: Asking questions (for science) and defining problems (for engineering), Developing and using models, Planning and carrying out investigations, Analyzing and interpreting data
Nature of Research: Basic Research
State: Texas
Target Audience: Major
CURE Duration: A full term

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.

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

Topography with Muons
Richard Lombardini, St. Marys University
Accuracy for 3D positioning is affected by surrounding media when using traditional techniques such as GPS. Other devices may need to be developed that produce readings unaltered by the conditions of the local environment (Tanaka 2020). The trajectory of highly energetic atmospheric muons experience very little change when traveling through different media, and the flux of particles is uniform and ubiquitous along surface of Earth. Using the TeachSpin muon detectors and theories of special relativity and quantum mechanics learned in class, students will determine the level of accuracy that they can achieve in the measurement of elevation at any location by directly measuring muon stopping rates.

Discipline: Physics:Quantum Physics
State: Texas
CURE Duration: A full term

Microbiome and Health in College Students
Susan Sturgeon, University of Massachusetts-Amherst

Genetically transformed plants as a tool for gene expression analysis
Alice Cheung, University of Massachusetts-Amherst
This CURE is the entry level of a 5-7 semester intense research experience course for undergraduates. It focuses on determining the expression patterns of genes from a family of cell wall modifying enzymes. The purpose is to use gene expression information data to predict potential functions and generate genetic material towards functional studies. At the conclusion of this entry level CURE, students will learn the basic principles of gene regulation, genetic transformation and transgenic organisms (plants) as tools to study biology. It is the plan that a subset WILL CHOOSE to advance to the next level (through 1 summer and 1 or more semesters), and a subset might CHOOSE TO FURTHER advance to complete their undergraduate semesters, and one of two of whom might be RECRUITED TO continue in a 5th year MS program. This cohort of students doing research in the lab will be tasked towards completing the goal of functional studies. These students will serve as future peer mentors for the entry level CURE course and rising students in the lab.

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.

Discipline: Life Sciences:Microbiology
Core Competencies: Planning and carrying out investigations, Asking questions (for science) and defining problems (for engineering), Analyzing and interpreting data
Nature of Research: Wet Lab/Bench Research, Basic Research, Applied Research
State: Massachusetts
Target Audience: Major, Upper Division
CURE Duration: A full term

Metabolic Engineering of terpene and cannabidiols in hemp cell culture
Jennifer Normanly, University of Massachusetts-Amherst

Investigating Neural Stem Cell Regulation in the Zebrafish Brain
Rolf Karlstrom, University of Massachusetts-Amherst
By now we have all heard about adult neural Stem Cells (nSCs) and the great promise they hold for treating neurological diseases, especially neurodegenerative diseases such as Parkinson's Disease or Alzheimer's Disease. We'll talk more about these cells in the course. In order to be useful in treating human disease, we must first learn what controls nSC division (proliferation), and what controls the types of neurons and glia that are produced (differentiation). Many labs around the world are working hard on these problems using a variety of lab animals; from worms to flies to fish to rodents to humans (using human induced Pluripotent Stem (iPS) cells). In this course we will take advantage of the experimentally accessible larval zebrafish to perform experiments designed to learn more about the regulation of nSCs and neurogenesis, the process of making new neurons and glial cells needed to make a functioning vertebrate brain.Why are new neurons (and glia, never forget glia) produced in the adult brain? One obvious answer is that this adult neurogenesis helps maintain the brain as it ages (e.g. replacing cells that die). While this may be true to some degree, especially for glial cells, we know that most cells in the brain simply aren't replaced when they die (a fact highlighted in neurodegenerative diseases) and it is not simple to replace functional neuronal connections. A relatively new idea is that new neurons and glia may be generated in parts of the brain as a normal part of the brains ability to function to guide behavior and respond to the environment. In this course students will learn about the regulation of stem cell proliferation and differentiation and we expore the idea that the generation of new neurons is part of normal brain function, helping zebrafish larvae to maintain internal physiology (homeostasis) in response to a changing environment. Students will become familiar with zebrafish embryonic and larval development, will design and implement experimental treatments of larvare, dissect larval brains, perform a chemical reaction to fluorescently mark proliferating cells, image larval brains using a fluorescent microscope, and count proliferating cells.