Mentors and Projects Available to Choose From Summer 2023
Chaoping Chen
Department of Biochemistry & Molecular Biology
Chen Lab
Research Profile
Research interests:
Retroviruses are enveloped RNA viruses, which comprise a large and diverse family including human immunodeficiency virus 1 (HIV-1), the pathogen that leads to AIDS. The laboratory focuses on characterization of the molecular and cellular mechanisms underlying the late stage of HIV-1 replication using a combination of biological imaging, cellular and molecular virology approaches.
Summer project:
This summer REU project is part of our ongoing research effort aiming to understand HIV-1 protease autoprocessing and drug resistant mechanism. This information is critical for identification of novel autoprocessing inhibitors with the action modes distinct from the currently available HIV-1 protease inhibitors. We have established a cell-based phenotypic assay that not only for the first time faithfully recapitulated the clinically reported drug resistance of a double mutation 77I82T but also precisely defined contributions of each point mutation to protease inhibitor (PI) susceptibility. The REU fellow will examine and determine how various mutations influence the responsiveness to HIV-1 protease inhibitors using this phenotype assay platform.
Mentoring plan:
The REU fellow will learn basic molecular biology techniques including SDS-PAGE, western blotting and subsequent quantification analysis, as well as fluorescence imaging and quantification protocols specifically established for the phenotype assay, under the guidance of the above-mentioned personnel. Results obtained will shed new lights into drug resistance mechanism. Through these research activities, the REU fellow will also develop skills of critical thinking, spoken and written communication, and being a productive team player.
Terry Engle
Department of Animal Sciences
Research Profile
Research Interests:
Ruminant Nutrition; Nutritional Biochemistry; Mineral and Lipid Absorption/Metabolism; Immunology and Nutrient Management
The summer project:
– Copper absorption in the bovine enterocyte.
– Bovine hepatic copper homeostasis.
– Understanding the development of liver abscesses in beef cattle.
– Influence of direct fed microbials on growth performance, carcass data, and immune function in finishing beef steers.
Mentoring plan:
I will meet with the REU student on a weekly basis (one-on-one meetings) and then we will have separate weekly meetings with my Ph.D. students. We will develop a plan for the REU student to work on several projects over the summer depending on the REU student’s interest. The REU student will also be required to keep a laboratory notebook/journal of their activities which the REU student and I will review on a weekly basis. All of my graduate students have mentored and/or are currently mentoring undergraduate students. I have taken several mentoring trainings and my graduate students have also had basic training in teaching students.
Arjun Khakhar
Department of Biology
www.arjunlab.com
Research Profile
Research Interests:
Plants are amazing because they make most of the things we need: delicious food, fabrics, building materials, hosts of molecules that make us healthier and happier, not to mention the beautiful biospheres that fill us with wonder and sustain us. Their biology is filled with intricate mechanisms that let them turn soups of molecules from their environments into complicated structures capable of producing all these things. Our lab seeks to understand how these mechanisms can be predictably re-engineered to create crops that are more productive, delicious, and resilient to the effects of climate change. We use synthetic biology to study and create new biological systems both in plants and the creatures that interact with them, including viruses and fungi, to achieve these goals.
The summer project:
Dwarfing is an agriculturally important trait that has the potential to dramatically increase crop yields. This project focuses on determining ways to use synthetic biology, a new kind of genetic engineering, to reprogram the metabolism and development of plants to create dwarfing phenotypes that will deliver these increased yield
Mentoring plan:
We have well structured training plans to onboard new students with no lab exp. to become proficient at plant care, molecular cloning, and experimentation. The student would be trained and once trained, assist a researcher with their project. If their mentor determined they were able to handle additional work, they would be given the opportunity to undertake a small independent project as well.
Graham Peers
Department of Biology
Research Profile
Research interests:
My primary research interests are: photosynthetic efficiency, how photosynthesis is regulated in a dynamic environment and algal stress physiology. Researchers in the laboratory employ forward and reverse genetics, ‘omics approaches and detailed physiology to investigate these areas. We are particularly interested how these processes differ across the vast evolutionary diversity of algal and cyanobacterial clades.
Summer project:
Our group has three potential focus areas for a summer project. The first involves developing synthetic biology tools to control gene expression in algae, the second involves characterizing the biochemistry of photosynthetic energy dissipation, the third involves exploring the anti-cancer activity of novel pigment molecules.
Mentoring plan:
Andrew Paton will participate in day-to-day mentoring with assistance from another graduate student and one research scientist. They will be responsible for teaching lab techniques and analyses. I will meet with the student(s) weekly both in lab meeting and one-on-one to discuss progress, identify roadblocks and also help in the lab when needed. Our goal will be to have the student(s) develop one figure (each) for a publication in a scientific journal.
Brad Reisfeld
Department of Chemical and Biological Engineering
Quantitative Systems Pharmacology and Toxicology Research Group
Research Profile
http://qspt.colostate.edu/
Research interests:
Dr. Reisfeld’s research interests lie in areas of biological, biomedical, and environmental science that are relevant to human health. His focus, at present, is in examining the fate and effects of xenobiotics (foreign compounds, such as drugs and toxicants) in the body, including issues such as biodistribution, clearance, metabolism, pharmacological effect, and toxicity. His work also includes projects in ‘one health’, with a focus on issues that interlink human, animal, and environmental health.
Summer project:
Students in Dr. Reisfeld’s group work on projects related to characterizing the effects of drugs and environmental pollutants on human and animal health. Bringing together concepts from physiology, biochemistry, and mathematics, students help to create models to predict how these chemical compounds are absorbed, distributed, metabolized, and excreted in the body and how they interact with biological systems to cause therapeutic or toxic effects. Models like these are often used in the pharmaceutical industry and in analyses related to protecting public health
Mentoring plan:
I will be the primary mentor for the student(s) and will provide
guidance on overall project aims and strategy. I will meet with the
student(s) weekly and on an ‘as needed’ basis. Detailed mentoring on
specific research topics will be provided by the graduate students
listed above. Aside from the above meetings, the REU student(s) will
participate in weekly group meetings.
Robyn Roberts
Department of Agricultural Biology
https://stem.colostate.edu/community/robyn-roberts-ph-d/
Research Profile
Research interests:
We study plant immunity, plant-microbe interactions, and pathology to better understand the infection process and why plants get sick. We hope that by better understanding plant immunity we can develop more resistant crops and reduce our reliance on pesticides, improve the economics and environmental impacts of agriculture, and contribute to an integrated pest management strategy. We focus on two crops for improvement: wheat and tomato.
Summer project:
The project will focus on discovering the molecular mechanisms behind the increased incidence and severity of a wheat-infecting virus, Triticum mosaic virus, in Colorado. The fellow will learn and execute various plant biology molecular research methods, such as DNA/RNA extraction, qPCR, viral inoculations, and more, and will also engage in computational biology/biofinformatics to analyze virus sequence changes and evolution.
Mentoring plan:
I will meet with the REU student 1:1 at least once per week to check on their progress, set short- and long- term goals, troubleshoot, and answer any questions. They will receive bench training from me, a graduate student (Diego), and/or an RA (Matt). I have trained over 20 undergraduate students and participated in the REU program in my postdoc (I just started at CSU in Aug 2020, so I haven’t had the opportunity to participate as a faculty member yet). Previous REU students trained by me have won poster and oral presentations as part of their REU experience and have been authors on my publications. I expect the student to be self-motivated, ask questions, make efforts to troubleshoot problems, and recognize mistakes. They will engage with their peers and colleagues in an inclusive and respectful environment. The student will participate in and present their work in lab meetings and other public speaking opportunities on campus.
Tom Santangelo
Department of Biochemistry & Molecular Biology
Research Profile
Research interest:
We investigate the information processing systems and metabolism of microbes that thrive in extreme environments. Using a combination of genetic and biochemical techniques we aim to understand the evolution, mechanisms, and interplay of archaeal transcription, DNA repair, DNA replication, and epigenetic modifications. In short, we strive to understand how microbes can survive under conditions where most would quickly perish due to temperatures, pressure, pH or salinity extremes. We regularly employ >10 undergraduates and >7 graduate mentors that direct independent research efforts towards these aims.
Summer project:
REU participants will master anaerobic microbiological techniques, culture, and genetically manipulate extremophiles, purify, and analyze enzyme and enzyme complexes, and contribute to a dynamic environment that explores life in the extremes. Efforts for summer 2023 students would likely be focused on discovery and analyses of new DNA repair pathways or investigate the role of modification to nucleic acids to support function at high temperatures.
Mentoring plan:
I am very familiar with the demands of the REU program, the mentoring philosophy and training format, and the need for assistance at the bench and with the totality of scientific training. I meet with REU students one-on-one each week; REU students present at weekly group meeting to solicit feedback and practice presentation skills. We also aim to socially incorporate REU students into our large group, an often overlooked yet critical feature of summer and scientific training. So much can be learned from informal gatherings and interactions that we aim to ensure full immersion in such.
Grant Schauer
Department of Biochemistry & Molecular Biology
Research Profile
Research interests:
The replisome is a multiprotein machine that orchestrates duplication of the genome—including the epigenome—with strikingly high accuracy despite a constant barrage of obstacles. These challenges to replication pose risks for mutagenesis and replication fork collapse. My lab is interested in auxiliary machinery that directly couples to the core replisome, handling these obstacles in coordination with the DNA replication apparatus to achieve high fidelity chromosome duplication. Using replisomes and chromatin reconstituted from protein complexes purified in yeast, we study these molecular mechanisms in detail with single-molecule fluorescence techniques in addition to traditional biochemistry.
Summer project:
The project will focus on DNA replication and related replication-coupled DNA damage tolerance pathways, and may include learning protein purification, in vitro biochemistry, and single-molecule fluorescence experiments.
Mentoring plan:
Alisa Shaw is the primary day-to-day mentor for incoming students. She has over 20 years experience at the bench at CSU and has trained over 100 students in molecular biology, biochemistry, cell biology, and microscopy techniques. Other members listed are able to help as well, depending on which project the student is assigned. My role as PI will be to meet with the student several times a week, tracking progress, helping with protocols and techniques, defining the research direction of the project as it evolves, and providing personalized input for growth as a scientist. The expectation is that the student learns to conduct experiments independently by the end of the summer, with the ultimate goal of a direct contribution on a peer-review research article.
Christopher Snow
Department of Chemical & Biological Engineering
Research Profile
Research interests:
The lab focuses on computer-guided protein and DNA engineering, particularly the engineering of crystals. Methods of particular interest include directed evolution, macromolecular crystallography, protein structure prediction, and new algorithms for reliable computational protein engineering. The lab works on designing and experimentally testing a new class of self-assembling crystals composed of both protein and DNA building blocks.
Summer project:
This project aims to realize one of the most transformative goals of nanotechnology – the ability to engineer complex macroscopic materials in which the constituent atoms are nonetheless positioned precisely. Precise control of the 3-D position of functional molecules will open the door for materials with unprecedented performance for diverse applications including biosensing, catalysis, energy conversion, biomedicine, and biotechnology. For example, enzyme positioning will enhance catalysis, chromophore positioning will enhance photonic materials, nanoparticle positioning will lead to superior hybrid materials, and conditional release of fluorescent and/or therapeutic proteins will lead to new biosensor and drug delivery materials.
Mentoring plan:
Orientation will commence with a one-day mini symposium in which the current graduate students and undergraduate students present 30-60 minute talks on their projects. The PI will also present a 1 hour talk on the context of the project within the larger research program. The next five days will include detailed laboratory tours and shadowing. Following these activities, the PI will meet for in-depth planning conversations with the REU student, and to provide introductory training on the molecular modeling and simulation aspects of the project. Orientation topics will include (a) the extent to which the student can operate independently of their mentor, (b) interaction with coworkers, (c) productivity including the importance of scientific publications, (d) work habits and laboratory safety, and (e) documentation of research methodologies and experimental details so that the work can be continued by other researchers in the future.
Kathryn Wilsterman
Department of Biology
Research Profile
Research interests:
Current projects in the lab are focused on understanding how reproductive physiology deals with hypoxic environments at high elevations. We use deer mice from Nebraska and Mount Evans, Colorado (over 14,000 ft elevation) to understand both how hypoxia limits reproduction, and how physiology in high elevation animals has overcome these challenges through physiological adaptation. We are combining in vitro approaches and organismal physiology to ask how tissues like the ovaries and uterine lining respond to chronic hypoxia. Over the course of the summer, the student will gain experience working with rodent models, histological approaches to reproductive physiology, and organismal biology.
Summer project:
Current projects in the lab are focused on understanding how reproductive physiology deals with hypoxic environments at high elevations. We use deer mice from Nebraska and Mount Evans, Colorado (over 14,000 ft elevation) to understand both how hypoxia limits reproduction, and how physiology in high elevation animals has overcome these challenges through physiological adaptation. We are combining in vitro approaches and organismal physiology to ask how tissues like the ovaries and uterine lining respond to chronic hypoxia. Over the course of the summer, the student will gain experience working with rodent models, histological approaches to reproductive physiology, and organismal biology.
Mentoring plan:
The REU student will work within a team in the lab and receive training from multiple mentors, including two technicians in the lab. I will meet with the student weekly to lay out goals, revise summer-long outcomes, and identify opportunities for further development. The student will have the opportunity to interact with a larger set of students in the laboratory and on the floor, including several graduate students in my lab and others. The student will be encouraged to participate in summer journal clubs and lab meetings.
