Mentors and Projects Available to Choose From Summer 2022

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:
It is part of our ongoing study aiming to understand HIV-1 protease autoprocessing and drug resistant mechanism. This information would be 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 has enabled high-throughput drug discovery but also provided an easy and powerful tool for analyzing mutations found in HIV-1 strains isolated from patients experiencing resistance to HIV-1 protease inhibitor treatment. The REU fellow will examine and determine how these mutations influence the responsiveness to HIV-1 protease inhibitors.

Mentoring plan:
The REU fellow will learn basic protein techniques including SDS-PAGE, western blotting and subsequent quantification analysis, and master these techniques to obtain reproducible results to shed new lights into drug resistance mechanism, under the guidance of research scientists or graduate students. Through these research activities, the REU fellow will also develop skills of critical thinking, spoken and written communication, and being a productive team player.

Karyn Hamilton
Director – Translational Research on Aging and Chronic Disease Laboratory Health and Exercise Science
Healthy Aging Center
Healthy Aging Center Research

Research Interests:
The overall objective of the TRACD laboratory is to understand the role of stress resistance, proteostasis, and maintenance of mitochondrial protein turnover and function in the context of slowing aging and age-related chronic disease.

Summer project:
The project would be focused on what we’ve been calling the “brain-muscle axis” in aging. We are interested in understanding mechanisms driving the co-existence of musculoskeletal decline and neurodegeneration/cognitive impairment with aging.

Mentoring plan:
During the trainee’s time in the TRACD lab, we will meet one-on-one weekly. The trainee will also participate in weekly whole lab meetings. Finally, the student will also have primary and secondary mentors from my lab team who will serve as  mentors for day-to-day work in the lab.

Seonah Kim
Department of Chemistry
https://Research Profile

Research interests:
Our research group’s central focus is the development of catalytic strategies to convert biomass (for example, corns, woods) into high-valued platform renewable chemicals, polymers, plastics, and biofuels using computational modeling. Three scientific challenges we are pursuing: Mechanism-Driven Discovery of Biopolymer Upgrading (quantum/molecular mechanics (DFT, MD)), Material Design for Catalytic Upgrading of Biomass (DFT, MD and Data Science), and Bottom-up Predictions/Design of (Bio)Fuel & Engine Performance (Cantera, DFT Chemical Kinetics).

Summer project:
Computational modeling/machine learning approaches in the renewable energy field to impact everyone and everyday life.

Mentoring plan:
I will arrange a weekly meeting with the student to discuss the research progress and discussion about the project. A postdoc and a graduate student will mentor REU students every day to teach the detailed computational methods and research approaches.

Julie Ann Moreno
CVMBS Environmental & Radiological Health Sciences Dept
Research Profile

Research interests:
The research focuses on the mechanisms of misfolding proteins in the brain during neurodegenerative diseases and aging that cause neuronal toxicity. Ongoing studies include: 1.) understanding the cellular mechanisms that allow neurons and glia to be vulnerable during aging and neurodegenerative misfolding proteins diseases, 2.) utilizing stem cell therapies to therapeutically intervene neuronal loss by decreasing the neuroinflammation, 3.) taking a multifaceted approach to neurodegenerative treatments by using genetic and/or small molecules to target cellular stress pathways.

Summer project:
Currently, there are no therapeutic treatments for prion diseases. A key to developing a successful therapy for prion disease is to target early neuroinflammation to reduce clinical signs and neuropathology. The first sign of disease is early inflammation of the brain caused by reactive astrocytes and the activation of microglia. This is due to the accumulation of PrPSc and results in oxidative stress, disruption of neural signaling, neuro inflammation and glial scarring A possible treatment avenue to reduce the early neuroninflammation is to use adipose-derived mesenchymal stem cells (AdMSCs) by the secretion of  anti-inflammatory cytokines and chemokines, neurotropic factors and growth factors in response to inflammatory conditions We are currently assaying the ability of these cells to protect mice infected with prions and determining the neurotoxic mechanisms that are inhibited by the secretion of anti-inflammatories.

Mentoring plan:
I will meet with the REU student and their graduate student mentor weekly. The student will also attend our weekly lab meetings.

Donald Mykles
Department of Biology and the director of the University Honors Program
Research Profile

Research interests:
The research focuses on the cellular and molecular mechanisms that control molting, muscle atrophy and limb regeneration in crabs. The species of crab studied in CSU’s Crab Lab is Gecarcinus lateralis, commonly known as the blackback land crab. These are fist sized, terrestrial crabs decorated with bright orange legs and claws with a splash of deep purple on their backs. Because G. lateralis is adapted to terrestrial conditions and does not require an aquatic environment, it is an ideal species to study in a laboratory setting.

Summer project:
The student will use bioinformatic tools to characterize signal transduction genes that control molting in decapod crustaceans. The student is expected to assist in laboratory experiments and animal care.

Mentoring plan:
Postdocs will mentor the REU student day-to-day. I meet with the student at least once a week.

Marc Nishimura
Department of Biology
Research Profile

Research interests:
The Nishimura lab explores the mechanistic underpinnings of plant-pathogen interactions. We want to understand how some plants are resistant to pathogens, while others become diseased. From the plant side, we need to know how the plant immune system functions. How do plants recognize potential pathogens and activate an appropriate immune response? From the pathogen perspective, what strategies can subvert the host and suppress immunity? Ultimately, how can we use all this knowledge to engineer the plant immune system to improve our crops

Summer project:
Understanding how plant and prokaryotic TIR immune receptors’s NADase activity generates an obscure class of signaling molecules, and how those molecules act to signal downstream disease resistance and cell death. These questions are important for engineering plant immune systems and understanding prokaryotic viral resistance.

Mentoring plan: 
Day to day, a graduate student or a postdoc will be mentoring the REU participant under my supervision. In past years, my role has been to help design a reasonable project that the summer student can have some ownership over, but that also meshes well with the mentor’s goals. I formally meet with the summer intern 3 times (begining, after 2 weeks, and end of summer). I expect the mentor to train the summer interns both on the practical aspects of the project as well as the larger scientific questions. The mentor also helps the intern prepare an end of project lab meeting presentation. The mentor and I collaboratively draft a recommendation letter for the intern as needed (typically one has been requested). Summer students are expected to work diligently, and keep a good lab notebook, to participate in the weekly PI/mentor meeting, and lab meeting/journal club.

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.

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 2022 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:
Each REU student is paired with a dedicated graduate student bench-mentor and will participate in weekly large- and small-group meetings. Previous REU students were assisted by many graduate and undergraduate mentors. REU students have daily access to the PI. 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.

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.

Jozsef Vigh
Department of Biomedical Sciences
Research Profile

Research interests:
The research focuses on visual signal processing in the retina, the lab is interested in how and why retinal nerve cells communicate with each other. Like everywhere else in the central nervous system, communication between retinal neurons occurs at synapses. Overlying modulatory processes tune the basic mechanisms of communication to physiological needs. Synaptically coupled neurons form microcircuits, and ultimately determine how the retina codes for three fundamental features of our visual environment: contrast, color and motion.

Summer project:
The project is related to the opioid regulation of circadian sleep/wake rhythms, and stems from the clinical observation that gradually worsening insomnia-type sleep problems, associated with daytime sleepiness abd/or depression, occur in approximately 90% of individuals who receive long-term opioid treatment for chronic pain (CP). Importantly, sleep disruption is a serious risk factor for suicidal ideation in CP patients receiving opioid therapy. The scientific goal would be to determine whether a given subpopulation of neurons in the pre-optic area express µ-opioid receptor (MOR) on their somato-denritic compartment (i.e. postsynaptically) and/or MORs expressed on their innervating axons arriving from the retina (i.e. presynaptically).

Mentoring plan:
The research methodology would include tissue preparation (sectioning, harvest would be done by qualified lab members), immunohistochemistry, in situ hybridization, and fluorescent image processing followed by statistical analysis. In addition, the training will include basics of ethical conduct of research, lab safety, hazardous waste management and LAR training in mouse handling. Project development/planning will be mentored by me as well as ethical conduct of research and lab safety as well as preparing for presentation of the acquired data. The REU student will participate in weakly lab meeting where progress reporting/trouble shouting/next step planning takes place, giving opportunity to practice presentation while enforcing continuous data processing.  In addition, I have an open-door policy for students, and lab members.

Joe Zadrozny
Department of Chemistry
Research Profile

Research interests:
Electronic and nuclear magnetic moments (spins) are present in nearly all matter. Our group is fundamentally interested in how to tune the properties of these spin systems in molecules and materials via the chemist’s toolkit: synthesis. Our goal is to use synthesis for the development of structure-property relationships. We leverage this fundamental science to develop solutions to pressing technological challenges, such as MRI detection of disease, discovery of new reactivity paradigms, and the design of transformative materials.

Summer project:
Students in the Zadrozny lab will work on a research program to develop molecules with metal ions as sensitive magnetic-resonance probes of chemistry at the molecular level. Students will chemically synthesize molecules to test key design parameters for either 59Co magnetic resonance imaging or electron paramagnetic resonance imaging. Over the course of the summer, students will prepare compounds, characterize prepared species for purity and identity, then perform the advanced magnetic resonance measurements to test for utility – learning all of the synthetic and spectroscopic techniques to do so along the way.

Mentoring plan:
The REU participant will be mentored by a graduate student or postdoc on a day-to-day basis, and I will hold an active role in training the graduate student/postdoc in mentorship. I will do the following: (1) meet with the student initially to give them an overview of the project they will be working on, (2) connect them with their in-lab mentor and trainer, (3) have daily walk-by meetings “what are you working on today?”, (4) have weekly face-to-face half hour meetings about research progress with their in-lab mentor, and (5) host group meetings where the student will present informal weekly research to the group via chalk talk, as well as present scientific papers. All of these are low-stakes ways of providing mentorship, guiding research progress, and some professional development (public speaking). Clear expectations for labwork and goals for the summer session will be given in the first meeting. I separately hold one on one meetings with current group members, and I will use those meetings as opportunities to discuss mentorship with the graduate/postdoc mentor throughout the summer.