Mentors and Projects Available to Choose From Summer 2024
Department of Microbiology,Immunology and Pathology
My laboratory studies the basic biology and pathogenesis of mycobacterial pathogens, including Mycobacterium tuberculosis and nontuberculous mycobacteria (NTM). We study the mycobacterial protein secretion pathways and the role they play in enabling intracellular survival of mycobacteria in macrophages. We also investigate novel therapeutics, including bacteriophage therapy, as treatments for drug resistant mycobacterial disease.
I am dedicated to mentoring trainees at all levels. At the start of the summer, I will meet with the student, and we will develop a list of agreed upon expectations for the summer research experience. I will then meet with the undergraduate student weekly to discuss their research project and progress. The student will also be assigned a ‘bench mentor’ who will meet daily with and advise the student in the lab. The student will participate in our weekly lab meetings and journal clubs. At the end of the summer, we will work with the student in writing an abstract on their summer research project and presenting their summer research at lab meeting.
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.
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 lab 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.
Santiago Di Pietro
Department of Biochemistry & Molecular Biology
This cell biology laboratory focuses on fundamental aspects of intracellular protein transport. We are particularly interested in clathrin mediated endocytosis and transport pathways to melanosomes, platelet granules and other lysosome related organelles (LROs). The physiological significance of these pathways is manifold. The endocytic pathway is required for nutrient uptake, down-regulation of signal transduction events, antigen presentation, and virus internalization, while the biosynthetic pathways to LROs are critical for the biogenesis and function of these organelles. A wide range of diseases are caused by defects in these pathways including heart disease, bleeding disorders and albinism. We have gained a solid expertise in the integrated use of biochemistry, biophysics, microscopy, mammalian and yeast cell biology, and genetics. We are applying that experience to identify new components of the transport machinery, to study novel mechanisms regulating clathrin coat formation, and to understand the link between the transport machinery and the actin cytoskeleton. Our work has implications not only in basic cell biology but also in deciphering the pathogenesis of diseases associated with defects in protein transport pathways.
The REU project will be directly related to our research in endocytosis, which is funded by an NSF grant that started in July 2023. This will comprise a mix of genetics, advanced live cell fluorescence microscopy, and biochemistry. Abdunaser Eadaim (postdoc) and Andrew Lamb (postdoc) are currently working on this project, and I expect they will provide most of the day-to-day mentoring. I will participate both in direct mentoring of the REU student as well as mentoring the mentors. I plan to meet with the REU student during weekly group meetings as well as meeting one-on-one on a regular basis in order to discuss the scientific question, experimental approaches and results. The expectation is that the REU student is motivated and focused. The main goal is for the student to learn how to design and execute experiments that test a hypothesis, and if possible, get results that will be published.
Department of Biology
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.
A senior level graduate student or postdoctoral scholar 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.
Department of Biochemistry & Molecular Biology
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.
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.
Department of Electrical and Computer Engineering
Our lab focuses on the architecture of mammalian cells. The main expertise of the team is in single-molecule biophysics experiments at the nanometer scale. We place particular emphasis on the actin-based cytoskeleton and its role in the dynamic organization of mammalian cells. The nature of this field is highly interdisciplinary, crossing the boundaries of Engineering, Physics, and Biology. The techniques we use in our research consist of stochastic processes, single-molecule detection and tracking, and superresolution imaging.
Day-to-day mentoring: A postdoc will be assigned to the day-to-day mentoring of the REU participant.
Interactions with the PI and other group members: The PI will meet at least twice per week with the mentor and the REU participant to discuss project progress and plan the work, once in a project-specific meeting and once during weekly group meetings. The group meetings will provide an opportunity for the participant to discuss the progress with the whole group. In addition, the REU participant will have the opportunity to participate in a weekly group lunch and a weekly journal club. Our group organizes outings (i.e., to the Poudre River or a hike in the mountains) and we always organize one of these outings when we have lab visitors.
Mentor training: Before the start of the project, the PI will thoroughly discuss with the mentor the responsibilities of the REU participant, the training of the participant, expected time commitment, and expected outcomes. The PI will meet with the mentor weekly during the project to assess the participant’s progress, to rapidly address any challenges, and to set new goals if needed.
Expectations and goals: The REU participant is expected to work in the lab 40 hours per week. The student will be given journal articles to read, and these articles will be discussed with the mentor and the PI. The REU participant is also expected to become familiar with appropriate lab safety protocols (these are achieved via online training) and maintain an electronic notebook. Depending on the specific project assigned to the student, they will be expected to achieve one of the following sets of goals.
i)Be trained in imaging in a confocal microscope. Understand the limits of diffraction-limited imaging and how to perform super-resolution imaging. Collect sperm or spermatid samples from mouse. Fix cells and label them for imaging. Optimize labeling conditions for immunofluorescence. Along this project the participant will be guided to think critically of the results and to test specific hypotheses.
ii)Perform statistical analysis of trajectories obtained by single-particle tracking in living cells. Model different modes of motion. Perform numerical simulations of random walks as a model for the motion of molecules in living cells. In this project, the participant will receive training in statistical methods using MATLAB tools.
iii)Perform live cell imaging under physiological conditions. Culture cells for track force microscopy. Obtain calibrated track force microscopy measurements where the cell exerts forces under different environmental conditions. In this project the participant will employ statistical methods and test specific hypotheses.
Evaluation and feedback: During the last two weeks of the project, the PI will gather the participant’s feedback on his experience, discuss research interests beyond the 10-week program and talk about career options. The student will give a short oral presentation where they discuss their work.
Department of Biology
My laboratory group specializes in investigating the intricate physiological adaptations occurring within biological systems to maintain homeostasis under the influence of external factors. Our primary research focuses on the equine gastrointestinal tract, where we investigate physiology at the gene expression level to improve our understanding of the complex relationship between the host and the microbiome. Our projects in this area involve analysis of both global and targeted expression patterns of protein-coding and non-coding genes. Additionally, we have a secondary research interest in studying the impact of high-altitude conditions on the cardiopulmonary system in cattle, with a particular emphasis on responses to hypoxia-induced pulmonary hypertension. Our lab is fully equipped for wet and bioinformatics work, with active projects in both areas.
Research Projects Available:
- Investigate the regulatory mechanisms of epithelial gene expression in the gastrointestinal tract.
- Examine the effects of hypoxia-induced pulmonary hypertension on gene expression in the bovine cardiopulmonary system.
By the end of the project, we anticipate that the student will:
- Gain practical experience in molecular biology techniques.
- Develop an understanding of data analysis and interpretation.
- Contribute to ongoing research and generate publishable results.
At the project’s onset, we will meet to discuss available research options and develop a customized plan for the chosen project.
- Training and Acclimatization: We will provide thorough training and guidance in laboratory techniques, experimental design, and data collection methods.
- Ongoing Support: Weekly scheduled meetings will be held to monitor progress, address any questions, and discuss any challenges the student may encounter. Informal interactions in the lab will also facilitate learning.
- Data Analysis: Toward the project’s conclusion, the student will participate in data analysis and interpretation.
- Final Report and Presentation: We will work together to summarize and interpret the results, culminating in a final report and presentation.
- Evaluation and Feedback: The project will conclude with an evaluation to identify strengths and areas for improvement in the research process.
The primary goal of this project is to provide students with hands-on research experience, teaching them essential molecular biology/genetic/bioinformatics techniques, fostering the ability to interpret results, and developing problem-solving skills in a research environment.
Department of Microbiology,Immunology and Pathology
The Dobos laboratory is focused on studies of Mycobacterium tuberculosis and other mycobacterial pathogens for the development of vaccines, diagnostic assays, and biomarkers of disease. The summer REU student will work with a Research Scientist and/or Graduate Research Assistant in the lab to learn some aspect of this research. Notably, our laboratory utilizes biological mass spectrometry, models of disease, and collaborations with clinical research groups to define macromolecules engaged in host-parasite interactions. This is accomplished through highly collaborative studies within CSU and outside of the University.
A Research Scientist and/or Graduate Research Assistant with demonstrated experience and credentialing in mentoring and advising will mentor the student(s) directly. This person(s) will be responsible for initial on-boarding, ensuring that the student completes their laboratory training, and weekly scheduling. Dr. Dobos will be involved in the summer student’s project including design, review, troubleshooting, meeting periodically, practicing the final presentation, as well as attending the final presentation and other events that Dr. Dobos and the co-mentors can make. All lab personal are expected to meet the minimum training requirements and sign and adhere to the mission and compact of our lab as baseline expectations for communication and goals. Specific goals to the project and time in lab will be discussed and agreed upon mutually and documented in this compact.
Department of Biology
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.
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.
Department of Biology
Research in the Williams Lab is taxonomically broad and highly interdisciplinary, spanning from molecular biology to population ecology. We focus primarily on systems characterized by high seasonal or inter-annual variability in resource pulses, with the goal of advancing our understanding of the mechanisms that underlie inter- and intra-specific variation in daily and seasonal timing. To explore the ecological and evolutionary drivers (and consequences) of this variation, we complement studies of free-living populations with lab- and field-based experiments and use a variety of tools including metabolic tracer techniques, molecular assays, gene-expression studies, and biologging. Below are some examples of current/recent projects in the lab.
Day-to-day mentorship will be led by my PhD student Cole Deal. Cole’s research is focused on understanding the neural mechanisms that turn off pre-hibernation fattening behavior immediately prior to the initiation of torpor in ground squirrels. The REU student project would likely focus on using digital droplet PCR to examine changes in gene expression in white adipose tissue between fattening and non-fattening ground squirrels, and/or using immunohistochemistry to examine changes in key neurons in the hindbrain. I would meet with the REU student and PhD mentor to outline expectations and goals of the project and to gain insight into the REUs student’s own goals/expectations for the research experience. We would discuss expectations are for the project, including safe research practices in the lab and conducting research in a manner that preserves scientific integrity. The REU student would also be required to read and adhere to the Williams Lab Code of Conduct (available on lab website under “join us” tab) which outlines expectations with regards to safety, professionalism, inclusivity, discrimination and harassment, and scientific integrity. The Code of Conduct also provides contact information for reporting various types of misconduct (and indicates protections exist for good-faith reporting). I would subsequently meet weekly with the REU student (or more frequently, if needed) to discuss progress on the project, as well as to ascertain whether the REU student’s goals are being met. I would also provide mentorship on completing final posters/reports and provide reviews/edits, as needed.