Mentors and Projects for the W2R/B2B Summer 2021 REU Program
Christie Peebles, Chemical and Biological Engineering Department
Lan Nguyen, Mentee
Project Title: Engineering a microbe to sense a low or no odor analyte and respond
Project Description: The overarching goal of the project is to determine whether we can engineer a microbe to sense a low or no odor analyte and respond by producing an output that has an odor that can work in the context of the nasal microbiome of rats. This project is broken into two parts. Part one uses a riboswitch to detect an analyte and produce the wintergreen scent and will test the functionality within the context of the rat nasal microbiome. The second part works to reduce the response time by engineering a protein switch using the principles of protein engineering. This project relies on multidisciplinary expertise in synthetic biology, protein engineering, microbiome analysis, and behavioral training of animals.
The project asks a fundamental question on whether or not we can engineer our sense of smell so that we can turn things we cannot smell into things we can smell. Just like sulfur is added to natural gas so we can smell a gas leak, we want to create a way to smell other molecules that maybe harmful to us.
There are several potential projects that the REU will participate in depending on the progress of the project.
A. One of the key aspects of this project is to develop a biocontainment circuit so that the engineered bacteria will not escape into the environment outside the context of the nasal microbiome. The REU student will work on second generation biocontainment strategies and will characterize the potential for genetic mutations to occur that will allow for escape from the biocontainment strategy.
B. The REU will have the opportunity to design, assemble, and test alternative gene circuit designs to sense the analyte and produce the wintergreen response.
The REU student will gain hands on skills in experimental design, implementation, and troubleshooting. You will learn a variety of molecular biology techniques including but not limited to PCR and restriction enzyme-based cloning (type II and IIS). You will also learn how to culture E. coli and Staphylococcus carnosus and how to detect and quantify protein expression in E. coli and S. carnosus.
Mentoring Plan: The day-to-day mentoring will be the primary responsibility of the postdoc scholar hired to work on the project. Each REU student will meet every week with Dr. Peebles (when I’m in town) to discuss career goals, and other research related topics. REU student will go through safety training at the start of the program. The REU student will receive in-lab safety training as well as an online safety course developed by CSU EHS. The REU student will be trained by his/her graduate student mentor in experimental techniques. The mentor will work closely with the REU student to plan and set-up experiments and interpret data. REU students will also receive guidance on how to search for research articles in online databases, read technical research articles, and report scientific findings in a poster format. Success of the REU experience will be evaluated through student and mentor feedback, through progress toward research goals, and through end of summer presentation.
Meghan A. Crabtree, Tri-Ethnic Center for Prevention Research, Psychology Department
Lori May, Mentee
Project Title: Survey of Substance Use by American Indian Youth
Project Description: The Tri-Ethnic Center for Prevention Research tracks substance use among American Indian teenagers in an ongoing survey study called Our Youth, Our Future. Every year, different American Indian youth who live on or near reservations across several geographic regions in the continental US complete this survey. This survey allows us to observe changes in substance use (or drug use) trends among these youth. We also use this survey to investigate the different environmental, social, and psychological factors that relate to American Indian adolescent drug use, with a special focus on identifying factors that might make some of these youth particularly resilient in spite of the challenges they experience in their day-to-day lives. This work is important, because it gives researchers and community members the information that they need to develop useful intervention and prevention tools to help students in these communities thrive and succeed.
The Tri-Ethnic Center for Prevention Research (TEC) has been funded by the National Institute on Drug Abuse (NIDA) to track the substance use of American Indian (AI) youth who live on or near AI reservations since 1974. Each year, youth across the country participate in the Our Youth, Our Future (OYOF) survey. Through systematic tracking of annual substance use of AI youth, we have been able to identify key trends that have marked significant reductions in levels of use as well as periods of marked increase. This type of epidemiological work is an important public health strategy, as identifying patterns and areas of heightened risk is critical for effective intervention . In addition, key risk and protective factors for substance use are examined. Identification of these etiological variables are important for the design of programs to prevent substance use and encourage healthy development.
As part of their training, participants will be involved in creating and organizing a fully annotated, psychometric codebook for the OYOF study, which will include summarizing all published research (coming out of TEC) utilizing each etiological measure within the OYOF survey, conducting brief reviews of the literature relevant to each measure, and conducting psychometric analysis (examining reliability, validity, multidimensionality, etc.) for each measure. Likewise, students will assist in providing a description of the nature of the samples collected year to year (e.g. sample sizes and demographic frequencies). While formulating and organizing the codebook, participants will familiarize themselves with measures that are of interest to them, they will formulate a research question and associated hypotheses, and conduct analyses to test these hypotheses using OYOF data.
Mentoring Plan: The participant will be mentored collectively by Drs. Meghan Crabtree (Research Scientist with TEC) , Kim Henry (Professor of Psychology and affiliated researcher with TEC), and Linda Stanley (Senior Research Scientist and Principle Investigator with TEC). Dr. Crabtree will mentor the participant in their day-to-day, introducing the participant to the OYOF project, overseeing and guiding the participant in organizing and structuring the OYOF psychometric codebook. Dr. Crabtree has strong experience mentoring undergraduate participants in similar NIH-funded research and training programs during her doctoral training (U-Research Training Initiative for Student Enhancement, or RISE program T34). In collaboration with Dr. Stanley and Dr. Henry, she will provide (virtual) “hands-on” mentorship of the participant in conducting psychometric analyses and other basic descriptive analyses in R and SPSS (statistical software programs), and other research tasks involved in conducting literature reviews, formulating research questions, and conducting analyses.
Mark Stenglein, Microbiology, Immunology and Pathology Department
Sydney Perkins, Mentee
Project Title: How Viruses Jump to New Host Species
Project Description: Most viruses that cause serious problems jumped into humans from animals. This is true for HIV, for new pandemic influenza viruses, and for SARS-CoV-2. Bunyaviruses are a less infamous but equally concerning type of virus that also have the potential to cause serious pandemics. We are working to understand what enables or prevents bunyaviruses from jumping into new species.
As the current pandemic illustrates, newly emerging viruses pose a serious threat to public health and the economy. This is true not just for coronaviruses, but also for a number of other types of viruses. One group of viruses of particular concern is the bunyaviruses, a large viral order that includes many serious human and animal pathogens. In fact, 3 of the 8 pathogens on the World Health Organization’s Priority Pathogen list are bunyaviruses (https://www.who.int/activities/prioritizing-diseases-for-research-and-development-in-emergency-contexts). The goal of this project is to generate a more detailed understanding of the processes that permit new potentially pathogenic bunyaviruses to emerge.
If the student can work in lab, this student will contribute to the development of a high-throughput assay to study bunyavirus reassortment. Ressortment is the shuffling of genes (on individual genome segments) from two parental viruses that can produce genetically novel viruses with new properties, like an expanded host range. This will involve molecular biology (cloning) and cell culture work. If the student can not work in the lab, the student will contribute to our analysis of genomics data related to this project.
Mentoring Plan: The student will primarily work day to day with Marylee Kapuscinski, a graduate student who is spearheading this project. I will meet with the student and Marylee weekly to guide their progress. I also have an ‘open door’ policy and students with questions can reach out to me anytime.
Michael Thomas, Neurocognitive Measurement Laboratory, Psychology Department
Sierra Sencenbaugh, Mentee
Project Title: Improving the Methods and Tools for Studying Psychiatric and Neurological Disorders
Project Description: This project seeks to improve the methods and tools used to study psychiatric and neurological disorders.
Students have the opportunity to be involved in two projects. The first seeks to identify neuronal biomarkers of healthy cognitive and brain aging. The second seeks to develop cognitive tasks that will be used in neuroimaging studies of psychosis. Neuroimaging (fMRI) data preprocessing, literature review, and (possibly) assistance in study appointments (including cognitive testing). Unfortunately, the bulk of this work (all but literature review) cannot be performed remotely and depends on a return to research approval.
The student will interact with others in the research group, conduct literature searches, carry out basic data analysis and modeling studies, and participate in group meetings and events.
Mentoring Plan: Day-to-day, the student will interact with graduate research assistants and our lab manager. The student will also participate in a weekly lab meeting. I will train graduate students and the lab manager in effective mentoring. Additionally, I will provide regular (at least biweekly) individual meetings with the student.
Nicole Kelp, Microbiology, Immunology and Pathology Department
Randy Vickery, Mentee
Project Title: Promoting Communication About Science Between Scientists and Non-Scientists
Project Description: How do scientists talk about science? How do non-scientists talk about science? And how can we break down barriers, helping different groups communicate about science together and solve scientific problems more effectively?
My lab has projects at the intersection of science communication and science education research. Thus, some projects are in collaboration with communication scholars and study the nuances of best practices of science/public health communication. Other projects examine the best ways to teach STEM students how to communicate effectively with diverse audience in a variety of media/venues. Finally, we are interested in the intersection of diversity, equity, and inclusion with science communication. Projects under development are focused on empowering members of diverse communities to communicate about science clearly and effectively.
While we are planning engagement activities in STEM classrooms and in informal learning environments, it is possible for all work to be done remotely due to COVID. Thus, the projects described below are chosen to be more focused on remote work.
REU or W2R students can participate in content analysis of qualitative data and/or statistical analysis of experimental survey data, depending on skills and interests. Additionally, students can help with literature reviews to help synthesize current theories in learning, in science education, and in public communication. Students will focus on examining the learning process involved in learning science communication skills. How do individuals of diverse backgrounds, such as first generation students or immigrants, learn how to think about and communicate about science? How can we better empower these individuals?
Mentoring Plan: I currently have several hourly student research assistants in my lab group who can help work with the REU student. I would be the main point of contact, however, as I don’t have a dedicated graduate student at this point.
Of note, I have a high teaching appointment in the new medical school branch, and we’ll be getting ready to launch in late July 2021. However, since the REU student would be working remotely I could easily do short daily check-in’s with them to guide their work as well as a longer session periodically. Additionally, they could join my biweekly lab group meetings with current students. I just wanted to let you know my appointment/schedule in case that would affect REU student experience.
Deborah Essert, Psychological Services Center Director, Psychology Department
Emily Pehlke, Mentee
Project Title: Investigation of the Increased Colorado Adult Suicidality During the COVID-19 Pandemic
Project Description: We are a team of mental health clinicians, substance use treatment providers, social workers and psychologists working together to address the increased suicidality among adults in Colorado during the COVID-19 pandemic. As part of our grant and services we are collecting data which we hope will help shed light on the psychosocial impact of the pandemic and will guide the ongoing response to the needs of our community.
Through our project we are addressing increased suicidality across Colorado through both direct therapy services and a prevention intervention offered to the community. Data is collected at multiple time points from participants receiving therapy services and will provide insights on aspects of mental health related to the COVID-19 pandemic, as well as treatment outcomes as they relate to the use of empirically-supported treatments for reducing suicidal thoughts and behaviors.
The REU Trainee will work with the Project Director and Assessment Director to examine preliminary data. They will also have the opportunity to join the treatment team meetings so they can gain experience with the implementation of an applied research project.
Mentoring Plan: The REU Trainee will be trained by the Project Director. They will work with the Project Director to learn about and the service/clinical side of the project and will work with the Assessment Director on the data collection aspects.