2025 SMART Research Projects

Global climate change is increasing the variability in precipitation patterns. The local balance between host and parasite will be sensitive to changes in salinity, pH, and water temperature. Understanding how trematode disease is affected by these conditions is imperative for understanding trends in infected host populations. The SMART student will be directly involved in experimental testing these effects. In addition the student will be involved in animal husbandry, break down and set up of an experiment, data collection and clean up, and statistical analysis. 

Prerequisites: No experience necessary. Students should be comfortable with microscopes, dissections of vertebrates, and use of animal for experimental biology (approved by IACUC).; Rising Juniors & Senior
Department: Ecology and Evolutionary Biology

This research project is focuses on how various gut bacteria impact neurodegenerative diseases like Parkinson's and Alzheimer's disease, a burgeoning field regarding the connection between gut bacteria and neurological disease. Using various nematode models, we have found that several bacteria (including human intestinal isolates) can dramatically enhance or decrease neurodegeneration. During these 10 weeks, I will teach this intern how to assess neurodegeneration and generate at least one transgenic nematode model (to assess molecular pathways). We will screen various models with different gut bacteria or individual candidate metabolites identified via mass-spectrometric analyses. Our SMART intern will gain expertise in basic C. elegans handling and genetics, fluorescent microscopy, and microbiology culture methodology. 

Prerequisites: No prerequisites are required, ideally someone who has connection to neurodegenerative diseases/aging and is interested in a career in biomedical science; Rising Sophomores & Juniors
Department: Molecular, Cellular, and Developmental Biology

Focusing on applying genome-wide association study methods to understand the genetics of complex traits like height, BMI, depression and alcohol use. We use a variety of statistical and computational approaches to identify genes that influence these traits, understand the molecular pathways in which those genes operate, determine genetic relationships among the traits, and predict trait values in external samples.  

Prerequisites: Coursework - Calculus Series, Differential Equations, Linear Algebra, & Chemistry; Rising Sophomores, Juniors & Seniors
Department: Ecology and Evolutionary Biology; Institute for Behavioral Genetics (IBG)

This project will use observational data and/or output from climate models to quantify the impact of southern hemisphere mid-latitude cyclones on physical properties such as temperature and salinity and biogeochemical properties such as oxygen and acidity, in the Southern Ocean.  

Prerequisites: Coursework - R coding is a must, knowledge of command line usage (linux/unix) is a big plus. Basic statistical knowledge is necessary (linear regression). Interest in genetics is necessary, but detailed knowledge of the methods, traits, and specific approaches can be learned during the summer; Rising Juniors & Seniors
Department: Atmospheric and Oceanic Sciences

We study human and mouse transcription and the control of gene expression by microRNAs.  We use approaches ranging from cell-based genome-wide assays, to biochemistry, and single molecule fluorescence.  The specific project will depend on student interests and research going on at the time the SMART Program starts.

Prerequisites: Rising Juniors & Seniors Only
Department: Biochemistry, Biophysics

Cells utilize transcription factors to orchestrate when and where transcription occurs. When a cell encounters a new stimulus in its environment, it can quickly respond by using stimulus-responsive transcription factors to temporarily change its transcriptional program. This project will look at the dynamics of these stimulus-responsive transcription factors. It will test the hypothesis that the mRNA transcripts coding for stimulus-responsive transcription factors don't persist as long in the cell as those of other transcription factors, and that this is a mechanism the cell uses to ensure its response is transient. This is a computational project and will be completed using bioinformatics and statistical methods. 

Prerequisites: None
Department: Molecular, Cellular, and Developmental Biology, BioFrontiers Institute

Bison play an important role in shaping and modifying many ecosystems, however  their impacts vary across site-specific conditions, including habitat type, time on the landscape, and herd density. The study of bison in certain habitat types are limited, including montane habitats in Colorado. With renewed interest in bison restoration in the state, there is a need to better understand how bison impact landscapes in Colorado. Therefore, this research studies the ecological impacts of a small and isolated bison herd at Genesee Park on the local plant community composition and occupancy of mid- to large-sized mammals. This field research utilizes plant cover sampling and camera traps across treatment (bison) and control (non-bison) pastures to understand the impacts from bison.

Prerequisites: Familiarity with plant ID  - Comfortable being outside for long periods of time and in extreme weather conditions (heat and sun exposure, high elevations)  - Detailed oriented; Rising Juniors & Seniors Only
Department: Environmental Studies

Approximating derivatives is well-understood in 1D. In higher dimensions, if one can choose the sampling points, then error decays quadratically in the spacing; but if one cannot choose the sampling points, error decays only linearly. We will investigate a processing technique that might achieve quadratic error given arbitrary points.

Prerequisites: Coursework - Linear algebra (SVD, eigenvalues). Numerical analysis is helpful but not necessary. Rising Juniors & Seniors Only
Department: Applied Mathematics

The calcium carbonate skeletons of marine organisms (e.g., corals, foraminifera) are important archives of past ocean properties like temperature and pH. This project will precipitate aragonite and calcite in the lab abiotically, under controlled temperature and rate conditions, to improve our understanding of skeletal chemistry. Characterization will include metal content (by inductively coupled plasma mass spectrometry), mineralogy (by Raman microspectroscopy), and crystal morphology (by scanning electron microscopy).

Prerequisites: Coursework and interest in Earth science and/or oceanography. Interest in geochemical lab work, but no experience required. Rising Juniors & Seniors Only
Department: Geological Sciences 

Individuals with Down syndrome experience chronic, elevated inflammation throughout their lives. This is associated with different susceptibility to infectious disease, but the mechanisms leading to this are not understood. This project seeks to provide more insight into differences in the immune system of individuals with and without Down syndrome by using cell culture models and stimulating them with different types of immune challenges to study the differences in response. This is a lab-based project that will involve cell culture and molecular biology techniques. 

Prerequisites: No experience required. Rising Sophomores, Juniors & Seniors 
Department: Molecular, Cellular, and Developmental Biology

This project will be conducted in collaboration with Denver Urban Gardens, an urban community garden collective. This study aims to examine landscape-level socioeconomic and biophysical features of urban landscapes and how they relate to arthropod community composition and ecosystem services. This project will involve lab work and fieldwork in Denver, CO. An undergraduate research assistant will assist with field data collection, insect identification, and greenhouse work with cucumber plants. They will additionally learn how to collect and analyze landcover data and multivariate biodiversity data. 

Prerequisites: Insect identification and R coding skills - preferred but not required. Rising Sophomores, Juniors & Seniors 
Department: Ecology and Evolutionary Biology

Genome Wide Association Studies (GWAS) of tobacco smokers have found several genes of interest that are associated with smoking behaviors. To better understand how these genes work, we are using cell culture to guide the creation of a mouse model for behavioral testing. We are currently performing transfections on cultured primary mouse astrocytes with CRISPR DNA plasmids to study the effects of several genes. Cultured astrocytes are assessed for dendritic branching using fluorescence microscopy. Once we find genes that affect the astrocytic response to nicotine, we are developing mouse models. Initially, with mice lacking the Akt2 gene, we found that astrocytes from mice exposed to chronic nicotine showed increased morphology consistent with intermediate astrogliosis. Astrocytes from wild type (WT) mice showed the opposite trend and were less complex. We will then perform behavioral testing including conditioned place preference (CPP), conditioned taste aversion (CTA), and prepulse inhibition (PPI). Our project will give SMART interns the chance to assist with handling mice, behavioral testing, fluorescence staining, cell culture,  and genotyping. We will also provide SMART interns with the opportunity to learn proper data collection and analysis, which will be complementary to the professional skills being taught through the program (e.g. grant proposal, elevator talk, presenting a poster and/or talk, writing a final manuscript-style report).

Prerequisites: Rising Sophomores, Juniors & Seniors 
Department: Institute for Behavioral Genetics