Summer Scholars Project Proposals

Summer 2021 Project Proposals

Comparative Biomedicine

Comparative Biomedicine

Project Title: Pathophysiology of emerging arboviruses
Contact: Dr. Matt Aliota, [email protected]

Project Description: Zika virus is dangerous to pregnant women and their fetuses/neonates throughout the Americas and beyond. This risk will persist for the foreseeable future, even if it is eventually curtailed by natural immunity and widespread vaccination. Therefore, we strive to provide important new tools for pregnant women and their health care providers to assess, and potentially reduce, the risk of congenital Zika syndrome. Therefore, we combine aspects of immunology, virology, and molecular genetics to understand how viruses like Zika virus emerge and how they subvert host immune defenses. Example topics for summer scholars to develop their proposal around include: (a) molecular evolution of Zika virus during transmission, (b) the role of antiviral signaling at the maternal-fetal interface, or (c) the impact of pre-existing immunity on flavivirus pathogenesis.

Techniques used: Cell culture, Molecular cloning, Flow cytometry, Classical virology approaches, RT-PCR, Immune assays


Project Title: Canine and human NK cell engineering for cancer therapies
Contact: Dr. Bruce Walcheck [email protected]

Project description: Our lab is actively involved in developing cancer immunotherapies for humans and companion animals. A focus of the lab has been on engineering human natural killer (NK) cells with enhanced Fc receptors that engage antibodies attached to tumor cells. Human NK cells engineered with one of our receptors are currently being examined in clinical trials at the University of Minnesota. We are also attempting to apply this same method in dogs to treat cancer. Our approaches include characterizing canine NK cells, designing and testing recombinant receptors to engage anti-tumor antibodies, and expressing them in NK cell platforms to examine their function. The summer scholar will be involved in these novel studies to help advance our goal of developing effective immunotherapies for cancer in dogs.

Techniques used: Techniques the summer scholar will be exposed to include cancer cell cytotoxicity assays, leukocyte functional assays, cell culture, and flow cytometry among others. The Summer Scholar will work with trained researchers to learn cutting edge techniques and develop an independent project and novel data.


Project Title: Developing immunosuppression free strategies for cell transplantation
Contact: Dr. Melanie Graham [email protected]

Project Description: Our lab uses an integrated interdisciplinary approach to address human and animal health and well-being. We have a unique focus on two closely related issues: 1) Developing methods to understand immunometabolism towards innovative therapies for diseases with high public health impact, e.g. diabetes, obesity, and infectious disease, and 2) Identifying the general reasons why animal models often fail to predict human outcomes, and providing solutions to improve the efficacy and well-being of animal models.  We are developing immunosuppression free strategies to transplant cells using immune tolerance strategies or device-based approaches.  Using islet cells, the insulin producing cells of the pancreas, as an example we have achieved of prolonged diabetes reversal in primates after porcine xeno-tx, the induction of robust tolerance to allografts, and have recently shown that cells survive for over 6 months using a bioartificial pancreas without any immunosuppression.  Taken together these technologies present a major paradigm shift in cell replacement therapy using unlimited cell sources (xeno- or stem cell- derived). The Summer Scholar will learn cutting edge techniques and develop an independent project and novel data in understanding factors that affect islet function and survival in the context of a complex translational animal model.

Techniques Used: PBMC functional assays; cell culture; cell transplant; flow cytometry; care and monitoring of animals used in research; digital spatial profiling.


Project Title: Modulating macrophage activation to alter behavioral outcomes following traumatic brain injury
Contact: Dr. Maxim Cheeran [email protected]

Project Description: It is known that traumatic brain injury (TBI), even when it does not result in loss of consciousness, can increase the risks for developing behavioral abnormalities, like cognitive impairment or addiction behavior, later in life. The specific mechanisms responsible for these long term behavioral outcomes is currently unknown, although it is known that persistent inflammation may have a part to play. The early response to injury in the brain is mediated by infiltrating macrophages. While the macrophage numbers return to baseline after the initial trauma, these macrophages exhibit a proinflammatory activation profile for several weeks which correlates with appearance of behavioral outcomes associated with TBI. This project investigates the role of these activated macrophages in the development of behavioral dysfunction. The hypothesis tested in our experiments is that classically activated macrophages (i.e. pro inflammatory) exacerbates neuronal dysfunction by remodeling synapses and inhibiting neurogenesis. Using this premise, we are testing ways to modulating the macrophage activation profile to an alternately activated state (anti-inflammatory) to promote neurogenesis and rebuilding of damaged neural circuitry. In the long run this would mitigate the impact of TBI on deleterious behavioral outcomes.

Techniques Used: Flow cytometry, IHC, behavior assays, and RT-PCR


Project Title: Reprogramming the tumor immune microenvironment in canine hemangiosarcoma
Contact: Dr. Erin Dickerson [email protected]

Project Description: Tumorigenesis is associated with the infiltration of various types of immune cells, including tumor associated macrophages (TAMs), which can evade the immune system and promote therapeutic resistance. Depending on the tumor microenvironment, TAMs are capable of promoting both anti- and protumor immune responses (M1 and M2 phenotypes, respectively). Canine hemangiosarcoma is an extremely aggressive cancer of blood vessel-formingcells with a high patient mortality. Because the accumulation of protumor (M2) macrophages is a feature of hemangiosarcoma, identifying mechanisms that drive immune-suppression and developing therapeutic approaches to program macrophages toward antitumor immune phenotypes will improve therapeutic responses. The metabolism of M1 macrophages favors glycolysis and low oxidative phosphorylation (OXPHOS). In contrast, the metabolism of M2 macrophages is characterized by fatty acid uptake, high levels of fatty acid oxidation (FAO), and OXPHOS. Preclinical studies support repurposing the beta adrenergic receptor antagonist, propranolol, as a treatment for hemangiosarcoma. Working with the Schwertfeger lab, we will determine if propranolol alters macrophage polarization and metabolism in vitro. We will treat mouse bone marrow derived macrophages (BMDMs) or macrophage cell lines with propranolol and evaluate changes in macrophage polarization and metabolism by flow cytometry and gene expression using standard markers.

Techniques Used: Cell culture, qRT-PCR, immunoblotting, flow cytometry, and metabolic assays.


Project Title: Vole prion proteins as substrates for RT-QuIC-based detection of CWD prions
Contact: Dr. Peter A. Larsen [email protected] 

Project Description: Significant progress has been made in the development of diagnostic tools capable of detecting prions responsible for transmissible spongiform encephalopathies (e.g., Creutzfeldt-Jacob Disease in humans; Chronic Wasting Disease (CWD) in cervids). An ultrasensitive prion amplification assay known as RT-QuIC has emerged as the gold standard for detecting infectious prions in a wide-variety of biological samples. An essential component of RT-QuIC is recombinant hamster prion protein, which is used as a substrate for prion amplification. However, recent data indicates that other rodent species, especially voles, have evolved prion proteins that are more suitable substrates for the RT-QuIC assay. Six species of voles occur in Minnesota and genetic analyses of their prion sequences warrant additional research with respect to RT-QuIC substrate functionality. The goal of this summer project is to conduct field-work aimed at collecting the target vole species and then examine how their prion protein products perform in RT-QuIC analyses. The summer scholar will work with an innovative team of experts who will assist with vole collection, isolation of target proteins, and assay performance. Outcomes from this project are anticipated to advance ongoing CWD and TSE biosurveillance efforts. 

Techniques used: Sherman live-trapping, PCR, RNA extraction, cDNA synthesis, molecular cloning, RT-QuIC


Project Title: Relationship between radiation therapy and brain inflammation
Contact: Dr. Davis Seelig [email protected]

Project Description: Cancer related cognitive impairment (CRCI) is a syndrome of decreased memory, attention, executive function, and processing speed that affects up to 76% of treated non-CNS cancer patients and persists for 5-10 years after treatment.  Although CRCI is currently thought to result primarily from the systemic effects of chemotherapy, it is unknown whether the non-target effects of ionizing radiation play a role.  Our previous studies have shown that hind-limb targeted, brain-sparing extracranial radiation therapy (ECRT) induces significant off-target brain inflammation and induces deficits in learning and memory in mice.  However, the mediators responsible for these distant effects and the impact of hypofractionation of RT on the development of CRCI are unknown.  Our central hypotheses are that ECRT induces distant brain inflammation via the circulatory delivery of pro-inflammatory mediators and that hypofractionated RT will result in more severe neuroinflammation and neurocognitive deficits than single fraction treatment.  To address this hypotheses, we will1) Characterize the circulating cytokine profile in irradiated mice, and 2) Evaluate the neuroinflammatory and neurocognitive impact of hypofractionated ECRT in mice.

Techniques used: Mouse behavioral analysis, Mouse dissection and tissue collection, Flow cytometry, Immunohistochemistry


Project Title: Lipid Metabolism and Osteoarthritis
Contact: Dr. Alonso Guedes [email protected]

Project description: This project focuses on understanding how lipid metabolism contributes to osteoarthritis (OA) pathophysiology. Specifically, our studies seek to determine both the therapeutic efficacy of cyclooxygenase (COX) and soluble epoxide hydrolase (sEH) inhibition in OA and understand the enzymes’ role in OA development/progression. Inhibition of arachidonic acid metabolism with COX inhibitors is first-line therapy for OA in animals and humans. sEH is an enzyme also involved in lipid metabolism that is receiving increasing attention for its role in pain relief and tissue repair. Our overall objectives are i) to elucidate the effect of a COX/sEH dual inhibitor on mobility and cartilage damage in a mouse model of OA and ii) characterize the expression of COX, sEH and related biomarkers in equine OA joint tissues. The proposed research is innovative because it will target the symptomatic and structural aspects of OA. It is significant because it is expected to provide strong evidence-based proof of principle for further development and future clinical trials of dual COX/sEH inhibitors, ultimately providing opportunities for the development of novel approaches to treat OA. 

Techniques used: Mouse models of OA, behavior assessment of pain and mobility, immunohistochemistry, western blots, PCR.


Project Title: Neuroinflammation associated with sequential traumatic brain injury in a rodent model
Contact: Dr. Maxim Cheeran [email protected]

Project Description: A concussion is the most common type of traumatic brain injury (TBI) and most patients recover without significant CNS pathology. But these patients are susceptible to the development of neurodegenerative and neuropsychiatric complications after a ‘second hit’ or repetitive TBI, which is common among soldiers and athletes. The present study hypothesizes that a second injury after a mild TBI will result in an enhanced neuroinflammatory response which persists longer and results in greater behavioral deficits. We also posit that treatment with a stem cell therapy will decrease the window of susceptibility for the second hit to elicit an exaggerated immune response in the brain.

Techniques Used: Flow cytometry, IHC, behavior assays and RT-PCR


Project Title: Reducing mastitis in the dairy cow by increasing the prevalence of beneficial polymorphisms in genes associated with mastitis resistance
Contact: Dr. Brian A. Crooker [email protected]

Project Description: Our premise is that previous selection practices have successfully increased the presence of genetic polymorphisms associated with increased milk yield but have decreased the presence of polymorphisms associated with disease resistance. We will use contemporary Holsteins and unique Holsteins that have not been subjected to selection since 1964 to determine differences in immune and inflammatory responses and mammary gene expression when unselected and contemporary Holsteins are subjected to intramammary challenges with E. coli or S. uberis. Pathogens will be infused into a quarter and blood and milk samples collected for analysis. The genome of the study cows will be sequenced to identify potentially beneficial polymorphic differences between the genotypes. The long-term goal is to increase the presence of polymorphisms in the Holstein cow to strengthen immune function and increase mastitis resistance.

Techniques used: Animal handling, milking, blood and milk sample collection, processing and analysis including ELISA cytokine assays


Project title: Investigating loss of function variants in the general equine population
Contact: Dr. Molly McCue [email protected]

Project description: Large-scale studies of genetic variation have been instrumental for facilitating the identification of disease-causing variants in human patients with genetic disease. One of the most surprising findings from these studies has been the higher than expected number of variants computationally predicted to have a detrimental effect on phenotype in apparently healthy individuals (the genetic burden). However, the genetic burden in many studies is inflated for several reasons, including inaccuracies in the reference genome and computational prediction program errors. A recent study of human loss of function (LOF) variants demonstrated that approximately 44% of the genetic burden are false positives and cannot be experimentally validated. We have developed the first large-scale study of genetic variation in the horse, and have established that the genetic burden in this population is 5,807 variants. The proportion of the genetic burden that represents false positives in the horse is not known, but is likely higher than humans due to the horse reference genome being less complete than the human reference genome. Therefore, the goal of this project is to use computational resources to validate the variants computationally predicted to have a detrimental effect on phenotype in the horse.

Techniques used: DNA isolation, Evaluation of whole genome sequencing analysis, Understanding of possible errors in the equine reference genome, Interpretation of the Integrative Genome Viewer for visualizing genome sequencing data, Computational evaluation of predicted highly detrimental variants, Investigation of genes containing LOF variants


Project title: Investigating of the genetic bases of cardiac arrhythmias in racehorses
Contact: Dr. Molly McCue [email protected]

Project description: Sudden death has a devastating impact on the racing industry and there are major safety concerns. Of the hundreds of horses that die on the track each year, the cause of death is not identified for 47% of them. Cardiac arrhythmias are thought to explain a large number of these cases. Most horses that develop arrhythmias have no underlying structural heart disease, making it virtually impossible to detect those that will develop arrhythmias. Arrhythmias in human athletes without underlying structural heart disease are almost exclusively caused by mutations in ion channel genes. These athletes frequently develop subtle ECG changes that are used for monitoring and to guide when retirement from high level athletic performance is recommended. Given the similarities between these arrhythmias in humans and horses, it is likely that mutations in genes responsible for cardiac arrhythmias in humans are associated with alterations in ECG measurements and the presence of arrhythmias in horses. This project will investigate if mutations in human arrhythmia causing genes are associated with changes in ECG measurements and cardiac arrhythmias in racehorses.

Techniques used: Collection of ECGs at rest, maximal intensity exercise, and immediately following exercise, Interpretation of ECGs at rest, during exercise, and following exercise in apparently healthy racehorses, Interpretation of cardiac ultrasound of apparently health racehorses with cardiac arrhythmias, State of the art application of genetics to improvement of equine health and welfare, DNA isolation, Agena Bioscience IPLEX bioassay genotyping, and statistical analyses, Candidate gene investigation.


Project Title: Magnetic Resonance Imaging of Degenerative Disc Disease
Contact: Dr. Casey P. Johnson, PhD, [email protected]

Project Description: Degenerative disc disease (DDD) is a major health problem for both dogs and humans. Degeneration of the intervertebral discs in the spine can lead to back pain and disc rupture, which can compress and damage the nerves of the spinal cord. There is a clinical need for new, noninvasive imaging techniques to predict whether a disc will rupture so that preventative treatment can be applied. Dogs are the only available large animal model that spontaneously develop DDD and thus have significant comparative advantages for studying DDD and its treatment.  The goal of this project is to investigate magnetic resonance imaging (MRI) techniques to detect and characterize disc degeneration in dogs. The summer scholar will analyze quantitative MRI measures of the biochemical and biomechanical properties of canine intervertebral discs. Several canine vertebral column specimens from the thoracolumbar region of the spine will be imaged ex vivo at 3T MRI and then subsequently analyzed with biomechanical testing, biochemical assays, and histology. This project will lay the groundwork for future in vivo studies in dogs. 

Techniques used: Techniques: magnetic resonance imaging, biomechanical testing, histology, data analysis, scientific communication (presentation and writing); Application – degenerative disc disease.


Project Title:  Metagenomic assessment of livestock commensal microbes
Contact: Dr. Noelle Noyes, [email protected] 

Project Description: Our lab is developing bioinformatic and statistical methods to identify signatures of transmission and persistence of commensal microbes within metagenomic datasets of various types. For this summer project, the student would join an interdisciplinary team to apply novel computational methods to existing data obtained from livestock animals of various species. The student will join weekly lab and relevant project meetings, and will take an active role in this collaborative work. Opportunities for on-farm sampling and/or molecular biology labwork may be possible, but depend on the COVID-19 situation during the summer. Note that all of the required work can be done remotely if needed.

Techniques used: Student will learn how to conduct bioinformatic and statistical analysis of shotgun sequencing data, and appropriate interpretation of analytic results.

Emerging, Zoonotic, and Infectious Disease

Emerging, Zoonotic, and Infectious Disease

Project Title: Nanopore-based adaptive sequencing for vector-borne disease surveillance
Contact: Dr. Peter A. Larsen [email protected]

Project Description: Single-molecule nanopore sequencing has emerged as a powerful tool for real-time sequencing-based biosurveillance and strain identification of pathogens. In particular, recent software advancements have made it possible to selectively enrich for viral and bacterial communities without the need for host depletion protocols. This approach is known as adaptive sequencing and it holds great promise for pathogen discovery and surveillance. Our research team is leveraging nanopore-based adaptive sequencing for a variety of domestic and international zoonotic disease surveillance projects, including tick-borne, rodent-borne, and bat-borne pathogens. The goal of this summer scholar project is to expand our adaptive sequencing method to include insect-borne pathogens found throughout Minnesota. The summer scholar will work with an innovative and vibrant team who are utilizing adaptive sequencing to phylogenetically characterize causative agents for a variety of zoonoses occurring in the state. The scholar will collect mosquitoes and midges from select areas, morphologically identify collected species, extract DNA and RNA, and perform RT-PCR and adaptive sequencing experiments. Outcomes from the research will directly support field-based biosurviellance initiatives that center on portable genomic technologies.

Techniques used: Insect collection, DNA and RNA extraction, PCR, RT-PCR, nanopore library prep and sequencing, phylogenetic analyses


Project Title: Spatio-temporal analysis of rabies animal cases in eastern North America
Contact: Dr. Meggan Craft [email protected]

Project Description: The current enzootic zone for raccoon rabies in eastern North America ranges from subtropical to cool temperate climates. This latitudinal climatic gradient profoundly affects raccoon ecology and disease dynamics. Information about latitudinal and seasonal variation in raccoon ecology remains incomplete, and is especially true for urban environments, which often exhibit distinct ecological conditions and disease dynamics. To assess whether eco-climatic variation has a generalizable effect on infection dynamics in urban and rural raccoon populations, we will analyze spatiotemporal outbreak patterns across decades from enzootic rabies virus circulation in raccoon populations of the eastern US. Here we ask: How do urban and rural outbreaks along a latitudinal gradient differ in terms of size, duration, and seasonality? We will use raccoon rabies surveillance data from the eastern US from 2006 to 2017. We will classify each data point as predominantly urban or rural. Data will be analyzed using a hurdle model. The student will have weekly (or as needed) mentoring meetings. Output will include (a) the opportunity to contribute to a peer-reviewed manuscript and (b) working with stakeholders to inform landscape level management strategies for enhanced control of raccoon rabies.

Techniques used/learned: statistical modeling in the program R; opportunity to work with public health officials and wildlife disease managers


Project Title: Understanding transmission dynamics of feline foamy virus in the Florida panther
Contact: Dr. Meggan Craft [email protected]

Project Description: Can the iconic Florida panther help to prevent the next pandemic? Panther researchers at the University of Minnesota have spent the last few years studying how best to protect panthers from a deadly virus called feline leukemia virus (FeLV), which caused a major outbreak in panthers in 2002-2004. Part of this work has involved testing if a non-disease causing virus closely related to FeLV, feline immunodeficiency virus (FIV), can help to predict FeLV transmission dynamics by identifying traits or individuals that are predictive of transmission events. Identifying these individuals could help to better predict, and even prevent, another FeLV outbreak before it can happen. Results of this work suggest that FIV is able to predict FeLV dynamics under some conditions, but these results would be strengthened by testing the same process with an additional non-disease causing virus, feline foamy virus (FFV). Here we propose a quantitative project for a motivated student with a computational background and interest to test FFV’s ability to predict FeLV dynamics, and then to share these results with both the scientific community and the public.

Techniques used/learned: statistical and simulation modeling in the program R; working with genetic sequences of FFV in Phyloscanner


Project Title: Developing a portable magnetic particle spectroscopy (MPS) platform for on-field detection of influenza a virus and mycoplasma hyopneumoniae
Contact: Dr. Maxim Cheeran [email protected]

Project Description: Porcine respiratory disease poses a major challenge to both veterinarians and pork producers. Conventional methods for identification of pathogens causing porcine respiratory disease are time consuming and require specialized laboratory facilities. It also involves multiple tests to detect different pathogens. MPS technology can be used to develop an accurate, affordable, fast and easy-to-use test for pathogen detection, including simultaneous detection of multiple pathogens in a single test. We are in the process of developing a portability MPS system that will enable early, rapid detection of two common porcine respiratory pathogens, allowing implementation of quick and effective prevention, and control strategies for these respiratory infections in swine. In order to develop these handheld tests we have generated monoclonal antibodies (Mabs) to M. hyopneumoniae that do not cross-react with other commensal or other pathogenic species of swine mycoplasma. Working with Dr. Maria Pieters we will characterize these antibodies for cross-reactivity to M. hyosynoviae and quantify its ability to detect M hyopneumoniae in common clinical sample matrices used for diagnosis of respiratory infection in pigs. We expect that these Mabs when used in a testing system with improved specificity, may provide the swine industry with a more effective tool for screening and monitoring M. hyopneumoniae infection in swine production systems.

Techniques used: ELISA development; purification and production of monoclonal antibodies; western blot 


Project Title: Immune drivers of PRRSV evolution
Contact: Dr. Maxim Cheeran [email protected] or Dr. Declan Schroeder or Dr. Kim Vander Waal

Project Description: Genetic variation and the presence of multiple co-circulating genetic strains, or "lineages," is the norm for many pathogens, particularly for rapidly evolving viruses, like PRRSV. Interactions between different lineages can occur if infection by one lineage confers partial cross-immunity to a related lineage, thus creating the potential for immune-mediated competition amongst co-circulating lineages. In this project will evaluate how immunity influences evolution of PRRSV using an experimental infection approach, where quasi-species evolution will be tracked via next generation sequencing. The project explores how immunity-driven factors, such as vaccination or prior infection, may impose selective pressures and alter transmission dynamics for multi-lineage pathogens, thus, advancing our understanding of the evolution, transmission and persistence of highly diverse viruses.

Techniques used: viral culture and purification, virological assays, RNA extraction, sequence analysis methods


Project Title:  Weather influences on PRRSV inter-farm transmission
Contact: Dr. Kimberly VanderWaal [email protected]

Project description: Understanding the spread of pathogens between swine farms is critical for disease control.  Adverse weather events may favor local transmission of pathogens, both through comprising biosecurity and facilitating environmental transport of pathogens. High winds may create breaches through which viruses can enter a farm; flooding can spread viruses that may be present in a manure lagoon over a larger area; and the disturbance in the area (lack of power, damaged infra-structure) may potentially increase absenteeism following the event, leading to inadequate or insufficient animal handling. Areas of the U.S. prone to adverse weather are often areas where swine production is also intense. This investigation will measure the association between the occurrence of PRRSv outbreaks in farms and extreme weather events in counties where those farms are located.  We will leverage farm status data already collected via the Morrison Swine Health Monitoring Project (MSHMP), which tracks the weekly status of sow farms of ~50% of the U.S. sow population. Data on extreme weather events per county will be collected from sources such as the National Oceanic and Atmospheric Administration (NOAA), which makes this data freely available online. Models evaluating the association will be constructed by the student under mentor’s supervision. 

Techniques used: The student will gain experience in epidemiology, transmission dynamics, spatial analysis, and data visualization. They will be involved in data collation, preparation and in the development of statistical models to evaluate our question. The student will gain skills in hypothesis formulation, development of epidemiological studies, data collection and processing, analysis and interpretation of study findings and potentially in publication of journal articles.


Project Title: Small fish, big problem: Solving the reproductive bottleneck of golden shiners
Contact: Dr. Nick Phelps [email protected]

Project description: The Minnesota aquaculture industry is the second largest producer of baitfish in the USA, with golden shiners being one of the most highly valued species. Significant efforts are underway to increase local production of golden shiners to meet a supply shortage that has been growing over the last decade. One major hurdle stands in the way: the ovarian parasite, Ovipleistophora ovariae, that effectively sterilizes female fish by age-2 and was recently confirmed to be present in both natural and manmade Minnesota golden shiner ponds. There are immediate and significant concerns that must be addressed. After thorough consultation with aquaculture producers, we have developed a long-term project plan that builds upon previous and ongoing research to address the highest priority needs. As part of this effort, the Summer Scholars student will assist the project team with field and laboratory research to identify O. ovariae-free populations of golden shiners to support industry development. This will include sampling of fish from across the Minnesota, conducting molecular and pathological diagnostic exams, and writing reports summarizing the results. The student will have an opportunity work with researchers, aquaculture producers, and natural resource managers to address a real-world problem.

Techniques used: A variety of field and laboratory techniques will be used during the course of the project, including trapping/seining fish from natural and manmade ponds, performing fish necropsies, performing molecular and histopathological diagnostic testing and interpretation of results, and communication with internal and external project partners. Previous experience with field and/or laboratory methods is preferred, but not required.


Project Title: Modeling dynamic microbial interactions
Contact: Dr. Amy Kinsley [email protected]

Project Description: The composition of various bacterial communities (i.e., microbiota) are complex, dynamic, and highly dependent on interactions between microbial species that range from mutualism to competition. The cumulative effect of these intraspecific interactions helps shape microbial ecosystems, which in-turn can contribute significantly to human, animal, and environmental health. One role that ‘heathy’ microbiota play in the context of biological homeostasis is the exclusion of opportunistic pathogens. The objective of the proposed project is to develop models of microbial interactions that can be used to understand and increase resistance to invasion and persistence of opportunistic bacterial pathogens. To achieve this, we will use an innovative combination of experimentation and mathematical modeling to understand the impact of interaction patterns on pathogen abundance. Results of this project will be used to inform the manipulation of microbial communities to enhance sustainable aquaculture systems.

Techniques used: 16S rRNA sequencing-sample collection and data analysis, Mathematical Modeling-Network models, Predator/Prey models, Aquaculture techniques (water quality, fish health, IACUC protocol implementation) 

Mentoring/Supervision plan:

Upon arrival, the student and faculty advisor will establish appropriate weekly goals that span the entire training period. These goals will be met through a combination of training including regular discussion of the topics indicated above, review of primary literature related to these topics, participation in ongoing research projects, training of methods, and weekly meetings with faculty advisor to discuss progress with training goals, training needs, and any additional topics of importance. 


Project Title: Enhancing CWD education and outreach in Tribal communities through community partnerships
Contact: Dr. Tiffany Wolf, [email protected]  and Dr. Roger Faust, [email protected]

Project Description: Chronic Wasting Disease (CWD) is a fatal, contagious disease of cervids in Minnesota and surrounding states. In 2019, our team learned that CWD information, including potential human health risks, was not reaching everyone. We were asked to facilitate CWD outreach to diverse hunting communities, including Tribal Nations. Given historic relationships and/or limited media sources, communication methods used by state management agencies may not reach disenfranchised communities. Effective engagement in Tribal communities on CWD risks to cervid populations, humans, and hunting heritage can lead to CWD hunting practices that align with science-based best practices and support for management of CWD by Tribal natural resource agencies. With that, our team is working with community partners to explore and understand cultural influences and understanding of deer and CWD through a community-based participatory research method. Community partners will lead interviews and/or focus groups in their community to gather this knowledge. Through these efforts we hope to accomplish the following goals: 1) enhance our understanding of Native American perceptions of and responses to wildlife disease, particularly related to CWD; 2) develop and engage in culturally-appropriate CWD outreach and education; 3) develop inclusive, community-specific CWD management plans integrating cultural values and science-based best practices. 

Techniques used: Qualitative data analysis;  Community partnership methodology;  Human dimensions of infectious diseases (CWD)

Population Systems

Population Systems

Project Title: Reducing dairy cow lameness
Contact: Gerard Cramer [email protected]

Project description: Lameness is a pervasive prevalent problem in the dairy industry that affects both animal welfare and farm profitability. A cow with lameness experiences negative changes in her physiology, behavior, and affective state. Current locomotion scoring in used to evaluate farms in dairy welfare assurance programs.  In this project, we will correlate those locomotion scores with more readily available hoof lesion data. This will require farm visits to locomotion score the herd and meetings with hoof trimmers to collect hoof trimming data.

Techniques used: Locomotion scoring, hoof trimming/lameness techniques, record analysis, data management 


Project Title: Capacity building for international animal disease surveillance
Contact: Andres Perez: [email protected] 

Project description: The Center for Animal Health and Food Safety (CAHFS) is the University of Minnesota College of Veterinary Medicine (CVM) service unit for issues related to veterinary public health. Our activities are ultimately intended to prevent or mitigate the risk associated with endemic, emerging, and foreign diseases that affect the health of animals, humans, and the environment. CAHFS is also one of 6 collaborating centers for capacity building of veterinary services designated by World Organisation for Animal Health (OIE) worldwide. CAHFS helps the CVM navigate the challenges of an increasingly interconnected world by bringing global solutions for Minnesotan challenges, and contributing Minnesotan solutions to global problems affecting animal and public health, and food security. The summer scholar/s will work with CAHFS staff in a combination of educational and research activities. Specifically, the summer scholar/s will collaborate on (a) the revision of educational material for capacity building projects targeting issues and trainees from East Africa, Latin America, and/or South East Asia, and (b) modeling and risk analysis assessments for infectious diseases, most likely, avian influenza and/or porcine reproductive and respiratory syndrome.

Techniques used: Analytical epidemiology (risk analysis, predictive modeling), and capacity building and trade of food animal products.


Project Title: Developing 3D models for training in disease surveillance and food safety
Contact:
Dr. Roxanne Larsen [email protected]

Project Description: Limitations on in-person activities highlight the increased need for a variety of educational simulation models (hands-on and virtual) for training professionals in disease surveillance, food safety, and animal health and welfare. Our CVM team will utilize the latest biomedical 3D printing and virtual technologies via the Earl E. Bakken Medical Devices Center (UMN) in creating models to assist in education and training of veterinary students, veterinarians, and meat inspection/processing personnel. These models will highlight key anatomical structures important for compliance and competence in disease testing and inspection. Access to and training from these models will directly impact food safety, meat inspection, animal welfare, veterinary public health, and production animal medicine. While working with a team, the student will assist in the development of 3D printed, digital, and virtual models as well as educational assessments to measure the impacts of the models on disease sampling and/or meat inspection procedures. This project will improve education and training programs by not only focusing on the technical skills required to accurately sample for foreign animal disease surveillance testing and specified risk materials in food safety, but also how to educate others on these processes using effective communication skills and theories in pedagogy.

Techniques used: anatomical dissection, basic radiological imaging, 3D and virtual model development and printing; educational research design; communication and education techniques for interacting with a wide variety of trainees and shareholders; reinforcement of skills in veterinary public health, production animal medicine, and food safety practices. 


Project Title: Randomized Placebo Controlled Field Trial Investigating the Effect of a Novel Probiotic (ProTernative®) Supplementation on Neonatal Dairy Calf Health and Performance
Contact: Dr. Whitney Knauer [email protected]

Project Description: High levels of dairy calf morbidity due to respiratory and diarrheal disease represent animal health, welfare, and antibiotic stewardship concerns, and result in economic losses through increases in labor, medication costs, death, culling, and impaired future performance. Non-antibiotic preventative products that help support health and growth throughout the pre-weaning period are needed. ProTernative®, a probiotic product containing Saccharomyces cerevisiae boulardii shows promise in improving dairy calves immune function, resistance to heat stress, and resilience to diarrheal disease during the pre-weaning period. However, large field trials are needed to investigate the short and long-term effect of this product under field conditions and natural disease exposure. Furthermore, as this product can be fed in both milk and starter grain, studies are needed to investigate the efficacy of supplementation during both the pre- and post-weaning period. The aimof this field trial is to describe the efficacy of feeding ProTernative® from birth on measures of dairy calf health and performance. The student will conduct research in a field laboratory setting on a commercial dairy farm in MN, and will have the opportunity to present the results of their project at the Annual Meeting of the American Association of Bovine Practitioners in 2022.

Techniques used: With the assistance of the PI (Knauer) and Co-PIs (Godden/Caixeta), the student will be responsible for all study related activities including data collection (calf health scoring; calf body weights; thoracic u/s), data management, analysis, and reporting. The student will become proficient at thoracic ultrasonography as well as increase their knowledge of calf health and management.


Project Title: A Forest to Fork Approach to Optimized Sustainable Food Security and Natural Resource Management with an Eye Toward Spillover Risk Management
Contact: Dr. Dominic Travis [email protected]

Project Description: Food Security can be defined as: “when all people, at all times, have physical and economic access to sufficient safe and nutritious food that meets their dietary needs and food preferences for an active and healthy life”. Unfortunately, an estimated 795 million people were food insecure before the current Pandemic, even with great investment. Access to sufficient protein is a significant contributor to this issue and wild meat is a significant source of easily accessible animal protein for landless, rural peoples throughout developing countries on every continent (Golden et al, 2011). It is also important for other nutrient and caloric metrics – such as fat - in many areas (Siren et al., 2008). The goal of the “forest – to – fork”  project is to answer the question: “what is wildlife’s contribution to global food security?” Built on a previous pilot study, we will design and conduct a modified systematic review for this topic across the domains of food security, ecosystem services and global health. The SS candidate will help design and conduct this study (in partnership with OIE and FAO), and then pick a sub question to analyze and present to partners.

Techniques used: The student will learn about the complexity and drivers of wildlife trade and bushmeat consumption and how it leads to the risk of spillover; complexity science and ecosystem health; systematic & scoping literature review – methods and analysis; and defining scientific questions within larger programmatic platform; communication with and to FAO/OIE.


Project Title: The effect of multimodal pain management strategies on acute pain, and subsequent health and performance associated with disbudding neonatal goat kids
Contact: Dr. Whitney Knauer [email protected]

Project Description: There are 14,000 dairy goats in the state of MN, many of which were disbudded as neonates without the use of any pain management. We are currently lacking comprehensive information about current disbudding and pain relief practices amongst dairy goat producers in Minnesota, but anecdotal evidence suggests that the use of any form of pain relief during disbudding is low to non-existent. Disbudding, or the removal of the cornual epithelium through thermal destruction, is well documented to elicit painful responses in goat kids. As such, the lack of pain management represents a significant welfare concern for dairy goat kids and the dairy goat industry. This research will deploy a novel pain mitigation strategy on a commercial farm to investigate longer-term health and performance measures. The results from this study will be directly applicable at the farm level, providing an immediate positive impact on dairy goat welfare, and the dairy goat industry in MN and beyond. The student will conduct this research in a field laboratory setting on a commercial dairy goat farm in WI, and will have the opportunity to present the results of their project at the Annual Meeting of the American Association of Small Ruminant Practitioners in the Fall of 2022.

Techniques used: With the assistance of the PI, student will be responsible for study related activities including sampling, data management, analysis, and reporting. The student will become proficient at disbudding dairy goat kids as well as increase their knowledge of common practices of dairy goat producers. 


Project Title: Behavioral Analysis of Wild Red-tailed Hawks During the Wildlife Rehabilitation Process
Contact: Dr. Julia Ponder [email protected]

Project Description: Stress monitoring in raptors is limited by the current methods for measuring acute stress in birds, which include plasma corticosterone, blood glucose, heart rate, and temperature.  The majority of these tests require stress-inducing handling, which limits the practical clinical use of these tests.  At this time, there are no scientifically validated, non-invasive methods for monitoring stress in raptors in a clinical setting.  This project will predominantly focus on the behavioral analysis portion of a larger ongoing research project at The Raptor Center (TRC), which is being performed to evaluate behavioral assessments as a method of identifying stress in wild red-tailed hawks during the rehabilitation process, by correlating behaviors with heart rates and plasma corticosterone values. 

The summer scholar’s work will focus on performing focal interval sampling of the behaviors displayed by red-tailed hawks in video recordings during episodes of rest and during/after a stressful event.  Video recordings will be obtained during the winter and spring of 2021, though additional data may continue to be collected throughout the summer pending caseload.  Student would also have the opportunity to learn general clinical skills, including venipuncture and training on raptor handling.  Potential for training in specialized laboratory procedures (corticosterone ELISA) as timing allows. 

Techniques used: Literature search, Raptor restraint/handling, venipuncture, Behavioral analysis in raptors, focal interval sampling techniques, Transdermal placement of remote heart rate sensors in raptors, ELISA techniques, Data collection, processing, and analysis, Scientific writing and communication


Project Title: Adapting high expansion foam for use in American systems for mass depopulation and on-farm culling
Contact: Dr. Marie Culhane, [email protected]

Project description: The scholar will assist with a newly funded USDA project to adapt high expansion nitrogen-gas filled foam anoxia (N2(g)-anoxia) for use as an acceptable routine method for on-farm euthanasia in American agricultural systems.  The student will work with veterinarians and animal scientists to deploy commercially-available, on-farm N2(g)-anoxia kits to three operations (swine, turkey, and dairy) in Minnesota. Under multiple environmental conditions and with animals of different biological parameters, we will evaluate the feasibility of these euthanasia carts for routine use on US farms. N2(g)-anoxia is in use in European agricultural systems, and the cart system used in Europe can be imported for use in the USA with smaller sized individual animals or groups of animals. For larger animals, we will test readily available farm equipment (such as small trailers or containers) to accommodate difficult to move animals such as nonambulatory cattle or sows. Our goal is to achieve a repeatable, humane, timely, contained complete system that results in death, is easy to use on farms for individual or small groups of pigs, turkeys, or cattle, that is acceptable and safe for animal caretakers and approved by welfare experts for culling during normal operation of the farm.

Techniques used: The scholar will learn techniques such as environmental measurements, physical exam, determining the time to reach anoxia (<2% oxygen) after filling the cart, time to unconsciousness, time to death, ease of carcass removal from the cart, and necropsy. More specifically, the scholar will learn how to perform an antemortem evaluation of the animals including body condition scoring, body temperature, recording clinical signs of disease, and activity level. The scholar will learn animal behavior by evaluating videos of the animals, specifically looking for aversive behaviors (head shaking, raising head and neck above bubbles, escape attempts, and finally, loss of posture).


Project Title: The contributions of wildlife rehabilitation to peer-reviewed scientific literature
Contact: Dr. Michelle Willette [email protected]

Project Description: While there is little doubt that humans have cared for injured and orphaned native wildlife throughout our history, the ‘profession’ of wildlife rehabilitation is relatively recent with professional associations first being formed in the early 1970s. Clinical wildlife medicine is a developing specialty in veterinary medicine for the diagnosis and treatment of individual, free-living wildlife.  It is estimated that over 500,000 wild animals are admitted to over 5,000 permitted wildlife rehabilitation facilities annually. ‘One Health’ is an approach that integrates human, domestic and wild animal, and environmental health and it is well-recognized that wildlife can serve as biosentinels for emerging diseases and as pathogen reservoirs for diseases in humans, livestock and poultry.  But clinical wildlife medicine has also created or advanced medical and surgical procedures that are applicable to exotic pet species, research species, and related companion animal species. Yet there have been no formal investigations into what relevant information is currently coming from wildlife rehabilitation facilities. Project – A review of the scientific literature will be conducted and prepared for publication. The specific focus of the review will be to identify types of information supported by data from clinical wildlife medicine and how to apply this information to clinical non-traditional species medicine and population level issues of human, animal and environmental health. A pilot project has already been conducted which will ‘jump start’ this project and move it quickly to completion. Additionally, the scholar will spend time working in The Raptor Center clinic obtaining experience in clinical procedures with raptors.

Techniques used: Literature search, Literature review, Retrospective study, Data collection/processing/handling, Scientific writing and communication, Data visualization, Clinical raptor medicine, surgery, and rehabilitation


Project Title: Reverse Trendelenburg and the Incidence of Gastroesophageal Reflux (GER) in Isoflurane-Anesthetized dogs
Contact: Dr. Erin Wendt-Hornickle [email protected]

Project description: The objective of this study is to determine if reverse Trendelenburg position (head-up tilt) has any effect in the incidence of GER during anesthesia in dogs. We will test the hypothesis that a 20° head-up tilt will significantly decrease incidence of GER during anesthesia. Thirty-six client-owned dogs admitted for elective knee surgical procedures will be recruited for inclusion into this prospective, randomized, parallel-arm study. All dogs will have comprehensive physical examination, followed by appropriate lab work. Dogs treated with gastric antacids or prokinetics within 1 month of surgery, with a history of GER, regurgitation, vomiting, esophagitis, or coughing will be excluded from the study. Dogs receiving treatment with nonsteroidal anti-inflammatory medications (NSAIDs) will be included in the study, but this will be recorded and factored into analysis. Owners of all dogs will sign an informed consent form before enrollment of their pet in the study. Immediately after induction of anesthesia, a 6.4-French (2.13-mm) esophageal multi-use pH probe, calibrated within 10 minutes of use in buffer solutions of pH 4.0 and 7.0, will be introduced into the esophagus via the oral cavity. Probe placement will be performed in all dogs by investigators skilled in placing esophageal temperature probes (a similarly shaped, albeit larger instrument) to ensure consistency in the positioning of the probe. Approximately half of the dogs will be tilted 20 degrees in a reverse Trendelenburg position. The other half will be positioned in the typical fashion. Esophageal pH will be recorded throughout anesthesia until extubation.

Techniques used: Client communication, patient enrollment, inclusion and exclusion criteria, data collection and analysis, poster completion and presentation, collaboration with clinicians.