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RESEARCH EXPERIENCES FOR UNDERGRADUATES FROM RURAL AND TRIBAL COLLEGES
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This REU Site, Genes & the Environment:  Research Experiences for Undergraduates from Rural and Tribal Colleges, will provide hands-on summer research experiences to undergraduate students.  The scientific focus of this REU program is environmental influences on gene expression.  Research will be conducted under the mentorship of faculty at the University of North Dakota in Grand Forks, ND.  Mentors will work closely with students to develop an independent research project.  Some possible research projects involve investigation into environmental influences on epigenetic regulation of cortical development, learning and memory in fish and mice, neural stem cell fate, sex-determination in turtles, stress tolerance in nematodes, and wing patterning in butterflies and moths.  Research activities being conducted by REU faculty mentors include:
ProjectExploring epithelial-to-mesenchymal transitions in Lyme arthritis
Mentor:  Catherine Brissette, Ph.D., Associate Professor
LocationDepartment of Biomedical Sciences, Neuroscience Building
Description: Lyme disease (LD) is caused by infection with the bacterial pathogen Borrelia burgdorferi (Bb) and is a prevalent and continually emerging vector-borne disease in the United States, Europe, and Asia.  Disseminated infection can lead to pathologies affecting the joints, heart, and central nervous system (CNS).  Despite antibiotic treatment, a proportion of patients continue to suffer from debilitating symptoms.  The mechanisms of CNS pathology as well as bacterial and host risk factors for these manifestations are poorly understood, largely due to the lack of a tractable laboratory model for the study of LD in the CNS.
The meninges serve as an interface between CNS and periphery.  The outermost layer of the meninges, the dura mater, possesses fenestrated blood vessels, lymphatic drainage, and a high density of resident immune cells capable of supporting a robust immune response.  We now show acute and persistent extravascular Bb colonization of the dura mater after both needle inoculation and tick transmission, accompanied by increases in expression of inflammatory cytokines; in addition, we observe a robust interferon (IFN) response in the dura mater comparable to that seen during murine Lyme arthritis.  Dura colonization is associated with leukocyte infiltration and mild meningitis, indicating an inflammatory state in the meninges of Bb-infected mice.  We also demonstrate an increase in IFN-stimulated genes in both the cortex and hippocampus of infected mice, despite a lack of detectable spirochetes in the brain parenchyma.  A sterile IFN response in the absence of Bb is unique to the brain parenchyma and could provide insights into the mechanism of inflammatory CNS pathology associated with this pathogen.
Our tractable model will allow us to directly assess potential risk factors leading to more severe inflammatory CNS involvement, as well as test potential interventions.


ProjectNeuroimmune changes in Alzheimer's disease
MentorColin Combs, Ph.D., Professor
Location:  Department of Biomedical Sciences, School of Medicine & Health Sciences
Description:  Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by dementia.  Therapeutic options for attenuating disease are limited.  Epidemiologic and genome wide association studies support the idea that immune system dysregulation contribute to disease progression.  This suggests that immunomodulatory interventions may serve as viable therapeutic approaches. Unfortunately, we still have much to learn regarding how immune changes may be influencing disease.  To address this problem, we utilize transgenic mouse models of Alzheimer's disease to study both age and disease-associated changes in immune cell behavior outside and inside of the brain.  In addition, we examine common comorbid, chronic inflammatory diseases such as periodontal disease, obesity, diabetes, atherosclerosis, asthma, and colitis to determine whether the immune changes of comorbid diseases increase the progression or severity of AD.  Our approach typically includes assessment of animal behavior, quantifying disease-related biochemical changes in the brain and diverse organs, defining histologic and cellular phenotype differences, and testing immunomodulatory interventions to improve AD.


Project  Agent-based model of chronic wasting disease in North Dakota deer
MentorBrian Darby, Ph.D., Associate Professor
Location:  Department of Biology, Starcher Hall
Description:  Chronic Wasting Disease (CWD) is one of the most significant threats to the deer, elk, and moose populations in North Dakota.  The disease is always fatal to members of the deer family and recent evidence suggests that high infection rates can lead to long-term population declines.  North Dakota is now at a critical point in time concerning the management of this disease.  A variety of "best management practices" have been proposed, but not thoroughly tested at a landscape level.  The objective of this project is to develop a spatially explicit model that can be used to predict the epidemiology of CWD in a state like North Dakota and test the effect of proposed best management practices.  The REU student will perform literature searches on the disease ecology of CWD and the landscape ecology of wild deer populations and use this information to create an agent-based model of CWD spread in wild deer populations.  If successful, the REU student will then create different model scenarios to predict the success of different best management practices.


ProjectBiological components of soil health in natural and agricultural soils
MentorBrian Darby, Ph.D., Associate Professor
Location:  Department of Biology, Starcher Hall
Description:  Microbiota are an active component of the soil ecosystem and impart key ecosystem services that maintain soil health, such as decomposition, nutrient cycling, pest reduction, and symbiotic relationships with plants. Federal programs, such as the Conservation Reserve Program, help landowners to take degraded lands out of production and build soil health. Additionally, the Natural Resources Conservation Service provides management recommendations for producers to build and maintain soil health, such as reducing soil disturbance, diversifying soil biota with plant diversity, keeping a living root in the ground year-round, and keeping the soil covered as much as possible (such as with a cover crop). The objective of this research project is to assess the success of these programs and management recommendations on building soil health. To accomplish this, we are measuring a variety of chemical, physical, and biological attributes of natural and agricultural soils that are susceptible to changes in land use, called dynamic soil properties. REU students will participate in various aspects of this broader project, such as sampling soil from natural and agricultural field experiments, processing soil samples in the laboratory, assaying dynamic soil properties (such as extracellular enzyme activity, invertebrate community composition, and microbial substrate use profiles), and analyzing these data statistically to identify how various land management schemes affect soil biota.


ProjectSoil health benefits of the Conservation Reserve Program
MentorBrian Darby, Ph.D., Associate Professor; and Kathryn Yurkonis, Ph.D., Associate Professor
Location:  Department of Biology, Starcher Hall
Description:   The Conservation Reserve Program is a Federally funded program that contracts with agricultural producers to convert marginal or environmentally sensitive pasture and cropland to a perennial cover mix of grasses, forbs, and legumes for 10 to 15 years.  The goal of this voluntary program is to improve soil health and prevent erosion on the acres enrolled.  Enrollment is also though to improve water quality by reducing nutrient runoff, and also improve critical habitat from waterfowl, songbirds, pollinators, and other wildlife.  The objective of this research project is to quantify the soil health benefits of the Conservation Reserve Program.  The REU students that take part in this project will have the opportunity to travel with a field crew to multiple states, measure vegetation cover, and collect soil samples from several dozen CRP enrolled fields and non-enrolled croplands.  The students may also assist in the laboratory with processing soil samples and conducting soil health assays, such as microbial respiration, substrate use profiles, enzyme activities, and plant-available nutrient pools.  The students will also learn how to graph and analyze the data they collect to characterize trends in soil health metrics over time and between enrolled and non-enrolled fields.


ProjectHow the brain comes together: neural-vascular interactions in cortex development 
MentorDiane Darland, Ph.D., Associate Professor (Not hosting REU participants Summer 2021)
Location:  Department of Biology, Starcher Hall
Description: Neural-vascular interactions can impact the development of the central nervous system as well as the plasticity of neural stem cells (NSC) and developing neurons while the brain is forming.  Among the current questions in the brain development field are: (1) how do blood vessels and neurons communicate while the brain is forming?; (2) what factors are involved in regulating these processes?; and (3) is epigenetic regulation of gene expression part of the micro-environmental signaling?  Neuro- genesis requires the coordinated regulation of NSC proliferation, initiation of differentiation with exit from the cell cycle, and acquisition of differentiated properties associated with a given cellular function (i.e., differentiated neuron).  My lab is investigating the coordinated regulation of heterotypic cell-cell interactions during brain angiogenesis, neurogenesis, and neural differentiation.  This project uses a tri-culture system consisting of primary brain endothelial cells and myofibroblasts cultured together in capillary-like tubes on one side of a Transwell™ membrane with primary neural precursors cultured on the other.  We are investigating the timing, molecular regulators, and epigenetic mechanisms involved in the NSC fate choice and the neural-vascular interactions.  Results of this project will help us to better understand the different cell-cell interactions that occur while the brain is forming, during post injury repair (stroke) or under stress (neuroinflammation or neurodegeneration).  REU students will learn microdissection, primary culture isolation and sterile tissue culture techniques, immunohistochemistry, apoptosis and proliferation detection, and confocal and standard microscopy as well as a variety of cell and molecular techniques ranging from PCR-subcloning and sequencing to RNA purification, cDNA synthesis, and quantitative real-time PCR.


ProjectGenetic and epigenetic modulation of classic conditioning in Zebrafish
MentorTristan Darland, Ph.D., Associate Professor (Not hosting REU participants Summer 2021)
Location:  Department of Biology, Starcher Hall
Description:  This research aims to understand how environment shapes an organism's ability to learn.  One of the most basic types of learning referred to as associative conditioning in which an organism learns to associate a primary stimulus, like food, with a secondary stimulus such as an auditory or visual cue.  Once an organism associates the two stimuli, it will respond to the secondary stimulus whether or not the primary stimulus is present.  This basic type of learning and memory is present in every vertebrate tested and even in some invertebrates.  The brain monoaminergic pathways have proven central to this type of learning.  In preliminary studies, we altered the ability of zebrafish to learn by classic conditioning by treating them with toxins during embryogenesis.  Since cocaine is a more potent and reliable stimulus than natural stimuli to induce this type of learning, we use it as a primary stimulus in adult behavioral tests.  We found that embryonic exposure to cocaine increases behavioral response to it later, while heavy metal treatment (cadmium) lowers drug responsiveness later.  Given the importance of monoamines in this type of learning, we are testing the hypothesis that these toxins modify gene expression in the monoaminergic neural pathways in opposite ways during embryo-genesis.  We will also test the hypothesis that epigenetic modification of chromatin underlies the basis for alteration of classic conditioning resulting from embryonic treatment of zebrafish with cocaine or cadmium.


Project:  Transcription factor dynamics during cell state transitions
MentorArchana Dhasarathy, Ph.D., Associate Professor
Location:  Department of Biomedical Sciences, Columbia Hall
Description:  Our laboratory aims to understand a deceptively simple yet unsolved question of how transcription factors choose from a multitude of available binding sites in the genome, to specifically activate only those genes that are relevant to the cell type and/or stimulus.  Transcription is a fundamental biological process with multi-layer regulation that results in the production of RNA from the DNA genome. Cellular identity is dictated by gene expression, therefore transcription is under tight control through multiple mechanisms (including epigenetic) that govern expression of individual genes, and organize them into network-level 'transcriptomes'.  At the earliest stages of transcription, proteins known as transcription factors bind to cognate DNA sequences at gene promoters to regulate gene expression, which in turn fine-tunes how cells respond to signals from their environment in diverse ways.  We study the epithelial to mesenchymal transition (EMT), which involves a cell state transition from an epithelial, attached and well-differentiated to a mesenchymal, migratory and less differentiated phenotype.  The process of EMT is controlled by several transcription factors, and the goal of this project is to understand which genes are regulated by these factors over the time course of EMT.  The end goal will be to understand changes in gene networks, signaling pathways and transcription factors during EMT.


Project:  Evolution of RNA vs. DNA binding abilities of transcription factors
Mentor: Archana Dhasarathy, Ph.D., Associate Professor; and Rebecca Simmons, Ph.D., Professor
Location:  Department of Biomedical Sciences, Columbia Hall; and Department of Biology, Starcher Hall
Description:  We study the epithelial to mesenchymal transition (EMT), which involves a cell state transition from an epithelial, attached and well-differentiated to a mesenchymal, migratory and less differentiated phenotype.  The process of EMT is controlled by several transcription factors.  While most research so far has focused on the DNA binding properties of transcription factors, RNA binding is being increasingly recognized as a property of some transcription factors, opening up new roles for these proteins in gene regulation.  Two questions we would like to answer are (a) are there different protein motifs/ domains that are unique to RNA vs DNA binding proteins; and (b) how did RNA and DNA binding proteins evolve in terms of dual RNA AND DNA binding, vs single/unique RNA OR DNA binding?  To answer this question, we will gather sequence data for loci that encode DNA and RNA binding proteins (DRBPs) across domains of life.  We will use phylogenetic approaches to align these sequences, establishing homology, and then will use model-based maximum likelihood and Bayesian approaches to construct evolutionary hypotheses for these genes.  These hypotheses will be compared to accepted phylogenies for these organisms to understand how ancestry and convergence shaped the functional groups of these important proteins.


Project:  Noradrenergic regulation of neurogenesis and cognitive function
MentorVan A. Doze, Ph.D., Associate Professor
Location:  Department of Biomedical Sciences, School of Medicine & Health Sciences
Description:  Norepinephrine (NE), an important neuromodulator in the brain, modulates cognitive function and synaptic plasticity.  NE mediates its effects via activation of adrenergic receptors (ARs).  We discovered that adult mice with chronically activated alpha1A-ARs exhibit significantly improved learning and memory, synaptic transmission, mood, and lifespan.  In contrast, we found that mice lacking alpha1A-ARs have reduced cognitive function, mood, and lifespan.  The mice with activated alpha1A-ARs also show increased neurogenesis in their hippocampi, an area of the brain critical for learning and memory.  The molecular cues and genes regulating this process include a wide range of growth and survival factors, but a direct link between NE activity, gene regulation, and neurogenesis, has not been explored.  This project will test the hypothesis that NE, through alpha1A-AR activation regulates differentiation and cell fate of neuronal and glial progenitors in the adult mouse brain, and subsequently enhances cognitive function.  Through immunolabeling, electrophysiology, behavioral studies, and confocal imaging, this project will characterize alpha1A-AR influences on adult neurogenesis and learning and memory.


ProjectRegulation of membrane transporters by palmitoylation
MentorJames Foster, Ph.D., Assistant Professor
Location:  Department of Biomedical Sciences, School of Medicine & Health Sciences
Description:  Over 5000 proteins have been identified as reversibly modified in the mammalian genome and evidence is growing which supports reversible palmitoylation as an important protein regulator. We have recently discovered that the dopamine transporter (DAT) and the sodium hydrogen ion exchanger isoform 1 (NHE1) is modified by S-palmitoylation, a post-translational modification in which C16 saturated palmitic acid is added to proteins via a thioester linkage to cysteine. S-palmitoylation of integral membrane proteins confers a variety of properties including control of activity, trafficking, turnover, and subcellular targeting. Palmitoylation is reversible and dynamic, conferring the ability of the protein to respond to physiological signals and participate in regulatory processes in a manner analogous to phosphorylation.  In this project we are examining the role of palmitoylation in regulating DAT and NHE1 activity, subcellular trafficking, membrane microdomain localization, and degradation.

For DAT, dysfunction mediated by altered palmitoylation may result in imbalanced transmitter levels found in DA disorders including Parkinson's disease, schizophrenia, depression, and bipolar disorder. For NHE1, multiple cellular processes are associated with NHE1 activity including coordinated cell migration, cellular proliferation, and control of cell volume. NHE1 also functions as a membrane anchoring and scaffolding protein resulting in the formation of different protein complexes that participate in regulating signaling pathways within the cell. Altered NHE1 function via changes in palmitoylation may alter these processes.  If remote participation is necessary because of COVID-19, students will be exposed to techniques and follow/direct experiments conducted by onsite personnel via live zoom. Students will analyze and plot the data using GraphPad Prism.


ProjectComputational modeling of interactions between psychoactive drugs and transporters  
MentorL. Keith Henry, Ph.D., Associate Professor
Location:  Department of Biomedical Sciences, School of Medicine & Health Sciences
Description:  Students will learn to generate 3D structures of small molecules such as antidepressants and drugs of abuse and then more complex 3D models of proteins such as the serotonin and dopamine transporters in different conformational states.  With the small molecule and the protein structures in hand, students will computationally refine the proteins followed by in silico docking to identify sites on the protein where the small molecules bind.  These results can help us understand the new compounds we have generated and how they may represent molecules with clinical promise.  Students will learn how to write UNIX and Pymol scripts to perform data analysis and generate structural models. The students will be introduced to biochemical, pharmacological, molecular and computational principles and methodologies which will benefit them no matter which path they choose in the future graduate careers.


ProjectEpigenetic changes induced by exposure to antidepressants
MentorL. Keith Henry, Ph.D., Associate Professor
Location:  Department of Biomedical Sciences, School of Medicine & Health Sciences
Description:  The project will focus on identification of epigenetic changes that occur after exposure to antidepressants.  Numerous animal studies now show that antidepressant exposure in early life leads to long-lasting physiological and behavior effects.  Our primary goal is to identify the molecular and epigenetic changes such as DNA methylation and histone modifications that underlie this reprogramming.  We utilize modern next-generation sequencing technologies and advanced molecular techniques.


Project:  Non-additive control of gene expression by long-range interactions between multiple regulatory elements
Mentor:  Manu Manu, Ph.D., Associate Professor
Location:  Department of Biology, Starcher Hall
Description:  The differentiation of cells during development relies on the fine control of gene expression by DNA sequences called enhancers.  In metazoans, most well-studied cell-fate genes are known to be regulated by multiple enhancers, with some loci having as many as 20.  Classical enhancers have long been regarded as acting independently - additively - in a distance independent manner.  Recent quantitative experiments with loci having multiple enhancers, however, do not support the classical assumptions and reveal non-additive behavior.  This implies that the cis-regulatory architecture of developmental genes is not modular but functions as an interconnected system.  The rules and molecular mechanisms by which enhancers influence each other's activities are not known.
Projects in our lab test the hypothesis that enhancers interfere with each other over long distances by modifying 3D chromatin conformation - looping interactions - or chromatin accessibility to produce nonlinear or non-additive responses.  The studies will culminate in the development of a new class of "whole locus" mathematical models of gene regulation that incorporate 3D chromatin conformation to simulate the regulation of genes by multiple enhancers.  These projects investigate interference between multiple co-expressed Cebpa enhancers uncovered recently by our lab.  Aim 1 will utilize a synthetic biology approach to measure the response of a gene regulated by two enhancers as a function of their strengths.  Aim 2 will utilize 3C techniques and ATAC-seq to test the hypothesis that enhancers interfere with the function of other enhancers by modifying the 3D chromatin conformation or accessibility of the locus.  Aim 3 will integrate looping interactions into sequence-based models of gene regulation to develop a new class of models capable of predicting the gene expression of complex multi-enhancer loci.


Project: Chromatin as an epigenetic regulator of the Simian Virus 40 lytic life cycle
MentorBarry Milavetz, Ph.D., Professor
Location:  Department of Biomedical Sciences, Columbia Hall
Description:  Using a virus, SV40, as a model to study the control of eukaryotic genes, we are dissecting the mechanisms responsible for epigenetic regulation.  Our studies use a combination of chromatin immunoprecipitation, next-generation sequencing, defective CAS9 fusion proteins, and small molecule inhibitors of epigenetic regulators to determine how the combination of nucleosome location and histone modifications regulate transcription and replication.  Our studies address fundamental questions related to eukaryotic molecular biology.  


Project:  Effect of peripheral immune responses on the brain function and behavior
MentorKumi Nagamoto-Combs, Ph.D., Assistant Professor
Location:  Department of Biomedical Sciences, School of Medicine & Health Sciences
Description:  Our research focuses on the interaction between the immune and the nervous systems.  Using a mouse model of cow's milk allergy, we investigate how the body's hypersensitivity responses to a food allergen alter the brain physiology.  REU students will learn basic immunology, intestinal and brain anatomy and histology, and various histochemical and/or molecular biological techniques for the analyses of experimental mouse tissues.


Project:  Organization of global transcriptomes by stepwise control of Pol II activity at gene promoters
Mentor:  Sergei Nechaev, Ph.D., Associate Professor
Location:  Department of Biomedical Sciences, Columbia Hall
Description:  While gene transcription is known to define cell identity, the underlying principles remain a mystery. This project will pursue the crucial, yet poorly understood mechanisms that, rather than regulating transcription of specific genes, affect RNA polymerase II (Pol II) machinery across the entire genome. The emphasis is on promoter-proximal RNA Pol II pausing, the most predominant form of Pol II enzyme on DNA. The project will examine how NELF and P-TEFb, two key factors involved in pausing, govern distribution of active Pol II across the genome.  Regulation by globally acting factors targeting Pol II at distinct steps of the transcription cycle may be a general property for generation of distinct, stable patterns from the same genome.  Laying the basis for this project, we previously developed small RNA-based technologies to profile Pol II pausing with nucleotide-level resolution and demonstrated surprisingly dynamic properties of Pol II at promoters.  By exploring Pol II pausing as a prominent but still poorly understood phenomenon, a new common principle organizing genes into networks may be uncovered.  REU students will be involved in all stages of the project and be able to choose if they want to do bench work (classic biochemistry and genomics), or computing-based bioinformatics.


Project: Genetics and epigenetics of temperature-dependent sex determination
MentorTurk Rhen, Ph.D., Professor
Location:  Department of Biology, Starcher Hall
Description:  Temperature-dependent sex determination (TSD) was first reported 50 years ago in a lizard. TSD has since been shown to occur in many reptiles as well as some fish and amphibians.  Yet, the molecular mechanism underlying TSD is unknown.  My lab has established the common snapping turtle, Chelydra serpentina, as a model for studying the molecular mechanisms underlying TSD.  We are using an integrative approach that combines classical genetics, genome-wide association studies, population genomics, ChIP-Seq, RNA-Seq, and experimental manipulation of gene expression to elucidate gene regulatory networks involved in TSD.  Our genetic studies and gene expression analyses have identified numerous candidate genes that may play a role in transducing temperature into a biological signal for the embryonic gonads to develop into ovaries or testes.  Among the candidates are genes that regulate epigenetic modifications like histone methylation.  Students will help characterize the role of various candidate genes in TSD.


ProjectCommunities within communities: Investigating the biodiversity of prairie pollinators and their endosymbionts
MentorRebecca Simmons, Ph.D., Professor
Location:  Department of Biology, Starcher Hall
Description:  North Dakota is the largest producer of honey in the US; both native and commercial pollinator species are central to the success of agriculture in the region. Despite their importance, pollinators are experiencing declining numbers both in the region and nationwide. These declines caused by many factors including, habitat destruction, pesticide/herbicide use, and diseases; loss of these species are a threat to economic growth in the region and national food security. While there are efforts to document the decline in pollinator species in the region, these surveys do not address the hidden diversity within pollinators themselves-microbes found in pollinator digestive tracts. In healthy individuals, these microorganisms synthesize vitamins, aid in honey production and provide other vital functions. To document and compare microsymbionts between pollinator species, REU students will collect and identify pollinators. Students will remove pollinator digestive systems which will be used to extract, amplify and sequence both pollinator and microsymbiont DNA. Students will then analyze resulting Illumina sequence data to identify species-specific and shared symbionts.


ProjectThe evolution of complex traits in mimetic tiger moths (Erebidae: Arctiinae: Euchromiina)
MentorRebecca Simmons, Ph.D., Professor
Location:  Department of Biology, Starcher Hall
Description:  Tiger moths, members of the subfamily Arctiinae, display bright coloration and often mimic noxious insects, such as bees and wasps.  These moths have evolved numerous traits allowing for precise mimicry of their models, such as clear wings, narrowed waists (=wasp waists), and behaviors (e.g., pseudo-stinging).  While these traits are well documented, it is not clear if these adaptations are the result of one evolutionary event in a group of closely related species, or convergent evolution between distantly related lineages.  We will investigate these possibilities by using a suite of genes that provide data allowing us to construct the evolutionary relationships of these moths (= phylogeny).  REU students will learn a variety of techniques including DNA extraction and amplification via PCR, Sanger sequencing, imagining specimens to document mimetic traits, and phylogenetic analyses.


ProjectGenetic factors behind wing loss in female tussock moths (Orgyia leucostigma)
MentorRebecca Simmons, Ph.D., Professor
Location:  Department of Biology, Starcher Hall
Description:  Tussock moths are responsible for large-scale defoliation of forests across North America.  The spread of tussock moths across North America is restricted by the female's limited flight capability.  Females in the genus Orgyia all lack wings, while males retain wings and can fly.  Wings develop normally in both males and females, but during the pupal stage, female wings degrade to small vestigial disks.  We plan to investigate the differential expression of wing pattern in male and female tussock moths throughout their larval and pupal development.  To accomplish this, we will extract and sequence RNA to determine if genes involved in wing development are differentially expressed between males and females.  REU students will learn a variety of techniques including DNA and RNA extraction, amplification via PCR, RNA seq, and appropriate analytical techniques.  Additionally, students will participate in rearing projects as well as imagining resulting phenotypes and image analysis.


ProjectMechanisms of gene expression changes in a model of metal-induced bladder cancer
MentorSeema Somji, Ph.D., Associate Professor; and Scott Garrett, Ph.D., Associate Professor
Location:  Department of Pathology, School of Medicine & Health Sciences
Description:  This project will investigate permanent gene expression changes induced by long-term exposure to two common environmental toxicants, cadmium and arsenite.  Current work focuses on characterizing the gene expression changes and transcriptional control mechanisms manifesting these permanent gene expression changes.  Specific effort has focused on investigating the mechanisms of permanent induced expression for enolase-2, metallothionein-3, keratin 6A, and metallothionein 1X, N-cadherin and elongation factor 1A2.  Research thus far as implicated the role of specific transcription factors and histone modifications.  Understanding how permanent gene expression changes occur due to long-term environmental exposure will help understand molecular mechanisms of cellular adaptation.     


ProjectDiscover epigenetic and therapeutic vulnerabilities of aggressive breast cancer through a pioneer transcription factor GATA3 mutations 
MentorMotoki Takaku, Ph.D., Assistant Professor
Location:  Department of Biomedical Sciences, Columbia Hall
Description:  Breast cancer is the most common cancer among women in
the US and the second leading cause of cancer-related deaths. GATA3 is a reliable biomarker for breast carcinomas and is frequently used to determine the tissue of origin to confirm a diagnosis. GATA3 is a special class of transcription factors that are capable of inducing cell-fate transition. For instance, GATA3 can induce mesenchymal-to-epithelial transition in breast cancer cells and iPSCs from fibroblasts. Recent large-scale genomic profiling of breast carcinomas identified frequent mutations in GATA3 and these mutations have been considered as breast cancer "drivers", yet the functional consequences of GATA3 mutations in breast cancer are underexplored. We recently generated GATA3 mutant cell clones by CRISPR-Cas9 genome editing and identified that GATA3 mutations can reprogram gene expression patterns and induce more aggressive breast cancer phenotypes. We also discovered a compound that specifically target GATA3 mutant luminal breast cancer cells. We are trying to understand molecular mechanisms of such therapeutic vulnerabilities in GATA3 mutant breast cancer cells by using genomics. REU students will learn cell culture, gene expression analysis (qPCR, RNA-seq), and many other chromatin biology techniques (ChIP-qPCR, ChIP-seq, CUT&RUN, etc).  As a virtual program, REU students will learn bioinformatics analysis of those genomics data.


Project:  Molecular study of avian malaria
MentorVasyl Tkach, Ph.D., Professor
Location: Department of Biology, Starcher Hall
Description: Malaria is one of the most serious infectious diseases of humans transmitted by mosquitoes and distributed mostly in tropical and subtropical regions of the world.  However, other animals, such as birds, reptiles and wild mammals, also may have malaria.  Moreover, while humans have only four species of malaria parasites, birds have hundreds worldwide.  They may be transmitted by mosquitoes and black flies common in our region.  Currently, more is known about avian malaria in tropical foreign countries than in the United States and especially in upper Midwest.  There was a very limited amount of previous research studies of bird malaria in Minnesota and practically none was done in North Dakota.  Research will include collecting samples in the field and screening them for avian malaria in the lab using DNA extraction, real time PCR, standard and nested PCR, and DNA sequencing.  This will be done together with faculty, graduate and possibly with other undergraduate students.


Project:  Revealing the agents of "swimmer's itch" in North Dakota and Minnesota
MentorVasyl Tkach, Ph.D., Professor
Location:  Department of Biology, Starcher Hall
Description: In summer time, people heading for recreation to lakes in our region (and elsewhere in the USA as well as other countries) often experience itching in their skin (mostly legs) associated with red dots and bumps not resulting from mosquito bites.  This itching only appears after contact in water.  The condition is commonly known as "swimmer's itch" while its scientific name is "cercarial dermatitis".  Few people know that it is caused by microscopical larvae of parasitic flukes found as adults in blood vessels of aquatic birds.  The larval stages live in snails and are released into water where they try to penetrate skin of ducks or humans, whichever comes first.  Fortunately, the parasites cannot develop in humans beyond causing temporary itch.  Currently, very little is known about these parasites in our region despite high diversity and numbers of birds and wide-spread swimmer's itch.  Student will participate in a variety of activities and learn a variety of techniques including collecting snails in the field, screening them for fluke larvae, light microscopy and digital imaging, scanning electron microscopy, DNA extraction, polymerase chain reactions, gel electrophoresis, sequencing reactions and analysis of the results.  The study will be conducted together with faculty, graduate and undergraduate students.


Project:  Causative agents of "black spot" disease in fishes of North Dakota and Minnesota
MentorVasyl Tkach, Ph.D., Professor
Location:  Department of Biology, Starcher Hall
Description: "Black spot" disease is the infection of fish skin due to penetration and encystment by larval stages of certain types of parasitic flukes (trematodes).  "Black spot" disease is widespread across the United States and is particularly common in the upper Midwest.  The disease is characterized by raised, black nodules on the skin, fins, and eyes of fish.  In cases of high intensity of infection, black spot disease can cause health issues ranging from mobility loss, increased vulnerability to predation and death.  While it is known that the disease is mostly caused by flukes parasitic as adults in fish-eating birds, the exact etiology and diversity of these parasites is not sufficiently studied and varies region to region.  Currently available molecular tools allow for matching DNA sequences of different life stages of these parasites and thus better understand their identity and life cycles in nature.  Student(-s) will participate in a variety of activities and learn a variety of techniques including collecting snails and fish in the field, their examination for fluke larvae, light microscopy and digital imaging, scanning electron microscopy, DNA extraction, polymerase chain reactions, gel electrophoresis, sequencing reactions and analysis of the results.  The study will be conducted together with Dr. Tkach and a graduate student.


Project:  Mining next generation sequence data for phylogenetic signal
MentorVasyl Tkach, Ph.D., Professor
Location:  Department of Biology, Starcher Hall
Description:  Next generation sequencing (NGS) technologies can be used for a number of purposes, from a variety of metagenomic approaches to clinical applications, functional, developmental and ecological genomics, etc.  One of the possible applications is obtaining data for evolutionary analysis.  NGS approach allows to obtain a large number of genes (up to a complete genome) that can be used for phylogenetic inference Dr. Tkach's laboratory has obtained several sets of next generation sequence data (using HiSeq technology) from parasitic flatworms.  While assembling and annotating large amount of NGS data is a highly demanding process requiring a significant background and experience, there are simpler, but nevertheless useful, ways to utilize some of this data.  The goal of this project will be to extract, assemble and annotate complete mitochondrial genomes (they are only 14,000-16,000 base pair long) from one to a few parasitic flatworm species, align them with previously published genomes and assess their utility for phylogenetic inference or/and differentiation among species.  To do this, student will need to learn several pieces of specialized installed and on-line software, some simple, some more complex.  This is a computer-based project.
  Manu Manu, Ph.D.
  Barry Milavetz, Ph.D.
  Kumi Nagamoto-Combs, Ph.D.
  Sergei Nechaev, Ph.D.
  Turk Rhen, Ph.D.
  Rebecca Simmons, Ph.D.
  Seema Somji, Ph.D.
  Motoki Takaku, Ph.D.
  Vasyl Tkach, Ph.D.

Catherine Brissette, Ph.D.

Colin Combs, Ph.D.

Brian Darby, Ph.D.

Tristan Darland, Ph.D.

Archana Dhasarathy, Ph.D.

Van A. Doze, Ph.D.

James Foster, Ph.D.

L. Keith Henry, Ph.D.

Manu Manu, Ph.D.

Barry Milavetz, Ph.D.

Kumi Nagamoto-Combs, Ph.D.

Sergei Nechaev, Ph.D.

Turk Rhen, Ph.D.

  Catherine Brissette, Ph.D.
  Colin Combs, Ph.D.
  Brian Darby, Ph.D.
  Diane Darland, Ph.D.
  Tristan Darland, Ph.D.
  Archana Dhasarathy, Ph.D.
  Van A. Doze, Ph.D.
  James Foster, Ph.D.
  Scott Garrett, Ph.D.
  L. Keith Henry, Ph.D.

Diane Darland, Ph.D.

Motoki Takaku, Ph.D.

Rebecca Simmons, Ph.D.

Vasyl Tkach, Ph.D.

Seema Somji, Ph.D.

Scott Garrett, Ph.D.