NSF-REU
RESEARCH EXPERIENCES FOR UNDERGRADUATES FROM RURAL AND TRIBAL COLLEGES 
~SUMMER 2017~
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 (UND) and Cankdeska Cikana Community College (CCCC) (Fort Totten, ND).  Mentors will work closely with students to develop an independent research project. Some possible research projects will involve investigation into how environmentally determined changes in gene expression influence learning in fish and mice, sex-determination in turtles, stress tolerance in nematodes, and wing patterning in butterflies and moths.  Research activities being conducted by REU faculty mentors include:


Kumi Combs (UND)

Brian Darby (UND)

Van A. Doze (UND)

Jane Dunlevy (UND)

Scott Garrett (UND)

Turk Rhen (UND)

Rebecca Simmons (UND)

Seema Somji (UND)

Brent Voels (CCCC)

Kurt Zhang (UND)


Investigator: Kumi Nagamoto-Combs, Ph.D.

Location: Department of Pathology, University of North Dakota School of Medicine & Health Sciences

Title: Gut-Brain Communication in Food Allergy

Description: Intestinal symptoms are often comorbid in patients suffering from neuropsychiatric conditions such as anxiety, depression, autism, and attention-deficit disorder. Recent studies have demonstrated that induction of food allergy in mice results in behavioral abnormalities similar to those observed in psychiatric disorders complete with altered neurochemistry in the brain. This observation suggests that allergy-mediated intestinal dysfunction may directly regulate behavior and brain physiology. More specifically, the immune changes initiated in the intestines during food allergy induction may directly communicate with the brain. Although the precise mechanism for this gut-brain cross-talk is not clear, we hypothesize that oral antigen sensitization leads to increased peripheral inflammatory factors or activated immune cells in the circulation which ultimately reach the brain to impair neuron and glial functions. Using the food allergy mouse model, we investigate various behavioral as well as biochemical and histologic changes that occur in the brains of allergic mice.


InvestigatorVan Doze, Ph.D.

Location:  Department of Basic Sciences, University of North Dakota School of Medicine

Title:  Noradrenergic regulation of neurogenesis and cognitive function

Description:  NE Norepinephrine (NE), an important neuromodulator in the brain, modulates cognitive function and synaptic plasticity, which is thought to underlie learning and memory.  NE mediates its effects through the activation of adrenergic receptors (ARs).  Recently, we discovered that adult mice with chronically activated alpha1AARs exhibit significantly improved cognitive functions, synaptic plasticity, mood, and lifespan.  These mice 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 alpha1AAR activation regulates differentiation and cell fate of neuronal and glial progenitors in the adult mouse brain, and subsequently enhances cognitive function.  This project will examine gene expression in the hippocampi and brain of mice with chronically activated alpha1AARs utilizing Illumina® MouseWG-6 v2.0 Expression BeadChips.  The global gene expression between treated and untreated mice will be compared and the significant differentiation in genes and signal pathways will be identified.  The change in expression for selected genes will be verified using real-time PCR.  Through immunolabeling, electrophysiology, and confocal/multi-photon imaging, this project will characterize alpha1AAR influences on cell migration, differentiation, fate/survival and function.  This research study will increase our understanding of the role of NE in adult neurogenesis and learning.


InvestigatorJane Dunlevy, Ph.D.

Location:  Department of Basic Sciences, University of North Dakota School of Medicine

Title:  Expression of the matricellular protein, SPARC

Description:  Matricellular proteins are extracellular matrix proteins that can bind to other matrix proteins, such as collagen, but function more like a growth factor or cytokine than as a structural component of the matrix.  SPARC, also known as osteonectin or BM-40, is one member of this family that plays a pivotal role in migration, angiogenesis, and anti-proliferation signaling. The primary interests in my laboratory are the mechanisms that control SPARC expression. Our results suggest that SPARC expression is drastically down-regulated, to a barely detectable level, by exposure to either arsenic or cadmium.  My lab is determining the regions of the SPARC promoter that are responsive to these heavy metals as well as the role of microRNAs, specifically miR-29a, b and c, in down-regulating SPARC protein expression.  Another focus involves how differences in SPARC glycosylation relate to its function in cell migration.


InvestigatorScott Garrett, Ph.D.

Location:  Department of Pathology, University of North Dakota School of Medicine

Title:  Cadmium-induced gene expression changes in cultures of proximal tubule cells

Description:  The accumulation of cadmium, an anthropogenic pollutant and low abundant soil metal, in the cortex of the kidney rivals nearly all potential toxins in the levels accumulated over a lifetime, and the proximal tubule cells of this tissue has been established as the target site of cadmium-induced renal damage.  The current approach to assess molecular determinants of chronic cadmium toxicity is to assess the changes in gene expression upon cadmium exposure to cultures of proximal tubule cells and to assess the gene expression changes from the forced expression of a cadmium-binding protein, metallothionein-3 (MT3), which confers enhanced epithelial character and vectorial active transport.


InvestigatorTurk Rhen, Ph.D.

Location:  Department of Biology, University of North Dakota

Title:  Epigenetics of temperature-dependent sex determination

Description:  Temperature-dependent sex determination (TSD) was first reported 45 years ago in a lizard.  TSD has since been shown to occur in some fish and amphibians and many reptiles.  Yet, the mechanism underlying TSD is not known in any species.  We used RNA-Seq to study transcriptional programs for ovary vs. testis determination in a species that is exquisitely sensitive to temperature.  We found rapid changes in expression of lysine specific demethylases (Kdm6A/Kdm6B) and Polycomb Repressive Complex 2 (PRC2), which plays a role in cell fate decisions in animals. PRC2 methylates histone H3K27 to produce an epigenetic mark associated with gene silencing.  In contrast, Kdm6A/Kdm6B derepress genes by demethylating histone H3K27.  Thus, differences in expression and targeting of PRC2 vs. Kdm6A/Kdm6B may determine whether key sex-determining genes are repressed or activated.  We will test the hypothesis that histone-modifying enzymes mediate temperature effects on sex determination in the snapping turtle, Chelydra serpentina.  Aim 1: We will use ChIP (chromatin immunoprecipitation) and PCR to analyze temperature effects on H3K27 methylation at sex-determining loci (e.g., FoxL2 and Sox9).  Aim 2: We will use ChIP-Seq to analyze temperature effects on genome-wide patterns of H3K27 methylation and correlate results with RNA-Seq data.  Aim 3: We will use PRC2 and Kdm6 inhibitors and RNA interference to test whether PRC2 and Kdm6A/Kdm6B regulate H3K27 methylation, gene expression, and organ fate.


Investigator: Rebecca Simmons, Ph.D.

Location:  Department of Biology, University of North Dakota

Title:  Interplay of host plant chemistry, patterning genes, and epigenetic mechanisms on wing patterns in Lepidoptera

Description:  The diversity of colors and patterns that decorate the wings of butterflies and moths has fascinated biologists for hundreds of years. The goal of this research is to address how environment, genetic and epigenetic factors affect both short term and evolutionary patterns in two related studies.   We will 1) examine evolution of wing patterning genes using the phylogeny of a group of charismatic moths (tiger moths) and 2) investigate if wing color polyphenism is an epigenetic phenomenon, via differences in caterpillar host plant chemistry.


InvestigatorSeema Somji, Ph.D.

Location:  Department of Pathology, University of North Dakota School of Medicine

Title:  Mechanisms of gene expression changes in an in vitro model of metal-induced cellular change.

Description:  This project will study permanent gene expression changes induced by long-term exposure to two common environmental agents, cadmium (Cd+2) and arsenite (As+3).  A cell line was transformed by exposure to each of the above metals and global gene expression was assessed after metal withdrawal.  Current work is focused on determining gene expression changes as well as identifying the transcriptional control mechanisms that manifest these permanent expression  changes.  Specifically, effort has focused on studying the mechanisms of permanent induced expression and research thus far as implicated the role of specific transcription factors and histone modifications in three genes, ENO2, MT3, MT1X, and KRT6A.  Knowing how permanent gene expression changes occur due to long-term environmental exposure will help realize molecular mechanisms of cellular adaptation.


InvestigatorBrent Voels, Ph.D.

Location:  Cankdeska Cikana Community College, Fort Totten, ND

Title:  Unique N- and C-Terminal Domains of Metallothionein-3 Influence Growth and Differentiation

Description:  Toxic insult from the heavy metal cadmium induces the expression of metallothioneins (MT) which are cysteine-rich heavy metal binding proteins six to seven kilo Daltons in size.  Previous research demonstrates that over-expression of Metallothionein-3 (MT-3) occurs in the majority of breast cancers and is associated with poor outcome.  Furthermore, MT-3 has been shown to inhibit the growth of breast cancer and prostate cancer cell lines.  The MT-3 protein contains seven additional amino acids that are not present in any other members of the MT gene family, a six amino acid C-terminal sequence and a Thr in the N-terminal region.  The unique N-terminal sequence appears to be responsible for the growth inhibitory activity of MT-3 in the neuronal system, while the function of C-terminal region remains unknown.  My lab is further characterizing the unique properties of the N- and C-terminal domain of MT-3 and the potential role that MT-3 may play in differentiation.  Specifically, this project is investigating the GAGE gene family antigens in MCF7 mutant cell lines containing either the N- or C-terminal of MT-3.  See also Garrett & Somji projects.


InvestigatorKurt Zhang, Ph.D.

Location:  Department of Pathology, University of North Dakota School of Medicine

Title:  Effects of genetic indels on tissue-specific gene expression

Description:  Expression quantitative trait loci (eQTL) are genetic variants that correlate with gene expression.  Studies of eQTL have contributed to knowledge of the underlying mechanism of gene regulation.  The majority of eQTLs are known to be tissue-dependent, but our information about human eQTL is limited because only a small number of tissues have been investigated and most studies have focused on cis-eQTL and single nucleotide polymorphism.  Our preliminary research with Illumina human body map project and development of an in-house RNA-Seq assembly tool enables us to locate genetic indels from transcriptome data and identify their association with gene expression.  The genetic indels for tissue-specific gene expression will be found by completing the following projects: 1) Develop a new RNA-Seq assembly tool for reliably identifying indels; the new assembler would be more accurate than the traditional assemblers while maintaining high computational efficiency by using new generation of high performance computing technology, and 2) apply our method of integrating analysis genetic variants and global gene expression to multiple genomic studies (e.g., Illumina body map, NIH genotype-tissue expression).