Genetics and Genomics Commons^™

Investigating Barriers Experienced By Underrepresented Minorities In Becoming A Competitive Genetic Counseling Applicant, Katie Huang

Dissertations and Theses (Open Access)

Representation for both racial/ethnic and gender identity minorities in genetic counseling (GC) remains the lowest among similar healthcare professions. Barriers that underrepresented minority (URM) individuals face in becoming a competitive GC applicant have not yet been described. Academic capital (AC) is a theoretical framework describing the social processes necessary for individuals to navigate and succeed in higher education. This study aimed to characterize barriers experienced by applicants who self-identify as underrepresented and to explore how AC could identify areas for intervention. Prospective GC applicants for the 2021/2022 cycles were recruited to complete an anonymous online survey in Qualtrics through a …

Rare Variant Association Studies In Crohn’S Disease And Colorectal Cancer: Methods And Applications, Jiun-Sheng Chen

Dissertations and Theses (Open Access)

Genetic factors account for a substantial portion of Crohn’s disease and colorectal cancer (CRC) risk. Patients with Crohn’s disease, a condition that causes chronic inflammation of the gastrointestinal tract, are at increased risk of colorectal cancer morbidity and mortality. Genome-wide association studies using single marker approaches have identified loci responsible for these diseases, but disease susceptibility from rare variants is incompletely understood. This dissertation includes three chapters, two association studies for Crohn’s disease and CRC, and a statistical method to improve the power of statistical tests.

For Crohn’s disease, we performed targeted sequencing of 101 genes in 205 children with …

Spectrum And Incidence Of Primary And Therapy-Related Hematologic Malignancies In Individuals With Brca1 And Brca2 Pathogenic Variants, Rosemary Rogers, Rosemary Rogers

Dissertations and Theses (Open Access)

Therapy-related myeloid neoplasms (t-MN) are rare and deadly hematologic malignancies that develop following exposure to cytotoxic therapies such as radiation, chemotherapy, and poly (adenosine diphosphate-ribose)-ADP polymerase (PARP) inhibitors. Preliminary evidence suggests that germline BRCA1 and BRCA2 pathogenic and likely pathogenic (P/LP) variants may increase susceptibility to t-MNs due to the genes’ established role in DNA damage response. There is also evidence that individuals with BRCA1/2 P/LP variants may be more susceptible to developing primary hematologic malignancies. We reviewed medical records of 706 individuals with BRCA1/2 P/LP variants to assess hematologic malignancy diagnoses and t-MN development. Our study population was 5.1% …

Mixture Model Approaches To Integrative Analysis Of Multi-Omics Data And Spatially Correlated Genomic Data, Ziqiao Wang

Dissertations and Theses (Open Access)

Integrative genomic data analysis is a powerful tool to study the complex biological processes behind a disease. Statistical methods can model the interrelationships of the involved gene activities through jointly analyzing multiple types of genomic data from different platforms (vertical integration), or improve the power of a study through aggregating the same type of genomic data across studies (horizontal integration). In this dissertation, we propose statistical methods and strategies for integrative multi-omics data in association analysis of disease phenotypes, with an emphasis on cancer applications.

We develop a new strategy based on horizontal integration by leveraging publicly available datasets into …

Examining The Role Of The Drosophila Melanogaster Unc13 Protein In Open Field Activity Using Rnai, Islam Orabi

Honors Theses

Unc13 are proteins in the presynaptic neurons essential in controlling synaptic vesicle fusion and synaptic transmission. Recently, the reduction of Drosophila melanogaster Unc13 proteins (Dunc13), were found to result in a resistance to alcohol, highly reminiscent of tolerance formation. I investigated whether genetically reducing Dunc13 activity in Drosophila brain regions leads to different forms of behavioral plasticity using an open field activity paradigm. In my approach, a Dunc13 RNAi transgene was expressed in the Drosophila brain within the mushroom body, the ellipsoid body, and in all neurons. The activities of the flies were examined in the open field paradigm to …

The Biodiversity Of Deadwood-Associated Arthropods In The Southern Appalachian Mountains, Isabelle Ong

Honors Theses

A biodiversity hotspot is a location that has significantly elevated levels of biodiversity including many species found nowhere else, and which is also in danger of losing much of this diversity. By identifying biodiverse regions, conservation efforts can be targeted to those locations where they are likely to have the most beneficial impacts. We looked at deadwood associated arthropods within the Southern Appalachian Mountains to examine centers of biodiversity. Nine logs were sampled, three of which were located in Bankhead National Forest and six were located in the Great Smoky Mountains. Polymerase chain reaction was used to amplify the mitochondrial …

Validation Of Anti-Oxidative Stress Genes From Genome-Wide Screening Of Escherichia Coli, Carson Ercanbrack

Chemistry & Biochemistry Undergraduate Honors Theses

The primary purpose of this project is to evaluate the genes that play a role in the oxidative stress response in Escherichia coli. In doing so, the entire genome of E. coli was subject to throughput in which individual genes were determined to have a role in the bacteria’s oxidative stress response. Moreover, this project focused on the validation of the genes that were able to pass the initial throughput stage. The genes were subject to two forms of validation. In the first validation technique, candidate genes were overexpressed and minimum inhibitory concentrations of hypochlorous acid were taken. Following, a …

Lotus: A Web-Based Computational Tool For The Preliminary Investigation Of A Novel Mst Method Utilizing A Library Of 16s Rrna Bacteroides Otus, Ginger Dewitte

Master's Theses

Microbial Source Tracking (MST) is a field of study that attempts to identify the source of fecal contamination in waterways in order to assist with development of remediation strategies. Biologists at Cal Poly Center for Applications in Biotechnology (CAB) are developing a new MST method using microbes from the genus Bacteroides. Bacteroides species are host-specific microorganisms that can theoretically be used to trace back to a single host species. After fecal samples are collected, biologists use Next-Generation Sequencing (NGS) techniques to obtain only the genetic sequences of microorganisms belonging to the phylum Bacteroidetes. Investigators hypothesize that similar sequences belong …

Dynamics Of Hybrid Zones At A Continental Scale, Bradley T. Martin

Graduate Theses and Dissertations

Hybridization has traditionally been viewed as a happenstance that negatively impacts populations, but is now recognized as an important evolutionary mechanism that can substantially impact the evolutionary trajectories of gene pools, influence adaptive capacity, and contravene or reinforce divergence. Physiographic processes are important drivers of dispersal, alternately funneling populations into isolation, promoting divergence, or facilitating secondary contact of diverged populations, increasing the potential for hybridization. In North America, glacial-interglacial cycles and geomorphological changes have provided a dynamic backdrop over the last two million years that promoted such oscillations of population contraction and expansion. These biogeographic processes have resulted in regional …

Molecular And Genetic Studies Of Robo2 Transcriptional Regulation In The Central Nervous System Of Drosophila Melanogaster, Muna Abdal Rahim Abdal Rhida

Graduate Theses and Dissertations

Drosophila Robo2 axon guidance receptor is a member of the evolutionarily conserved Roundabout (Robo) protein family that is involved in directing axons that cross the midline to the other side of the animal body. Robo2 roles mainly depend on two factors: The functional domains of the Robo2 protein, which is extensively studied, and the dynamic transcription of robo2 in various subsets of cells throughout embryogenesis which is not fully understood. Thus, knowing robo2 enhancers that transcriptionally regulate robo2 during embryogenesis is significant. To investigate robo2 potential enhancers, we screened 17 transgenic lines of Drosophila that were generated by Janelia Research …

Epigenome-Wide Association Study Of Kidney Function Identifies Trans-Ethnic And Ethnic-Specific Loci, Charles E. Breeze, Anna Batorsky, Mi Kyeong Lee, Mindy D. Szeto, Xiaoguang Xu, Daniel L. Mccartney, Rong Jiang, Amit Patki, Holly J. Kramer, James M. Eales, Laura Raffield, Leslie Lange, Ethan Lange, Peter Durda, Yongmei Liu, Russ P. Tracy, David Van Den Berg, Nhlbi Trans-Omics For Precision Medicine (Topmed) Consortium, Topmed Mesa Multi-Omics Working Group, Kathryn L. Evans, William E. Kraus, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

BACKGROUND: DNA methylation (DNAm) is associated with gene regulation and estimated glomerular filtration rate (eGFR), a measure of kidney function. Decreased eGFR is more common among US Hispanics and African Americans. The causes for this are poorly understood. We aimed to identify trans-ethnic and ethnic-specific differentially methylated positions (DMPs) associated with eGFR using an agnostic, genome-wide approach.

METHODS: The study included up to 5428 participants from multi-ethnic studies for discovery and 8109 participants for replication. We tested the associations between whole blood DNAm and eGFR using beta values from Illumina 450K or EPIC arrays. Ethnicity-stratified analyses were performed using linear …

Changes In Gene Sequence That Cause Discordances Involving Disease In Monozygotic Twins, Kacie Jacques

Thinking Matters Symposium

Identical twins or, monozygotic twins, occur when the egg in a mother is fertilized, but one zygote divides into two separate embryos. Monozygotic twins are considered to be genetically identical, but most twins often display discordances, some involving diseases or disorders. Some of these differences are due to environmental factors. For example, one twin may have diabetes due to diet. Recent literature has shown that some differences in monozygotic twins may be due to changes in gene sequence, as opposed to random, environmental or epigenetic factors. Identical twins from pedigrees with familial disease often show discordances. When looking at schizophrenia …

The Genetic Links Between Archaic And Modern Humans, Maria J. Orellana Rosales

Thinking Matters Symposium

Our modern physiology is the mixture of many archaic humans that once roamed our planet. The evidence of these archaic humans is still present in our DNA. This poster reviews how our understanding of ancient human genetics has drastically changed due to advances in molecular genetics. Neanderthal and Denisovan remains have been sequenced for nuclear and mitochondrial DNA. Neanderthal and Denisovan genetic ancestry have been identified by genomic studies in modern human populations across Eurasia and Pacific Island regions. Studies have shown a gene flow of 4±1% from Neanderthals to present-day Eurasians. Whereas, Papuan and Melanesian individuals share 4±0.7% more …

The Genes Of Pain, Alina Semenova

Thinking Matters Symposium

Pain is an important defense mechanism that protects us from environmental factors that might harm us. Our body's response to pain helps us to avoid injury. However, constant pain is a problem. Management of constant pain is an important area of research. Studies have shown that genetic variation contributes to pain sensitivity.

Numerous pain-related genes and their functional polymorphisms (CYP450, MOR-1, COMT, GCH1, etc.) have been identified in the past ten years. In particular, three opioid receptors (OPRM, OPRD and OPRK) are associated with pain sensitivity. One of the most studied human functional polymorphisms is the debrisoquine/sparteine polymorphism of CYP2D6 …

Genetically Modified Organisms Are Important But Also Controversial, Masen Pelletier

Thinking Matters Symposium

Genetically modified organisms (GMOs) are organisms containing a set or multiple sets of genes that have been introduced into the organism using laboratory techniques. In the instance of agriculture, the genes introduced provide advantages for the farmer and consumer by yielding plants that produce greater yields, longer growing seasons, longer shelf lives, greater concentrations of vitamins or add additional vitamins that are novel to the plant. There are two general ways that GM (genetically modified) crops are produced: the addition or removal of genes. This review focuses on an example of each strategy. An example of the latter is GM …

Understanding The Genetics Of Schizophrenia, Matthew Toohey

Thinking Matters Symposium

Schizophrenia has been considered heritable for a long time, but only with the advent of new technologies such as whole-genome sequencing and genome-wide association studies can we begin to identify specific molecular causes of schizophrenia. This poster will review some of the genetic variants that research groups have associated with schizophrenia. Current research has indicated that schizophrenia is a polygenic disease and has been linked to many genes. Some of these common risk variants are in protein coding sections of the DNA. These proteins are often linked to neurological development or immune system function. Other variants that have been associated …

Importance Of Understanding Genetic Predisposition, Andrew Carter

Thinking Matters Symposium

Hypersensitivity reactions can be sudden and are often fatal. Many of these reactions occur as a result of allergies to prescribed medication. Adverse drug reactions or (ADR’s) were show in a recent study to affect over 6% of hospitalized patients and resulted in over 100,000 deaths a year in the US alone. This poster will review the importance of understanding genetic predisposition, through articles about possible genetic causes of allergies to penicillin and other beta-lactams. Changes in a specific HLA gene located on chromosome 6 showed a correlation to penicillin reactions in over 600,000 participants. Another study found a conclusive …

The Evolution Of Mimicry; The Doublesex Gene, Aisha Hill

Thinking Matters Symposium

Many butterfly species use mimicry in order to increase their chance of survival. In Batesian mimicry, non toxic butterflies mimic the wing patterns, colors, and shapes of another species that is toxic to predators. Swallowtail butterflies (Papilio polytes) are well-known Batesian mimics, and also display sexual dimorphism with distinct differences between the sexes. Sex limited mimicry is common. The female butterfly may mimic an inedible red-bodied swallowtail, such as the common rose (Pachliopta aristolochiae), or she may be non-mimetic. The male butterfly is non-mimetic. This is a review of recent research into the origin and evolution …

Association Of Trim Gene Variation And Lpdv Infection Patterns In Wild Turkeys, Bennett Fry

Honors Theses

Emerging infectious diseases pose a serious threat to various species throughout the globe, including humans. The lymphoproliferative disease virus (LPDV) in wild turkeys is an example of disease virus whose impact on its host requires additional study. Although the first description of lymphoproliferative disease came from outbreaks in domestic turkey flocks in Europe, it is now known that LPDV is widespread in wild turkey populations in North America. In an effort to understand what may affect an individual turkey’s susceptibility to this virus, variation in part of the anti-viral TRIM62 gene was investigated. DNA was extracted from hunter-collected, turkey blood …

Identification Of Mitochondrial Transfer Sequences In Homologs Of A Folic Acid Metabolism Gene, Alyson Hally

Biology Student Work

Neural tube defects (NTDs) are common malformities resulting in exposed spinal cord or brain tissues caused by the inability to close the neural tube in embryogenesis. Previous research has shown folate deficiency increases the risk of NTDs. A folic acid metabolism gene, serine hydroxymethyltransferase (SHMT) is responsible for the synthesis of thymidylates, purines, and methionine which are important for DNA replication especially during embryogenesis. Typically, eukaryotes have two copies of SHMT which are either localized to remain in the cytosol or transferred to the mitochondria. The different localizations are a result of mitochondrial target sequences on the N-terminus. Interestingly, the …

Detection Of European Aspen (Populus Tremula L.) Based On An Unmanned Aerial Vehicle Approach In Boreal Forests, Anton Kuzmin, Lauri Korhonen, Sonja Kivinen, Pekka Hurskainen, Pasi Korpelainen, Topi Tanhuanpää, Matti Maltamo, Petteri Vihervaara, Timo Kumpula

Aspen Bibliography

European aspen (Populus tremula L.) is a keystone species for biodiversity of boreal forests. Large-diameter aspens maintain the diversity of hundreds of species, many of which are threatened in Fennoscandia. Due to a low economic value and relatively sparse and scattered occurrence of aspen in boreal forests, there is a lack of information of the spatial and temporal distribution of aspen, which hampers efficient planning and implementation of sustainable forest management practices and conservation efforts. Our objective was to assess identification of European aspen at the individual tree level in a southern boreal forest using high-resolution photogrammetric point cloud …

Rewired Pathways And Disrupted Pathway Crosstalk In Schizophrenia Transcriptomes By Multiple Differential Coexpression Methods, Hui Yu, Yan Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao

School of Medicine Faculty Research

Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or intercoordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired …

Identification Of A Chlorovirus Pbcv-1 Protein Involved In Degrading The Host Cell Wall During Virus Infection, Irina V. Agarkova, Leslie C. Lane, David D. Dunigan, Cristian F. Quispe, Garry A. Duncan, Elad Milrot, Abraham Minsky, Ahmed Esmael, Jayadri S. Ghosh, James L. Van Etten

Nebraska Center for Virology: Faculty Publications

Chloroviruses are unusual among viruses infecting eukaryotic organisms in that they must, like bacteriophages, penetrate a rigid cell wall to initiate infection. Chlorovirus PBCV-1 infects its host, Chlorella variabilis NC64A by specifically binding to and degrading the cell wall of the host at the point of contact by a virus-packaged enzyme(s). However, PBCV-1 does not use any of the five previously characterized virus-encoded polysaccharide degrading enzymes to digest the Chlorella host cell wall during virus entry because none of the enzymes are packaged in the virion. A search for another PBCV-1-encoded and virion-associated protein identified protein A561L. The fourth domain …

Novel Genetic Mutations In Genes Agbl5 And Tulp1 For Presumed Unilateral Retinitis Pigmentosa Managed With Low Vision Rehabilitation: A Case Report And Review, Maggie Man Ki Ho Od, Ms, Faao, Stephanie Schmiedecke-Barbieri Od, Faao, Abcmo, Dip Low Vision, Patricia C. Sanchez-Diaz Phd, Dvm, Faao, Carolyn E. Majcher Od, Faao, Fors

Optometric Clinical Practice

Background: Retinitis pigmentosa is a group of hereditary retinal diseases characterized by the degeneration of rod and cone photoreceptors. It commonly results in night blindness followed by tunnel vision and central vision reduction. The classic triad of clinical signs includes pigmented bone spicules, waxy disc pallor, and arterial attenuation. Unilateral retinitis pigmentosa is rare and can be supported with ancillary testing including genetic and laboratory studies to rule out differential diagnoses.

Case Report: A 68-year-old Hispanic female was referred to the low vision rehabilitation clinic due to progressive vision loss in the left eye (OS) that began 15 years ago. …

The Analysis Of Folate-Dependent Transcription Factor Zinc Finger Protein 410, Feifan Xu

Senior Honors Theses

A previous study that introduced dietary folate to mice in the form of folic acid to determine if gene activity would be altered based on this biological molecule demonstrated that mice without folic acid had cognition deficits, and this phenomenon was correlated with altered gene expression in their brains. The included bioinformatic analysis revealed two main transcription factors that bind to proteins in the nucleus, and one is known as the Zinc Finger Protein 410 (Zfp410). Due to the lack of literature explaining the function of this transcription factor, this project is intended to analyze Zfp410 in detail from scratch. …

Detection And Quantification Of Γ-H2ax Using A Dissociation Enhanced Lanthanide Fluorescence Immunoassay, Felicite K. Noubissi, Amber A. Mcbride, Hannah G. Leppert, Larry J. Millet, Xiaofei Wang, Sandra M. Davern

Biology Faculty Research

Phosphorylation of the histone protein H2AX to form γ-H2AX foci directly represents DNA double-strand break formation. Traditional γ-H2AX detection involves counting individual foci within individual nuclei. The novelty of this work is the application of a time-resolved fluorescence assay using dissociation-enhanced lanthanide fluorescence immunoassay for quantitative measurements of γ-H2AX. For comparison, standard fluorescence detection was employed and analyzed either by bulk fluorescent measurements or by direct foci counting using BioTek Spot Count algorithm and Gen 5 software. Etoposide induced DNA damage in A549 carcinoma cells was compared across all test platforms. Time resolved fluorescence detection of europium as a chelated …

208— Describing Genetic Diversity In A Non-Native Ant-Mimicking Spider, Cassidy Mills, Jennifer L. Apple

GREAT Day Posters

The ant-mimicking spider Myrmarachne formicaria (Salticidae) is a species native to Eurasia and was first identified in North America in 2001. It has since been found in many locations in the Northeast including western New York, western Pennsylvania, northeastern Ohio, and southern Ontario. Little is known about its introduction to North America and how it has dispersed since. By characterizing the mitochondrial genetic diversity of this species, we can learn about its introduction history and dispersal patterns in North America. Sequencing of a 600-bp mitochondrial DNA gene region spanning the 16s rRNA, leucine tRNA, and part of the ND1 gene …

307— Cooperation Of Selfish Genetic Elements In Stalk-Eyed Flies, Suhani Patel, Ben Mcpherson

GREAT Day Posters

SGEs are selfish genetic elements that increase the likelihood of their own transmission regardless of the host’s best interest. Transposable elements (TEs) and meiotic drivers are both types of SGEs. SGEs subsequently result in genetic conflict as they disrupt functional elements in the genome. We are working to better understand the cooperation of selfish genetic elements in Stalk-Eyed flies. Transposable elements are counteracted by small non-coding RNA molecules called piRNA. These RNA molecules work by reducing the expression of TEs by degrading TE RNA transcripts. Prior work in stalk-eyed flies has shown that TEs are expressed at a higher rate …

Annotation Of The Genome Of Drosophilia Ananassae, Landon Kehr

Celebration of Scholarship 2021

This project involves the use of software to annotate the genome of D. ananassae in collaboration with the Genomics Education Partnership. Annotations include coding regions and transcription start sites for specific genes that are homologous to D. melanogaster genes.

Comparative Genomics For D. Ananassae, Hailey Chang, Tia Watkins

Celebration of Scholarship 2021

The purpose of this project is to utilize comparative genomics tools to characterize specific genes in D. Ananassae. This is done in collaboration with the Genomics Education Partnership.