Genetics and Genomics Commons^™

Aging Induces B Cell Defects And Decreased Antibody Responses To Influenza Infection And Vaccination, Daniela Frasca, Bonnie B. Blomberg

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Background: Aging is characterized by a progressive decline in the capacity of the immune system to fight influenza virus infection and to respond to vaccination. Among the several factors involved, in addition to increased frailty and high-risk conditions, the age-associated decrease in cellular and humoral immune responses plays a relevant role. This is in large part due to inflammaging, the chronic low-grade inflammatory status of the elderly, associated with intrinsic inflammation of the immune cells and decreased immune function.

Results: Aging is usually associated with reduced influenza virus-specific and influenza vaccine-specific antibody responses but some elderly individuals with higher pre-exposure …

The Effects Of Parental Factors And Personal Attributes On Birth Control Use Under The Genetic Influences Of 5-Httlpr Among Adolescents, Hyun-Jin Cho

Legacy Theses & Dissertations (2009 - 2024)

The purpose of this study was (a) to examine relationships between parental influences and personal attributes on birth control use and (b) to identify genetic influences on such relationships by comparing the frequencies of common genetic variants—short allele vs. long allele—in 5-HTTLPR among adolescents (N = 5,852). Data from the Wave 1 and Wave 4 of the National Longitudinal Study of Adolescent Health were used to examine the birth control use of adolescents who were in 7th through 12th grade in 1994–1995. Multi-group Structural Equation Modeling analyses were used to identify the relationship among factors. Results did not find significant …

Role Of Microrna-483 In Pancreatic Β-Cells, Jackson Waugh

Dissertations, Master's Theses and Master's Reports

Insulin is an essential hormone produced by β-cells in the pancreas. The release of insulin is tightly regulated in healthy people in order to control blood sugar level in our body. However, people with Type 2 Diabetes have insufficient insulin secretion from pancreatic β-cells, leaving to high blood sugar (hyperglycemia) and β-cell failure. microRNAs (miRNAs or miR) are newly discovered small regulatory molecules and have emerged as important regulator of cell growth, differentiation, and organ function. Altered miRNA function has been implicated in the pathogenesis of a variety of human disease, including diabetes. In this report, we focus on dissecting …

Genome-Wide Sequence Analyses Of Ethnic Populations Across Russia, Daria V. Zhernakova, Vladimir Brukhin, Sergey Malov, Taras K. Oleksyk, Klaus Peter Koepfli, Anna Zhuk, Pavel Dobrynin, Sergei Kliver, Nikolay Cherkasov, Gaik Tamazian, Mikhail Rotkevich, Ksenia Krasheninnikova, Igor Evsyukov, Sviatoslav Sidorov, Anna Gorbunova, Ekaterina Chernyaeva, Andrey Shevchenko, Sofia Kolchanova, Alexei Komissarov, Serguei Simonov, Alexey Antonik, Anton Logachev, Dmitrii E. Polev, Olga A. Pavlova, Andrey S. Glotov, Vladimir Ulantsev, Ekaterina Noskova, Tatyana K. Davydova, Tatyana M. Sivtseva

Biology Faculty Articles

The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show …

Host Transcriptional Response To Persistent Infection With A Live-Attenuated Porcine Reproductive And Respiratory Syndrome Virus Strain, Jayeshbhai Chaudhari, Chia-Sin Liew, Aspen M. Workman, Jean-Jack Riethoven, David J. Steffen, Sarah Vitosh-Sillman, Hiep Vu

Nebraska Center for Virology: Faculty Publications

Both virulent and live-attenuated porcine reproductive and respiratory syndrome virus (PRRSV) strains can establish persistent infection in lymphoid tissues of pigs. To investigate the mechanisms of PRRSV persistence, we performed a transcriptional analysis of inguinal lymphoid tissue collected from pigs experimentally infected with an attenuated PRRSV strain at 46 days post infection. A total of 6404 differentially expressed genes (DEGs) were detected of which 3960 DEGs were upregulated and 2444 DEGs were downregulated. Specifically, genes involved in innate immune responses and chemokines and receptors associated with T-cell homing to lymphoid tissues were down regulated. As a result, homing of virus-specific …

Geographic Distribution Of Bacillus Thuringiensis Cry1f Toxin Resistance In Western Bean Cutworm (Lepidoptera: Noctuidae) Populations In The United States, Brad S. Coates, Craig A. Abel, Katharine A. Swoboda-Bhattarai, Debra E. Palmquist, Débora Goulart Montezano, Sarah N. Zukoff, Yangzhou Wang, Jeffery D. Bradshaw, Christina D. Difonzo, Elson Shields, Kelley J. Tilmon, Thomas Hunt, Julie A. Peterson

West Central Research and Extension Center, North Platte

The western bean cutworm (WBC), Striacosta albicosta (Lepidoptera: Noctuidae), can be a severe pest of transgenic corn in the western Plains and Great Lakes regions of North America, including on hybrids expressing the Bacillus thuringiensis (Bt) Cry1F toxin. The level and geographic distribution of Cry1F resistance are not completely known. Neonate S. albicosta from 10 locations between Nebraska and New York state were subjected to dose–response trypsin-activated native Cry1F toxin overlay bioassays. In 2017, the mean estimated lethal concentration causing 50% larval mortality (LC50) ranged from 15.1 to 18.4 μg Cry1F cm−2, and were not significantly different among locations. In …

Assessing Pepper Pungency By Using Rt-Qpcr To Measure Pun1 Expression, Sam Blechman

Williams Honors College, Honors Research Projects

Capsicum spp. evolved capsaicin as a chemical defense to deter consumption of its fruits by mammals, allowing birds to disperse the seeds throughout a greater range. The Pun1 locus codes for a capsaicin synthase (CS), the expression of which is a direct determinant of capsaicin accumulation. RT-qPCR was used to measure low-abundance mRNA transcripts. The aim of this study was to use RT-qPCR to measure Pun1 expression in cDNA synthesized from total RNA extracted from placental tissue of Capsicum annuum and chinense cultivars. A secondary aim was to troubleshoot the protocol designed for this experiment to verify the efficacy of …

Structural Biology Of The Enterovirus Replication-Linked 5'-Cloverleaf Rna And Associated Virus Proteins, Steven M. Pascal, Ravindranath Garimella, Meghan S. Warden, Komala Ponniah

Chemistry & Biochemistry Faculty Publications

Although enteroviruses are associated with a wide variety of diseases and conditions, their mode of replication is well conserved. Their genome is carried as a single, positive-sense RNA strand. At the 5′ end of the strand is an approximately 90-nucleotide self-complementary region called the 5′ cloverleaf, or the oriL. This noncoding region serves as a platform upon which host and virus proteins, including the 3B, 3C, and 3D virus proteins, assemble in order to initiate replication of a negative-sense RNA strand. The negative strand in turn serves as a template for synthesis of multiple positive-sense RNA strands. Building on structural …

Temperate Eurasian Origins Of Hawaiian Chenopodium (Amaranthaceae) Plus Description Of A New Species Endemic To Moloka‘I, Jason T. Cantley, Angela J. Mcdonnell, J Branson, S R. Long, W Garnett, Christopher T. Martine

Faculty Journal Articles

Chenopodium taxa of Hawai‘i are tetraploids distinguished from other members of the circumglobally distributed genus by minute morphological characters. Because of these reasons, the geographic origin of Hawaiian Chenopodium has remained unclear. Across the Hawaiian Archipelago, Chenopodium taxa are morphologically variable and grow in highly disparate xeric habitats, especially in terms of precipitation, temperature, wind, salt spray, and solar irradiation. Habitats include dry subalpine shrublands, sandy beach strand of atolls in the Northwest Hawaiian Islands, dry forests, and precipitously tall sea cliffs of northwestern Moloka‘i. From the Moloka‘i sea cliffs, which are battered by high energy winds, salt spray, and …

Investigating The Effect Of Ethanol On Wnt7a And Its Potential Implications In Fetal Alcohol Spectrum Disorder, Erika Lytle

Honors Undergraduate Theses

Fetal Alcohol Spectrum Disorders (FASDs), are caused by maternal alcohol consumption during pregnancy [3]. FASD encompasses a wide variety of cardiac and neural anomalies, while also associated with improper limb development, abnormal craniofacial features, problems within the central nervous system (CNS), and disabilities in learning and communication. Gene-regulating FASDs have not been well studied during the crucial phases of early embryonic development. Genes within the Wnt/Beta-catenin pathway control a vast amount of embryonic developmental processes. Among them is the Wnt7a gene, a significant downstream gene regulator which positively controls neural stem cell proliferation and cardiomyocyte differentiation on a large scale …

Regulation Of The Egfr Epigenetic Landscape In Glioblastoma Multiforme, Anishaa Sivakumar

Honors Undergraduate Theses

Glioblastoma Multiforme (GBM) is the most lethal subtype of glioma (brain tumor), with a 5-year survival rate of merely 5.6% post diagnosis¹. The traditional study of glioblastoma has investigated the role of multiple genes in advancing its progression, including the upregulation of Epidermal Growth Factor Receptor (EGFR). However, there is at yet little research into the epigenetic factors that control EGFR, both in the precursor astrocytes and in glioblastomas themselves². EGFR and its regulation may play a significant role in the progression and development of GBM from astrocytes. Through modification of genomic pathways as observed in …

Association Between Maoa U Vntr Genetic Polymorphism And Aggression, Gender, And Race In Adolescents, Almaz Adair Johnson

Walden Dissertations and Doctoral Studies

A genetic polymorphism found in the upstream region of the monoamine oxidase A (MAOA) gene upstream variable number tandem repeat (u VNTR) has been shown to have an influence on aggression with mixed results. The purpose of this quantitative study was to examine the association between the u VNTR genetic polymorphism of the MAOA gene and aggression in an adolescent population 13–18 years of age. The conceptual framework was based on the biosocial model of antisocial behavior that indicates genes can influence aggressive behaviors with or without environmental influences. Data (N = 2506) from the National Longitudinal Adolescents and Adult …

Predicting Patterns Of Gene Family Evolution In Taxa With Similar Ecological Niches, Kim Vertacnik

Theses and Dissertations--Biology

To fully understand the genetic basis of adaptation, we need to know its predictability—the extent to which specific selective pressures and contexts can yield corresponding genetic changes. In particular, the repeated colonization of similar, specialized environments by different taxa is ideal for assessing the frequency of reoccurring changes in the same genes or functions. But compared to a growing body of literature on the convergent evolution of individual genes, far less is known about the repeatability of gene family evolution, where families (defined here as groups of genes that share sequence and functional similarity from common ancestry) can expand (gain …

Investigation Into The Roles Of Her9 And Capn5 During Retinal Development And Regeneration, Cagney Coomer

Theses and Dissertations--Biology

The formation of a healthy and functioning eye requires coordinated interactions between numerous signaling pathways and gene regulatory networks within the developing neural retina. Tight regulation of gene expression is required for cell specification and differentiation in this multilayered, light sensitive tissue. The photoreceptors are the light detecting cells of the retina, capable of functioning in both intense sunlight and dim light at night. When pigment cells of the photoreceptor outer segment are activated by light, a complex chain of events called phototransduction leads to the electrical signal cascade that is transmitted through the retina and ultimately to the brain …

Combination Of Investigational Cell-Based Therapy And Deep Brain Stimulation To Alter The Progression Of Parkinson’S Disease, Nader El Seblani

Theses and Dissertations--Pharmacy

Parkinson’s disease (PD) is the second most common neurodegenerative disorder and the motor symptoms are caused by progressive loss of midbrain dopamine neurons. There is no current treatment that can slow or reverse PD. Our current “DBS-Plus” clinical trial (NCT02369003) features the implantation in vivo of autologous Schwann cells (SCs) derived from a patient’s sural nerve into the substantia nigra pars compacta (SNpc) in combination with Deep Brain Stimulation (DBS) therapy for treating patients with advanced PD.

The central hypothesis of our research is that transdifferentiated SCs within conditioned nerve tissue will deliver pro-regenerative factors to enhance the survival of …

Apoe As A Metabolic Regulator In Humans, Mice, And Astrocytes, Brandon C. Farmer

Theses and Dissertations--Physiology

Altered metabolic pathways appear to play central roles in the pathophysiology of late-onset Alzheimer’s disease (AD). Carrier status of the E4 allele of the APOE gene is the strongest genetic risk factor for late-onset AD, and increasing evidence suggests that E4 carriers may be at an increased risk for neurodegeneration based on inherent metabolic impairments. A new appreciation is forming for the role of APOE in cerebral metabolism, and how nutritional factors may impact this role. In chapter 1, the literature on nutritional interventions in E4 carriers aimed at mitigating disease risk is reviewed. Studies investigating the mechanism by which …

Effects Of Thinning Regimes On Genetic Variation Of White Oak (Quercus Alba L.) In Upland Oak Forests Of Eastern Kentucky, Rachel Gayle Thunder

Theses and Dissertations--Forestry and Natural Resources

This research assesses the effects of silvicultural thinnings, varying in residual basal area and number of thinnings, on genetic diversity and relatedness of white oak (Quercus alba L.). The objectives were to (1) develop microsatellite DNA markers (simple sequence repeats, SSRs) for assessing the genetic diversity of white oak and (2) determine if thinnings significantly change the degree of diversity and relatedness in white oak stands. For objective 1, 84 primer pairs from previously predicted genomic SSRs of white oak were evaluated for consistent PCR amplification and polymorphism. Twenty of the 84 primer pairs amplified consistently and were confirmed …

Identification And Characterization Of Epigenetic Regulators In The Yellow Fever Mosquito, Aedes Aegypti, Shankar C. R. R. Chereddy

Theses and Dissertations--Entomology

Due to the increased interactions between the sylvatic and urban cycles of Aedes aegypti life cycle, there has been an increase in the incidence of vector-borne diseases. The risk involved through the transmission of viruses like Dengue, Zika, Yellow-fever and Chikungunya calls for an effective control method for the deadly vector. The possibility of pesticide resistance and the costs involved in producing new pesticides have pushed Sterile Insect Technique (SIT) into prominence. However, current methods used to sterize insects for SIT are not highly efficient. This study tackles current issues in mosquito control by identifying and characterizing epigenetic regulators that …

Current Dog Breeding Practices Impacts On Health And Preservation Of Purebred Dogs, Bridget E. Baker

Honors Theses and Capstones

No abstract provided.

Development Of Highly Sensitive Environmental Dna Methods For The Detection Of Bull Sharks, Carcharhinus Leucas (Müller And Henle, 1839), Using Droplet DigitalTm Pcr, Katherine E. Schweiss, Ryan N. Lehman, J. Marcus Drymon, Nicole M. Phillips

Faculty Publications

Background: As apex and mesopredators, elasmobranchs play a crucial role in maintaining ecosystem function and balance in marine systems. Elasmobranch populations worldwide are in decline as a result of exploitation via direct and indirect fisheries mortalities and habitat degradation; however, a lack of information on distribution, abundance, and population biology for most species hinders their effective management. Environmental DNA analysis has emerged as a cost‐effective and non‐invasive technique to fill some of these data gaps, but often requires the development of species‐specific methodologies.

Aims: Here, we established eDNA methodology appropriate for targeted species detections of Bull Sharks, Carcharhinus …

Monitoring Mammal Community Shifts Across Silvicultural Treatments Utilizing Camera Traps And The Development Of Invertebrate- Derived Dna In Hardwood Forests Of North America, Shallen Gurtler

Dissertations, Master's Theses and Master's Reports

Mammal distribution and diversity is quickly changing as humans modify the landscape. In particular, silviculture, which is the practice of controlling the growth, structure, and quality of forests to meet the needs of society and the landowner, influences the habitat usage of mammals. Utilizing camera traps, I monitored shifts in mammal communities across different silviculture treatments in the northern hardwood forests of the Great Lakes region in North America. I assessed the community composition across six canopy treatments and three understory treatments with a total of 2,018 active camera trap nights with 3,321 detections over the course of 147 days. …

Genetic Variation Within A Broadly Distributed Chewing Louse Genus (Thomomydoecus), Clarissa Elizabeth Bruns

Honors Program Theses

No broad study has been conducted to examine the genetics of Thomomydoecus species and their patterns of geographic variation. Chewing lice and their parasite-host relationships with pocket gophers have been studied as a key example of cophylogeny (Demastes et al., 2012). Despite this, genetic data on interspecific and intraspecific variation in Thomomydoecus is unexplored, and prior studies consisted within the narrow frame of one complex or species and its relative host gopher. This project collected, and analyzed genetic data, then generated phylogenetic trees. Many of the existing relationships between Thomomydoecus species was confirmed, and there were a number of unexpected …

Investigation Of The Phenotypic Effect Of Mutating A Highly-Conserved Cysteine Residue In The Rna Polymerase Beta Prime Subunit Of E. Coli Rna Polymerase, Meg Dillingham

Mahurin Honors College Capstone Experience/Thesis Projects

All bacteria contain a multi-subunit RNA polymerase (RNAPs) that is essential for gene expression. Because of the centrality of these enzymes in cellular life, the structure and function of the various subunits is intensely studied. The primary sequence of the RNAP β’ subunit contains five cysteine residues that are highly conserved. Four of the cysteines coordinate a zinc atom and form the beta prime subunit zinc binding domain (ZBD). Mutation of any one of the ZBD cysteines is lethal to the cell. However, the role of the fifth residue (C58), which is located upstream of the ZBD cysteines, has not …

Biological Pathways Associated With Wild And Domestic Animals, Cayla Steemer, Laura Carson, Jim Hu, Gloria Regisford

Pursue: Undergraduate Research Journal

Background: Zoonotic diseases are problematic, in that, they impact both wild and domestic animals alike. Thus, there is a need to investigate the genomes of wild and domestic. Gene ontology (GO) is a major bioinformatics initiative, whereby descriptions of gene products across the database are developed and unified to describe all species. This process is performed by biocurators, who gather, annotate, and validate information on the databases, consequently affording easy access to accurate and updated data. In this study, we investigated the biocuration of two biological processes, DNA integration, which is used for DNA coding, and the tricarboxylic acid (TCA) …

Spatial And Temporal Genetic Structure Of Winter-Run Steelhead (Oncorhynchus Mykiss) Returning To The Mad River, California, Steven R. Fong

Cal Poly Humboldt theses and projects

Distinct populations of steelhead in the wild are in decline. The propagation of steelhead in hatcheries has been used to boost population numbers for recreational fisheries and for use in conservation. However, hatchery breeding practices of steelhead can result in changes in genetic structure. I investigated the genetic structure of winter-run steelhead (Oncorhynchus mykiss) returning to the Mad River, California, where a hatchery has been used enhance production for recreational fisheries since 1971. Genetic variability in Mad River steelhead was evaluated using 96 single nucleotide polymorphisms (SNPs) among 4203 individuals, including the Mad River and nearby locations, and …

Snp Population Genetic Data For The Seagrass Halodule Uninervis From Pilbara Region, Western Australia, Kathryn Margaret Mcmahon, Richard Evans

Research Datasets

This dataset contains 80 SNP loci from 15 locations with 25-47 samples per locations. Each column contains data from two alleles. All genotyped samples are included. Prior to population genetic analysis clone mates were identified and removed.

Predictors Of Marine Genetic Structure In The Indo-Australian Archipelago, Kathryn M. Mcmahon, Udhi Eko Hernawan

Research Datasets

This is the dataset extracted from 101 publications on 99 marine species from eight taxonomic groups in the Indo Australian Archipelago. Data extracted includes measures of genetic structure and the potential predictors.

Population-Based Case-Control Study Revealed Metabolomic Biomarkers Of Suboptimal Health Status In Chinese Population—Potential Utility For Innovative Approach By Predictive, Preventive, And Personalized Medicine, Hao Wang, Qiuyue Tian, Jie Zhang, Hongqi Liu, Xiaoyu Zhang, Weijie Cao, Jinxia Zhang, Enoch Odame Anto, Xingang Li, Xueqing Wang, Di Liu, Yulu Zheng, Zheng Guo, Lijuan Wu, Manshu Song, Youxin Wang, Wei Wang

Research outputs 2014 to 2021

Background: Suboptimal health status (SHS) is a subclinical stage of chronic diseases, and the identification of SHS provides an opportunity for the predictive, preventive, and personalized medicine (PPPM) of chronic diseases. Previous studies have reported the associations between metabolic signatures and early signs of chronic diseases. Methods: This study aimed to detect the metabolic biomarkers for the identification of SHS in a case-control study. SHS questionnaire-25 (SHSQ-25) was used in a population-based health survey to measure the SHS levels of participants. The liquid chromatography-mass spectrometry-based untargeted metabolomics analysis was conducted on plasma samples collected from 50 SHS participants and 50 …

Sampling The Local Fare: Fishes At The Sam Israel House Pit (45gr76), Soap Lake, Washington, Adam Fruge

All Master's Theses

The Sam Israel site is a precontact archaeological complex with numerous fish bones at the north end of Soap Lake, Washington. Excavated in 1976, the fish remains recovered from there were never fully analyzed prior to this research. Since this inland Columbia Plateau site had thousands of fish bones, it contained untapped potential for our understanding of ancient local fish procurement. As such, I conducted a detailed analysis of 2,862 fish bone specimens from the Sam Israel House Pit locus to: study a larger sample of fish bones in greater detail than was done before; compare the distribution of fishes …

Environmental Dna Is An Effective Method To Monitor Species In Various Freshwater Habitats, Kayleigh Mullen

All Master's Theses

This research investigated the use of DNA shed from individuals into the environment (eDNA) to monitor three amphibian species and two trout species associated with habitat intersected by Interstate-90 in Snoqualmie Pass, Washington. This included a large catchment area within creeks and nearby wetlands historically affected by I-90, including sites where significant habitat improvements had been made. Species-specific primers were used to detect three focal amphibians of varying local abundance and two focal trout species. This study showed successful detection of species across both lentic and lotic systems throughout the study area through efficient multiplexing (detection of multiple species in …