Genetics and Genomics Commons^™

Data From: Phylogenomic Species Delimitation Of Studfishes (Fundulidae: Fundulus): Evidence For Cryptic Species In Agreement With The Central Highlands Vicariance Hypothesis, Kayla M. Fast, Peter J. Hundt, Zachariah D. Alley, Michael W. Sandel

CFR Publications

The Central Highlands ecoregion of the eastern United States represents a hotspot of freshwater biodiversity, with replicated patterns of vicariant speciation east and west of the Mississippi River. Previous phylogeographic investigation of the studfishes (Fundulus subgenus Fundulus) revealed evidence for vicariant speciation in the Central Highlands, but data were limited to a small number of gene sequences generated with Sanger sequencing. We used double digest restriction-site associated DNA sequencing (ddRADseq) to improve resolution of phylogeographic patterns and better characterize population genetic variation. Our sample design included individuals from the Fundulus catenatus species group (F. catenatus, F. bifax, …

Quantitative Trait Loci Influencing Elemental Content In Grapevine Leaves, Jesse L. Krokower

Graduate Theses/Dissertations

In grapevine, the influence of the plant’s elemental composition (the ionome) on fruit and wine quality is well established, but its genetic underpinnings have received limited scientific attention. In this study, I analyzed the leaf ionome of 131 interspecific F1 hybrid progeny plants from a cross between a Vitis rupestris Scheele (♀) and a Vitis riparia Michx (♂) parents, which were replicated in four different environments: Southwest Missouri, Central Missouri, South Dakota, and New York. I sampled leaves at three different times during the growing season at all four locations and had the concentration of 20 elements measured using ICP-MS. …

Rare Variant Analyses Validate Known Als Genes In A Multi-Ethnic Population And Identifies Antxr2 As A Candidate In Pls, Tess D. Pottinger, Joshua E. Motelow, Gundula Povysil, Cristiane A. Martins Moreno, Zhong Ren, Hemali Phatnani, The New York Genome Center Als Sequencing Consortium, Timothy J. Aitman, Javier Santoyo‑Lopez, Scottish Genomes Partnership, Hiroshi Mitsumoto, Als Cosmos Study Group, Pls Cosmos Study Group, Gtac Investigators, David B. Goldstein, Matthew B. Harms

Neurology Faculty Publications

Background Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 300,000 people world‑ wide. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts physical function. Approximately, 15% of individuals diagnosed with ALS have a known genetic variant that contributes to their disease. As therapies that slow or prevent symptoms continue to develop, such as antisense oligonucleotides, it is important to discover novel genes that could be targets for treatment. Additionally, as cohorts continue to grow, performing analyses in ALS subtypes, such as primary lateral sclerosis (PLS), becomes possible …

Functional Analyses Of The Polycomb-Group Genes In Sea Lamprey Embryos Undergoing Programmed Dna Loss, Cody Saraceno

Theses and Dissertations--Biology

During early embryonic development, the sea lamprey (Petromyzon marinus) undergoes programmatic elimination of DNA from somatic progenitor cells in a process termed programmed genome rearrangement (PGR). Eliminated DNA eventually becomes condensed into micronuclei, which are then physically degraded and permanently lost from the cell. Previous studies indicated that many of the genes eliminated during PGR have mammalian homologs that are bound by polycomb repressive complex (PRC) in embryonic stem cells. To test whether PRC components play a role in the faithful elimination of germline-specific sequences, we used a combination of CRISPR/Cas9 and lightsheet microscopy to investigate the impact …

Caenorhabditis Elegans Rapgef Promotes Synaptic Development Through A Small G Protein Signaling Cascade, Reagan Em Lamb

Theses and Dissertations--Neuroscience

Synaptic dysfunction is a major contributor toward the development of many neurological disorders. For proper development, synapses require a series of signaling pathways to guide them, but not all the mechanisms underlying these processes are understood. Here, we used the neuromuscular junction of Caenorhabditis elegans as a model circuitry for examining underlying pathways that mediate proper development of synapses. We hypothesized that the C. elegans RapGEF2 and RapGEF6 orthologue, PXF-1, contributed toward development of cholinergic synapses at the neuromuscular junction. Using behavioral assays and fluorescence microscopy, we found that pxf-1 mutant animals had decreased neuromuscular junction function and decreased synaptic …

Contributions Of The Replication Initiator Protein Dnaa To Physiology And Virulence Of The Lyme Disease Spirochete, Andrew Krusenstjerna

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Borrelia burgdorferi, the etiological agent of Lyme disease, is the most prevalent vector-borne disease in the United States. The spirochetal population is naturally maintained by consistently cycling between Ixodid ticks and small vertebrates. To survive within these diverse niches, B. burgdorferi has evolved a unique physiology and regulatory network to sense and respond to environmental fluxes. Replication is a hallmark of the Lyme spirochete’s enzootic life cycle, specifically at the nymphal tick-to-vertebrate interface. The mechanisms and regulatory schema for the basic cellular processes in B. burgdorferi, or indeed any member of the phylum spirochaetota, are largely unknown. The central hypothesis …

Practical Challenges In Delivering Dsrna For Woody Plant Protection, Zachary Bragg

Theses and Dissertations--Entomology

Unprecedented weather events associated with climate change, coupled with extensive anthropogenic stresses, have reduced the effectiveness of traditional forest pest management approaches, which can no longer keep pace with invasive species overwhelming naïve landscapes and native pests experiencing eruptive and expansive outbreaks. Double-stranded RNA-(dsRNA) mediated gene silencing, a type of RNA interference (RNAi), has been coopted for use as a biopesticide against a multitude of agricultural and horticultural pests and could serve as a powerful tool for woody plant protection. While effective initiation of gene silencing and subsequent mortality have been demonstrated in multiple tree pests, effective and efficient methods …

Determining Population Structure In Kentucky Parascaris Univalens Specimens, Constance Finnerty

Theses and Dissertations--Veterinary Science

Parascaris univalens is a highly pathogenic nematode that affects the gastrointestinal system of young horses. When unaddressed, this parasite causes severe intestinal impactions and even death. Parascaris univalens is also found to have an emergence of anthelmintic resistances, causing a concern for horse owners. Despite its clinical significance, very little work has been done on Parascaris univalens to identify its population structure. This study aimed to determine the population structure of Parascaris univalens through Illumina next generation sequencing (NGS) on three hierarchical categorizations: within a horse, within an isolated herd, and within horses in the state of Kentucky. A total …

Genomic Studies Of The Equine Bloodworm, Strongylus Vulgaris, Nichol Ripley

Theses and Dissertations--Veterinary Science

Strongylus vulgaris is the most pathogenic nematode parasite of grazing horses worldwide. This gastrointestinal parasitic nematode is in the family Strongylidae under the subfamily Strongylinae, or Strongylins. While the epidemiology, complete life cycle, and high pathogenicity of the fourth and fifth larval stages of S. vulgaris are well established, we understand very little about its biology. This parasite is renowned for its unique life cycle and capacity to cause arterial damage, leading to significant health and economic impacts for the equine industry. It also is the most intensively documented Strongylin; however, S. vulgaris has yet to gain drug resistance as …

Exploring 3d Genome Interaction And Epigenetic Regulation Via Swi/Snf Complex And Deep Learning Models, Ruoyun Wang

Dartmouth College Ph.D Dissertations

The three-dimensional organization of the genome is fundamental in regulating gene expression and maintaining cellular function. This organization's complexities, influenced by epigenetic marks and chromatin remodeling complexes, are crucial for understanding genomic regulation. Among these, the SWI/SNF complexes are key, facilitating chromatin accessibility and regulating gene activity across cell types. The first part of my dissertation focuses on SWI/SNF complexes, exploring their role in chromatin remodeling and their impact on 3D genome architecture. Utilizing next-generation sequencing (NGS) techniques, this section investigates the interplay between these complexes and chromatin structure. During my research on the SWI/SNF complex, I was intrigued by …

Contribution Of The Transcription Factor Red Nac To Low Nitrogen Phenotypes In Poplar, Shane Alexander Spence

Dissertations, Master's Theses and Master's Reports

Greenhouse grafting and field trials were conducted to examine the contribution of the RED NAC transcription factor on low nitrogen phenotypes in hybrid poplar (P. tremula x P. alba). Reciprocal grafting trials showed both root and shoot expression contribute to phenotype under low nitrogen conditions, and shoot expression has a leading role in contribution to low-nitrogen phenotype. The impact of RED NAC expression level on auxin polar transport was investigated using a DR5::GUS auxin-responsive reporter gene line as rootstock for RED NAC modified scions. Pilot studies indicate the rate of auxin transport from apex to roots is slower through shoots …

Genetic Diversity Of Paxistima Canbyi A. Gray: Conserving A Rare Plant Species Endemic To The Eastern United States, Isaac Buabeng

Master’s Theses

Premise: The glacial cycles of the Pleistocene period likely had a profound impact on the genetic diversity and phylogeographic patterns of numerous plant taxa in North America. However, the genetic diversity of rare, limestone-endemic woody species has not been highlighted. This study assesses genetic diversity in Paxistima canbyi A. Gray (Canby’s mountain lover or rat stripper), a rare limestone endemic small woody plant.

Methods: We investigated the genetic diversity of P. canbyi using genomic Single Nucleotide Polymorphism (SNP) data from 165 individuals from 14 populations sampled from across the entire range distribution. We first; de novo assembled the SNP …

Inflammation And Tumor Progression: The Differential Impact Of Saa In Breast Cancer Models, Daniel Wilhelm Olivier, Carla Eksteen, Manisha Du Plessis, Louis De Jager, Lize Engelbrecht, Nathaniel Wade Mcgregor, Preetha Shridas, Frederick C. De Beer, Willem J. S. De Villiers, Etheresia Pretorius, Anna-Mart Engelbrecht

Saha Cardiovascular Research Center Faculty Publications

Background: Previous research has shown that the Serum Amyloid A (SAA) protein family is intricately involved in inflammatory signaling and various disease pathologies. We have previously demonstrated that SAA is associated with increased colitis disease severity and the promotion of tumorigenesis. However, the specific role of SAA proteins in breast cancer pathology remains unclear. Therefore, we investigated the role of systemic SAA1 and SAA2 (SAA1/2) in a triple-negative breast cancer mouse model.

Methods: Syngeneic breast tumors were established in wild-type mice, and mice lacking the SAA1/2 (SAADKO). Subsequently, tumor volume was monitored, species survival determined, the inflammatory profiles of mice …

Examining Potential Causal Associations Of Sedentary Time And Physical Activity With Heart Failure Using Subjective And Objective Measures: A Mendelian Randomization Analysis, Jessica Geller

UNF Graduate Theses and Dissertations

Purpose: The objective of this study was to assess the causal relationship between both subjectively and objectively measured sedentary time (ST) and physical activity (PA) with heart failure (HF) risk, utilizing Mendelian Randomization (MR) approach.

Methods: The present MR used genetic instruments identified for self-reported ST and PA extracted from 51 genome wide association studies (GWAS), encompassing data from 703,901 individuals. The GWAS identified 89 independent single nucleotide polymorphisms (SNPs) associated with leisure screen time. Eleven loci were reported to be associated with moderate to vigorous physical activity (MVPA). From another GWAS examining accelerometer-based activities, three loci were found to …

Range-Wide Analysis Of The Genetic Diversity And Genetic Structure Of The Spotted Turtle (Clemmys Guttata), Madison S. Whitehurst

Theses and Dissertations

Understanding the spatial distribution of genetic diversity and structure in endangered species is vital for effective conservation management. This research discusses the results of an initial analysis of the genetic structure and variation of the spotted turtle (Clemmys guttata), a species of conservation interest. The study sampled 913 individuals from 78 unique locales across 16 states in the eastern portion of the species' range. Utilizing ddRADSeq, a de novo genome assembly was developed to identify nearly 20,000 potential loci. A total of 926 were selected for this analysis. Results revealed no spatial clustering of genetic diversity or structure, …

Cyp6g2 Is The Major P450 Epoxidase Responsible For Juvenile Hormone Biosynthesis In Drosophila Melanogaster, Qiangqiang Jia, Liu Yang, Jiamin Wen, Suning Liu, Di Wen, Wei Luo, Weihua Wang, Subba R. Palli, Li Sheng

Entomology Faculty Publications

Background Juvenile hormones (JH) play crucial role in regulating development and reproduction in insects. The most common form of JH is JH III, derived from MF through epoxidation by CYP15 enzymes. However, in the higher dipterans, such as the fruitfly, Drosophila melanogaster, a bis-epoxide form of JHB3, accounted most of the JH detected. Moreover, these higher dipterans have lost the CYP15 gene from their genomes. As a result, the identity of the P450 epoxidase in the JH biosynthesis pathway in higher dipterans remains unknown.

Results In this study, we show that Cyp6g2 serves as the major JH epoxidase responsible for …

Go West: Population Genomics Reveals Unexpected Population Fluctuations And Little Gene Flow In Western Hemisphere Populations Of The Predatory Lady Beetle, Hippodamia Convergens, Arun Sethuraman, Schyler O. Nunziata, Angela Jones, John J. Obrycki, David W. Weisrock

Entomology Faculty Publications

Hippodamia convergens—the convergent lady beetle, has been used extensively in aug- mentative biological control of aphids, thrips, and whiteflies across its native range in North America, and was introduced into South America in the 1950s. Overwintering H. convergens populations from its native western range in the United States are com- mercially collected and released across its current range in the eastern USA, with little knowledge of the effectiveness of its augmentative biological control. Here we use a novel ddRADseq-based SNP/haplotype discovery approach to estimate its range- wide population diversity, differentiation, and recent evolutionary history. Our results indicate (1) significant population …

N(Alpha)-Acetyltransferase 40-Mediated Histone Acetylation Plays An Important Role In Ecdysone Regulation Of Metamorphosis In The Red Flour Beetle, Tribolium Castaneum, Sharath Chandra Gaddelapati, Smitha George, Anilkumar Moola, Karthi Sengodan, Subba Reddy Palli

Entomology Faculty Publications

Histone acetylation, a crucial epigenetic modification, is governed by histone acetyltransferases (HATs), that regulate many biological processes. Functions of HATs in insects are not well understood. We identified 27 HATs and determined their functions using RNA interference (RNAi) in the model insect, Tribolium castaneum. Among HATs studied, N-alpha-acetyltransferase 40 (NAA40) knockdown caused a severe phenotype of arrested larval development. The steroid hormone, ecdysone induced NAA40 expression through its receptor, EcR (ecdysone receptor). Interestingly, ecdysone-induced NAA40 regulates EcR expression. NAA40 acetylates histone H4 protein, associated with the promoters of ecdysone response genes: EcR, E74, E75, and HR3, and causes an increase …

The Mechanoreceptor Piezo Is Required For Spermatogenesis In Bombyx Mori, Zhongjie Zhang, Xiaojing Liu, Bo Hu, Kai Chen, Ye Yu, Chenxin Sun, Dalin Zhu, Hua Bai, Subba Reddy Palli, Anjiang Tan

Entomology Faculty Publications

Background The animal sperm shows high diversity in morphology, components, and motility. In the lepidopteran model insect, the silkworm Bombyx mori, two types of sperm, including nucleate fertile eupyrene sperm and anucleate unfertile apyrene sperm, are generated. Apyrene sperm assists fertilization by facilitating the migration of eupyrene spermatozoa from the bursa copulatrix to the spermatheca. During spermatogenesis, eupyrene sperm bundles extrude the cytoplasm by peristaltic squeezing, while the nuclei of the apyrene sperm bundles are discarded with the same process, forming matured sperm.

Results In this study, we describe that a mechanoreceptor BmPiezo, the sole Piezo ortholog in B. mori, …

Contemporary Vs. Traditional Dna-Based Mutation Testing To Detect Hereditary Breast And Ovarian Cancer Syndrome (Hboc) In Women: A Meta Narrative Review, Hannah Olivia Cantu, Jacob Hipp, Nyela Y. Lopez, Duc Duy Nguyen

Research Methods Poster Session 2024

No abstract provided.