Genetics and Genomics Commons^™

Leveraging The Genomic Tools To Explore The Molecular Basis Of Salinity Tolerance In Rice And Soybean, Rajat Pruthi

LSU Doctoral Dissertations

Salinity stress significantly challenges agricultural productivity, particularly affecting major crops like rice and soybean. This research investigates the genetic basis of salt tolerance in both crops through high-resolution genetic mapping, genome-wide association studies (GWAS), and RNA-Seq analysis. In rice, we examined quantitative trait loci (QTLs) associated with salt tolerance at the seedling and flowering stages using a population of advanced backcrossed introgression lines (ILs). A genetic map, constructed with 14,230 polymorphic SNP markers, identified distinct QTLs and candidate genes for salt tolerance at both stages, suggesting differential genetic controls. Notable genes such as OsHAK13 and OsCYP21-4 were upregulated under salt …

Conservation Genomic Investigation Of A Threatened Trout Species Endemic To The Gila River, David Thomas Camak

Biology ETDs

Climate change is a looming threat to the persistence of species, especially aquatic, imperiled species. Species native to desert streams are at a particular disadvantage, as many species already face drought, floods, wildfires, and threats from nonnative species, all of which are thought to be exacerbated by climate change. Species such as the threatened Gila Trout (Oncorhynchus gilae) already have small ranges and persist in fragmented and isolated habitats that limits gene flow between populations. Therefore, it is important to understand the current genomic status of such populations to be able to predict the future effects of climate …

Role Of Sds-22/Pp1 Phosphatase In Polarizing The Germplasm Of Caenorhabditis Elegans Embryo, Aparna Nurni Ravi

Dartmouth College Ph.D Dissertations

During asymmetric cell division, cell polarity and cell cycle are tightly coupled to ensure robust segregation of cell fate determinants and generation of cellular diversity. In the one-cell C. elegans embryo, multiple cell cycle kinases regulate cell polarization and posterior segregation of germline fate determinants (germplasm). For example, PLK-1 kinase inhibits the retention of its germplasm substrate POS-1 in the anterior, driving POS-1 segregation to the posterior (Han et al., 2018). Additionally, MBK-2 kinase disassembles P granules in the anterior through phosphorylation of the P granule scaffold MEG-3, helping to drive P granule segregation to the posterior (Wang et al., …

Functional And Structural Analysis Of The Neimann-Pick Disease Type C Pathway To Include Caveolin-1, Anthony Michael Seat

Chemistry and Chemical Biology ETDs

Human disease is often thought of as an all or nothing prospect, either one has the disease or one does not. This does not bear out in clinical or personal experiences, instead demonstrating that disease occurs within a spectrum ranging from presumed unaffected to demonstrably and detrimentally affected.Neimann-Pick disease is one example of this spectrum look into diseased states, with multiple named versions of a phenotypically similar disease. We focus on Neimann-Picktype C (NPC), which is the result of a disruption in the efflux of cholesterol and sphingolipids from the endocytic pathway. NPC demonstrates this concept of a spectrum of …

Evaluation Of The Capacity And Effective Angle Of Thalamic Damage For 2 Commercially Available Captive Bolt Tool Types On Cadaver Heads From Sows >200 Kg Body Weight, Karly N. Anderson, Ruth Woiwode, Ashlynn A. Kirk, Jennifer Berger, Arquimides A. Reyes, Perle E. Zhitnitskiy, Kurt D. Vogel

Department of Animal Science: Faculty Publications

This study evaluated the ability of 2 penetrating captive bolt (PCB) types (PISTOL, INLINE) to reach and disrupt the thalamus when applied in 2 placements (FRONTAL, BEHIND EAR) to chilled cadaver heads (N = 60) from sows >200 kg. Heads were randomly distributed across 6 treatments (n = 10): FRONTAL-INLINE, FRONTAL-PISTOL, FRONTAL-NO SHOT, BEHIND EAR-INLINE, BEHIND EAR-PISTOL, and BEHIND EAR-NO SHOT. The FRONTAL shot was placed 3.5 cm superior to the optic orbits at the midline; the BEHIND EAR shot was placed directly caudal to the pinna of the ear on the same plane as the eyes and targeting the …

L-2-Hydroxyglutaric Aciduria In Two Palestinian Siblings With A Novel Mutation In The L2hgdh Gene, Imad Dweikat, Bassam Abu Libdeh, Iman Abu-Libdeh, Motee Ashhab, Haneen Zitawi

Journal of the Arab American University مجلة الجامعة العربية الامريكية للبحوث

L-2-Hydroxyglutaric aciduria is a rare autosomal recessive neurometabolic disorder caused by deficiency of L-2-hydroxyglutarate dehydrogenase. This enzyme catalyses the conversion of L-2-hydroxyglutarate to alpha-ketoglutarate and its deficiency causes accumulation of L-2-hydroxyglutarate which is s toxic to the brain leading to the leukoencephalopathy.

The researchers reported a novel mutation in the L2HGDH gene in two siblings with L-2-Hydroxyglutaric aciduria and described clinical phenotype. The symptoms were presented with developmental delay, cerebellar ataxia, tremor and speech regression. Urine organic acid analysis revealed massive excretion of 2-Hydroxyglutaric acid. Brain magnetic resonance imaging showed the characteristic leukodystrophy involving the subcortical cerebral white matter and …

Associations Between Covid-19 Therapies And Outcomes In Rural And Urban America: A Multisite, Temporal Analysis From The Alpha To Omicron Sars-Cov-2 Variants, A. Jerrod Anzalone, William H. Beasley, Kimberly Murray, William B. Hillegass, Makayla Schissel, Michael T. Vest, Scott A. Chapman, Ronald Horswell, Lucio Miele, J. Zachary Porterfield, H. Timothy Bunnell, Bradley S. Price, Sharon Patrick, Clifford J. Rosen, Susan L. Santangelo, James C. Mcclay, Sally L. Hodder

School of Medicine Faculty Publications

Purpose: To investigate the enduring disparities in adverse COVID-19 events between urban and rural communities in the United States, focusing on the effects of SARS-CoV-2 vaccination and therapeutic advances on patient outcomes. Methods: Using National COVID Cohort Collaborative (N3C) data from 2021 to 2023, this retrospective cohort study examined COVID-19 hospitalization, inpatient death, and other adverse events. Populations were categorized into urban, urban-adjacent rural (UAR), and nonurban-adjacent rural (NAR). Adjustments included demographics, variant-dominant waves, comorbidities, region, and SARS-CoV-2 treatment and vaccination. Statistical methods included Kaplan-Meier survival estimates, multivariable logistic, and Cox regression. Findings: The study included 3,018,646 patients, with rural …

Ocular Gene Transfer In The Spotlight: Implications Of Newspaper Content For Clinical Communications, Shelly Benjaminy, Tania M. Bubela

Office of the Provost

Background: Ocular gene transfer clinical trials are raising hopes for blindness treatments and attracting media attention. News media provide an accessible health information source for patients and the public, but are often criticized for overemphasizing benefits and underplaying risks of novel biomedical interventions. Overly optimistic portrayals of unproven interventions may influence public and patient expectations; the latter may cause patients to downplay risks and over-emphasize benefits, with implications for informed consent for clinical trials. We analyze the news media communications landscape about ocular gene transfer and make recommendations for improving communications between clinicians and potential trial participants in light of …

Exploring The Functional Significance Of A Yap1 Missense Variant Of Uncertain Significance In Caenorhabditis Elegans, Nathan Jones

Theses

Polycystic ovary syndrome (PCOS) is a complex disorder with various implications, such as polycystic ovaries, visceral obesity, and increased risk of cancer. YAP1 was recently identified as a gene of interest in the development of PCOS. Researchers have established that single nucleotide variants in YAP1 are likely to play a role in PCOS development. This project aims to provide insight into the potential impact of a YAP1 variant of uncertain significance (VUS). Studies in C. elegans have established yap-1 as a nematode ortholog for human YAP1. A YAP1 VUS was identified through ClinVar, YAP1 c.1015A>G (p.Asn339Asp). Evolutionary conservation …

Hybridization Between The Rare Gray-Headed Chickadee And The Abundant Boreal Chickadee In The Midst Of Shifting Climate, Matthew R. Armstrong

School of Natural Resources: Dissertations, Theses, and Student Research

As species respond to changing climate, distributions and abundances may shift and alter species interactions. Hybridization, a relatively widespread phenomenon becoming more common with climate change, can have beneficial and detrimental effects on population growth rates and genetic integrity. Beneficial effects due to the introduction of advantageous alleles and increased genetic diversity may result from hybridization. Species may also accrue fitness costs associated with changing climates if mismatches occur between environmental variables and phenotypes. The gray-headed chickadee, Poecile cinctus lathami, is an extremely rare songbird that has experienced marked declines in recent decades within its restricted distribution in Alaska …

Interleukin 24 Induces Apoptosis Through Glycogen Synthase Kinase-3 Beta Inactivation In Prostate Cancer Cells, Sual J. Lopez, Moira Sauane

Theses and Dissertations

Interleukin 24 (IL-24) is a tumor-suppressing protein currently in clinical trials. IL-24 induces cancer-specific apoptosis by activating endoplasmic reticulum (ER) stress and mitochondria dysfunction. We have previously demonstrated that IL-24 leads to apoptosis in cancer cells by protein kinase A (PKA) activation in human breast cancer cells. To further understand the mechanism by which IL-24 induces apoptosis, I analyzed the role of glycogen synthase kinase-3 (GSK3), a highly conserved and normally active serine/threonine kinase in cancer cells and downstream target of PKA. The work reported here provides direct evidence that GSK3 was inhibited following IL-24 treatment in human prostate cancer …

Identifying And Training Deep Learning Neural Networks On Biomedical-Related Datasets, Alan E. Woessner, Usman Anjum, Hadi Salman, Jacob Lear, Jeffrey T. Turner, Ross Campbell, Laura Beaudry, Justin Zhan, Lawrence E. Cornett, Susan Gauch, Kyle P. Quinn

Computer Science and Computer Engineering Faculty Publications and Presentations

This manuscript describes the development of a resources module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox at the beginning of this Supplement. This module delivers learning materials on implementing deep learning algorithms for biomedical image data in an interactive format that uses appropriate cloud resources for data access and analyses. Biomedical-related datasets are widely used in both research and clinical settings, but the ability for professionally trained clinicians and researchers to interpret datasets becomes difficult as the size and …

New Insights On Hybridization In Potamogeton Floridanus (The Florida Pondweed), Kaitlyn R. Sampson

Graduate Theses and Dissertations (2019 - present)

Freshwater ecosystems are some of the most important and highest threatened habitats in the world, and aquatic plants play an important, but often-overlooked, role in maintaining them. Potamogeton is a diverse and ecologically important aquatic plant genus well known for taxonomic difficulty and rampant hybridization. lbis study aimed to 1) test the hypothesis that Potamogeton jloridanus (Florida pondweed) is a hybrid between P. oakesianus and P. pulcher, and 2) to investigate correlations in ecological conditions for the focal species. This study revealed the discovery of a new population of P. jloridanus in Big Coldwater Creek in Santa Rosa Co., FL, …

Heat Stress Changes The Bovine Methylome And Transcriptome And Investigation Of Two Novel Genetic Defects In Cattle, Rachel Renae Reith

Department of Animal Science: Dissertations, Theses, and Student Research

Heat stress is a major concern for livestock producers due to its negative impact on animal health and productivity. Heat stress does so by altering expression of genes through different regulatory mechanisms such as DNA methylation. Understanding how heat stress alters gene expression will help elucidate the genetic basis of physiological changes as well as identify targets for possible heat stress mitigation. The purpose of the first study was to understand how heat stress alters the adipose and skeletal muscle transcriptomes in zilpaterol-fed Brahman, as zilpaterol improves muscle growth and may mitigate the effects of heat stress. Differential expression and …

Heat Stress Changes The Bovine Methylome And Transcriptome And Investigation Of Two Novel Genetic Defects In Cattle, Rachel Renae Reith

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Heat stress is a major concern for livestock producers due to its negative impact on animal health and productivity. Heat stress does so by altering expression of genes through different regulatory mechanisms such as DNA methylation. Understanding how heat stress alters gene expression will help elucidate the genetic basis of physiological changes as well as identify targets for possible heat stress mitigation. The purpose of the first study was to understand how heat stress alters the adipose and skeletal muscle transcriptomes in zilpaterol-fed Brahman, as zilpaterol improves muscle growth and may mitigate the effects of heat stress. Differential expression and …

Optimizing The Expression Of Polyethylene Terephtalate Hydrolase-Encoding Synthetic Gene In Escherichia Coli Arctic Express (De3), Jocelyn Nataniel, Maria Ulfah, Dini Achnafani, Niknik Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, Abinawanto Abinawanto, Is Helianti

Makara Journal of Science

The waste of polyethylene terephthalate (PET) plastic waste in Indonesia is a pressing concern due to its slow degradation and potential environmental damage. One promising solution is to utilize polyethylene terephthalate hydrolase from Ideonella sakaiensis (IsPETase), an enzyme that specifically degrades PET. However, inducing the expression of IsPETase synthetic gene in Escherichia coli BL21 (DE3) has been challenging because much of it remains insoluble. This study aimed to express IsPETase in E. coli Arctic Express (DE3) and optimize the conditions to enhance its production. First, pET22b(+)pelB-IsPETase was inserted into E. coli Arctic Express (DE3). The …

Evaluating Past Progress And Assessing Prediction Breeding Strategies For Sustained Genetic Gains In The Louisiana Sugarcane Variety Development Program, Brayden A. Blanchard

LSU Doctoral Dissertations

The aim of this dissertation is to outline important considerations for the Louisiana Sugarcane Variety Development Program (LSVDP) as it pertains to historical progress, impact, goal setting, and new strategies for continued genetic gains. Industry progress was evaluated with robust regression models to quantify rates of productivity gains. Over the last 50 years, statistically significant productivity gains were identified in sucrose content (45%), cane yield (32.2%), and sugar yield (93%) while pairwise comparisons of decades showed that progress was incremental rather than rapid and sustained once achieved. The decade from 1990-1999 was identified as the only decade with a significant …

Association Of Longitudinal Changes In 24-H Blood Pressure Level And Variability With Cognitive Decline, Jesus D. Melgarejo, Kristina Vatcheva, Silvia Mejia-Arango, Sokratis Charisis, Luis J. Mena, Rosa P. Mavarez, Antonio Garcia, Ney Alliey Rodriguez, John Blangero, Gladys Maestre

School of Medicine Publications

Objective:

A high office blood pressure (BP) is associated with cognitive decline. However, evidence of 24-h ambulatory BP monitoring is limited, and no studies have investigated whether longitudinal changes in 24-h BP are associated with cognitive decline. We aimed to test whether higher longitudinal changes in 24-h ambulatory BP measurements are associated with cognitive decline.

Methods:

We included 437 dementia-free participants from the Maracaibo Aging Study with prospective data on 24-h ambulatory BP monitoring and cognitive function, which was assessed using the selective reminding test (SRT) and the Mini-Mental State Examination (MMSE). Using multivariate linear mixed regression models, we analyzed …

The Influence Of Childhood Trauma On Dna Methylation Patterns And Sex-Specific Cortisol Stress Reactivity: A Secondary Analysis, Isabella F. Correia

USF Tampa Graduate Theses and Dissertations

Childhood trauma has been shown to significantly impact physical and mental health outcomes, leading to conditions such as heart disease, diabetes, depression, and difficulties in decision-making and maintaining relationships. Exposure to such trauma has the potential to dysregulate an individual’s stress response system, resulting in abnormal cortisol levels. Many studies suggest a lasting impact of early-life stress on DNA methylation patterns and, separately, cortisol stress reactivity. In addition, there are known sex differences in exposure to childhood trauma and cortisol reactivity; yet studies to date have not investigated whether there is an association to DNA methylation. This study utilized a …

Porphyrin Overdrive In Cancer: Unraveling The Mechanisms And Therapeutic Potential, Pravin D. Meshram

USF Tampa Graduate Theses and Dissertations

The increased understanding of cancer cell metabolism has shown options for novel treatment strategies. This thesis looks at the role of heme metabolism, specifically "porphyrin overdrive," in cancer progression and treatment. Cancer cells are hypermetabolic and rely on heme synthesis. When treated with δ-aminolevulinic acid (ALA), they abnormally accumulate heme intermediates. This metabolic weakness presents an opportunity to exploit heme synthesis in targeted cancer therapy. In this study, we suggest a "Bait and Kill" technique that uses exogenous ALA to induce protoporphyrin IX (PpIX) buildup in cancer cells, making them more susceptible to oxidative stress. We investigate the possibility of …