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American Eel (Anguilla Rostrata) And Other Fishes As Surveyed By Environmental Dna In The Bronx River And Hudson River Watershed, Sam C. Chin 2023 The Graduate Center, City University of New York

American Eel (Anguilla Rostrata) And Other Fishes As Surveyed By Environmental Dna In The Bronx River And Hudson River Watershed, Sam C. Chin

Dissertations, Theses, and Capstone Projects

Mounting an effective response to the threats faced by freshwater fish may require expansions to aquatic biomonitoring in excess of what is feasible using the capture-based survey techniques currently relied upon by natural resource managers. Methods for analyzing environmental DNA (eDNA) are emerging as a minimally invasive and cost-effective approach for surveying fish and other organisms. By detecting taxon-specific DNA sequences recovered from environmental samples (e.g. water, sediment), eDNA methods are able to infer species presence from samples that can be collected rapidly with simple equipment. In many cases, eDNA detection rates of fish species have been shown to meet …


Rhetorics Of Species Revivalism And Biotechnology – A Roundtable Dialogue, Eva Kasprzycka, Charlotte Wrigley, Adam Searle, Richard Twine 2023 University of British Columbia

Rhetorics Of Species Revivalism And Biotechnology – A Roundtable Dialogue, Eva Kasprzycka, Charlotte Wrigley, Adam Searle, Richard Twine

Animal Studies Journal

This informal dialogue contextualises and explores contemporary practices of nonhuman animal gene-modification in de-extinction projects. Looking at recent developments in biotechnology’s role in de-extinction sciences and industries, these interdisciplinary scholars scrutinise the neoliberal impetus driving ‘species revivalism’ in the wake of the Capitalocene. Critical examinations of species integrity, cryo-preservation, techno-optimism, rewilding initiatives and projects aimed at restoring extinct animals such as the woolly mammoth and bucardo are used to map some of the necessary restructuring of conservation policies and enterprises that could secure viably sustainable – and just – futures for nonhuman animals at risk of extinction. The authors question …


Effects Of Depth, Distance To Shore, And Water Velocity On Organismal And Extra-Organismal Environmental Dna Concentrations In A Large River, Dylan Keel 2023 Humboldt State University

Effects Of Depth, Distance To Shore, And Water Velocity On Organismal And Extra-Organismal Environmental Dna Concentrations In A Large River, Dylan Keel

Cal Poly Humboldt theses and projects

Environmental DNA (eDNA) is a sensitive tool for detection of aquatic species and concentrations of eDNA in water samples have been useful for estimating abundance. This study evaluated the effects of depth, distance to shore, and water velocity on the concentration of organismal and extra-organismal eDNA concentrations in the Klamath River, California (basin area ≅ 40,000 km2). At each of six river cross sections 32 water samples were collected, including surface samples and depth samples evenly distributed across the cross section, and eDNA concentrations were determined for the parasite Ceratonova shasta and Chinook salmon, Oncorhynchus tshawytscha, using …


Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan Jimenez 2022 University of Nebraska-Lincoln

Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan Jimenez

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Wheat (Triticum aestivum L.) is a staple cereal that provides 20% of the calories and proteins in human intake (Ray et al., 2013). Global population is projected to increase to 9.7 billion by 2050. Food production must increase by 70% to feed this future population. Wheat production is in crisis due to political and environmental challenges and is projected to decline by 0.8% in 2022 (FAO, 2022). To ensure food security yield genetic gain must increase by around 1.4% annually. Taking advantage of heterosis, hybrid wheat has the potential to boost grain yield. However, hybrid wheat seed production systems …


Data-Driven Biomarker Panel Discovery In Ovarian Cancer Using Heterogenous Data Fusion On Exosomal And Non-Exosomal Microrna Expression Data, Paritra Mandal 2022 Clemson University

Data-Driven Biomarker Panel Discovery In Ovarian Cancer Using Heterogenous Data Fusion On Exosomal And Non-Exosomal Microrna Expression Data, Paritra Mandal

All Dissertations

Ovarian cancer (OC) is an aggressive gynecological cancer and is currently the 5th leading cause of deaths due to cancer in women. High mortality rates are attributable to the vague pathogenesis and asymptomatic nature of the early stages. The development of a liquid biopsy for routine OC screening could help identify the disease at an earlier stage, making treatments more likely to be effective thereby increasing survival rates. Exosomes, small (~100nm) extracellular vesicles present in body fluids, have been shown to contain cancer-progression, onset, and related factors, making them good candidates for use in liquid biopsies. However, to date, only …


Identification Of Quantitative Trait Loci (Qtls) For Resistance To Bacterial Leaf Streak: Xanthomonas Translucens Using Qtl And Association Mapping In Three Populations Of Soft Red Winter Wheat, Benjamin Tyler Meritt 2022 Louisiana State University and Agricultural and Mechanical College

Identification Of Quantitative Trait Loci (Qtls) For Resistance To Bacterial Leaf Streak: Xanthomonas Translucens Using Qtl And Association Mapping In Three Populations Of Soft Red Winter Wheat, Benjamin Tyler Meritt

LSU Doctoral Dissertations

Bacterial leaf streak (BLS) and black chaff, caused by Xanthomonas translucens pv. undulosa (Xtu), can be a very destructive disease of wheat, especially in the warmer, wetter areas of the Southeastern U.S. Yield losses of up to 40 percent have been recorded in some cases in southern wheat growing regions. With no effective agronomic or chemical method of disease control, identification of genetic resistance is seen as a promising solution. Three soft red winter wheat populations (GAWN, ARK-SNP, and AGS 2060- AGS 2035 DH) representative of soft red winter wheat germplasm in the southeastern U.S. developed by …


Identification And Characterization Of Epicuticular Proteins Of Nematodes Sharing Motifs With Cuticular Proteins Of Arthropods, Bruno Betschart, Marco Bisoffi, Ferial Alaeddine 2022 University of Neuchâtel

Identification And Characterization Of Epicuticular Proteins Of Nematodes Sharing Motifs With Cuticular Proteins Of Arthropods, Bruno Betschart, Marco Bisoffi, Ferial Alaeddine

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Specific collagens and insoluble proteins called cuticlins are major constituents of the nematode cuticles. The epicuticle, which forms the outermost electron-dense layer of the cuticle, is composed of another category of insoluble proteins called epicuticlins. It is distinct from the insoluble cuticlins localized in the cortical layer and the fibrous ribbon underneath lateral alae. Our objective was to identify and characterize genes and their encoded proteins forming the epicuticle. The combination between previously obtained laboratory results and recently made available data through the whole-genome shotgun contigs (WGS) and the transcriptome Shotgun Assembly (TSA) sequencing projects of Ascaris suum allowed us …


Investigation Of Basil Downy Mildew Pathogen Survival, New Pathotype Development And Sources Of Quantitative, Kelly S. Allen 2022 University of Massachusetts Amherst

Investigation Of Basil Downy Mildew Pathogen Survival, New Pathotype Development And Sources Of Quantitative, Kelly S. Allen

Doctoral Dissertations

Basil downy mildew (BDM) caused by the oomycete pathogen Peronospora belbahrii, threatens sweet basil (Ocimum basilicum) production worldwide. Chemical and cultural control options for BDM are limited, and resistant cultivars have only recently become available for commercial production. To address this challenging agricultural disease, this research investigates BDM epidemiology, occurrences of new pathotypes, and molecular plant-pathogen interactions leading to host resistance or susceptibility. A reproducible low-resource inoculation protocol was developed to harvest P. belbahrii inoculum and propagate BDM for further research. The survival of P. belbahrii sporangia was examined using an in vitro assay to assess germination …


Radiation Exposure Determination In A Secure, Cloud-Based Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Peter Rogan 2022 Cytognomix Inc

Radiation Exposure Determination In A Secure, Cloud-Based Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Peter Rogan

Biochemistry Publications

Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI …


The Effect Of Infection Risk On Female Blood Transcriptomics, Brenna M. G. Gormally, Patricia C. Lopes 2022 Chapman University

The Effect Of Infection Risk On Female Blood Transcriptomics, Brenna M. G. Gormally, Patricia C. Lopes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Defenses against pathogens can take on many forms. For instance, behavioral avoidance of diseased conspecifics is widely documented. Interactions with these infectious conspecifics can also, however, lead to physiological changes in uninfected animals, an effect that is much less well understood. These changes in behavior and physiology are particularly important to study in a reproductive context, where they can impact reproductive decisions and offspring quality. Here, we studied how an acute (3 h) exposure to an immune-challenged male affected female blood transcriptomics and behavior. We predicted that females paired with immune-challenged males would reduce eating and drinking behaviors (as avoidance …


Evaluating Non-Invasive Environmental Methods For Detecting Tropical African Pangolin Species To Inform Conservation Actions, Ichu Godwill Ichu 2022 Mississippi State University

Evaluating Non-Invasive Environmental Methods For Detecting Tropical African Pangolin Species To Inform Conservation Actions, Ichu Godwill Ichu

Theses and Dissertations

Tropical African pangolin species are threatened throughout their range due to habitat loss and illegal take. Limited knowledge on distribution has rendered conservation efforts challenging. Methods commonly used for other wildlife species need to be tested for each pangolin species as each has variable ecologies requiring specific detection and monitoring techniques. This thesis evaluates the efficacy of two non-invasive environmental methods for detecting tropical African pangolin species, and consists of two complementary studies; a proof of concept study using soil sourced eDNA from a white-bellied pangolin enclosure in the Columbus Zoo, Ohio, to detect the species, and a field study …


Chromosome Number Evolution, Phylogeography, And The Effects Of Climate Change On Species Distributions In Polyploid Plant Systems, Courtney H. Babin 2022 University of New Orleans

Chromosome Number Evolution, Phylogeography, And The Effects Of Climate Change On Species Distributions In Polyploid Plant Systems, Courtney H. Babin

University of New Orleans Theses and Dissertations

Polyploidy, a term used to describe organisms with cells having more than two paired sets of chromosomes, is a significant driver of diversification among land plants. Over a century of research has advanced our understanding of polyploidization in some taxa, but polyploid organisms remain understudied. In this dissertation, I investigate chromosome number evolution, phylogeographic structure, genetic differentiation, and the effects of climate change on ploidy level distribution using polyploid plant systems. In the first chapter, I inferred a molecular phylogeny of Allium, an economically important genus that includes cultivated crops and ornamentals, to investigate evolutionary transitions in chromosome number …


Roles Of Oxidative Stress And Dna Methylation In Cigarette Smoking-Induced Accelerated Acute Myeloid Leukemia Progression, Mary Figueroa 2022 The Texas Medical Center Library

Roles Of Oxidative Stress And Dna Methylation In Cigarette Smoking-Induced Accelerated Acute Myeloid Leukemia Progression, Mary Figueroa

Dissertations & Theses (Open Access)

Acute myeloid leukemia (AML) is a commonly diagnosed cancer in smokers. When current or former smokers have AML, they have worse survival compared to never smoking patients. This has been observed clinically for decades, but then it is unknown how smoking leads to worsened AML survival. Smoking causes oxidative stress and altered DNA methylation that persists for decades in peripheral blood mononuclear cells, but these changes from smoking have not been evaluated in the context of AML. We hypothesize that smoking-induced molecular changes, including altered DNA methylation associated with poor AML prognosis, promote AML. We developed a novel model to …


Clinical And Molecular Characterization Of Key Features Of Phelan-Mcdermid Syndrome And Potential Approaches To Clinical Trials, Bridgette Moffitt 2022 Clemson University

Clinical And Molecular Characterization Of Key Features Of Phelan-Mcdermid Syndrome And Potential Approaches To Clinical Trials, Bridgette Moffitt

All Dissertations

Phelan-McDermid Syndrome (PMS) is a rare neurodevelopmental disorder that involves chromosomal abnormalities on 22q13.3 and pathogenic variants with the SHANK3 gene. SHANK3 encodes for a critical scaffolding protein that is important in post-synaptic density, function, and maintenance of excitatory synapses. Haploinsufficiency of SHANK3 is considered the major cause of the neurological phenotype of PMS. These studies focused on further characterizing the neurologic phenotype of sleep disturbances in individuals with PMS.

Sleep disturbances are a common feature of PMS, however there is little research available on the subject matter. We reviewed the literature on sleep disturbances and used the Phelan-McDermid Syndrome …


Genetic Protocols For Dna Extraction From White-Tailed Deer Cast Antlers To Confirm Individuality, Zach Carter, Brian C. Peterson, Casey W. Schoenebeck, Kimberly A. Carlson 2022 University of Nebraska at Kearney

Genetic Protocols For Dna Extraction From White-Tailed Deer Cast Antlers To Confirm Individuality, Zach Carter, Brian C. Peterson, Casey W. Schoenebeck, Kimberly A. Carlson

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

White-tailed deer (Odocoileus virginianus) are the most sought-after deer species in America. The antlers of mammals, such as deer, are one of the fastest regenerative tissues in the world and are grown and naturally cast every year. Research on cast antlers have been used for a variety of purposes including population comparisons and impacts of deer health due to climatic stressors. When investigating cast antlers, it is important to confirm individuality of match sets in addition to antlers of the same individual between years. Therefore, individuality must be confirmed genetically, and protocols must be developed and established to …


Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci 2022 University of Tennessee, Knoxville

Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci

Doctoral Dissertations

Nearly all organisms exist in proximity to microbes. These microbes perform most of the essential metabolic processes necessary for homeostasis, forming the nearly hidden support system of Earth. Microbial symbiosis, which is defined as the long-term physical association between host and microbes, relies on communication between the microbial community and their host organism. These interactions among higher order organisms (such as animals, plants, and fungi) and their bacteria links metabolic processes between interkingdom consortia. Many questions on microbial behavior within a host remain poorly understood, such as the colonization efficiency among different microbial species, or how environmental context changes their …


Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., Justin T. Kos 2022 University of Louisville

Genomic Tools And Models For Investigating The Role Of Germline Diversity In Mouse Antibody Repertoire Development., Justin T. Kos

Electronic Theses and Dissertations

Given the diversity and complexity within immunoglobulin (IG) loci, effective mouse models first require characterization of intra-strain differences and construction of high-quality reference assemblies for IG loci in several representative strains. To understand light chain germline diversity across biomedically significant mouse strains, we profiled the expressed IGK and IGL repertoires of 18 commonly used laboratory mouse strains using AIRR-seq. Across strains, we observed germline IGKV sequences shared by three different IGK haplotypes and a more conserved IGLV germline repertoire among common laboratory strains. Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing was used to sequence and assemble bacterial artificial chromosomes (BAC) …


Invisible Disabilities, Academic Capital And Competitiveness Of Genetic Counseling Applicants, Natalie E. Stoner, Meagan Choates, Carla McGruder, Debra Murray, Theresa Wittman, Sara Wofford, Claire N. Singletary 2022 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Invisible Disabilities, Academic Capital And Competitiveness Of Genetic Counseling Applicants, Natalie E. Stoner, Meagan Choates, Carla Mcgruder, Debra Murray, Theresa Wittman, Sara Wofford, Claire N. Singletary

Dissertations & Theses (Open Access)

The field of genetic counseling has historically lacked diversity. Recent research has begun to explore how visible diversity may present barriers to a genetic counseling applicant becoming competitive, but has not yet characterized potential barriers with invisible diversities, such as being a first-generation college student, or a part of the LBGTQ+ community. Therefore, this study aimed to address this gap among those with invisible diversities, as well as explore their academic capital (AC), a theoretical framework used to identify factors that make students more likely to succeed in post-secondary work including supportive networks, trustworthy information, family uplift, college knowledge, overcoming …


The Synthesis And Purification Methodology Of An Intermolecular Pyrophosphate Sensor: Applications For The Quantitative Polymerase Chain Reaction, Ethan Gevedon 2022 Bowling Green State University

The Synthesis And Purification Methodology Of An Intermolecular Pyrophosphate Sensor: Applications For The Quantitative Polymerase Chain Reaction, Ethan Gevedon

Honors Projects

The optimized synthesis and purification methodology for an intermolecular pyrophosphate sensor scaffold molecule was performed: high performance liquid chromatography afforded the scaffold in excellent purity and yield. The applications of the sensor assembly in the quantitative polymerase chain reaction were discussed, and preliminary results show that


Liquid Biopsies For Type 2 Diabetes Mellitus: Biomarkers For Disease Risk And Diagnosis, Stephanie Chidester 2022 University of Missouri-St. Louis

Liquid Biopsies For Type 2 Diabetes Mellitus: Biomarkers For Disease Risk And Diagnosis, Stephanie Chidester

Dissertations

Background: Type 2 diabetes mellitus (T2DM) has reached epidemic proportions in the United States. There is a critical need for earlier and more effective screening and diagnostic tools. Innovative liquid biopsy technologies may play a key role in meeting this need. Liquid biopsies are a non-invasive, adjunctive tool for determining diagnosis, prognosis, and therapeutic response. This dissertation focuses on two potential applications of liquid biopsy technologies to T2DM: (1) epigenome-wide association studies to identify epigenetic markers of risk for T2DM, and (2) extracellular vesicle (EV)-based biomarker studies to identify and detect markers associated with T2DM development and progression. Dissertation studies: …


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