Life Sciences Commons^™

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

Association Mapping For Soybean (Glycine Max L. Merr.) Protein And Oil Content, Joseph Najjar

Graduate Theses and Dissertations

Soybean [Glycine Max (L.) Merrill] is an important economic crop because of its high content of seed protein and oil. Seed oil and protein content are quantitative inherited traits. The genetics of seed protein and oil levels have been extensively studied, with 367 QTL reported for protein and 475 QTL reported for oil to date. Validation of such QTLs, and identification of easily-automatable molecular markers around these QTL will aid the progression of breeding for such traits. The focus of this research was to discover novel and verify previously reported QTL related to protein and/or oil content via Genome-Wide Association …

Molecular Genetic Analysis Of Drought Resistance And Productivity Traits Of Rice Genotypes, Yheni Dwiningsih

Graduate Theses and Dissertations

Rice (Oryza sativa L.) is the staple food for a majority of the world’s population, and uses 30% of the global fresh water during its life cycle. Drought at the reproductive stage is the most important abiotic stress factor limiting grain yield. The United States is the third largest exporter of rice, and Arkansas is the top rice-producing state. The Arkansas rice-growing region in the Lower Mississippi belt is among the 10 areas with the highest risk of water scarcity. Adapted U.S. rice cultivars were screened for drought resistant (DR) traits to find sources for breeding U.S. rice cultivars for …

The Design And Validation Of A Qpcr-Based Approach To Cell Quantification Of Fungal-Algal Symbioses, Isabelle Katherine Garlotte

Honors Theses

Symbiotic relationships are extremely common in virtually all species. These relationships between organisms, particularly mutualistic symbioses, can have an incredibly large impact and can greatly affect the evolution of the species involved. Of particular interest is the suspected mutualistic relationship between green algae and fungi that may hold key evidence of how terrestrial plants evolved. In this experiment we established a method of quantifying the cells of each species involved in these symbioses through qPCR analysis to determine if the relationships are truly mutualistic. We developed a system for using DNA copies as a proxy for cell count in co-cultures …

P53 Drives A Transcriptional Program That Elicits A Non-Cell-Autonomous Response And Alters Cell State In Vivo, Sydney Moyer

Dissertations & Theses (Open Access)

Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion of Mdm2, a gene which encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 ChIP-sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes which included Mdm2 but not p21. Global p53 activation …

Identification And Characterization Of Novel Genes And Genetic Interactions That Influence Iba Metabolism, Vanessica Jawahir

Dissertations

Indole-3-butyric acid (IBA) is an endogenous storage auxin important for maintaining appropriate indole-3-acetic acid (IAA) levels that influences primary root elongation and lateral root development. IBA is metabolized into free IAA in the peroxisome in a multistep process similar to fatty acid β-oxidation. Although many components specific to IBA metabolism and peroxisome function have been identified, our understanding is incomplete. I sought to identify novel components of IBA metabolism or peroxisome function by conducting a forward genetic screen for Arabidopsis thaliana plants with enhanced resistance to IBA. I identified Long chain acyl-CoA synthetase 4 (LACS4) as a novel gene functioning …

Identifying Positive Selection In Multiple Subspecies Of Xylella Fastidiosa, Daniel Doroteo Flores

Theses and Dissertations

For this study, we will be looking to identify positive selection in eight genomes of the bacterial plant pathogen Xylella fastidiosa. A previous study used a branching method that identified 2 genes with positive selection along with a site-specific method identifying 34 genes showing positive selection. This current study focused specifically on the site-specific method, resulting in 28 genes (of 1,039 tested) showing positive selection. Of the 28 genes showing positive selection, 12 of them come from the pathogenicity, virulence and cellular structural categories. The remaining genes are found in the biosynthesis, metabolism, macro metabolism, and cellular process categories. …

An Investigation Into Multi-View Error Correcting Output Code Classifiers Applied To Organ Tissue Classification, Daniel Alvarez

UNLV Theses, Dissertations, Professional Papers, and Capstones

Large amounts of data is being generated constantly each day, so much data that it is difficult to find patterns in order to predict outcomes and make decisions for both humans and machines alike. It would be useful if this data could be simplified using machine learning techniques. For example, biological cell identity is dependent on many factors tied to genetic processes. Such factors include proteins, gene transcription, and gene methylation. Each of these factors are highly complex mechanism with immense amounts of data. Simplifying these can then be helpful in finding patterns in them. Error-Correcting Output Codes (ECOC) does …

A Strategic Plan To Thread Genomics Competencies Into Undergraduate Curriculum, Holly Mathis

Dissertations

Problem: Genomics in undergraduate nursing education has experienced slow adoption in the United States. Various approaches have been proposed but do not address barriers to successful implementation.

Methods: A strategic plan was developed to increase the amount of genetics and genomic content in the curriculum of an undergraduate nursing program. A gap analysis was performed on the curriculum revealing a paucity of content. A SWOT analysis informed the strategic plan, which included a faculty education program using the ANA/ISONG’s Essentials of Genetic and Genomic Nursing: Competencies, Curricula Guidelines and Outcome Indicators (2^nd ed.) (2009) as a foundation.

Results: Faculty …

Epigenetics A Decolonizing Science, Wade Paul

Electronic Thesis and Dissertation Repository

Epigenetics is the study of gene expression that does not entail alterations to the actual DNA. Decolonization is a theoretical and political movement that seeks to deconstruct colonial institutions and ideologies and reconstruct new and balanced approaches that accept and respect Indigenous worldviews. This project studies the decolonizing potential of epigenetics. Using genealogy as the method, the study establishes a long history of reductionist and deterministic thought that shaped the study of genetic science. Particular instances like thrift gene theory are explored to highlight how genetic explanations have been detrimental to the health and wellbeing of Indigenous people and illustrate …

Genetic Architecture Of Salt And Drought Tolerance In Cowpea, Waltram Second Ravelombola

Graduate Theses and Dissertations

Cowpea [Vigna unguiculata (L.) Walp.] is a diploid and nutrient-dense legume species. It provides affordable source of protein to human. Cowpea cultivation is prevalent in Africa, Asia, the western and southern U.S., and Central and South America. However, earlier reports have shown that drought and salt stress can be devastating to cowpea production. The objectives of this study were to screen for salt and drought tolerance in cowpea and to identify molecular markers associated with these traits. Simple methodologies to screen for drought (Chapter 2) and salt tolerance were developed (Chapter 3). Results suggested that: 1) a total of 14, …

Determining The Genetic Control Of Neural Tube Malformation Through Genetic Interactions With Idgf3, Elli N. Fox

Honors Projects

Genetic mutations disrupting human neural tube formation can lead to birth defects such as spina bifida and anencephaly. Defects can result in lack of neural tube closure in either the caudal (spina bifida) or cranial (anencephaly) regions. Little is known about the genes that cause these malformations. Researchers have been using the model organism Drosophila melanogaster in an attempt to determine genes responsible for neural tube malformations. Recently, an ortholog of human chitin-like protein, imaginal disc growth factor 3 (Idgf3), has been identified as important in the proper formation of Drosophila egg dorsal appendages. However, the molecular mechanism responsible for …

The Embark® Protocol: Dog Genomics In Genetics Laboratories, Alexandra Kissel

Honors Theses

In a world of ever-advancing technology, it is imperative that young pre-health professionals are educated according to the most relevant research. One of the most fundamental, foundational concepts of health is genetics. This field is rapidly expanding, and quickly engraining itself into the realm of healthcare. Genetic testing and gene therapies, once subjects of science fiction, have become commonplace. It is more important than ever that health professionals have a concrete knowledge of genetics, and this begins with the proper education of pre-health students.

With this idea in mind, a laboratory protocol was designed for students of the Bisc 336 …

Evaluation Of The Bax-Vdac Interaction And Their Influence On Apoptosis In Drosophila Melanogaster, Frances Marie Gatlin

Honors Theses

Apoptosis, also known as programmed cell death, is a cellular process used for development or for when cells undergo injury or stress. The Bcl2 family of proteins includes both pro-apoptotic and anti-apoptotic proteins that control the intrinsic pathway of apoptosis. Understanding the mechanisms and influence these proteins have on apoptosis is an important area of research focused on in Dr. Jones’s lab. Evidence shows a homology amongst the Bcl2 family of proteins at the BH3 domain. Dr. Jekabsons' lab has found a potential homology amongst VDAC 1-3 and the Bcl2 family at the BH3 domain.

Specifically, our lab is using …

Population Genetics Of A Recent Range Expansion By The Southern Pine Beetle, Dendroctonus Frontalis, Into The Northeastern United States, Megan Stubbs

Honors Theses

Population genetics as a field of study aims to determine the genetic variation among individuals in a population, and differences among populations. Certain population genetic analyses can provide such information and be used to better understand the biological aspects to a species’ expansion beyond its native range. The southern pine beetle (SPB), Dendroctonus frontalis, has become an invasive pest to pine forests in northeastern United States with its recent range expansion. Nine microsatellite loci were first developed and then used in analyses. To determine what the genetic variation is among individuals in SPB populations across its entire range, including …

Identifying Phenotypic Effects In Sporisorium Reilianum And Ustilago Maydis Lacking The Alternative Oxidase Gene., Caroline D. Culver

College of Arts & Sciences Senior Honors Theses

Ustilago maydis and Sporisorium reilianum are both dimorphic fungi that cause infection in the host plant, corn (Zea mays). In order for infection to be successful, compatible haploid mating types must form a dikaryon that later leads to the development and dispersal of teliospores. In order to sustain growth, energy is produced via the electron transport chain within the mitochondrion. Host plants often produce harsh reactive oxygen species, resulting in the need to use an alternative respiration pathway such as employing an alternative oxidase. Therefore, this study attempted to investigate the role of the aox gene in pathogenicity …

Mapping Quantitative Trait Loci For Peach (Prunus Persica) Resistance To Xanthomonas Arboricola Pv. Pruni (Xap) And Determining The Diversity And Virulence Of A United States Xap Collection, Maxwell Vonkreuzhof

Graduate Theses and Dissertations

Bacterial spot, caused by the bacterium Xanthomonas arboricola pv. pruni (Xap), is a threat to the peach [Prunus persica (L.) Batsch], Japanese and European plum (P. salicina L. and P. domestica L.), and tart and sweet cherry (P. cerasus L. and P. avium L.) industries. Markers for fruit resistance to bacterial spot have been developed however, markers associated with foliar resistance have yet to be developed. A total of 130 progeny and 13 parents (n=143) were evaluated for foliar and fruit Xap resistance in 2013, 2014, and 2015, and 162 progeny and eight parents (n=170) in 2017 and 2018 as …

Associations Among Beef Cattle Genotypes, Neospora Caninum Infection, And Reproductive Performance, Ryan James Page

Graduate Theses and Dissertations

Reproductive performance is crucial for sustained financial success in the beef cattle industry. This dissertation includes a population study that quantified the incidence of Neospora caninum infections in the central region of the United States and tested its relationship with reproductive performance in beef cattle. Trial one of that study concluded that 6.9% of open, replacement heifers (n = 1306) tested seropositive. The second trial in that project found that 9.6% of the breeding age females (n = 500) tested were seropositive for Neospora caninum; and that state in which the cattle lived and age impacted (P < 0.05) infection rate. Breed composition, number of farm dogs on the ranch, and use of total mixed rations were not associated (P > 0.1) with seropositive …

Characterization Of The Broad-Spectrum Inhibitory Capability Of Alcaligenes Faecalis And A. Viscolactis Against Potential Pathogenic Microorganisms, Andrew Fuqua

Undergraduate Honors Theses

The recent rise of multidrug resistant microorganisms has grown from an isolated concern to a massive public health crisis. It has become imperative that scientists look for new ways to combat this issue. Due to the selective pressures of competition, bacteria and other microbes possess a host of defenses and weapons designed to exploit vulnerabilities in other microorganisms. Consequently, the study of these systems and microbial interactions has much to reveal in the search for novel antimicrobial treatments. Previous research from our laboratory has discovered that both Alcaligenes faecalis and Alcaligenes viscolactis, two rarely studied and generally non-virulent bacteria, …

Advanced Phenotyping Of Otosclerosis In An Ontario Population And Two Large Newfoundland Families, Matthew B. Lucas

Electronic Thesis and Dissertation Repository

Otosclerosis is a relatively common hearing loss disorder characterized by abnormal bone growth in the otic capsule leading to stapes fixation. In approximately half of cases, otosclerosis is inherited as an autosomal dominant trait. Typically, gene discovery efforts rely on surgical confirmation, audiometry and occasionally acoustic reflexes to identify affected cases of otosclerosis within families, requiring that the otosclerosis was at an advanced stage to be detected. This makes it difficult to identify individuals with early otosclerosis. The use of advanced phenotyping to identify cases of otosclerosis was tested in an Ontario otosclerotic population as well as in two large …

Revisiting The Essential Informational Needs Of Parents Receiving A Diagnosis Of Down Syndrome, Margaret Jean Wilkes

Theses and Dissertations

Down syndrome is a condition characterized by varying degrees of intellectual disability (ID), distinctive facial appearance, and congenital anomalies that results from the presence of a third 21st chromosome. Down syndrome is the most common chromosomal condition, affecting approximately 12.6 per 10,000 live births in the United States, making it imperative that we determine which information is most essential to impart to parents when first presenting the diagnosis. The aim of the present study is to reassess the informational needs of parents during the presentation of a Down syndrome diagnosis. In 2009, data were collected to define the essential information …

The Now Trial: A Pragmatic Randomized Controlled Trial Of Personalized, Genetic-Based Lifestyle Advice, Justine Rochelle Horne

Electronic Thesis and Dissertation Repository

Background: The impact of nutrigenomics and lifestyle genomics interventions on health outcomes and behaviours remains controversial and under-explored.

Objectives: To determine the short-term (3-month), moderate-term (6-month) and long-term (12-month) impact of providing personalized, genetic-based lifestyle information and advice on anthropometric measures, as well as dietary intake and adherence.

Methods: The nutrigenomics, overweight/obesity and weight management trial (NOW Trial) is a pragmatic randomized controlled trial that was incorporated into the Group Lifestyle Balance™ (GLB) program (N=140). Inclusion criteria: overweight or obesity (BMI ≥ 25 kg/m²), ≥ 18 years of age, English-speaking, having access to internet at least …

Using Crispr-Cas9 As A Restriction Enzyme, Zack Crawley

Master's Theses

Restriction digests are a commonly utilized process for cleaving DNA at specific, but relatively common sites. Restriction enzymes have widespread use in DNA manipulation. CRISPR/Cas9 is a recently identified endonuclease which utilizes a customizable guide sequence to recognize and cut specific ~20 bp sites located in a DNA sequence. This preliminary research aimed to exploit the potential benefit of DNA restriction using the CRISPR/Cas9 procedure through alterations of different components involved in that system. We sought to refine existing CRISPR/Cas9 protocols and make a budget friendly, user-selectable CRISPR/Cas9 restriction digest protocol. The motivation for this research was to simplify and …

Addressing The Issue Of Missing Heritability: The Importance Of Apoptosis In Hereditary Breast And Ovarian Cancer And Functional Assessment Of Tp53i3-S252*, Sophia Chaudhry

Wayne State University Dissertations

A quarter of all cases of ovarian cancer (OVCA) cases are due to inherited factors. However, much of the genetic risk remains unknown. We have previously established the importance of whole exome sequencing to answer the question for missing heritability. We identified clinically actionable and novel risk loci in the DNA repair and cell cycle regulation pathways by assessing a cohort of women diagnosed with OVCA, wildtype for BRCA1/BRCA2 and suspected to be hereditary due to family history of breast cancer/OVCA. Equally as important was the exploration and discovery of novel risk loci in the apoptosis pathway. A total of …

Mef2-Bound Genes May Influence Ethanol Sedation In Drosophila Melanogaster, Katlyn M. Myers

Theses and Dissertations

Alcohol Use Disorder (AUD) is a global health issue that affects millions of people every year. This disorder has serious negative mental and physical consequences. Currently, treatment options for this disorder are largely limited to psychological therapy, with very few medications available to treat it. Being able to identify the environmental and genetic components that influence AUD can help improve diagnosis and treatment options. Previous studies in humans have shown a link between initial sensitivity and risk for alcohol abuse. Our laboratory uses Drosophila melanogaster as a model to study the genetic and environmental components of alcohol-related behaviors. Previous lab …

The Effects Of Internal Physiology On Polyphenic Horn Development In The Dung Beetle Onthophagus Taurus, Naomi Garrett Williamson

Graduate Theses, Dissertations, and Problem Reports

An organism’s phenotype can be affected in development by alterations to gene expression based on environmental inputs. Nutrition is one such environmental input and the central regulator of development of large horn or small horn phenotypes in the dung beetle species, Onthophagus taurus. However, little is known about the nature of chemical compounds that are critical to this plastic horn development. To better understand these compounds, we are utilizing an untargeted metabolomic approach as well as a targeted gene approach. Through the metabolomic approach, it was uncovered that environmental conditions tend to have a greater impact on metabolomic composition …

Impact Of Sire Selection And Breed On Parasite Resistance In Sheep, Andrew Ryan Weaver

Graduate Theses, Dissertations, and Problem Reports

Selection within and among breeds are strategies to mitigate the impact of parasitism given failing chemotherapeutics. While Texels have improved marketability compared to other parasite-resistant breeds, the mechanism by which Texels reduce fecal egg count (FEC) is unclear. The immune response to Haemonchus contortus (Hc) was compared in Texel, parasite-resistant St. Croix, and parasite-susceptible Suffolk sheep. Adult worms exposed to St. Croix- and Texel-derived peripheral blood mononuclear cells and serum in vitro had greater binding around the reproductive structures than Suffolk and worm egg release tended to be affected by breed (P = 0.09). Resistance in Texels …

Optimization And Validation Of The Neurolux Wireless Optoelectronics System For Optogenetics, Karis Courey, Su Hyun Lee Ph.D., Adam Smith Ph.D., Nicholas Cilz Ph.D., Sarah K. Williams Avram Ph.D., Adi Cymerblit-Sabba Ph.D., June Song, Nicholas Leipzig Ph.D., W. Scott Young M.D., Ph.D.

Williams Honors College, Honors Research Projects

Utilizing light and genetic engineering, optogenetics permits the manipulation of events within cells via light using the light-sensitive properties of single-component microbial opsins. Microbial opsins are activated by a light source, such as lasers, light-emitting diodes, and incandescent sources that deliver light to the region of interest either directly or indirectly, such as through fiberoptics. In classical in vivo optogenetics, the wiring of optic fibers necessitates tethering of animals by the optic fiber to the light source. The novel NeuroLux wireless optoelectronic system for optogenetics circumvents issues pertaining to classical optogenetics by utilizing near-field power transfer via magnetic coil antennae …

Genetic And Functional Approaches To Understanding Autoimmune And Inflammatory Pathologies, Abbas Raza

Graduate College Dissertations and Theses

Our understanding of genetic predisposition to inflammatory and autoimmune diseases has been enhanced by large scale quantitative trait loci (QTL) linkage mapping and genome-wide association studies (GWAS). However, the resolution and interpretation of QTL linkage mapping or GWAS findings are limited. In this work, we complement genetic predictions for several human diseases including multiple sclerosis (MS) and systemic capillary leakage syndrome (SCLS) with genetic and functional data in model organisms to associate genes with phenotypes and diseases.

Focusing on MS, an autoimmune inflammatory disease of the central nervous system (CNS), we experimentally tested the effect of three of the GWAS …

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

Honors Theses and Capstones

No abstract provided.