Biology Commons^™

Periocular Mesenchyme Heterogeneity During Morphogenesis Of The Vertebrate Ocular Anterior Segment, Kristyn L. Van Der Meulen

Theses and Dissertations--Biology

The vertebrate eye is a complex organ, responsible for the primary sense with which we interact with our environment: vision. Development of the eye is a tightly regulated process, controlled by a vast network of genes. This process begins with eye morphogenesis, when the eye structure is formed through a series of morphogenetic movements and culminates in the creation of the optic cup, lens, and presumptive optic stalk. Next, retinal differentiation creates the critical cell layers of the retina needed to process light waves that enter the eye, including rod and cone photoreceptors, interneurons, and support cells. Failure in either …

Transactivation And Mitochondrial Activity Are Affected By High Temperature In C. Elegans Sperm, Jacqueline Mcvay

Scripps Senior Theses

Sexual reproduction has a conserved flaw in that it is temperature sensitive. Exposure to high temperature leads to male infertility, but little is known about the underlying mechanism. Understanding these mechanisms is important for agriculture and reproductive medicine. Using C. elegans, we investigated two potential aspects of male fertility that may be affected by high temperature conditions: activation of sperm by seminal fluid and sperm mitochondrial activity. There are two pathways for sperm activation in C. elegans: the SPE-8 pathway in hermaphrodites and the TRY-5 pathway in male seminal fluid. Hermaphrodite sperm with a mutation in spe-8 can …

Exploring The Genetic Variability Of Zebra Mussels Dreisenna Polymoprha, Maxwell Carr

Journal of Earth and Life Science

Zebra Mussels Dreisenna polymorpha are one of the most well-known invasive species here in the United States. This species can take over watersheds very quickly, causing damage to both the ecosystem and man-made structures. The basic physical behavior of this species has been well documented, but the invasive North American Zebra Mussel is much more aggressive and therefore causes more damage in the Great Lakes region compared to its native waters. Genetic variation may be playing a very large role in how and why D. polymorpha is causing such large problems for stakeholders in the United States. This review cites …

Modulation Of Pharyngeal Health In Bacterial Diet-Dependent Survival, Deniz Sifoglu

Wayne State University Dissertations

ABSTRACT

MODULATION OF PHARYNGEAL HEALTH IN BACTERIAL DIET-DEPENDENT SURVIVAL

by

DENIZ SIFOGLU

August 2021

Advisor: Dr. Joy Alcedo Major: Biological Sciences Degree: Doctor of Philosophy Both diet and bacterial microbiome modulate insulin signaling, which regulates key physiological processes that are important for survival. However, the mechanisms through which diet and the microbiome modulate insulin signaling remain unclear. To understand these mechanisms, I turned to the nematode worm C. elegans, whose diet consists of different types of bacteria. Like humans and other animals, C. elegans has to modulate its responses to its diet and to bacteria to optimize its survival. Because …

Molecular Mechanisms Regulating Optic Fissure Fusion During Zebrafish Eye Development, Megan Weaver

Theses and Dissertations--Biology

Vertebrate retinal development requires timely and precise fusion of the optic fissure. Failure of this event leads to congenital vision impairment in the form of coloboma. Recent studies have suggested hyaloid vasculature to be involved in OF fusion. In order to examine this link, we analyzed optic fissure fusion and hyaloid vasculogenesis in the zebrafish pax2a noi mutant line. We first determined that pax2a^-/- embryos fail to accumulate F-actin in the optic fissure prior to basement membrane (BM) degradation. Furthermore, using 3D and live imaging we observed reduced OF hyaloid vascularization in pax2a^-/- embryos. When examining the connection …

Composition And Homology In The Taxonomic Classification Of Escherichia Coli, Tanya Irani

Theses and Dissertations (Comprehensive)

As new techniques have been introduced, specifically the possibility of complete genome sequencing, better methods of defining bacterial species have also been proposed. One of the most recently proposed methods, using bioinformatic techniques, is to calculate the average nucleotide identity (ANI) between the homologous genome segments of different isolates. Another method for species discrimination that has been tested successfully is the similarity of DNA compositional signatures. However, in a recent update, DNA signatures split the available Escherichia coli complete genomes into three groups. To check if this result was consistent with such genomes belonging to different species, we tested methods …

Creating A Georgia Southern Spider Collection: Can Dna Barcoding Help?, Guy B. Hobbs

College of Graduate Studies: Theses & Dissertations

With over 280 spider (Araneae) species recorded within the State of Georgia, USA, the need for a well-documented natural history collection with a usable voucher system is critical to continually assess spider diversity and their future ecological impact in this region. Spider identification can be daunting for the inexperienced taxonomist; it is time consuming and sometimes requires destructive procedures. Previous works have successfully used an alternative method, DNA barcoding, to correctly identify spider species while preserving their morphology. This study set forth to create the core of a well-documented spider collection within Georgia Southern University’s Institute for Coastal Plain Science …

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 …

Modeling Neurofibromatosis Type Ii In Zebrafish, Hannah Nuszen

University Honors Program Senior Projects

Neurofibromatosis Type 2 (NF2) is a rare genetic disorder, classified as a neurocutaneous syndrome inherited through an autosomal dominant genetic mutation or deletion of the NF2 gene in humans. The tumor suppressor gene NF2 encodes the cytoskeletal protein MERLIN to promote apoptosis and inhibit abnormal cellular proliferation. Mutations in NF2 lead to a deficiency of functional MERLIN in humans and can result in hearing loss, disability, and premature death. These symptoms are due to uncontrollable growth of schwann cells generating bilateral benign tumors (schwannomas) within the nerve sheath of cranial nerve VIII. Here we seek to understand the function of …

Assessment Of Genetic Diversity In Largetooth Sawfish, Pristis Pristis, Populations Over The 20th Century, Ann Fearing

Master's Theses

The Critically Endangered Largetooth Sawfish, Pristis pristis, experienced global declines in range and abundance over the past century and Australia is now their last stronghold. This research aimed to understand whether these declines have been accompanied by a reduction in levels of genetic diversity. Using P. pristis tissue samples sourced from natural history specimens, three fragments (616-bp, 386-bp, 141-bp) in the mitochondrial DNA (mtDNA) control region were PCR-amplified. At each fragment, significant genetic structure was found in P. pristis overall (Φ_ST=0.946, N=9; 0.813, N=54; 0.771, N=99). The Indo-West Pacific and Atlantic/Eastern Pacific each harbor genetically distinct lineages of …

Neogene And Quaternary Events Shaped Diversification And Speciation In Bhutanese Rheophilic Fishes Of The Family Nemacheilidae (Cypriniformes) And Sisoridae (Siluriformes), Karma Wangchuk

Graduate Theses and Dissertations

Biogeography of the Himalayan region [to include the Qinghai-Tibetan Plateau (QTP)] evolved over a ~30M year span, catalyzed by the collision of the Indian and Eurasian plates. The resulting uplift produced major ecological and climatic effects, that in turn drove the diversification of biodiversity. As a result, the QTP is designated as a global biodiversity hotspot particularly vulnerable to cumulative climatic effects, including shrinking distributions, declining numbers, and local extinctions. Understanding how the biodiversity within the Himalaya/ QTP was established and maintained is a necessary first step in prioritizing conservation efforts.

Fishes in global montane regions, such as the Himalaya, …

Evaluation Of The Xpert Carba-R Nxg Assay For Detection Of Carbapenemase Genes In A Global Challenge Set Of Pseudomonas Aeruginosa Isolates, Fred C. Tenover, Christian M. Gill, Tomefa E. Asempa, Isabella A. Tickler, Caitlin M. Dela Cruz, David P. Nicolau

Biology Faculty Publications

The growing prevalence and diversity of carbapenemase producers among carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates warrants an expansion of detection capabilities. The purpose of this study was to evaluate the performance of the commercially available Xpert Carba-R (Carba-R) and the research-use-only Xpert Carba-R NxG (Carba-R NxG) in a global collection of P. aeruginosa. The challenge set included 123 P. aeruginosa clinical isolates from 12 countries. Isolates were previously categorized via PCR or whole-genome sequencing. Carbapenemase classes tested include VIM, IMP, NDM, SPM, KPC, and GES. Non-carbapenemase (non-CP)-harboring isolates were also tested (negative control). Isolates were tested using the Carba-R NxG and …

Quantifying Structure And Variation In Complex Phylogenetic Data, Genevieve Geraldine Mount

LSU Doctoral Dissertations

Identifying the source and structure of variation in nature is crucial to understanding fundamental aspects of evolution. Despite a recent plethora of genetic and morphological data, many interesting questions about the relationships between different groups remain unresolved. My dissertation evaluates three approaches for identifying and quantifying the variation within phylogenetic datasets. Characterizing variation within datasets and across analytical methods gives insight into biologically interesting characters, unusual evolutionary processes, and areas for model improvement.

Network-based community detection approaches offer a powerful tool to describe variation in phylogenetic signal across the genome (i.e., gene tree variation). In Chapter 2, I investigate the …

The Nature Of Genes Expressed Differently After Environmental Drug Exposure, Nicci Siffel

Scholars Week

The Nature of Genes Expressed Differently after Environmental Drug Exposure

N. Siffel, S. Anderson, B. Subedi, D.R. Hammond-Weinberger

Drug use, of prescription or illicit varieties, alter bodily functions in different ways, especially in the nervous system. These drugs are found in sources of drinking water because they are not removed by wastewater treatment facilities. To investigate the effects of these drugs as they appear in mixtures, we exposed groups of zebrafish embryos to cocktails of drugs and screened for genes that were differentially expressed between the experimental and control groups and could thus give more insight into their biological functions. …

Inheritability Of Ciprofloxacin-Induced Mitochondrial Mutations From Parental To Offspring Generation Using Quantitative Polymerase Chain Reaction, Rose Mccoy

Honors Program: Senior Projects (Public)

In all eukaryotes, mitochondria are known as the powerhouse of the cell (Siekevitz, 1957). In plants, however, their mitochondrial genome is especially strange. Plant mitochondrial genomes are extremely large and contain both linear and circular subgenomic DNA fragments. Plant mitochondrial genomes undergo a significant amount of mutations in the form of rearrangements. However, it is not known how often these rearrangements are inherited by the next generation. It is thought that plant cells that are still dividing have higher rates of DNA repair, such as double-strand break repair, to ensure the quality of that plant lineage. As follows, it is …

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 …

Herb-Layer Dynamics In An Old-Growth Forest: Vegetation–Environment Relationships And Response To Invasion-Related Perturbations, Taylor M. Buskey, Margaret E. Maloney, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Temperate forests of eastern North America are subject to multiple invasions from non-native species that have the potential to drive long-term dynamics in biodiversity. Garlic mustard (Alliaria petiolata (M. Bieb.) Cavara and Grande) is an invasive plant in many deciduous forests, and management efforts often focus on removing this species to initiate native species restoration. Agrilus planipennis Fairmaire (emerald ash borer; Coleoptera: Buprestidae) is a non-native insect pest that has caused substantial loss of ash trees (Fraxinus spp. L.) in North America. Our goal was to understand how the herbaceous layer in an old-growth forest responded to the removal of …

Does The Presence Of Multiple Β-Lactamases In Gram-Negative Bacilli Impact The Results Of Antimicrobial Susceptibility Tests And Extended-Spectrum Β-Lactamase And Carbapenemase Confirmation Methods?, Fred C. Tenover, Caitlin M. Dela Cruz, Scott Dewell, Victoria M. Le, Isabella A. Tickler

Biology Faculty Publications

Objectives: Many multidrug-resistant Gram-negative bacilli (MDR-GNB) harbour multiple β-lactamases. The aim of this study was to assess the impact of multiple β-lactamase carriage on the accuracy of susceptibility tests and extended-spectrum β-lactamase (ESBL) and carbapenemase confirmation methods.

Methods: A total of 50 MDR-GNB, of which 29 carried multiple β-lactamases, underwent broth microdilution (BMD) and disk diffusion (DD) testing as well as confirmation tests for ESBLs and carbapenemases. Whole-genome sequencing (WGS) was used for β-lactamase gene identification.

Results: Categorical agreement of BMD and DD testing results ranged from 86.5 to 97.7% for 10 β-lactam agents. BMD and DD algorithms for ESBL …

The Influence Of Riparian Invasion By The Terrestrial Shrub Lonicera Maackii On Aquatic Macroinvertebrates In Temperate Forest Headwater Streams, Michelle N. Little, Kevin W. Custer, Eric B. Borth, Julia I. Chapman, Mitchell J. Kukla, Corey Kuminecz, Margaret E. Maloney, Michaela J. Woods, Ryan Mcewan

Biology Faculty Publications

The ecology of headwater streams is tightly linked to the riparian zone through organic matter subsidies which are highly susceptible to alteration due to biological invasion. Lonicera maackii is a non-native shrub that is a highly successful invader of headwater stream riparian zones in the American Midwest. We assessed effects on benthic macroinvertebrates across a gradient of invasion intensity from references sites with minimal invasion to a site that had a very heavy invasion. Benthic macroinvertebrates were sampled throughout the year and compositional differences were assessed using Non-metric Multidimensional Scaling ordination, and by comparing the prevalence of sensitive (Ephemeroptera, Plectoptera, …

Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso

LSU New Orleans Theses and Dissertations

One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …

Arabidopsis Heat Shock Granules Exhibit Dynamic Cellular Behavior And Can Form In Response To Protein Misfolding In The Absence Of Elevated Temperatures, Rosalie Lawrence , '12, Nicholas J. Kaplinsky

Biology Faculty Works

No abstract provided.

Wild Mice With Different Social Network Sizes Vary In Brain Gene Expression, Patricia C. Lopes, Barbara König

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

Appropriate social interactions influence animal fitness by impacting several processes, such as mating, territory defense, and offspring care. Many studies shedding light on the neurobiological underpinnings of social behavior have focused on nonapeptides (vasopressin, oxytocin, and homologues) and on sexual or parent-offspring interactions. Furthermore, animals have been studied under artificial laboratory conditions, where the consequences of behavioral responses may not be as critical as when expressed under natural environments, therefore obscuring certain physiological responses. We used automated recording of social interactions of wild house mice outside of the breeding season to detect individuals at both tails of a distribution …

Inactivation Of Hippo And Cjun-N-Terminal Kinase (Jnk) Signaling Mitigate Fus Mediated Neurodegeneration In-Vivo, Ankita Sarkar, Abijeet Singh Mehta, Prajakta Deshpande, Madhuri Kango-Singh, Udai Bhan Pandey, Amit Singh

Biology Faculty Publications

Amyotrophic Lateral Sclerosis (ALS), a late-onset neurodegenerative disorder characterized by the loss of motor neurons in the central nervous system, has no known cure to-date. Disease causing mutations in human Fused in Sarcoma (FUS) leads to aggressive and juvenile onset of ALS. FUS is a well-conserved protein across different species, which plays a crucial role in regulating different aspects of RNA metabolism. Targeted misexpression of FUS in Drosophila model recapitulates several interesting phenotypes relevant to ALS including cytoplasmic mislocalization, defects at the neuromuscular junction and motor dysfunction. We screened for the genetic modifiers of human FUS-mediated neurodegenerative phenotype using molecularly …

Elucidating The Role Of Apl-1, The C. Elegans Ortholog Of The Human Amyloid Precursor Protein, Adanna G. Alexander

Dissertations, Theses, and Capstone Projects

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, impacting approximately 6 million Americans. AD is the leading cause of dementia amongst the aged population. Post mortem analysis of the brains of AD patients shows high quantities of extracellular Aβ peptide deposits, which are derived from cleavage of the amyloid precursor protein (APP). Mutations in APP and proteins responsible for APP cleavage, PSENs, greatly increase the incidence of developing AD at an early age. Despite its strong correlation to the progression of AD, the role of APP remains unclear.

Here we investigate the role of the Caenorhabditis elegans ortholog, APL-1. We …

Elucidating The Role Of The High Aliphatic Glucosinolate ( Hag ) Genes In Pennycress ( Thlaspi Arvense L. ) Glucosinolate Production, Dalton Williams

Theses and Dissertations

Pennycress (Thlaspi arvense L.) is a Brassica species being developed into an oilseed-producing winter cash cover crop. Similar to its relatives, rapeseed (Brassica napus L.) and camelina (Camelina sativa L.), pennycress seeds produce high levels of oil and protein (~34% oil and ~19% protein dry weight). For pennycress to be economically viable and environmentally sustainable as a crop, both the oil and seed meal must be utilized. Pennycress like other Brassicaceae, produces high levels of glucosinolates in the seed coat. Glucosinolates taste bitter and can be metabolized by the enzyme, myrosinase, into toxic isothiocyanates, nitriles, and epithionitriles. Seed meal containing …

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 …

Generation And Characterization Of A Rack1 Knockout Cell Line, Roy Missall

Seton Hall University Dissertations and Theses (ETDs)

The µ-opioid receptor (MOR) is an important regulator of nociception, bearing the largest role in analgesia of all opioid receptors. This function has made MOR an effective drug-target for the clinical treatment of pain. However, opioid drugs such as morphine and fentanyl are highly addictive, and prolonged abuse can be fatal due to respiratory depression. A key determinant in the cellular and systemic responses to opioids is MOR. At the transcriptional level, MOR is positively regulated by the transcription factors, including poly-C binding protein 1 (PCBP1). Using the two-hybrid screening, PCBP1 was found to interact with receptor for activated C …

Genetic Analysis Of Flower Color Differences Between A Hummingbird-Pollinated And A Self-Pollinated Monkeyflower (Mimulus) Species, Caitlin Foster

University Scholar Projects

Flower color plays an important role in pollinator discrimination and speciation. Understanding the genetic contributions to flower color differences between two closely related species, Mimulus cardinalis and Mimulus parishii, can improve understanding of how they developed different pollination syndromes and diverged from a recent common ancestor. M. cardinalis is hummingbird-pollinated and has large, bright red flowers while M. parishii is self-pollinated and has small, pale pink flowers. An F2 hybrid population between these two species was created to establish a platform for analysis of the genetic architecture controlling the differences in anthocyanin pigmentation. Statistical analysis of anthocyanin concentration distribution …

Efficient Conditional Inactivation Of Rdh10 Reveals Important Role Of Retinoic Acid During Lung Branching Morphogenesis., Nhut Quang Huy Tran

Electronic Theses and Dissertations

Birth defects are complicated pathological processes. Many birth defects can be traced back to disrupted regulation of molecular signaling pathways during embryogenesis. One of the most important gene regulatory factors during embryo development is retinoic acid (RA). However, studying the specific roles of RA in each organ during embryogenesis in vivo is challenging. The Sandell laboratory has a conditional mutant mouse model that can potentially be used for studying the role of RA during embryogenesis by inducing stage-specific RA deficiency. This model allows retinol dehydrogenase 10 (Rdh10), a gene required for RA production, to be inactivated at a …

Investigation Of The Individual Soybean Root Nodule Microbiome, Parris Mica Mayhood

Graduate Theses/Dissertations

Soybean is a valuable crop that establishes a symbiotic association with nitrogen-fixing microorganisms. Previous research suggests members of the genus Bradyrhizobium are the major nitrogen-fixing inhabitants of soybean root nodules. However, results from recent studies identified the presence of other bacteria, so called non-rhizobial endophytes (NREs), inside root nodules. All previous research has pooled nodules of different plants for bacterial community analysis, but this study investigated the presence and relative abundance of rhizobia and NREs within multiple root nodules of a single plant. Three sites were selected on Kendrick Farm in Springfield, MO, where three plants and rhizosphere soil were …