Biology Commons^™

Development Of A Neutropenic Murine Model For Invasive Candida Auris Infection, Steven Torres

Legacy Theses & Dissertations (2009 - 2024)

In less than a decade, the emerging fungal pathogen Candida auris has become a major public health threat due to its multidrug resistant (MDR) phenotype, high transmissibility, and high mortality rates that range between 30%-60%. Unlike other Candida species, C. auris has acquired high levels of resistance to an already limited arsenal of antifungals. As an emerging pathogen, there are currently a limited number of documented murine models of C. auris infection. These animal models using a range of inoculums from 105 –108 cells per mouse, and the environmental and occupational exposure of working with these models has not been …

Butterflies As Charismatic Indicators : Can Study Of Impact Of On-Farm Habitat Enrichment On Butterfly Populations Provide Insight About Habitat Quality For Other Insects?, Erin Allen

Legacy Theses & Dissertations (2009 - 2024)

Populations of insect pollinators have been declining precipitously across the Northern Hemisphere, due to disease, insecticide application, and habitat degradation and loss. As a result, crop pollination services are at risk, and the ecological insurance provided by biodiversity is in jeopardy. Regional efforts to combat the decline of pollinator diversity and abundance include the New York State Pollinator Protection Plan to assess regional pollinator health, strategies to enhance wild pollinator habitat, as well as on-farm habitat enhancement strategies to augment pollinator populations in and around crops. One such habitat enhancement strategy involves improving native floral resource availability, which is often …

Inteins From Pathogenic Microbes As Regulatory Elements And Potential Drug Targets, Cathleen Maria Schiraldi

Legacy Theses & Dissertations (2009 - 2024)

Inteins are self-splicing elements that orchestrate the autocatalytic process of protein splicing, during which the intein excises itself from a host polypeptide. This multistep reaction involves a series of coordinated nucleophilic attacks and peptide bond rearrangements that remove the intein and reassemble the flanking halves, called exteins, to form the mature host protein. Some inteins are also mobile elements, and can spread to the same or ectopic sites using an internal homing endonuclease domain.

The Effect Of Anthropogenic Environmental Modifications On Malaria Vectors In Amazonian Peru And Brazil, Catharine Prussing

Legacy Theses & Dissertations (2009 - 2024)

Malaria is the most deadly vector borne disease, causing substantial morbidity and hundreds of thousands of deaths worldwide each year. In the Americas, the incidence of malaria has increased steadily since 2014. The factors driving continued malaria transmission are complex and highly variable across endemic areas. These factors include inadequate access and financial commitment to prevention, diagnosis, and treatment, and a failure to target interventions to heterogeneous malaria transmission patterns and vector populations. Nyssorhynchus darlingi (formerly Anopheles darlingi), the predominant malaria vector in Latin America, is known for behavioral, phenotypic, and genetic variability across its range, which allow it to …

Examining The Mechanisms Of Nucleic Acid Structural Rearrangements Using Nanospray Ionization Mass Spectrometry, Botros Toro

Legacy Theses & Dissertations (2009 - 2024)

RNA’s diverse gene regulatory functions are tied to its ability to adopt and rearrange between an ensemble of three-dimensional structures. This concept is illustrated by the process of genome dimerization in HIV-1 and other retroviruses, which is mediated by the dimerization initiation site (DIS) of viral RNA. This essential stem-loop domain establishes a metastable kissing complex (KC) intermediate that seeds the structural rearrangements necessary to stabilize genome dimerization. Most approaches applied to study RNA structure provide us with a snapshot of RNA at equilibrium, leaving key details on dynamics concealed. This thesis explored the merits of nanospray ionization mass spectrometry …

Contrasting Roles Rna Binding Proteins G3bp1 And Hur Influence Zika Virus And A Proposed Mechanism By Which Zika Virus Induces Neurological Complications, Gaston Bonenfant

Legacy Theses & Dissertations (2009 - 2024)

Globalization and climate change have contributed to the rampant spread of mosquitos from tropical and subtropical climates into more moderate climates, and thus also the spread of a number of vector-borne viruses. As of 2016, the World Health Organization (WHO) estimates that of all human infections world-wide, 16% result from vectors such as flies, ticks, and mosquitos. The spread of such viruses has encouraged expedient evolutionary pressures resulting in more pathogenic viruses that continually pose a serious threat to public health. First discovered in 1947, Zika virus (ZIKV) has only recently presented as a detriment to public health. The importance …

Infestation Of Japanese Honeysuckle (Lonerica Japonica) Shows Variation In Soil Microbial Community Composition And Species Diversity In Wvu Core Arboretum, Jackie Mullins

Undergraduate Student Research

Invasive species are found to cause alteration of biodiversity, competition with native species, and other environment and ecological changes across the globe. Also, invasive species have economic implications. When specifically talking about invasive plant species, an important influence is soil microbes that can altered or are altered after growth of invasive plant species. One invasive plant, Lonerica japonica, is extensively spread across the globe but has had little research done, specifically in if it alters the microbes of the soil. Having L. japonica readily available in the West Virginia University Core Arboretum, soil samples were collected from sites of …

Role Of Geographic Distance In Clonal Propagation Of Asimina Triloba Subpopulations Of Northern West Virginia, Kari Fontana

Undergraduate Student Research

Clonality prevails as reproductive strategy of choice in several plant species, including Asimina triloba. More commonly known as the North American Paw Paw tree, this plant yields high domestication potential and well as scientific value. Clonality and inbreeding are highly common in Paw Paw which can pose a threat to the species’ success due the effect on genetic variation. The goal of this experiment was to examine geographic distance in the context of clonality by determining the number of individuals and clones within and among subpopulations. Methodology includes analysis of plant genetic makeup through extraction, amplification, and iSSR analysis. Data …

Differences In Soil Bacterial Diversity After Treatment With Benzyl Isothiocyanate, An Allelopathic Secondary Metabolite Derivative Of Alliaria Petiolata (Garlic Mustard), Samantha Pagel

Undergraduate Student Research

The species, Alliaria petiolata (garlic mustard), has overtaken the understory of North American forests for over a century, but how the plant has become invasively successful is not well understood. There is some indication that the secretion and breakdown of its allelopathic metabolic compounds, known as glucosinolates, contribute to its success. Benzyl isothiocyanate, an end product of garlic mustard glucosinolate breakdown, has been found in previous studies to inhibit seed germination and the growth of certain mycorrhizal fungi species. Soil bacterial communities, in addition to fungi, play an important role in the surrounding abiotic and biotic environment. This study aims …

A Fragment Of Apolipoprotein E4 Leads To The Downregulation Of A Cxorf56 Homologue, A Novel Er-Associated Protein, And Activation Of Bv2 Microglial Cells, Tanner B. Pollock, Jacob M. Mack, Noail F. Isho, Raquel J. Brown, Alexandra E. Oxford, Brad E. Morrison, Eric J. Hayden, Troy T. Rohn

Biology Faculty Publications and Presentations

Despite the fact that harboring the apolipoprotein E4 (APOE4) allele represents the single greatest risk factor for late-onset Alzheimer’s disease (AD), the exact mechanism by which apoE4 contributes to disease progression remains unknown. Recently, we demonstrated that a 151 amino-terminal fragment of apoE4 (nApoE4_1-151) localizes within the nucleus of microglia in the human AD brain, suggesting a potential role in gene expression. In the present study, we investigated this possibility utilizing BV2 microglia cells treated exogenously with nApoE4_1-151. The results indicated that nApoE4_1-151 leads to morphological activation of microglia cells through, at least in part, …

Using Isoconversional Methods To Study The Effect Of Antioxidants On The Oxidation Kinetics Of Milk Fat, Khalid Ahmed Alsaleem

Electronic Theses and Dissertations

Milk fat is a versatile ingredient because of its nutritional value, functionality, and flavor. During processing and storage, milk fat may undergo oxidation resulting in many undesirable changes such as unpleasant flavor and aroma, and formation of toxic compounds. A common practice to prevent the oxidation of milk fat is by the addition of antioxidants. It is worth to mention that little is known on the effect of antioxidants on the oxidation kinetics. In this work, the effect of selected antioxidants on the oxidation kinetics of anhydrous milk fat (AMF) under non-isothermal conditions was investigated. AMF with an addition of …

Increasing Accumulation Of Glyceollins In Soybeans Via Optimization Of The Fungal Incubation Process, Stephanie Wootton

Electronic Theses and Dissertations

Continual use of antibiotics in the feed of food animals was viewed a solution to the problem of disease outbreaks in livestock produced in confinement operations. This practice also improved animal performance, likely due to the reduction in sub-clinical infections. Unfortunately, this practice led to a new problem, the development of antibiotic resistant microbes. This increase in antibiotic resistance reduced the direct benefits of antibiotics in animal production. Moreover, as antibiotic resistance spread from animal to human pathogens, this practice created a major public health concern. This led the FDA to enact the Veterinary Feed Directive in 2017 that greatly …

The Evolution Of Coral Snake Mimicry, Renan Janke Bosque

Electronic Theses and Dissertations

Scientists have regarded mimicry as one of the most amazing examples of the power of natural selection. Early observations by naturalists of the mimetic association between venomous New World coral snakes of the genus Micrurus and harmless mimics has stimulated an intense debate about the causes and consequences of mimicry that persists today. Despite its medical, evolutionary and historical importance our understanding of evolution within the genus Micrurus is negligible. My dissertation explores the evolution of mimicry within South American coral snakes and their mimics using a multi-scale framework involving macroevolutionary (Chapter I), geographic/morphological concordance (Chapters II and III), behavioral …

Extended Adolescence: The Ecology And Endocrinology Of Facultative Paedomorphosis, Jason R. Bohenek

Electronic Theses and Dissertations

Phenotypic plasticity is an adaptation to unpredictable environments whereby an organism of a single genotype may express more than one phenotype under differing environmental conditions. Phenotypic plasticity can manifest as polyphenisms, which is an extreme form of phenotypic plasticity that produces two or more discrete, alternative phenotypes. The expression of alternative phenotypes is controlled by biotic and abiotic environmental factors, which variably affect the strength and direction of phenotypic outcomes. Using a model polyphenic salamander, I sought to understand the ecological and hormonal processes that regulate alternative phenotype expression. The mole salamander (Ambystoma talpoideum) and eastern newt ( …

Engineering Stem Cell Cardiac Patch With Microvascular Features Representative Of Native Myocardium, Zichen Qian, Dhavan Sharma, Wenkai Jia, Daniel Radke, Timothy Kamp, Feng Zhao

Michigan Tech Publications, Part 1

The natural myocardium is a highly aligned tissue with an oriented vasculature. Its characteristic cellular as well as nanoscale extracellular matrix (ECM) organization along with an oriented vascular network ensures appropriate blood supply and functional performance. Although significant efforts have been made to develop anisotropic cardiac structure, currently neither an ideal biomaterial nor an effective vascularization strategy to engineer oriented and high-density capillary-like microvessels has been achieved for clinical cardiovascular therapies. A naturally derived oriented ECM nanofibrous scaffold mimics the physiological structure and components of tissue ECM and guides neovascular network formation. The objective of this study was to create …

Memory Formation In Matter, Joseph Paulsen, Nathan C. Keim, Zorana Zeravcic, Srikanth Sastry, Sidney R. Nagel

Physics - All Scholarship

Memory formation in matter is a theme of broad intellectual relevance; it sits at the interdisciplinary crossroads of physics, biology, chemistry, and computer science. Memory connotes the ability to encode, access, and erase signatures of past history in the state of a system. Once the system has completely relaxed to thermal equilibrium, it is no longer able to recall aspects of its evolution. The memory of initial conditions or previous training protocols will be lost. Thus many forms of memory are intrinsically tied to far-from-equilibrium behavior and to transient response to a perturbation. This general behavior arises in diverse contexts …

Vertical Sleeve Gastrectomy Improves Ventilatory Drive Through A Leptin-Dependent Mechanism, Deanna M. Arble, Alan R. Schwartz, Vsevolod Y. Polotsky, Darleen A. Sandoval, Randy J. Seeley

Biological Sciences Faculty Research and Publications

Obesity hypoventilation syndrome (OHS) is a serious disorder characterized by daytime hypercapnia, disordered breathing, and a reduction in chemosensitivity. Vertical sleeve gastrectomy (VSG), a bariatric surgical procedure resulting in weight loss and weight-independent improvements in glucose metabolism, has been observed to substantially improve sleep-disordered breathing. However, it is unclear if the ventilatory effects of VSG are secondary to weight loss or the marked change in metabolic physiology. Using preclinical mouse models, we found that VSG leads to an improvement in the hypercapnic ventilatory response (HCVR) and reductions in circulating leptin levels independent of reductions in body mass, fat mass, and …

Detection Of Sickle Cell Disease-Associated Single Nucleotide Polymorphism Using A Graphene Field Effect Transistor, Kandace Fung

CMC Senior Theses

Sickle Cell Disease (SCD) is a hereditary monogenic disorder that affects millions of people worldwide and is associated with symptoms such as stroke, lethargy, chronic anemia, and increased mortality. SCD can be quickly detected and diagnosed using a simple blood test as an infant, but as of now, there is currently limited treatment to cure an individual of sickle cell disease. Recently, there have been several promising developments in CRISPR-Cas-associated gene-editing therapeutics; however, there have been limitations in gene-editing efficiency monitoring, which if improved, could be beneficial to advancing CRISPR-based therapy, especially in SCD. The CRISPR-Chip, a three-terminal graphene-based field …

Generating Genome Browsers To Facilitate Undergraduate-Driven Collaborative Genome Annotation, Luke Sargent, Yating Liu, Wilson Leung, Nathan Mortimer, David Lopatto, Jeremy Goecks, Sarah C.R. Elgin

Biology Faculty Research

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. Undergraduates can become skilled annotators, and in the process learn both about genes/genomes and about how to utilize large datasets. Data visualizations provided by a genome browser are essential for manual gene annotation, enabling annotators to quickly evaluate multiple lines of evidence (e.g., sequence similarity, RNA-Seq, gene …

Phenogeneranker: A Tool For Gene Prioritization Using Complete Multiplex Heterogeneous Networks, Cagatay Dursun, Naoki Shimoyama, Mary Shimoyama, Michael Schläppi, Serdar Bozdag

Computer Science Faculty Research and Publications

Uncovering genotype-phenotype relationships is a fundamental challenge in genomics. Gene prioritization is an important step for this endeavor to make a short manageable list from a list of thousands of genes coming from high-throughput studies. Network propagation methods are promising and state of the art methods for gene prioritization based on the premise that functionally-related genes tend to be close to each other in the biological networks.

In this study, we present PhenoGeneRanker, an improved version of a recently developed network propagation method called Random Walk with Restart on Multiplex Heterogeneous Networks (RWR-MH). PhenoGeneRanker allows multi-layer gene and disease networks. …

Comparative Optic Nerve Head Physiology: Glaucoma Induced Retinal Ganglion Cell Apoptosis By Disruption Of The Translaminar Pressure Gradient And Reduced Neurotrophic Signaling, Cassidy Christopherson

Biology and Microbiology Graduate Students Plan B Research Projects

Glaucoma is the leading cause of irreversible blindness, and the second leading vision loss neurodegenerative disease affecting millions worldwide. Glaucoma is characterized as a group of eye disorders which are initially asymptomatic but may progress to significant optic nerve head damage and vision loss with time. Early stages of glaucoma often go undetected, leading to irreversible damage to the optic nerve head prior to patients seeking medical care. Glaucoma leads to vision loss via death of retinal ganglion cells. Retinal ganglion cell apoptosis is thought to begin due to interference with the normal transmission of neurotrophic signals that arrive by …

Irritable Bowel Syndrome With Constipation (Ibs-C) Treatment Efficacy And The Emerging Importance Of Serotonin, Meghan Schenk

Biology and Microbiology Graduate Students Plan B Research Projects

Irritable bowel syndrome with constipation (IBS-C) affects a large proportion of the population. It decreases quality of life for the patient both physically and mentally. Patients report higher levels of mental health issues and other gastrointestinal maladies compared to the normal population, in addition to an IBS diagnosis. Patients have increased healthcare visits and costs, raising insurance rates for all, and also results in more missed time from work. There are limited treatments available for IBS-C, and medicinal and non-medicinal modalities are differentially prescribed to patients throughout the country. Recently, serotonin has emerged as a key mediator of normal gut …

A Review: The Association Of Asthma And The Microbiome, Kathleen Olson

Biology and Microbiology Graduate Students Plan B Research Projects

The microbiome gut-lung axis has been associated with asthma. Asthma is a respiratory disease that presents itself in many different ways. The microbiome is the bacteria, fungi, protozoa, and viruses found in a particular environment. The association of the microbiome gutlung axis in an asthmatic individual compared to a healthy individual has shown that different types and/or concentrations of bacterial genera are present in an asthmatic individual compared to a healthy individual. A causal relationship between the microbiome and asthma has not yet been identified. The aim of this review is to present the association of asthma and the microbiome …

Pathogenesis Of Cte: A Review Of Ptau, Lewy Bodies, And Cytokine Involvement In Cte, Karter Keefer

Biology and Microbiology Graduate Students Plan B Research Projects

Chronic Traumatic Encephalopathy (CTE) is a neuropathological disease that develops years after experiencing repetitive traumatic brain injuries. In recent years, this disease has been gaining recognition from professional, college, and high school teams that participate in contact sports. The purpose of this paper is to review available information about this neurodegenerative disease. Only limited published experiments are available on this disease. Research on CTE has been limited by the fact that patients can only be diagnosed with the disease by a post mortem autopsy. Many experiments were analyzed regarding different CTE pathologies, symptoms, and treatments. Articles used in this paper …

Non-Native Ant Invader Displaces Native Ants But Facilitates Non-Predatory Invertebrates, Robert Warren, Madeson C. Goodman

Biology Faculty Datasets

Many invasive ants, such as the European fire ant (Myrmica rubra), are particularly successful invaders due to their ability to form multi-nest, multi-queen 'supercolonies' that appear to displace native invertebrates in invaded regions. Myrmica rubra has invaded many areas in the Northeastern United States, including Western New York. Myrmica rubra invasion corresponds with decreases in native invertebrates, particularly ants, an effect which may be attributable to direct displacement, or because M. rubra prefers habitat unsuitable for native ants. We surveyed Western New York parklands to investigate native ant and non-ant invertebrate abundance in M. rubra-invaded and …

Regional-Scale Environmental Resistance To Non-Native Ant Invasion, Robert Warren

Biology Faculty Datasets

A successful invasion of novel habitat requires that non-native organisms overcome native abiotic and biotic resistance. Non-native species can overcome abiotic resistance if they arrive with traits well-suited for the invaded habitat or if they can rapidly acclimate or adapt. Non-native species may co-exist with native species if they require novel, underused resources or if they can out-compete similar native species. We investigated abiotic and biotic resistance to the progression of a Brachyponera chinensis invasion in the southeastern U.S. relative to the dominant native woodland ant (Aphaenogaster). We used observational data from long-term plots along the elevation gradient …

The Role Of Antarctica In Biogeographical Reconstruction: A Point Of View, Manuel De La Estrella, Sven Buerki, Thais Vasconcelos, Eve J. Lucas, Félix Forest

Biology Faculty Publications and Presentations

Premise of research. The opening of the Drake Passage in the Miocene (disconnecting Antarctica and South America and resulting in the establishment of the Circumpolar Current preventing warm waters from the north to reach the polar continent) has led to the formation of the ice sheets and the retreat of the temperate to tropical vegetation that had covered Antarctica for millions of years. With only two current native vascular plant species, Antarctica has been virtually ignored in biogeographical reconstructions and, when considered, only a posteriori invoked as a route of dispersal to reconcile inferred disjunct biogeographical patterns.

Methodology. Here, we …

Do Humans Possess The Capability To Regenerate?, Chasha Wuensch

The Science Journal of the Lander College of Arts and Sciences

Urodele amphibians, including newts and salamanders, are amongst the most commonly studied research models for regeneration. The ability to regenerate, however, is not limited to amphibians, and the regenerative process has been observed in mammals as well. This paper discusses methods by which amphibians and mammals regenerate to lend insights into human regenerative mechanisms and regenerative potential. A focus is placed on the urodele and murine digit tip models, both of which share critical regenerative stages including wound healing, histolysis, and blastema formation. Formation of the blastema proved to be a crucial process necessary for regeneration, and is responsible for …

Degeneration Of Rods And Cones In Retinitis Pigmentosa, Rachel Stern

The Science Journal of the Lander College of Arts and Sciences

Retinitis Pigmentosa, most commonly characterized by night blindness and loss of peripheral vision, is a rare genetically inherited group of diseases affecting the retina of the eye. It is estimated that 1 in 4000 people in the USA are affected by some form of the disease. Retinitis Pigmentosa (RP), is caused by a mutation or change in one or more of 55 genes. There are many causes to this disease as RP presents with many different symptoms and biological effects on the eye. These are then grouped together because they share a common result, deterioration of vision. Presently, there is …

Energy Drinks: Cardiovascular Effects And The Specific Components Responsible, Malka B. Gelbfish

The Science Journal of the Lander College of Arts and Sciences

Energy drink usage as a stimulant is on the rise among adolescents and young adults. While these drinks have positive energizing effects, they pose significant health concerns. This paper examines the adverse cardiovascular effects of energy drinks and the components that could possibly be responsible. Analysis was conducted by reviewing and comparing many studies available in this area of research. Studies of energy drinks in general and energy drinks versus drinks containing caffeine alone were analyzed. Additionally, this review investigated studies of the specific ingredients in energy drinks such as caffeine, taurine, guarana, and sugar. This review found that energy …