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Of Transcription Factor And Transformation: Elucidating Gene Function In The Common Ice Plant, Mesembryanthemum Crystallinum, Chinenye Lilian Izuegbunam

Dissertations and Theses

Abiotic stresses negatively affect plant growth and development across the globe, which also affect the production of food, feed, biofuel, and fiber to meet the demands of a growing population. Thus, developing novel strategies to increase abiotic stress tolerance in crops is necessary. One of these strategies is exploring transcription factors (TFs) in Crassulacean Acid Metabolism (CAM) plants to improve plant abiotic stress tolerances. Therefore, the first objective of this dissertation determine the abiotic stress tolerance function of a CAM TF, McHB7opt in Arabidopsis. This study found that McHB7opt increased stress-responsive pathways related to seed germination and early seedling development. …

An Analysis On How Housing Status Influences The Gut-Brain-Axis For Populations In And Around The Skid Row Area Of Los Angeles, California, Mauricio Guzman

Pitzer Senior Theses

Over recent years, the “microbiota-gut-brain axis” (MGBA) has garnered significant attention in the scientific community. Specifically, perturbations of the MGBA via stress and dietary intake have been linked to a wide-range of diseases including gastrointestinal diseases, metabolic diseases, mood disorders, and cognitive diseases. However, most studies have been solely conducted on mice models and have yet to consider the more complex, intricate systems that impact the human body. In addition, researchers have yet to consider the populations who may be most susceptible to chronic stress and negative dietary outcomes. Drawing from the fields of medical sociology, non-invasive human biology, and …

Propagation, Physiology And Biomass Of Giant Cane (Arundinaria Gigantea) For Conservation And Restoration, Sanjeev Sharm

Graduate Theses/Dissertations

Giant cane (Arundinaria gigantea) is a native species to 22 states in the U.S. The species and its ecosystem are considered critically endangered, and the species has been reduced to 2% of its original extent. The species has a long cultural and conservation history. Large canebrakes were commonly found in Missouri in bottomland forests, stream and riverbanks, and margins of lakes. My research goals were to: 1) examine methods for propagation success from field to greenhouse to field; 2) examine the physiology of cane at one of the few current canebrakes, for greenhouse propagated plants, and field planted …

The Role Of Insulin-Like Growth Factor I In The Development Of The Cerebellum In Euthyroid And Hypothyroid Mice, Prathibha Mangedarage

All Graduate Theses, Dissertations, and Other Capstone Projects

Thyroid hormone deficiency during development is known to cause anatomical defects in the cerebellum that lead to neurological deficits. It has been observed that insufficient thyroid hormone levels also decrease the levels of brain derived Insulin-like growth factor 1 (Igf-1). Given that the deficits caused by low Igf-1 levels are similar to those caused by low thyroid hormone, we designed this study to investigate if the deficits caused in the development of the cerebellum by low thyroid hormone levels may be due to the lack of sufficient Igf-1. We also sought to determine if ectopic over expression of Igf-1 in …

"Effects Of Chronic Clothianidin Exposure On Various Aspects Of Oncorhynchus Mykiss (Rainbow Trout) Development", Jacob Schmid

All Graduate Theses, Dissertations, and Other Capstone Projects

Agricultural run-off is one of the leading sources of environmental pollution in the United States. One major pollutant within this is insecticides, and among these, neonicotinoids which have become the most used insecticide class across the world. Neonicotinoids act as an agonist on the nicotinic acetylcholine receptor (nAChR) in the central nervous system of insects. Neonicotinoids are perceived to have low toxicity on non-target organisms however recently extensive literature has been published showing various effects on non-target organisms. Clothianidin is one of the most applied compounds belonging to the neonicotinoid class, yet few studies have investigated its chronic effects on …

Excess Dietary Sugar Alters Colonocyte Metabolism And Impairs The Proliferative Response To Damage, Ansen H.P. Burr, Junyi Ji, Kadir Ozler, Heather L. Mentrup, Onur Eskiocak, Brian Yueh, Rachel Cumberland, Ashley V. Menk, Natalie Rittenhouse, Christopher Marshall, Pailin Chiaranunt, Xiaoyi Zhang, Lauren Mullinax, Abigail Overacre-Delgoffe, Vaughn S. Cooper, Amanda C. Poholek, Greg M. Delgoffe, Kevin P. Mollen, Semir Beyaz, Timothy W. Hand

Biological Sciences Faculty Research and Publications

Background & Aims

The colonic epithelium requires continuous renewal by crypt resident intestinal stem cells (ISCs) and transit-amplifying (TA) cells to maintain barrier integrity, especially after inflammatory damage. The diet of high-income countries contains increasing amounts of sugar, such as sucrose. ISCs and TA cells are sensitive to dietary metabolites, but whether excess sugar affects their function directly is unknown.

Methods

Here, we used a combination of 3-dimensional colonoids and a mouse model of colon damage/repair (dextran sodium sulfate colitis) to show the direct effect of sugar on the transcriptional, metabolic, and regenerative functions of crypt ISCs and TA cells. …

Effect Of Soil Transplantation On Fungal Communities During Restoration, Thomas Luehl

All Master's Theses

Ectomycorrhizal fungi are integral parts of natural ecological systems that provide access to nutrients that would otherwise be unavailable by forming symbiotic relationships with plants. Relationships with ectomycorrhizal fungi are known to improve plant growth rate, increase plant resistance to pathogens, and improve survival. Current revegetation practices often ignore this relationship between fungi and plants. During the revegetation of the Interstate 90 Keechelus Lake wildlife overcrossing (Easton, WA), soil from forest sites adjacent to the restoration area were collected and used to inoculate a set of experimental plots to determine whether ectomycorrhizal fungi would become established in the plots and …

Emerging Applications Of 3d Engineered Constructs From Plant Seed Extracts, Sedat Odabaş, Bora Gari̇pcan, Rihab Ksouri

Turkish Journal of Biology

Seeds, by-products derived from various plants such as mango, quince, and apples, are considered waste, though they have emerging commercial potential, and have been used in biological, industrial, and physiological research. Seed-derived natural macromolecules- mainly polysaccharides, mucilage, gums, and cellulose-have physicochemical and structural diversification, giving the potential for forming gels, texturing, thickening, and providing interfacial adsorption. Seed-derived natural macromolecules have been widely used during the last few years in cell research and tissue engineering applications. Their widespread approachability and safety, high rate of biodegradability, biocompatibility, supporting cell proliferation, and extracellular matrix synthesis are the main properties making plant seed derivatives …

Ascophyllum Nodosum Seaweed Extract Application As A Possible Mechanism For Mitigating Salt Stress In Soybeans (Glycine Max), Elena Hoang

Honors Program Theses

Soil salinity, an abiotic stressor associated with climate change effects, inhibits the normal growth and development of sensitive crop species. The excessive accumulation of salt ions in plant tissue induces oxidative stress, which is characterized by an increased production of reactive oxygen species (ROS) damaging plant organelles and disrupting normal metabolic functions. Seaweed extracts (SWE) may be a solution for mitigating the effects of salt stress on crop yield and quality, as they introduce bioactive ingredients that are able to regulate gene expression and enhance natural physiological processes in plants. However, the positive benefits of SWE applications differ between plant …

Producing Grnas For Use In Crispr-Cas9 Dna Editing Applications Via In Vivo T7 Rna Polymerase Transcription In Escherichia Coli., Christian A. Santiago

Honors Program Theses

The development of the CRISPR-Cas9 system is widely considered to be a breakthrough advancement in gene editing. Compared to traditional technologies, CRISPR is generally regarded as the most accessible, effective, and precise tool for inducing stable and inheritable gene edits in vivo. The CRISPR-Cas9 gene editing complex relies on the complementary binding of guide RNAs to specifically target a DNA sequence for endonuclease cleavage and mutagenesis. The production of gRNAs for use in CRISPR applications can become exceedingly complex and costly, as in vivo methodologies generally require the use of RNA polymerases that interfere with gRNA sequence identity and in …

Sdf-1 Induces Directional Chemotaxis Of Endogenous Bmscs At The Intervertebral Fusion Site And Promotes Osteogenic Differentiation By Regulating Wnt/Ss-Catenin In The Bone Marrow Chimera Spinal Intervertebral Fusion Mouse Model, Qiwen Zhang, Ning Liang, Bin He, Siyou Wu, Depeng Wen, Xiaoyong Tang, Xiongcheng Shen

Turkish Journal of Biology

Clinical observations show that the current spinal fusion with internal fixation has a nonfusion rate of 5%-35%; however, methods to promote spinal fusion are limited. This study aimed to investigate the role of SDF-1-induced directional chemotaxis of BMSCs in bone marrow chimera spinal intervertebral fusion mouse model. BMSCs were isolated from bone marrow and identified by detecting CD44/CD34 positive cells. BMSCs (GFP-BMSCs) were labeled with GFP for tracking in vivo. Mice were inoculated with GFP-BMSCs to construct bone marrow chimera spinal intervertebral fusion model, which were divided into BM-SIF model, BM-SIF+SDF-1, BM-SIF+SDF-1-Anta group. The callus area of intervertebral fusion site …

Methionine Restriction And Cancer Treatment: A Systems Biology Study Of Yeast To Investigate The Possible Key Players, Esra Börklü

Turkish Journal of Biology

Background/aim: Dietary restriction, mainly carbon and/or methionine restriction are among the upcoming supporting interventions along with chemotherapy in various cancers. Although dietary restriction has been proven to be beneficial, the main cellular machineries affected by its administration lacks deeper information considerably, a notable pitfall in its use as a personalized nutritional approach. Materials and methods: In this study, cellular effects of methionine restriction on a yeast model are explored via systems biology approaches. The methionine biosynthesis network, constructed by integrating interaction data with gene ontology terms, was analysed topologically, and proved to be informative about the intertwined relationship of methionine …

The Effects Of Sex On Zebrafish Bone Metabolism, Simon Bagatto

Williams Honors College, Honors Research Projects

I investigated the effects of diet and sex on zebrafish bone metabolism. Zebrafish were subjected to either a high-calorie or low-calorie diet over a five-week period. After this diet, zebrafish scales were used to measure alkaline phosphatase (ALP) and tartrate-resistant acid phosphatase (TRAP) enzyme activity with a fluorescent substrate. The enzyme activities were markers of the osteoblasts (ALP) and the osteoclasts (TRAP). These data were compared among sex and diet of the zebrafish using a repeated measures ANOVA statistical test. I also measured the number of resorption lacunae per scale (another indicator of osteoclast activity). The results showed higher TRAP …

To What Extent Do Non-Native Shrubs Support Higher Trophic Levels?, Ari Zakroff

Browse all Theses and Dissertations

Invasive species threaten ecosystems and economies. Globally, biological invasions are estimated to have cost over $2.1 trillion since 1970. In Eastern North American woodlands, invasive plants are rapidly displacing natives. This is concerning, because invasive plants may not support the diverse and abundant arthropod communities essential to ecosystem function. Despite the conceptual understanding of invasive shrubs’ potential to transform forest communities, scant research has focused on the effect of invasive plants on higher trophic levels here in Ohio. To address this gap, I examined the diversity and abundance of arthropod communities, caterpillar performance, and caterpillar predation on two invasive shrubs, …

Exploring The Metabolic Capabilities And Biotransformation Potential Of Environmental Lactococcus Strains, Desirée Román Naranjo

Theses

The aim of this thesis is to characterize environmental Lactococcus strains to identify different and diverse metabolic capabilities that could be applied to microbial biotransformation, defined as the conversion of a cheap/waste substrate into a value-added product. Due to the increased amounts of food processing waste generated worldwide and the impact of climate change, new sustainable approaches are necessary to contribute to waste valorization and the circular bioeconomy. We ask to what extent and in what ways environment isolated Lactococcus strains could contribute to food biotransformation by metabolizing a different range of substrates. We do so to further understand and …

Isolation And Characterisation Of Soil-Derived Bacteria With Antimicrobial Activity Against Antibiotic Resistant Pathogens, Ellen Twomey

Theses

Bacteriocins are a diverse range of ribosomally synthesized bioactive peptides, recognised predominantly for their potent antimicrobial activity against other strains closely related to the producer. The focus of this thesis was to explore this activity and examine the potential of bacteriocins to inhibit the growth of clinically relevant pathogens. Although evidence exists in the literature to suggest that bacteriocins could be applied in a similar fashion to conventional antibiotics, to date they are only utilised as preservative in food to prevent the growth of foodborne illness causing organisms. Isolating and screening bacterial strains in order to identify bacteriocin producers has …

Deep Learning-Based Technique For The Perception Of The Cervical Cancer, Aya Haraz, Hossam El-Din Moustafa, Abeer Twakol Khaleel, Ahmed H. Eltanboly

Mansoura Engineering Journal

In third-world countries, cervical cancer is the most prevalent and leading cause of death. It is affected by a variety of factors, including smoking, poor nutritional status, immunological inadequacy, and prolonged use of contraception. The Pap smear test, which is intended to prevent cervical cancer, finds preneoplastic changes in cervical epithelial cells. This study framework classified cervical cancer cells from Pap smears into five specified cell types using machine learning-based classification algorithms. The SIPaKMeD database is used in this investigation. This public dataset, which was manually cropped from 966 cluster cell images taken from Pap smear slides, has 4045 isolated …

Examining The Effects Of Hyperglycemia On Retinal Regeneration, Emmanuella Ec Kyllians

Theses and Dissertations--Biology

Diabetes is a disease that affects how the body processes glucose, leading to a cascade of other complications, one of which is diabetic retinopathy (DR). DR is a neurovascular disease that affects the retina and research has revealed the role of retinal neurodegeneration in its development. Animal models like zebrafish have emerged as important tools for studying the molecular and cellular mechanisms underlying DR. On the other hand, retinitis pigmentosa (RP) is a degenerative disease that involves the progressive degeneration of rods and cones, and hyperglycemia has been found to impair regeneration. Therefore, this study aims to examine the effects …

Parental Effects On Offspring Reaction Norms: Consequences For Complex Phenotypes In Variable Environments, Alexandra G. Cones

Theses and Dissertations--Biology

Organismal traits all exhibit some degree of environmental sensitivity, and both the strength and direction of these phenotypically plastic responses to the environment can evolve in adaptive ways. For example, parents can use information about their own environment to precondition the traits of their offspring so that they thrive in their future environment. This transgenerational plasticity can also alter the plasticity of offspring, but explicit investigations of this specific phenomenon are rare. I begin with a review of the literature and provide a quantitative genetic framework to investigate this phenomenon, which I then explore empirically using avian embryos. The metabolic …

Viral Chemotaxis Of Paramecium Bursaria Altered By Algal Endosymbionts, Huy V.N. Ho, David Dunigan, Miranda E. Salsbery, Irina Agarkova, Zeina Al-Ameeli, James L. Van Etten, John Delong

School of Biological Sciences: Faculty Publications

Chemotaxis is widespread across many taxa and often aids resource acquisition or predator avoidance. Species interactions can modify the degree of movement facilitated by chemotaxis. In this study, we investigated the influence of symbionts on Paramecium bursaria’s chemotactic behavior toward chloroviruses. To achieve this, we performed choice experiments using chlorovirus and control candidate attractors (virus stabilization buffer and pond water). We quantified the movement of Paramecia grown with or without algal and viral symbionts toward each attractor. All Paramecia showed some chemotaxis toward viruses, but cells without algae and viruses showed the most movement toward viruses. Thus, the endosymbiotic …

Stochasticity Directs Adaptive Evolution Toward Nonequilibrium Evolutionary Attractors, John Delong, Clayton E. Cressler

School of Biological Sciences: Faculty Publications

Stochastic processes such as genetic drift may hinder adaptation, but the effect of such stochasticity on evolution via its effect on ecological dynamics is poorly understood. Here we evaluate patterns of adaptation in a population subject to variation in demographic stochasticity. We show that stochasticity can alter population dynamics and lead to evolutionary outcomes that are not predicted by classic eco-evolutionary modeling approaches. We also show, however, that these outcomes are governed by nonequilibrium evolutionary attractors— these are maxima in lifetime reproductive success when stochasticity keeps the ecological system away from the deterministic equilibrium. These NEEAs alter the path of …

The Consumption Of Viruses Returns Energy To Food Chains, John Delong, James L. Van Etten, Zeina Al-Ameeli, Irina Agarkova, David Dunigan

School of Biological Sciences: Faculty Publications

Viruses impact host cells and have indirect effects on ecosystem processes. Plankton such as ciliates can reduce the abundance of virions in water, but whether virus consumption translates into demographic consequences for the grazers is unknown. Here, we show that small protists not only can consume viruses they also can grow and divide given only viruses to eat. Moreover, the ciliate Halteria sp. foraging on chloroviruses displays dynamics and interaction parameters that are similar to other microbial trophic interactions. These results suggest that the effect of viruses on ecosystems extends beyond (and in contrast to) the viral shunt by redirecting …

Pathways Of Density Dependence And Natural Selection In Modern Humans, John Delong

School of Biological Sciences: Faculty Publications

Living things depend on a flow of energy and materials to grow, reproduce, and maintain their bodies. Populations are aggregations of individuals, so they too depend on resources. Humans use many fuels derived from the Earth’s photosynthetic energy, which in turn support a population that often occurs at unusually high densities for a mammal. Like most populations, growing human populations may experience negative feedbacks from population size unless the socio-economic system in which the population lives grows fast enough to maintain resource flows to individuals and to limit the downsides of high density. I map out a simple view of …

Use Of Amino Acid Isotope Analysis To Investigate Capital Versus Income Breeding Strategies In Migratory Avian Species, Nico Lübcker, John P. Whiteman, Oliver N. Shipley, Keith A. Hobson, Seth D. Newsome

Biological Sciences Faculty Publications

1. Income and capital breeding represent opposing ends of a continuum of reproductive strategies. Quantifying nutrient allocation to reproduction is challenging, but recent advances in compound-specific stable isotope analysis hold promise for tracing the source of individual compounds allocated to reproduction.

2. Here, we describe a novel approach of using measured carbon (δ13C) and nitrogen (δ15N) isotope values of individual amino acids (AAs) in pectoral muscle of egg-laying females and egg yolk as a useful tool to quantify the reliance on income versus capital breeding in migrating species. We used white-fronted (Anser albifrons frontalis), lesser snow (A. …

Grizzly Bears And Humans At Alpine Moth Sites In Wyoming, Usa, Erika A. Nunlist, Dan Tyers, Andrew Pils, Bok F. Sowell

Human–Wildlife Interactions

Army cutworm moths (Euxoa auxiliaris; moths) are an important seasonal higher elevational food source for grizzly bears (Ursus arctos horribilis; bears) in the Greater Yellowstone Ecosystem (Wyoming, Montana, and Idaho, USA). Increased human interaction with bears at moth sites is an important management issue because of the potential for displacing bears and the concern for human safety. Managers will need better information regarding human–bear interactions at high-density moth sites that are also accessible to humans to mitigate potential conflicts. In the summers of 2017 and 2018, we studied human–bear interactions at 2 of the most human …

Ecological Niche Comparison Among Closely Related Tree Species Of Lauraceae Using Climatic And Edaphic Data, Laura J. Giraldo-Kalil, Gonzalo E. Pinilla Buitrago, Andrés Lira-Noriega, Francisco Lorea-Hernández, Juan Núñez-Farfán

Publications and Research

ABSTRACT:

Edaphic specialization is considered to promote ecological differentiation among closely related species of Damburneya (Lauraceae) occurring in sympatry. However, little is known about the effects of soil and other key environmental factors like climate on the ecological niche and distribution of these tree species. Here, we assessed the role of climate and soil on niche divergence and potential distribution of four Damburneya species whose distributions span Central America and Mexico. We performed ecological niche modeling with MaxEnt using three sets of environmental data: climatic-only, edaphic-only, and a combination of both, to characterize species niches and suitable distribution areas. Niche …

Tcga Expression Analyses Of 10 Carcinoma Types Reveal Clinically Significant Racial Differences, Brian Lei, Xinyin Jiang, Anjana Saxena

Publications and Research

Epidemiological studies reveal disparities in cancer incidence and outcome rates between racial groups in the United States. In our study, we investigated molecular differences between racial groups in 10 carcinoma types. We used publicly available data from The Cancer Genome Atlas to identify patterns of differential gene expression in tumor samples obtained from 4112 White, Black/African American, and Asian patients. We identified race-dependent expression of numerous genes whose mRNA transcript levels were significantly correlated with patients’ survival. Only a small subset of these genes was differentially expressed in multiple carcinomas, including genes involved in cell cycle progression such as CCNB1 …

Salinization Impacts On Heterotrophic Respiration, Ecosystem Respiration, And Plant Productivity In Tidal Freshwater Marshes, Kelsie J. Moses

Theses and Dissertations

Tidal freshwater marshes have preserved substantial stocks of soil carbon, which represents carbon dioxide that is no longer in the atmosphere. There is conflicting evidence in the literature about how disturbances such as sea level rise and associated wetland salinization impact the accumulation and long-term stability of this stored carbon. The goal of this experiment was to quantify how salinization impacts total ecosystem respiration and its component parts, autotrophic and heterotrophic respiration. This was a microcosm experiment using a C4 plant (Spartina cynosuroides) grown in soil derived from C3 plant matter and exposed to different salinities (0 to …

The Effect Of Larval Competition On Adult Life History Traits And The Immune Response Of Adult Cat Fleas (Ctenocephalides Felis), Piper N. Zellner, Lisa D. Brown

Honors College Theses

In holometabolous insects, conditions during the larval stage can affect the adult stage. For instance, in mosquitoes, reduced larval food and high density can make adults more susceptible to infection. Fleas (Siphonaptera), like mosquitoes, go through complete metamorphosis and have adult stages that exclusively feed on the blood of vertebrates, including humans. However, flea larvae have chewing mandibles and rely on nutrients from dried fecal matter containing vertebrate blood proteins. Their limited mobility and unique nutritional needs confine their development to specific areas, likely leading to frequent larval competition in natural conditions. Yet, the influence of larval density on the …

Identification And Creation Of Novel Bacteriocins With Potential Food And Clinical Applications, David Lynch

Theses

Bacteriocins represent a heterogeneous group of small, ribosomal-synthesized, potent antibacterial peptides produced by bacteria, capable of inhibiting bacteria both closely related or indeed those from other genera than the producer. In addition to their role as food preservatives, bacteriocins have potent activity against medically significant pathogens and are considered attractive alternatives to antibiotics, due to their inherent heat stability, potency at nanomolar scale, resistance to proteases and low levels of acquired resistance in commercial applications. The aim of this thesis was to identify, purify and bioengineer novel bacteriocins from Staphylococcus and Lactic Acid Bacteria (LAB), with a view to expanding …