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The Role Of Semaphorins In Response To Injury In C. Elegans Neurons, Maria Belen Harreguy Alfonso

Dissertations

When neural tissue is injured by trauma, delicate neuronal processes such as axons and dendrites are prone to lesion damage and often disconnect. The molecular, cellular, and circuit mechanisms that underlie the regrowth and reconnection of these processes and the recovery of behavior are major challenges in the fields of neuroscience, regeneration, and resilience. At the molecular and cellular levels, signaling pathways that mediate neuronal growth cone guidance during development can play a role in neuronal regeneration and recovery from injury. One family of signaling proteins involved in this process comprises the highly conserved semaphorins and their receptors, the plexins. …

Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin

Dissertations

Clustering analysis has been conducted extensively in single-cell RNA sequencing (scRNA-seq) studies. scRNA-seq can profile tens of thousands of genes' activities within a single cell. Thousands or tens of thousands of cells can be captured simultaneously in a typical scRNA-seq experiment. Biologists would like to cluster these cells for exploring and elucidating cell types or subtypes. Numerous methods have been designed for clustering scRNA-seq data. Yet, single-cell technologies develop so fast in the past few years that those existing methods do not catch up with these rapid changes and fail to fully fulfil their potential. For instance, besides profiling transcription …

Novel Photobase Generators For Photoinduced Polymerization And Ph Regulation, Shupei Yu

Dissertations

Photochemistry encompasses the investigation of chemical processes instigated by light absorption. As important branches of photochemistry, photosensitive and optical materials have attracted extensive research interests in both academia and industry. Photosensitive and optical materials are composed of polymers / small molecules with photo-responsive properties. These materials not only can absorb light in the desired energy spectrum, but also exhibit chemical / physical reactions, which can be applied to different fields such as photoredox, photo-heat, phototherapy, solar cells, diodes, etc. Among them, photobase generators (PBGs) are a series of photosensitive compounds, which absorb the incident light, then release the basic species …

Assessing Neurobehavioral Deficits And Neuroinflammation Following Rllb In A Transgenic Mouse Model, Aakaash Gosain

Theses

As global conflicts are escalating, military personnel have long faced the constant threat of explosions, heightening the risk of blast-induced traumatic brain injury (bTBI). The recent increase in war conflicts and combat zones worldwide not only puts the military, service members, and police forces at risk but also innocent civilians who are caught in the crossfire. While moderate to severe bTBIs have been extensively studied, the pathology of repeated low-level blasts (rLLB) remains less understood. This research addresses the gap in knowledge regarding the long-term consequences of rLLB injuries in the neural anatomy. A transgenic mouse model was subjected to …

Covalent Inhibition Of Enzyme Sortase A As A New Pathway Against Bacterial Resistance Of Staphylococcus Aureus, Umyeena Bashir

Master's Theses

The continued rise of antibiotic-resistant bacteria, such as MRSA (methicillin-resistant Staphylococcus aureus), has made the discovery of novel antibiotics critical. While bacteriostatic and bactericidal antibiotics inevitably exert evolutionary pressure on bacteria to develop resistance, small molecules that target mechanisms of bacterial virulence present a promising alternative for treatment. Sortase A (Srt A), a cysteine protease of S. aureus, promotes bacterial virulence by covalently attaching proteins such as pilin to the bacterial surface, enabling bacterial adhesion to mammalian cells. Inhibitory studies of this enzyme have gained prominent interest as a new pathway for drug development since blocking this enzyme's ability to …

Assessing Medication Compliance And The Usage Of Complementary Therapies Effecting Hba1c Among Patients With Type 2 Diabetes Mellitus In A Tertiary Care Hospital In Karachi, Pakistan, Neelam Nasruddin

Theses & Dissertations

Background: Diabetes Mellitus is a chronic illness. It remains to be a major public health matter and a financial burden on the medical system worldwide. This condition can be managed and better treatment strategies and compliance can reduce the risk of complications. In 2022, there will be around 33,000,000 new cases of diabetes worldwide, with 26.7% of the adults in Pakistan being affected, predicts the (International Diabetes Federation, 2022). However, it is observed that most individuals turn to complementary and alternative methods (CAM)/Traditional medicine because of the rising cost of therapy, adverse effects of anti-diabetic medications, and accessibility concerns.
Purpose: …

Isolation And Characterization Of Bacteriophages From Fish Tank Samples, Oluwaseyi Oluwagbeminiyi Oladele-Ajose

Electronic Theses and Dissertations

Bacteriophages (phages) are viral obligate intracellular parasites that infect bacteria. Research has been carried out on alternative treatment plans for bacterial infections due to the increase in antibiotic resistance. Phages have been proposed as an alternative to antibiotics. This research focused on the isolation and characterization of bacteria from small aquariums. A total of 42 bacterial isolates were isolated from seven different fish tank water samples and were tested to determine if they possessed phages. Spot plaque assay revealed presence of lytic phage for only one of the isolated bacterial strains, which was determined to belong to Enterobacteriaceae family based …

Characterizing The Ecology Of Plains (Spilogale Interrupta) And Eastern (Spilogale Putorius) Spotted Skunks: A Systematic Literature Review And Population Assessment In Kansas, Jenell De La Peña

Electronic Theses & Dissertations

The plains spotted skunk (Spilogale interrupta) has recently been recognized as a distinct species from the eastern spotted skunk (Spilogale putorius). While once abundant across the central and eastern United States, both species have experienced population declines, resulting in their review for listing under the Endangered Species Act (1973). In Kansas, the plains spotted skunk has suffered a particularly dramatic decline, the last detection in the state having occurred in 2020. Additionally, due to the recent taxonomic split, many past studies reporting on S. putorius ecology actually describe findings of two species, potentially complicating our understanding …

Developing Regulated Crispr Systems To Control Bacterial Microbiomes, Gregory M. Pellegrino

Electronic Thesis and Dissertation Repository

Changes to the human microbiome’s composition and metabolome are associated with numerous diseases and alterations to xenobiotic metabolism. As such, targeting the human microbiome is an increasingly popular option for therapeutic interventions. However, traditional therapies that target the microbiome such as antibiotics lack specificity, which can affect the beneficial species of the microbiome and cause adverse health outcomes such as the rise of antimicrobial-resistant bacteria. Therefore, the research and development of specific, targeted antimicrobial therapies is crucial to effectively treating microbiome dysbioses.
CRISPR and CRISPRi provide easily modifiable, RNA-guided mechanisms mediated by the Cas9 or dCas9 enzymes to induce sequence-specific …

Adaptation Reshapes The Distribution Of Fitness Effects, Diego Tenoch Morales Lopez

Electronic Thesis and Dissertation Repository

The process of adaptation has been of interest since the XIX century, when Darwin first proposed the idea of natural selection. Since then, there has been a myriad of theoretical and empirical works that have expanded the field. From the many evolutionary insights these works have produced, a foundational idea is that spontaneous mutations in the genome of organisms can produce changes to their reproductive success that might confer an advantage for the mutant organisms with respect to their peers. Therefore, mutations drive adaptive evolution by virtue of their heritable effects on fitness. Empirical measures of the distribution of these …

Interactive Effects Of Sublethal Concentrations Of Fracking Biocides And Abandoned Mine Drainage On Amphipod Behavior, Kelly Lenhart

Electronic Theses and Dissertations

This thesis examined the sublethal effects of three pollutants, namely glutaraldehyde, 4,4-dimethyloxazolidine (DMO), and abandoned mine drainage (AMD), on amphipods. The primary objective was to investigate their combined effects on amphipods. The three pollutants, despite having the potential to combine in the environment, have not been studied to determine their potential for detrimental interactive effects which could result in unexpected environmental damage.

The research employed a series of experimental setups involving controlled exposure of amphipods to varying, putatively sublethal, concentrations of the chemicals of interest. Subsequently, effects were assessed via both behavioral and feeding assessments. To facilitate this analysis, novel …

Dna Methylation-Based Epigenetic Biomarkers In Cell-Type Deconvolution And Tumor Tissue Of Origin Identification, Ze Zhang

Dartmouth College Ph.D Dissertations

DNA methylation is an epigenetic modification that regulates gene expression and is essential to establishing and preserving cellular identity. Genome-wide DNA methylation arrays provide a standardized and cost-effective approach to measuring DNA methylation. When combined with a cell-type reference library, DNA methylation measures allow the assessment of underlying cell-type proportions in heterogeneous mixtures. This approach, known as DNA methylation deconvolution or methylation cytometry, offers a standardized and cost-effective method for evaluating cell-type proportions. While this approach has succeeded in discerning cell types in various human tissues like blood, brain, tumors, skin, breast, and buccal swabs, the existing methods have major …

Targeting Macrophytes: Increased Water Quality Through Optimized Vegetation Considerations For Constructed Wetlands, Austin Mcbrady

Masters Theses

This study of constructed wetland design investigated relationships between macrophyte species selection and planting density for water quality improvement. A lab-scale wetland was compared against a pilot-scale wetland in San Antonio, Texas at Mitchell Lake to measure differences in effluent water quality improvement using three native macrophyte species. Using a novel, two-phase method, a targeting macrophyte was identified from among other species based on its marked capability for improving water quality factors, then was planted in varied majority densities to compare differences in treatment effectiveness. The results of this study showed that this complimentary approach to wetland design displayed significant …

Developing Novel Food Packaging Products With High Barrier Properties, Enabled By Cnf, Nabanita Das

Electronic Theses and Dissertations

In recent times, plastic has become a highly favored choice for packaging due to its exceptional microbial, damage, and water-resistant properties. However, the alarming rise in plastic usage has led to adverse environmental pollution. This study aims to develop innovative food packaging solutions using renewable and compostable cellulose nanofibrils (CNFs). This thesis comprises two related studies on the barrier performance of novel food packaging materials, including oxygen barrier and oil/grease barrier properties. The goal of the first study was to enhance the mechanical and barrier properties of the cellulose nanofibril (CNF) films by inducing fibrils orientation for food packaging applications. …

Regeneration Response To Salvage Logging Following Tornado Disturbance, Colby K. Bosley-Smith

Electronic Theses and Dissertations

In an era of increasing natural disturbances, successful tree regeneration has grown more difficult to achieve. Salvage logging, a common management response to disturbance, may further impede regeneration success, although published literature currently remains inconclusive. In 2013, a rare tornado in northcentral Maine, USA, and subsequent salvage operation created three clear ‘treatments’ for evaluation of post-disturbance regeneration: blowdown, blowdown followed by salvage logging and an undisturbed control. In the summers of 2022 and 2023, (nine and ten) years post-tornado, we revisited this site to examine regeneration outcomes.

During the summer of 2022, we evaluated stand structure and regeneration success of …

Integrating Remote Sensing And Machine Learning To Assess Forest Health And Susceptibility To Pest-Induced Damage, Rajeev Bhattarai

Electronic Theses and Dissertations

Spruce budworm (Choristoneura fumiferana; SBW) outbreaks are cyclically occurring phenomena in the northeastern USA and neighboring Canadian provinces. These outbreaks are often of landscape level causing impaired growth and mortality of the host species namely spruce (Picea sp.) and balsam fir (Abies balsamea (L.) Mill.). Acknowledging the recent SBW outbreak in Canadian provinces like Quebec and New Brunswick neighboring the state of Maine, our study devised comprehensive techniques to assess the susceptibility of Maine forests to SBW attack. This study aims to harness the power of remote sensing data and machine learning algorithms to model and map the susceptibility of …

Assessing The Role Of The Microbiome, Parasite Infections, And Movement In Avian Health, Olivia N. Choi

Electronic Theses and Dissertations

Avian health encompasses the physical, physiological, and behavioral well-being of birds. Assessing avian health is not only important for the conservation and management of wild birds and the recreational economy, but also for the management of infectious diseases that threaten public health and agriculture. Birds, comprising approximately 10,000 species and an estimated 50 billion individuals worldwide, are known to be involved in the spread of pathogens, some of which are zoonotic (from animals to humans), such as avian influenza and West Nile viruses. Individual measures of avian health may include physical measurements (e.g., body mass, wing length), pathogen infection status, …

Forest Management In A Changing Climate: Integrating Social And Biopysical Sciences To Inform Adaptive Responses To Future Uncertainty, Peter Breigenzer

Electronic Theses and Dissertations

Forests provide numerous ecological and socio-economic benefits, yet climate change is creating novel and extreme conditions that threaten forests and disrupt traditional management practices. To address future uncertainty about how to manage forests amid a rapidly changing climate, researchers have developed adaptive management strategies that move away from using historical ecological baselines as management goals. However, despite increases in adaptive forest management frameworks, there are still concerns that private woodland owners (PWOs; also known as family forest owners or non-industrial private landowners) are not adopting beneficial practices. Additionally, since tree canopies often buffer understory microclimates (i.e., fine scale variation in …

Interactions Between Streptococcus Agalactiae And Candida Albicans Affect Persistence And Virulence, Kathryn Patenaude

Electronic Theses and Dissertations

Streptococcus agalactiae (Group B Streptococcus or GBS), a Gram-positive bacterium, and Candida albicans, a polymorphic fungus, are commensal microbes in most of the population they colonize but are also capable of causing severe and sometimes fatal infections in certain patient groups. Both organisms share similarities including the colonization the same tissue environments and causing infections in specific patient groups including those who are newborn, pregnant, suffering from chronic conditions like diabetes and HIV, as well as elderly patients. Previous research discovered that GBS and C. albicans can synergize to enhance the colonization of GBS in the bladders of mice, but …

Habitat And Demography Of The Ozark Chinquapin (Castanea Ozarkensis) At Roaring River State Park In Barry County, Missouri, Danielle Evilsizor

Electronic Theses & Dissertations

The Ozark chinquapin, Castanea ozarkensis Ashe, is a chestnut tree with a range concentrated in the Interior Highlands of North America. Like other North American members of Castanea, it was reduced from an overstory tree to an understory shrub by the invasive chestnut blight fungus (Cryphonectria parasitica [Murrill] M.E. Barr) during the early 20^th century. However, relatively little is known about the habitat of this species or its health and reproductive capability post chestnut blight. Chapter one of this study analyzed the habitat of this species through a random forest species distribution model (SDM) to predict where …

Effects Of Sous-Vide Processing And Acidic Marination On Physicochemical Quality, Shelf-Life, And Consumer Acceptability Of Blue Mussel (Mytilus Edulis) Meats, Sara Gundermann

Electronic Theses and Dissertations

Sous-vide cooking is a thermal processing method in which a raw food is vacuum sealed in a pouch and then placed into water below 100°C for a controlled amount of time. It is particularly good for cooking meats because of its precise control over temperature and time, which results in an ideal food texture for consumers. This method also prevents the food from coming in contact with oxygen, which can lead to spoilage that reduces product quality and shelf life. Acidification is a food preservation method that utilizes acids to lower the pH of foods, making the environment less conducive …

On The Anti-Adipogenic Function Of Collagen Triple Helix Repeat-Containing Protein 1, Matthew E. Siviski

Electronic Theses and Dissertations

Adipogenesis is regulated by the coordinated activity of adipogenic transcription factors, including PPAR-gamma (PPARG) and C/EBP alpha (CEBPA). Thus, dysregulated adipogenesis predisposes adipose tissues to adipocyte hypertrophy and hyperplasia. We have previously reported that mice possessing a homozygous null gene mutation in collagen triple helix repeat-containing protein 1 (CTHRC1) have increased adiposity compared to wildtype mice, supporting the concept that CTHRC1 regulates body composition. Herein, we investigated the anti-adipogenic activity of CTHRC1. Using 3T3-L1 preadipocytes, we showed significantly reduced adipogenic differentiation in the presence of CTHRC1 commensurate to marked suppression of Cebpa and Pparg gene expression. In addition, CTHRC1 increased …

Unbridled Insights: Exploring Equine Behavior Through Gps Tracking And Analysis, Madison L. Philbrick

Electronic Theses and Dissertations

Horse behavior in pasture and grazing environments remains understudied, despite the substantial domestic horse population in the United States. This paper explores the utilization of Global Positioning System (GPS) technology to detect equine behavior, specifically focusing on grazing behaviors. By analyzing GPS data from (n=9) Standardbred horses, this study aims to establish the capabilities and accuracy of the Columbus P-1 data logger as a low-cost GPs unit for equine research, without the use of accelerometers. Through the data provided by the GPS unit, a model to distinguish grazing, resting, drinking, walking, trotting, and running was developed with satisfactory detection rates. …

Mobilizing Indigenous Research Methodologies And Wabanaki Knowledge In Biophysical Research To Restore Wabanaki Sweetgrass Harvesting In Acadia National Park And Identify Basket Quality Black Ash Habitat For Emerald Ash Borer (Agrilus Planipennis) Preparedness, Suzanne Greenlaw

Electronic Theses and Dissertations

Black ash (wikpiyik/Fraxinus nigra) and sweetgrass (suwitokolasol/Anthoxanthum nitens) are two culturally important species to Wabanaki (Passamaquoddy, Penobscot, Maliseet, Mi’kmaq, and Abenaki) people, and to many other Native American tribes across the species’ ranges. Wabanaki relationships with black ash and sweetgrass include creation stories, generational stewardship practices, important economic markets, and cultural identity. Land use patterns, changes in access, invasive species, and climate change are negatively affecting both the health of black ash and sweetgrass and Wabanaki people’s relationship to these species. This dissertation consists of five chapters that mobilize Wabanaki knowledge and address Wabanaki access to sweetgrass and an invasive …

Pseudomonas Aeruginosa Enhances Fluconazole Activity Against Candida During Polymicrobial Infection, Siham Hattab

Electronic Theses and Dissertations

Polymicrobial infections pose a significant challenge in the field of medicine due to our incomplete understanding of how pathogens interact during infection and how these interactions impact the effectiveness of drug treatments. Among the opportunistic pathogens, Candida albicans and Pseudomonas aeruginosa stand out, as they are often found in similar infection sites, such as burn wounds, the lungs of patients with cystic fibrosis and those on mechanical ventilation. Candida albicans is an opportunistic fungus responsible for invasive candidiasis, a condition associated with a high mortality rate of 40% in hospitals. Pseudomonas aeruginosa, on the other hand, is the primary pathogen …

Population Trends And Trophic Ecology Of The Invasive Peacock Eel (Macrognathus Siamensis) In The Florida Everglades, Grace Kahmann

Electronic Theses and Dissertations

Invasive species threaten the ecological integrity of ecosystems worldwide, including the Florida Coastal Everglades. This study investigated the ecological role of the peacock eel (Macrognathus siamensis) within this ecosystem, emphasizing its population trends and the environmental factors that affect its population performance, and the potential for interactions with native fish assemblages and coastal food webs. I used 19 years of electrofishing data to investigate the population trends of peacock eels at the marsh-mangrove ecotone of the Shark River Estuary, Everglades National Park (Florida, USA). I found that peacock eel populations have increased since their first detection in 2002, and their …

Investigating The Soil Mycobiome Of American Ginseng, Rachel Amelia Rajsp

Electronic Thesis and Dissertation Repository

American ginseng (Panax quinquefolius L.) is a perennial herbaceous plant cultivated for its medicinal properties. Growers report that when ginseng is replanted in a field previously used to cultivate ginseng, it soon succumbs to disease, known as ginseng replant disease. I examined changes in composition in the ginseng mycobiome throughout cultivation in a newly planted garden and beyond (i.e., 3–14 years post-harvest) with a third-generation metabarcoding approach (Pacific Biosciences, single-molecule real-time sequencing). Amplicons of about 600 nucleotides from the nuclear ribosomal internal transcribed spacer (ITS) region and translation elongation factor 1-α gene were chosen to help discriminate between closely …

Freezing Tolerance Of Herbaceous Legumes Within Southwestern Ontario: Evidence Of Disproportionate Freezing Sensitivity, Samuel L. Rycroft

Electronic Thesis and Dissertation Repository

Legumes (Fabaceae) represent a diverse and ecologically significant plant taxon; most described legumes form mutualisms with diazotrophic rhizobia, potentially fixing substantial quantities of nitrogen within habitats where they are well-established. Stressors causing lethal or sub-lethal impacts in legumes or rhizobial symbionts may therefore impact the nitrogen dynamics of such habitats. In recent decades, variability of winter temperatures, precipitation, and soil freeze-thaw cycling has increased in temperate regions. Without adequate snow cover to insulate roots and shoot bases, herbaceous plants will likely be exposed to more frequent or severe freezing. In southwestern Ontario, a pattern of disproportionate freezing sensitivity relative to …

Effect Of Timing Of Energy Intake On Blood Glucose And Body Composition In Women With Overweight Or Class One Obesity, Michael Wade Smith

Theses and Dissertations

Overweight and obesity has increased in the U.S. Unfortunately, this increases the risk of metabolic dysfunction, such as diabetes. Meal timing has recently shown promise as viable options to minimize the risk of overweight or obesity and metabolic dysfunction. The primary purpose of this study, therefore, was to investigate the effect of timing of energy intake on blood glucose in females with overweight or class one obesity (BMI=27-35 kg/m2). This study utilized crossover design with two conditions counterbalanced in random order. Participants completed two 2-week 1500kcal dietary interventions: 1) a big breakfast diet or BB (50% of energy intake between …

Status Survey Of Eight Rare Aquatic Macroinvertebrates In East Texas, Alexandra Randall

Biology Theses

Freshwater is essential to human existence. The health of each freshwater source is connected to the survival of pollution intolerant species of aquatic macroinvertebrates in the orders Ephemeroptera, Plecoptera, and Trichoptera (EPT taxa). A higher presence of EPT taxa equates to better water quality because their water bound larvae assist in maintaining clean freshwater environments and will not survive in highly polluted water. Human disruption to natural environments is causing increases in polluted freshwater, leading to decreases in the presence of EPT taxa. Texas Parks and Wildlife Department documentation shows major concern for the populations of eight EPT species of …