Life Sciences Commons^™

Single Nuclei Transcriptomics Reveals Cellular Diversity In Tsc Subependymal Giant Cell Astrocytomas, Jennie C. Holmberg, Vijay Shankar, Rachel A. Lyman, Trudy F.C. Mackay, David M. Feliciano

Publications

Tuberous sclerosis complex (TSC) is a genetic disorder characterized by benign growths called hamartomas that are a significant cause of morbidity and mortality. Hamartomas are found along the neurocutaneous axis including along the brain’s ventricles near the boundaries of the striatum. They can be categorized by size and include small subependymal nodules (SENs) or larger subependymal giant cell astrocytomas (SEGAs). Here, we describe a quantitative analysis of SEGA cell identities based on single nuclei RNA sequencing. SEGAs contain several cell types. In contrast to unaffected samples, SEGAs have pronounced vasculature, more endothelial cells, increased perivascular macrophages, less myelination, and altered …

Enhancing Preparedness: A Genetic Study Of Sar-Cov-2 And Other Microbial Public Health Threats In Wastewater From A College Town, Christian N. Hutchinson

Master's Theses

Problem

The SARS-CoV-2 (COVID-19) pandemic revealed both the systemic vulnerabilities of our healthcare system as well as the importance of timely, localized data for informing public health responses. Traditional testing approaches were essential but often failed to capture the full extent of viral spread, especially in those with mild or asymptomatic conditions that relied on at home testing. This underreporting hindered effective allocation of resources and made developing effective intervention strategies difficult. We also realized the potential for wastewater surveillance to be applied to tracking antimicrobial resistance gene markers. Taken together, this approach should have important implications for improving public …

Miscanthus × Giganteus Increases Soil Maximum Water Holding Capacity Compared To Maize, Jessica T. Nelson, Maoz Dor, Andy D. Vanloocke, Jacob E. Studt, Perla K. Schrock, Marshall D. Mcdaniel

School of Earth, Environmental, & Marine Sciences Faculty Publications

Soil ecosystem services, like the ability to store water, have been depleted after a century of conventional, annual cropping, and perennial crops offer a solution to this and other agricultural environmental issues. We assessed the impact of Miscanthus × giganteus (miscanthus), a perennial biomass crop, on soil water holding capacity and structure compared to continuous maize (Zea mays L.) at two sites in Iowa. After three growing seasons, we measured the following: (1) maximum water holding capacity (MWHC) with and without soil structure, and (2) total porosity and pore size distribution (PSD) via micro-computed tomography (microCT). Miscanthus increased MWHC …

Crispr-Cas9 Gene Editing In Tomato: Development And Characterization Under Stress, Jun Guo

Tennessee State University Alumni Theses and Dissertations

Transcription factor (TF) families played essential roles in plant responses to abiotic stress, contributing significantly to stress tolerance and adaptation. The basic helix-loop-helix (bHLH) TF family included 161 members in tomato (Solanum lycopersicum). Previous proteomic analysis identified TF bHLH148 (Solyc01g058670) as being upregulated under aluminum (Al) stress, suggesting a potential role in Al tolerance. To investigate this, CRISPR-Cas9 was used to generate SlbHLH148 knockout mutants in the ‘Black Vernissage’ tomato cultivar. Two homozygous T2 lines, Slbhlh148-1 and Slbhlh148-2, were confirmed to contain frameshift mutations that resulted in truncated proteins lacking the bHLH_AtIBH1_like domain, as shown by protein modeling. Phenotypic evaluation …

Dietary Modulation Of Obesity-Specific Gut Microbial Signatures And Their Functional Roles, Anjula Swathi Sagam

Tennessee State University Alumni Theses and Dissertations

Obesity remains a major global health concern, contributing significantly to chronic diseases. While diet is a well-known driver of obesity, emerging evidence suggests the key role of gut microbiota in mediating diet-related metabolic outcomes. Numerous epidemiological and microbiome studies suggested diet-microbiome-obesity associations. However, consistent microbial markers and mechanistic insights remain limited. To address this gap, this study aimed to identify consistent microbial species associated with obesity and investigate how diet influences their growth and function. A review of over 200 publicly available 16S rRNA and shotgun metagenomic studies revealed consistent microbial patterns in obesity, including members of Firmicutes and Bacteroidetes. …

Effects Of Straw Return On Crop Yield, Soil Organic Carbon And Greenhouse Gas Emissions, Maazeera Fatima

Tennessee State University Alumni Theses and Dissertations

Global crop residue production was substantial, at approximately 3758 × 106 mg annually. The practice of straw return, was found to enhance soil organic matter content, increase crop yield, and mitigate soil greenhouse gas emissions. However, individual studies showed inconsistent results. While meta-analyses synthesized multiple individual studies and provided overall effects of straw return, but their conclusions were varied. We evaluated meta-analyses on the effects of straw return on crop yield, soil organic carbon, and greenhouse gas emissions and proposed a grand mean response ratio to estimate an overall effect and the impacts of different properties. The result showed that …

Genetic Profiling Of Tennessee Johnsongrass And Pigweed Accessions Per Weedicide Resistance And Agronomic Traits, Gouse Mohiddin Shaik

Tennessee State University Alumni Theses and Dissertations

Herbicide-resistant weeds pose an escalating threat to crop productivity in Tennessee, leading to notable economic losses and complicated conventional weed control strategies. Among the most persistent species, Sorghum halepense (Johnsongrass) and various Amaranthus species (pigweeds) have exhibited remarkable adaptability and increasing resistance to widely used herbicides. Addressing this growing issue necessitates a thorough understanding the genetic and biochemical mechanisms that drive herbicide resistance. This study conducted an extensive genetic analysis of Pigweed and Johnsongrass samples collected from a broad range of counties across Tennessee, ensuring representation from both the northern and southern portions of the state’s Eastern, Central, and Western …

Heat Stress On Germinating Tomato Pollen And The Molecular Mechanisms For Heat Response Using Single Cell Type Proteomics, Dibya Thapa Magar

Tennessee State University Alumni Theses and Dissertations

The primary objective of this study is to develop the technical workflow for collecting homogenous germinating pollen samples. Two tomato varieties, Black Vernissage (BV) and Micro Tom (MT), were grown in temperature-controlled plastic greenhouses. For the non-heated control conditions, greenhouse temperature was set at 25C/21oC (16/8 hours; day/night). For the heat-treated greenhouse, temperature was set at 32/25 oC (16/8 hours; day/night). Supplemental light was provided using plant growth LED light. Ten freshly opened flowers were collected and pollen were released into 2ml pollen germination medium (PGM) in 5-ml centrifuge tubes. After centrifugation, pollen pellets were washed three times in 2 …

Opportunities And Impacts For Recreational Fishing From The Westport Development: Final Report, Matt Navarro, Michael Burton, Abbie Rogers, Joanna Pearce, Julian Clifton, Milena Kim, Clara Obregón

Reports accepted as research outputs

Executive summary: This project employs a mixed methods approach to evaluate the significance of Cockburn Sound for recreational fishers, examine the potential effects of the proposed port development on recreational fishing experiences, and understand fishers' preferences for initiatives to improve recreational fishing in Cockburn Sound. Initial qualitative interviews with six local recreational fishing stakeholders were conducted to establish an early understanding of the primary issues and contextual factors with respect to opportunities and impacts of the proposed Westport development. These were followed by on-site surveys at boat ramps and shore access points across Cockburn Sound and the surrounding region. In …

Fisheries Science Update - West Coast Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Science Updates

The Department of Primary Industries and Regional Development (DPIRD) monitors the status of Western Australia’s demersal scalefish resources by undertaking regular stock assessments on indicator species.

This summary provides key outcomes of the 2025 assessment of the West Coast Demersal Scalefish Resource (Resource Assessment Report No. 2).

Fisheries Science Update - Gascoyne Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Science Updates

The Department of Primary Industries and Regional Development (DPIRD) monitors the status of Western Australia’s demersal scalefish resources by undertaking periodic stock assessments on key indicator species.

This summary provides key outcomes of the 2024 Gascoyne Demersal Scalefish Resource Stock Assessment (Resource Assessment Report No. 3).

Shallow Coastal Bays As Sediment Carbon And Nutrient Reservoirs In The Baltic Sea, Betty Gubri, Joakim P. Hansen, Sofia A. Wikström, Martin Snickars, Martin Dahl, Martin Gullström, Emil Rydin, Pere Masqué, Andrius Garbaras, Mats Björk, Christoffer Boström

Research outputs 2022 to 2026

Coastal vegetated ecosystems are being increasingly recognized for their capacity to capture carbon, provide long-term biogenic storage, and alleviate nutrient pollution. To assess the ability of shallow, vegetated coastal bays to function as blue carbon and nutrient (nitrogen and phosphorus) sinks, we collected sediment cores in nine shallow enclosed bays (representative of the EU Habitats 1153 and 1154) in the archipelago areas of Sweden (Stockholm), Åland Island, and southwestern Finland. Our study showed strong uniformity of carbon and nutrient storage, substantial accumulation of carbon and nutrients, and minimal regional differences in carbon, nitrogen, and phosphorus sediment stocks. These findings are …

Evaluation Of Tracheal And Cecal Microbial Composition In Heat Stressed Broilers Supplemented With Phytogenic Additives, Andressa Silveira Stein

Graduate Theses and Dissertations

The rise in global temperatures has become a concern due to its significant impact on the agricultural sector, including poultry production. Heat stress caused by high temperatures directly affects animal welfare, health and productivity, leading to major losses in the poultry sector. In broilers, heat stress affects feed consumption, weight gain, mortality and may also lead to changes in the microbiome, which can increase the predisposition to disease and impact the overall performance of these animals. The aim of this thesis was to reproduce field conditions, simulating an increase in temperature, and to evaluate possible changes in the respiratory and …

Understanding Glufosinate Resistance In Palmer Amaranth And Examination Of Additives For Improved Weed Control, Pamela Carvalho-Moore

Graduate Theses and Dissertations

The aim of this dissertation was to: 1) provide an in-depth review about the potential use of natural and synthetic glutathione S-transferase (GST) inhibitors to enhance herbicidal activity or induce crop safety; 2) determine if the addition of metabolic inhibitors to glufosinate is an effective approach to enhance weed control; 3) investigate the mechanism conferring resistance to glufosinate in a highly-resistant Palmer amaranth accession; 4) characterize the genomic rearrangement involved in glutamine synthetase 2 amplification in a Palmer amaranth accession resistant to both glufosinate and glyphosate; 5) quantify the distribution of glufosinate resistance among Palmer amaranth accessions within a 15-km …

Spatial Distribution Of Microsporidia Mb Along Clinal Gradient And The Impact Of Its Infection On Pyrethroid Resistance In Anopheles Gambiae S.L. Mosquitoes From Nigeria And Niger Republic, Lamine M. Moustapha, Muhammad M. Mukhtar, Abdoul Nasser H. Sanda, Shuaibu Adamu, Yusuf Y. Aliyu, Hadizat K. Einoi, Maryam U. Maigari, Peter C. Okeke, David E. Nwele, Abiodun Obembe, Udoka C. Nwangwu, Jeremy K. Herren, Sulaiman S. Ibrahim

All Peer-Reviewed Publications

Microsporidia MB (MB), a promising biological control agent, suppresses Plasmodium falciparum transmission in Anopheles mosquitoes. This study examined the spatial distribution of MB infection in natural populations of An. gambiae s.l. mosquitoes collected in Nigeria and Niger Republic, and its association with insecticide susceptibility in the mosquitoes. Microsporidia MB has wide geographic distribution across Nigeria and Niger Republic. The overall prevalence of MB in F0 mosquitoes was 12.25% (95% CI: 7.76–16.75%); 25 mosquitoes out of 204 were positive. Geographic variation was observed, with a higher prevalence (5/15 mosquitoes) in Ebonyi State (33.33%, CI: 9.48–57.19%, Fisher’s exact test, p = 0.008). …

An Integrated Skeletal Muscle Methylome-Transcriptome Profile In Pre-Clinical Colorectal Cancer Cachexia Models And Chemotherapy Aggravating The Effects Of Cachexia, Ana Regina Cabrera Ayuso

Graduate Theses and Dissertations

Cancer cachexia is a wasting syndrome characterized by the loss of skeletal muscle affecting cancer patients’ independence and quality of life. Cancer cachexia affects up to 80% of cancer patients and is responsible for 30-40% of cancer-related deaths. Previous studies have demonstrated sex-specific differences in the onset and progression of cancer cachexia; however, these differences remain underexplored. To date, pharmacological and nutritional interventions are largely ineffective in preventing or reversing cachexia. Chemotherapy, a first-line cancer treatment, is known to trigger cachexia by itself complicating prognosis and therapy response. In addition, epigenetic alterations, such as DNA methylation (DNAm), are known to …

Impact Of Retail Display Case On Shelf-Life, Palatability, And Color-Stability Of Fresh Beef Steaks, Stephanie Elizabeth Shimer

Graduate Theses and Dissertations

The objective of the study was to determine: the impact of two retail display cases, three beef muscles, and three packaging schemes on palatability traits, flavor development, lipid oxidation, objective and subjective evaluation of color stability, and microbial shelf-life. No muscle × package × case × day interactions were observed for any instrumental or panelist color evaluation (P > 0.851). No retail case effect was observed for TBARS, consumer sensory evaluation, or cook loss (P >0.05). A muscle × case × package interaction was observed for L* and b* (P< 0.05). No muscle × case × package observations were observed for shelf-life or palatability analyses (P > 0.05). No significant two-way or three-way interactions were observed for evaluation …

Investigation Of Motor Neuronal And Circuit Level Mechanistic Determinants Of Spinal Excitability Following Cst Injury, Thelma Bethea

Dissertations, Theses, and Capstone Projects

The corticospinal tract (CST) is the primary descending motor pathway in mammals, essential for precise, dexterous movements, especially in humans and nonhuman primates. Damage to the CST, such as from spinal cord injury (SCI), impairs skilled motor function and triggers maladaptive changes including aberrant proprioceptive afferent sprouting and increased spinal excitability. These changes are closely linked to both muscle weakness and the development of hyperreflexia, compounding the functional deficits. Animal models of SCI are valuable for investigating mechanisms of injury and recovery, though traditional models often limit the ability to isolate circuit-specific contributions. To address this, I employed selective unilateral …

The Evolution And Reproduction Of Andean Miconia (Melastomataceae), Juan Angulo

Dissertations, Theses, and Capstone Projects

Understanding the factors that shape diversification and distribution in tropical plant lineages is central to explaining the origins of Neotropical biodiversity. Assessing evolutionary history with trait evolution and climatic niche dynamics provides key insights into the drivers of diversification and biogeography, while natural history data remains critical for these evolutionary studies. The Tropical Andes, with its exceptional biodiversity and environmental heterogeneity, offers an ideal setting to explore these processes. In this dissertation, I investigate how reproductive systems, climatic niche dynamics, and pollination strategies influence the evolution and biogeography of Miconia III, a large and ecologically diverse clade in the …

Systematics, Biogeography, And Comparative Morphology Of Emerald And Tigertail Dragonflies (Anisoptera: Synthemistidae & Corduliidae), Aaron M. Goodman

Dissertations, Theses, and Capstone Projects

Dragonflies and damselflies (Odonata Fabricius, 1793) are among the most widely recognized and charismatic insect groups, whose significance have permeated throughout artwork, culture, and religion. They are highly mobile predators, currently consisting of ~ 6,500 species, and possessing some of the complex visual color systems, visual acuity, and flight patterns on Earth. Odonata are the among the earliest flying insects, with proto-odonates (Griffinflies) dating back to the Carboniferous (~360mya), with crown-odonata fossils stretching back to the Triassic (~250mya). Overall, dragonflies and damselflies are considered models of ecological and evolutionary research due to their long evolutionary history, range of habitats, and …

From Sequence To Allostery: How Amino Acid Differences Rewire Coupled Conformational Heterogeneity In The Ptp Enzyme Family, Shivani Sharma

Dissertations, Theses, and Capstone Projects

Protein Tyrosine Phosphatases (PTPs) are critical regulators of cellular signaling, and their activity is often modulated through allosteric mechanisms. Allostery is defined as a chemical or conformational change in one site of the protein due to a binding event at another site. Although several studies have investigated aspects of allostery in PTPs, the mechanistic foundations underlying allosteric regulation remain poorly understood. Despite a highly conserved catalytic domain across PTPs, regions with low or no conservation suggest potential "rewiring" of allosteric networks. This raises key questions about the universality versus individuality of allosteric mechanisms across the PTP family.

In this work, …

Potential Role Of A Ruthenium-Based Compound Ru-Im In The Treatment Of Triple Negative Breast Cancer, Rachele Rameau

Dissertations, Theses, and Capstone Projects

Triple negative breast cancer (TNBC) is an aggressive and heterogeneous molecular subtype of breast cancer that has limited available treatments. The organometallic cationic ruthenium derivative Ru-IM was found to be highly water soluble, was differentially toxic for breast cancer cells and tumors, and was involved in the pI3K/AKT/mTOR pathway. However, a full understanding of genetic and epigenetic factors that can be part of regulatory mechanisms of Ru-IM is yet to be determined. Epigenetic assays including DNA methylation, histone acetylation and histone deacetylation were performed with the half inhibitory concentration (IC50) values of Ru-IM. Bisulfite sequencing of untreated and treated MDA-MB-231 …

Ai-Powered Multi-Omics Integration For Predictive Modeling Of Genotype-Environment-Phenotype Relationships, You Wu

Dissertations, Theses, and Capstone Projects

This dissertation presents a series of machine learning frameworks for modeling genotype–environment–phenotype relationships through integrative predictive modeling of multi-omics data. The work addresses three major axes of biological complexity: modeling biological information transmission cross-levels from genes to proteins to phenotypes, predicting molecular features cross-scale from cells to tissues to organisms, and translating phenotypes cross-species from model systems to humans. Each proposed method also tackles key machine learning (ML) challenges in the biomedical domain, including data scarcity, domain shift, out-of-distribution (OOD) generalization, and hierarchical modeling. Specifically, this dissertation introduces five novel deep learning algorithms: MultiDCP predicts drug-induced transcriptomic and viability responses …

Retinal Precursor Cell Enriched Multiomic And Pseudo-Time Analysis Of Developing And Reprogrammed Photoreceptors, Brendon M. Patierno

Dissertations, Theses, and Capstone Projects

The vertebrate retina is a complex tissue made up of seven major cell subtypes which during development must differentiate and localize into a highly organized structure. These neuronal cells do not regenerate if damaged or diseased, and the progressive deterioration of cone photoreceptor cells is the leading cause of age related blindness. Currently there are no cures for this disease, but one promising therapeutic avenue is cell transplantation research. If we can further elucidate the gene regulatory networks that define cone cell development, this knowledge could be applied to the generation of healthy cone cells in clinically relevant models.

The …

Origin And Maintenance Of The Andean Bird Fauna, Elkin A. Tenorio

Dissertations, Theses, and Capstone Projects

The origin and maintenance of the tropical montane diversity have been evaluated over multiple decades using various techniques and perspectives. Despite major progress in understanding phylogenetic relationships, diversification patterns, distributional data, and general ecology in the Andean biota, large gaps in our understanding remain, particularly in the synthesis across scales. To fill these gaps, I aimed to explore patterns and processes that underlie species diversification in birds of the tropical Andes of South America by combining different approaches using phenotypic, phylogenetic, and genomic data in multiple temporal and spatial scales.

In the first chapter, I examined the macroevolutionary patterns of …

The Sonic Hedgehog Effector Smoothened Modulates Cholinergic Interneuron Activity, Physiology, And Striatum-Dependent Behaviors, Santiago Uribe-Cano

Dissertations, Theses, and Capstone Projects

The striatum is a central node in action selection and associative learning, integrating cortical, thalamic, and neuromodulatory input. Among its principal modulators, dopamine (DA) and acetylcholine (ACh) are known for their temporally coordinated yet mechanistically distinct influences on striatal output. However, the upstream signals that regulate their dynamic interplay, particularly within cholinergic interneurons (CINs)—the primary source of striatal ACh—remain incompletely characterized. This dissertation investigates the role of Smoothened (Smo), a G protein-coupled receptor (GPCR) effector of Sonic Hedgehog (Shh) signaling, in modulating ACh signaling dynamics in the striatum.

Building on evidence that midbrain DA neurons co-release Shh and that CINs …

Non-Linear Heart Rate Variability: Investigating Cardiac Complexity Of Psychopathic Traits, Khaya A. Roach

Dissertations, Theses, and Capstone Projects

Psychopathy is a complex personality disorder characterized by distinct emotional and interpersonal deficits, and affects approximately 25% of the prison population and 4.5% of nonincarcerated populations. The manifestation of psychopathy can be understood through two distinct variants, each demonstrating unique etiological pathways and clinical presentations. Primary psychopathy is characterized by core interpersonal and affective deficits, including shallow emotions and manipulativeness, while demonstrating reduced autonomic responsivity and lower anxiety levels. Secondary psychopathy presents with higher levels of impulsivity, anxiety, and emotional dysregulation, showing stronger associations with various psychopathologies. Treatment outcomes also vary between the variants, with primary psychopaths typically showing poor …

Bmp Signaling Co-Regulation Of Immune Response And Lipid Metabolism, Katerina K. Yamamoto

Dissertations, Theses, and Capstone Projects

The Bone Morphogenetic Proteins (BMPs) are secreted peptide ligands of the Transforming Growth Factor beta (TGF-β) family, initially identified for their roles in development and differentiation across animal species. They are now increasingly recognized for their roles in physiology and infectious disease. In the nematode Caenorhabditis elegans, the BMP ligand DBL-1 controls fat metabolism and immune response, in addition to its roles in body size regulation and development. DBL-1 regulates classical aspects of innate immunity, including the induction of anti-microbial peptides. We theorized that BMP-dependent regulation of fat metabolism could also promote resilience against microbial pathogens. We found that …

Investigating The Role Of Early Growth Response 1 (Egr1) Gene In Riluzole-Induced Apoptosis In Osteosarcoma, Syeda Maryam Azeem

Dissertations, Theses, and Capstone Projects

Osteosarcoma is a rare but aggressive bone malignancy most commonly affecting adolescents and young adults (AYA). With 5-year survival rate stagnating over the last four decades despite the advancements in multi-modal therapy, drug repurposing offers a rapid path to new osteosarcoma treatments. Recent studies suggest that Riluzole, a drug approved for amyotrophic lateral sclerosis (ALS), may be repurposed for osteosarcoma treatment due to its ability to slow tumor progression and induce apoptosis. Previously, we have shown that Riluzole increases reactive oxygen species (ROS), activating c-Abl, which phosphorylates YAP in the nucleus. YAP then forms a complex with p73 to enhance …

Inhibition Of Return And Attentional Blink: Aspects Of A Singular Attentional Process?, Kathleen Rowe

Dissertations, Theses, and Capstone Projects

Inhibition of Return (IOR) and Attentional Blink (AB) are two distinctly defined phenomena that display some intriguingly similar properties. They both describe suppression effects following a visual stimulus that has captured attention, both may be preceded by an enhancement, and both share partially overlapping effect time windows which can be manipulated by task difficulty. The current study attempted to measure the two phenomena simultaneously to test our hypothesis that behavioral indices of AB and IOR will display significant spatial and temporal overlap, suggesting the two phenomena may reflect, at least in part, different aspects of a singular attentional process. To …