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Gene Expression Of Anthocyanin Pigments In The California Native Plant Leptosiphon Parviflorus: Interactions Between Flower Color Morphology And Abiotic Stressors, Weston Gonor

Master's Theses

For plants to survive in harsh conditions imposed by abiotic stressors, they must develop mechanisms of adaptation. One of the common types of adaptation seen in plants is the production of anthocyanin pigments, which have been shown to protect plants from UV radiation, metabolic stress, and drought. In this study, we used the flower color polymorphic species Leptosiphon parviflorus to investigate the role of anthocyanin pigments in protecting plants from abiotic stress. To accomplish this, RNA samples were taken from flower, leaf and root tissue of different flower color morphs of Leptosiphon parviflorus (Polemoniaceae) grown in high magnesium and water …

Alpine Plants And Climate Change: Tracking Community Shifts In Yosemite National, Brooke L. Wallasch

Master's Theses

As climate change progresses, alpine plant communities are predicted to shift upslope as they track temperature over time. Relative to lowland environments, alpine areas are experiencing a faster rate of temperature change due to a phenomenon referred to as elevation-dependent warming. A common approach for tracking plant communities shifts over time, is to conduct resurveys of the same area at several time points, as the Global Observational Research Initiative in Alpine Environments (GLORIA) has done on mountain summits around the world since 2001. In 2011-2013, GLORIA developed a supplemental survey method whereby belt transects were established downslope of summits in …

Identification And Characterization Of Peptide Responsive Histone Modification Genes During Root Nodule Symbiosis In Medicago Truncatula, Shivani Dharam

Tennessee State University Alumni Theses and Dissertations

Nitrogen (N) is an essential but limiting macronutrient for crop growth in agroecosystems. Biological Nitrogen Fixation (BNF) is a critical biological process where atmospheric Nitrogen is converted into ammonia by Nitrogen fixing the bacteria called rhizobia, forming mutualistic relationships with legume plants. These interactions are mediated by several signaling pathways and may involve epigenetic modifications like DNA methylations, histone modifications, where gene expression is altered without any change in DNA sequence. Histones are proteins provide structural support to DNA. However, genes encoding enzymes for these post translational modifications are poorly investigated in the Leguminosae family. This project aims to answer …

Understanding Performance And Egg Quality Parameters In A Pastured Egg-Type Poultry Breed, Biswajit Kumar Biswas

Tennessee State University Alumni Theses and Dissertations

This study investigated the effects of rearing systems on performance, egg quality, and ileal amino acid (AA) digestibility in laying hens (65 weeks of age). A total of 66 hens were distributed into two rearing systems: Cage (2 birds/replication, total 12 birds in 6 replications) and pasture (9 birds/replication, total 54 birds in 6 replications), and reared on three levels of energy diet (11.50 MJ/kg, 12.50 MJ/kg, and 13 MJ/kg). The birds were reared from d 1 to 14 (diet 1), d 15 to 28 (diet 2), and d 29-42 (diet 3). The average temperature, wind speed, and humidity were …

Root Exudates: The Rhizospheric Frontier For Advancing Sustainable Plant Protection, Muhammad Rahil Afzal, Misbah Naz, Youbo Yu, Lisha Yan, Peiyi Wang, Janaki Mohotti, Gefei Hao, Jing-Jiang Zhou, Zhou Chen, Libo Zhang, Qian Wang

Faculty Publications

Root exudates (REs), a diverse array of bioactive metabolites secreted by plant roots in response to environmental stimuli, serve as key mediators of rhizosphere ecology and plant defense responses, offering a promising avenue for sustainable pest management and eco-friendly plant protection. While earlier reviews primarily focus on root exudates in the context of general rhizosphere dynamics and plant-microbial interactions, critical knowledge gaps persist in REs-plant-pest tripartite interactions, the mechanistic basis of REs-mediated plant defense, and their practical integration with integrated pest management (IPM) frameworks. This review provides a synthesis of the latest literature on the biochemical diversity and functions of …

Fisheries Occasional Publication No. 149 - Economic Contribution Of Wild-Catch Fishing In Western Australia, 2024: Beyond Gross Value Of Production, Dipesh Maharjan, Vilaphonh Xayavong, Ben Fraser, Rebecca Thomas

Fisheries Occasional Publications

The wild-catch fishing industry plays a significant role in Western Australia’s economy, particularly in regional communities. This report summarises the economic contribution of the commercial wild-catch fishing sector in 2024, based on REMPLAN’s input-output (I-O) modelling methodology and DPIRD data and analysis. This report focuses on key economic indicators including total economic output, gross value added (GVA), and employment (FTEs).

Key findings:

• Total Economic Output of the wild-catch fishing industry is $1.22 billion (total value of goods and services produced, including intermediate inputs)
• Gross Value Added (GVA) of the wild-catch fishing industry is $487 million (value of profit, wages, salaries …

Comparative Analysis Of Vermicomposting Practices Utilizing Agroforestry Farm Materials, Theresa Nemesis P. Ocampo Maria, Armie Janica R. Pleto Ma., Reden D. Macalagay, Wilfredo O. Banasihan

The Philippine Agricultural Scientist

Vermicomposting is an effective and eco-friendly method of converting biodegradable materials into fertilizers that promote plant growth and development. This study aimed to assess the efficiency and quality of vermicompost and vermiworms produced using combinations of biodegradable farm materials in agroforestry systems. The materials used for the 6 treatments included combinations of the following materials: fresh leaves of leguminous plants (Gliricidia sepium, Flemingia macrophylla, and Senna spectabilis), fresh cattle manure, and other plant materials (rice straw and banana trunk). Using a 90:10 ratio of plant residues and cattle manure, respectively, a substrate of 100 kg was prepared for each treatment …

Comparison Of Gonad Development Between Wild And Hatchery-Bred Silver Therapon Leiopotherapon Plumbeus (Teleostei: Terapontidae) During An Annual Reproductive Cycle, Frolan A. Aya, Samantha Ally V. Bismonte, Mary Jane P. Sayco, Luis Maria B. Garcia

The Philippine Agricultural Scientist

This study compared gonad development between wild-sourced and hatchery-bred silver therapon Leiopotherapon plumbeus. Wild fish from the east bay area of Laguna de Bay, Philippines, and hatchery-bred stocks grown to adult size in outdoor tanks were sampled, and somatic condition, gonad histology, gonadosomatic index (GSI), gut index (GI), and hepatosomatic index (HSI) were assessed during the annual reproductive cycle. Hatcherybred fish condition was generally better than that of wild-sourced fish as a consequence of readily available food resources and environmental conditions. Hatchery-bred male GSIs were significantly higher than in wild male fish in November to February, coinciding with low water …

Evaluation Of Semen Characteristics And The Impact Of Storage Time In Dong Tao And Ho Indigenous Chickens, Phan Nhan, Nguyen Thi My Phuong

The Philippine Agricultural Scientist

This study aimed to evaluate the semen quality of 2 indigenous Vietnamese chicken breeds, Dong Tao and Ho, and to assess their reproductive potential for breeding and conservation programs. Semen samples were collected from 10 roosters of each breed and analyzed for macroscopic and microscopic traits. The results indicated that both breeds exhibited semen quality within acceptable physiological ranges. Mean semen volume was 0.47 mL in Dong Tao and 0.48 mL in Ho roosters; pH values were 7.47 and 7.42, respectively. Semen color scores (2.39 vs. 2.35), sperm concentrations (2.11 vs. 1.92 × 109/mL), and mass activity scores (3.79 vs. …

Summer Field Report, June–July 2025, W. Ross Silcock

Nebraska Bird Review

I have mentioned previously the breeding categories that are available to observers in eBird checklists. This database is becoming more comprehensive and useful, and I encourage observers to use this eBird feature.

Usefulness of Merlin-derived checklists continues to be an issue. As an example, Merlin seems to love White-winged Doves; there were 52 undocumented Merlin reports of this species this summer, no doubt some correctly identified and acceptable if observers had taken a minute to add even minimal observation details to support Merlin’s identifications.

A vexing issue for me is determining the status of midsummer (i.e. between spring and fall …

The Nebraska Bird Review (September 2025) 93(3), Whole Issue

Nebraska Bird Review

Summer Field Report, June–July 2025, by W. Ross Silcock

First Confirmed Nebraska Breeding Record of the Common Raven (Corvus corax) since the 19th Century, by Eugene A. Huryn and Jacob C. Cooper

2024 (36th) Report of the NOU Records Committee, by Mark A. Brogie

The Official List of the Birds of Nebraska: 2024, compiled by Mark A. Brogie

Subscription and Organization Information

2024 (36th) Report Of The Nou Records Committee, Mark A. Brogie

Nebraska Bird Review

The functions and methods of the Nebraska Ornithologists’ Union Records Committee (NOURC) are described in its bylaws (NOURC 2010). The committee’s purpose is to provide a procedure for documenting unusual bird sightings and to establish a list of all documented birds for Nebraska. Species for which the NOURC seeks documentation (NOURC Review List) can be found at the NOU website: www.NOUbirds.org.

Starting in 2020, the NOURC decided to deal mainly with those species deemed as Accidental on the “Official List of the Birds of Nebraska.” Casual species and out-of- range species are now summarized in the “Seasonal Reports” of 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 …

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 …

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 …

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 …

Detecting Sonic Hedgehog Expression In The Adult Mouse Brain Using A Gene Expression Tracer, Kendra Stephens-Jones

Dissertations, Theses, and Capstone Projects

Sonic Hedgehog (Shh) is best known for its role in development, yet evidence supports Shh signaling plays a functional role in the adult brain. Previous work demonstrated that Shh is expressed by dopamine (DA) neurons in the ventral midbrain and that loss of Shh from these neurons leads to late-onset motor and structural abnormalities resembling Parkinson’s disease. However, the extent of Shh expression and its connectivity to the striatum in the adult mouse brain remain unclear due to the lack of reliable antibodies for Shh detection. To address this gap, the present study employed Shh ^L/L and DAT-Cre^+/- mice …

Mechanisms Of Sleep Regulation In Drosophila Melanogaster, Anfal A. Abuhilal

Dissertations, Theses, and Capstone Projects

Sleep is a fundamental biological need, and sufficient sleep is required for physical and mental well-being. Sleep is regulated by two biological mechanisms: sleep-wake homeostasis and circadian rhythm. Circadian rhythms are near 24-h rhythms in behavior and physiology that are generated by endogenous mechanisms. In mammals, the suprachiasmatic nucleus (SCN) is the central circadian pacemaker, which is known to receive a significant amount of serotonergic input that likely modulates sleep rhythms. In addition to circadian modulation, sleep is subject to homeostatic regulation. Several neuromodulators have been proposed as mediators of sleep homeostasis. Serotonin has been implicated in sleep drive and …

Structural Characterization Of A Tarantula Toxin And Its Interactions With Lipid Bilayers And Voltage-Gated Sodium Channels, Krishnakoli Adhikary

Dissertations, Theses, and Capstone Projects

Voltage-gated ion channels are membrane protein complexes. They allow the selective flow of their respective ions down an electrochemical gradient through a central ion conduction pore surrounded by four voltage-sensing domains (VSDs). Various neurological and cardiovascular diseases are caused by mutations in voltage-gated ion channels (VGICs). One of the biggest challenges today is addiction to opioid medication. Coming up with non-opioid drug leads can be a real blessing for society. This is where voltage-gated sodium channel research comes in. Na_v1.7, Na_v1.8, and Na_v1.9 are responsible for pain sensations. Loss or gain of function in …

Cardiovascular And Aortic Wave Reflection Responses To Evening Binge Alcohol Consumption, Grant Thivierge, Ian Greenlund, Jeremy Bigalke, Carl Smoot, Jason R. Carter, John J. Durocher

Michigan Tech Publications

Evening binge alcohol consumption contributes to sleep disruption and autonomic dysregulation that persists into the following morning. However, its impact on morning-after arterial stiffness and aortic wave reflection remains unknown. Using a randomized, crossover, fluid-controlled design, we hypothesized that heart rate (HR), carotid-femoral pulse wave velocity (cfPWV), aortic augmentation index (AIx), and aortic pulsatile load (APL) would be increased acutely after binge drinking at night (study 1) and the morning-after binge drinking (study 2). Participants (n=33, 18 females, 15 males, age 25±1 years, BMI: 27±1 kg/m) completed binge alcohol (4-5 drink equivalent) and fluid control protocols. Study 1 examined cardiovascular …

Assessment Of Microbial Quality And Safety, Including Aflatoxin B1, In Buckwheat Flour And Groats, La Fontaine Bahatsi

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Buckwheat (Fagopyrum esculentum), a gluten-free pseudocereal, has gained popularity in global food markets for its nutritional value and functional properties. However, despite its health-promoting potential, buckwheat is vulnerable to microbial contamination and mycotoxin accumulation during cultivation, processing, and storage. These factors present significant food safety concerns that remain understudied, particularly in North America.

This study investigated the microbiological quality and mycotoxin contamination of buckwheat flour and groats collected from different suppliers via online sourcing. Samples were collected in two consecutive years (2024-2025). Microbiological quality, including aerobic plate counts (APC), Enterobacteriaceae, coliforms, E. coli, yeasts, and molds, was evaluated …

Tetrigidae Of Ethiopia: First Species Delimitation Via Dna Barcoding And Description Of Three New Species †, Tarekegn Fite, Hendrik Devriese, Dustin Kulanek, Josip Skejo, Niko Kasalo, Manaye Misganaw, Tadele Tefera, Jandouwe Villinger, Martin Husemann

All Peer-Reviewed Publications

Tetrigidae is a caeliferan family of Orthoptera constituting a diverse and relatively ancient lineage of small Orthopterans, which has its greatest diversity in tropical and subtropical areas. However, to date, few studies have been conducted on the identification and description of Tetrigidae species in Ethiopia, and even fewer molecular data are available. Hence, we performed the first species delimitation study via DNA barcoding of species belonging to the genera Paratettix, Leptacrydium, Dasyleurotettix, and Morphopoides from Ethiopia. We provide 35 new sequences of the COI gene belonging to six species of these genera. We show that Ethiopian Tetrigidae can be successfully …

Helminth And Malaria Co-Infection Among Pregnant Women In Battor And Adidome Towns Of The Volta Region Of Ghana, Navneet Kaur, William K. Anyan, Abraham K. Anang, Nilanjan Lodh

Clinical Lab Sciences Faculty Research and Publications

Aim: In sub-Saharan Africa, approximately 40 million pregnant women are exposed to parasitic diseases such as malaria caused by Plasmodium falciparum, Schistosome parasites, and soil-transmitted helminths (STHs). When parasitic diseases share the same habitat and overlap in distribution, then high co-infection rates occur. The co-infection can lead to consequences for the child, such as intrauterine growth retardation, low birth weight, pre-term delivery, and neonatal mortality.

Methods: The objective of the study was to determine the nature and extent of coinfection from 100 samples collected from the Battor (50) and Adidome (50) towns of Ghana in collaboration with the Noguchi …

Resource Assessment Report No. 4: North Coast Demersal Scalefish Resource - Kimberley 2025 Assessment, Fabian Trinnie, Rubie Evans-Powell, Ainslie Denham, Sybrand A. Hesp, Corey Wakefield, Craig L. Skepper, Brett Crisafulli, Stephen J. Newman

Resource Assessment Reports

The North Coast Demersal Scalefish Resource (NCDSR) comprises ecological suites of tropical demersal fish species that occur predominantly in inshore waters (20–250 m deep) and offshore waters ( > 250 m deep) of the North Coast Bioregion (NCB). More than 60 demersal species are landed by fisheries operating in the Kimberley and Pilbara regions of the NCB each year, including high-value snappers (Lutjanidae), groupers (Epinephelidae), and emperors (Lethrinidae). As outlined in the NCDSR Harvest Strategy (DPIRD, 2017), the Kimberley resource is currently monitored through annual reviews of total removals and catch rate trends of indicator species, as well as periodic (every …

Impact Of Varied Dietary Macronutrient Ratios On The Nutrition Status Of Swiss Albino Mice, Hellen Kinyi, Charles Kato, Gertrude Kiwanuka

Biomedical Sciences, East Africa

The nutrition status of an organism depends on the balance between nutrient intake and utilization. Malnutrition results not only from inadequate caloric intake but also from imbalanced macronutrient ratios, which can affect aging, metabolism, and health. While many studies focus on individual nutrients, this study used purified, isocaloric diets with varying macronutrient ratios to assess dietary effects on nutrition markers in Swiss albino mice.

Mice were randomized into 6 dietary groups, each containing 6 males and 6 females housed separately. Each group received an isocaloric diet with different carbohydrate, protein, and lipid ratios for 15 weeks. Animal weight, body mass …

The Role Of Liver Macrophages In Viral Liver Pathogenesis, Alexis Brantly, Kyle Yeakle, Michael J. Bouchard, Peter J. Gaskill, Michael R. Nonnemacher

Kimmel Cancer Center Faculty Papers

Liver macrophages play important roles in the pathophysiology of liver fibrosis and hepatocellular carcinoma. However, liver macrophages are a heterogenous population and have differing roles in maintenance of liver function and response in disease. In a healthy liver, macrophages play a critical role in antigen processing, maintaining tolerance to the high levels of gut-derived bacterial products, and regulating inflammation through cytokine response. However, macrophages also play a critical role in liver pathology, specifically in the context of viral infection. The liver is targeted by multiple viruses, including human immunodeficiency virus, hepatitis B virus, and hepatitis C virus, which dysregulate macrophage …

A Co-Design Approach To Integrating Gender Into The Cacao Value Chain In Davao City, Philippines, Mia Barbara Aranas, Aileen Lapitan, Mitchiko Lopez, Nico Jayson Anastacio, Canesio Predo, Mara Faylon, Emmanuel Flores, Claire Estelle Cruz, Anjelyn Joy Enong

The Philippine Agricultural Scientist

The specific needs and challenges of women and their contributions are often not integrated when developing interventions and policies targeted to improve agricultural value chains. Therefore, this study developed a codesign approach to creating solutions to improve gender relations in agri-food value chains. Specifically, it focused on the cacao value chain in Davao City, which is located in the southern Philippines. Co-design is a highly participatory approach in which solutions are designed with, and not just for, the people who have lived experiences of the problems being addressed. The approach emphasizes understanding gender-related barriers and opportunities to inform government interventions …

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 …