Life Sciences Commons^™

Variation In Bat Activity Across Upland Embedded Wetlands In The Cumberland Ranger District Of The Daniel Boone National Forest, Brittany Ryan

Online Theses and Dissertations

Within the Daniel Boone National Forest (DBNF) in Kentucky, over 800 upland-embedded wetlands (UEWs) have been constructed in past decades to provide habitat for bats and other wildlife. This research focused on identifying differences in bat activity and occupancy across natural and constructed UEWs. Acoustic detectors were deployed at 9 natural and 31 constructed UEWs across the Cumberland Ranger District of the DBNF. Each UEW was surveyed across 3 intervals from May – August 2022, and each recording session spanned >3 consecutive nights, yielding a total of 413 detector nights. Occupancy modeling and AIC model selection were used to evaluate …

Software Jimenae Allows Efficient Dynamic Simulations Of Boolean Networks, Centrality And System State Analysis, Martin Kaltdorf, Tim Breitenbach, Stefan Karl, Maximilian Fuchs, David Komla Kessie, Eric Psota, Martina Prelog, Edita Sarukhanyan, Regina Ebert, Franz Jakob, Gudrun Dandekar, Muhammad Naseem, Chunguang Liang, Thomas Dandekar

All Works

The signal modelling framework JimenaE simulates dynamically Boolean networks. In contrast to SQUAD, there is systematic and not just heuristic calculation of all system states. These specific features are not present in CellNetAnalyzer and BoolNet. JimenaE is an expert extension of Jimena, with new optimized code, network conversion into different formats, rapid convergence both for system state calculation as well as for all three network centralities. It allows higher accuracy in determining network states and allows to dissect networks and identification of network control type and amount for each protein with high accuracy. Biological examples demonstrate this: (i) High plasticity …

Climate Change And The Shifting Geography Of Coral-Reef Development, Victor Rodriguez-Ruano

Theses and Dissertations

Coral-reef development is modulated by growth processes that deposit calcium carbonate onto the reef, such as calcification, and destructive processes that remove calcium carbonate from the reef, such as bioerosion. Wherever calcification rates exceed bioerosion rates, there is a net accretion of the reef through time, but where bioerosion rates exceed calcification rates, there is a net destruction of the reef through time. A reef’s framework is the legacy of the interaction of these processes throughout a reef’s history. Studying the fossil frameworks of reefs can shed light on the environmental factors that have controlled reef development in the past, …

Expanding Recognition And Inclusion Of Animal-Free Organic Agriculture In The Sustainable Agriculture Movement, Mona Seymour

Urban and Environmental Studies Faculty Works

Animal-free organic agriculture resides at the margins of sustainable agriculture discourse, practice, and imaginaries, which center animal-based forms of farming. However, the concerns and goals of sustainable agriculture are overwhelmingly consistent with those of many forms of animal-free organic agriculture (AFOA), described as organic farming sans animal production, labor, and byproducts. Despite this sidelining, AFOA has great potential to contribute to a more robust sustainable agriculture movement. In order to emphasize the continuities between animal-based and animal-free sustainable agriculture, this Perspective identifies a number of key similarities between animal-free and animal-based sustainable farming, including mutual foci on soil health and …

Overexpression Of Ubtf Correlates With Aggressive Phenotypes Of Prostate Cancer Cells, Guillermo Andres Saldana

Theses and Dissertations

Prostate cancer (PrCa) is one of the most common malignancies in men globally and the second leading cause of cancer associated deaths in developed countries. Accumulating evidence have demonstrated involvement of various molecular and cellular factors in the development, progression and chemoresistance of PrCa and many of them were successfully established as potential molecular targets for therapy. Despite these advancements, the underlying mechanisms of PrCa occurrence is still unclear, which limits the diagnosis and therapy. Therefore, it is an urgent need to discover potential molecular targets which can be used in rational design of new strategies for the prevention and …

Aedes Aegypti Host Preference On Canines Versus Human Volatile Skin Compounds, Melissa Bernadette Rosalez

Theses and Dissertations

It is critical to understand how Aedes aegypti mosquitoes detect hosts through cues such as volatile skin compounds. In South Texas, evidence suggests that this mosquito is showing a feeding preference for canines over humans. This shift may impact the transmission of Dirofilaria immitis, canine heart worms, in local dog populations. Our study is set to explore Ae. Aegypti attraction to hosts using canine and human volatile compounds. Volatile skin compounds will be collected using a volatile collection system. Compounds will be analyzed using gas chromatography/mass spectrometry. It is anticipated that the main volatile skin compounds amongst humans are nonanal, …

Growth Rates, Morphology, And Potential For Mariculture Of The Southern Population Of Crassostrea Virginica In The Lower Laguna Madre, Texas, Jerad Lee Fuelling

Theses and Dissertations

The Eastern Oyster also known as Crassostrea virginica, is an important resource here in the United States. Historically, this species has been overfished, poorly managed, and plagued by disease. Oyster mariculture is a growing industry here in the United States and is a sustainable solution to producing oysters. Texas has become the last coastal state to legalize oyster mariculture which means there is now a vast coastline with many unique bay systems that are open to this industry. One bay system that is particularly unique is the Lower Laguna Madre which is a hypersaline lagoon. Little is known about …

Effects Of Short-Term Pesticides Exposure On Swimming Behavior, Tissue Morphology, Oxidative-Nitrative Stress, Antioxidant Expression, And Cellular Apoptosis In Kidneys Of Goldfish, Esmirna Cantú

Theses and Dissertations

The prevalence of pesticides in the aquatic environment continues to increase due to anthropogenic activities and poses a threat to aquatic organisms. The aim of this study was to determine the short-term exposure (one-week) of pesticide mixtures (metolachlor, linuron, isoproturon, tebucanazole, alconifen, atrazine, pendimethalin; azinphos-methyl) on swimming behaviors, kidney morphology, and expression of nitrotyrosine protein (NTP), dinitrophenyl protein (DNP), superoxide dismutase (SOD), catalase (CAT), renin, and cellular apoptosis in goldfish (Carassius auratus). Results indicated that both low- and high-dose pesticide mixtures decreased the distance swimming behavior. Histological analysis showed pesticide exposure alters kidney morphology. DNP, NTP, and renin expressions, and …

Synthesis Of Bacterial Glycerophospholipids For Biomembrane Model Studies: A Means To Advanced Biofuels, Felix Adulley

Electronic Theses and Dissertations

To reduce reliance on fossil fuels, sustainable biofuels are being pursued, especially advanced biofuels like 1-butanol that have higher energy content and greater compatibility with existing infrastructure than ethanol. A persistent challenge is the yield-limiting toxicity of biofuels and process solvents, such as tetrahydrofuran, to the microbes that ferment biomass into biofuel. The cell membrane is a focal point of toxicity, and understanding how it interacts with fuels and solvents is key to improving yield. Phospholipid bilayers are the core of biomembranes, and model biomembranes of defined composition provide the ideal platform for biophysical studies. To this end, glycerophospholipids characteristic …

Intestinal Microbiome, Fecal Fermentation Profile, And Health Indices In Hiv Infected Men Versus Non-Infected Controls, Mary Andreae, Mary C. Andreae Mrs

Electronic Theses and Dissertations

Many HIV-positive (HIV+) males on Highly Active Anti-Retroviral Therapy (HAART) experience metabolic abnormalities, including Non-Alcoholic Fatty Liver Disease (NAFLD) and lipodystrophy. The intestinal microbiota and short chain fatty acids (SCFA), participate in bidirectional communication with their host. Dysbiosis in HIV+ males on HAART demonstrate a Prevotella-rich enterotype shaped by multiple factors including, medications, adiposity, diet, intestinal permeability, and lifestyle; our objective was to investigate these factors. 19 HIV+ and 21 HIV- males were enrolled. BMI and hip-to-waist ratio (H:W) were obtained, and FibroScan for liver health. Intestinal permeability markers Claudin-21, flagellin, and intestinal fatty acid binding protein (IFABP) in …

Adoption And Continued Use Of Irrigation Management Practices In Arkansas, Evelyn Osei

Graduate Theses and Dissertations

The paper assesses row crop producers continued use of irrigation management practices, namely the decision to continue rather than stop the use of irrigation practices, using a probit with a sample selection model. To better explain and increase user acceptance, we must understand why producers adopt and continue using irrigation management practices. Past studies have researched the adoption of management practices. However, it is also essential to consider what factors influence continued use and why producers discontinue irrigation practices after adoption. This is the first study to investigate factors influencing the continued use of irrigation management practices in Arkansas. Producers …

Flavonol Glucosylation: A Structural Investigation Of The Flavonol Specific 3-O Glucosyltransferase Cp3gt, Aaron S. Birchfield

Electronic Theses and Dissertations

Flavonoid glycosyltransferases (GTs), enzymes integral to plant ecological responses and human pharmacology, necessitate rigorous structural elucidation to decipher their mechanistic function and substrate specificity, particularly given their role in the biotransformation of diverse pharmacological agents and natural products. This investigation delved into a comprehensive exploration of the flavonol 3-O GT from Citrus paradisi (Cp3GT), scrutinizing the impact of a c-terminal c-myc/6x histidine tag on its enzymatic activity and substrate specificity, and successfully achieving its purification to apparent homogeneity. This established a strong foundation for potential future crystallographic and other structure/function analyses. Through the strategic implementation of site-directed mutagenesis, a thrombin …

Elucidation Of The Role Of Avocado Wri1 And Wri2 And Their Ability To Affect Oil Content And Composition When Co-Expressed With Pdat1 And Dgat1, Jyoti Ranjan Behera

Electronic Theses and Dissertations

Plants synthesize and store oil, mostly as triacylglycerols (TAG), in seeds that is transcriptionally controlled by WRINKLED1 (WRI1), an APETALA2 (AP2) transcription factor. Among the four Arabidopsis WRI paralogs, WRI2 is nonfunctional, while the others are expressed in a tissue-specific manner. Additionally, two rate-limiting enzymes, diacylglycerol acyltransferase (DGAT) and phospholipid diacylglycerol acyltransferase (PDAT) catalyze the terminal step in TAG assembly and contribute to oil accumulation. Avocado (Persea americana) mesocarp, a non-seed tissue, accumulates significant amounts of TAG (~70% by dry weight) enriched with heart-healthy oleic acid. The oil accumulation stages in mesocarp coincide with the high expression of …

Cyclin D1 Extensively Reprograms Metabolism To Support Biosynthetic Pathways In Hepatocytes, Heng Wu, Betsy T. Kren, Andrew N. Lane, Teresa A. Cassel, Richard M. Higashi, Teresa Whei-Mei Fan, George S. Scaria, Laurie L. Shekels, Mark A. Klein, Jeffrey H. Albrecht

Markey Cancer Center Faculty Publications

Cell proliferation requires metabolic reprogramming to accommodate biosynthesis of new cell components, and similar alterations occur in cancer cells. However, the mechanisms linking the cell cycle machinery to metabolism are not well defined. Cyclin D1, along with its main partner cyclindependent kinase 4 (Cdk4), is a pivotal cell cycle regulator and driver oncogene that is overexpressed in many cancers. Here, we examine hepatocyte proliferation to define novel effects of cyclin D1 on biosynthetic metabolism. Metabolomic studies reveal that cyclin D1 broadly promotes biosynthetic pathways including glycolysis, the pentose phosphate pathway, and the purine and pyrimidine nucleotide synthesis in hepatocytes. Proteomic …

Immunization With The Amino-Terminus Region Of Dense Granule Protein 6 (Gra6) Of Toxoplasma Gondii Activates Cd8+ Cytotoxic T Cells Capable Of Removing Tissue Cysts Of The Parasite Through Antigen Presentation By Human Hla-A2.1, Rajesh Mani, Corinne Mercier, Marie-France Delauw, Yasuhiro Suzuki

Markey Cancer Center Faculty Publications

CD8þ T cells from HLA-A2.1-transgenic mice, but not wild-type mice, immunized with the amino- terminus region (aa 41e152) of dense granule protein 6 (GRA6Nt) of Toxoplasma gondii secreted large amounts of perforin and granzyme B in response to GRA6Nt through antigen presentation by HLA-A2.1 in vitro. When those CD8þ T cells were transferred into chronically infected HLA-A2.1-expressing NSG mice deficient in T cells, cerebral cyst burden of the recipients of HLA-A2.1-transgenic T cells, but not of WT T cells, became significantly less than that of control mice with no cell transfer. Furthermore, the significant reduction of the cyst burden by …

Md_Harmonize: A Python Package For Atom-Level Harmonization Of Public Metabolic Databases, Huan Jin, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

A major challenge to integrating public metabolic resources is the use of different nomenclatures by individual databases. This paper presents md_harmonize, an open-source Python package for harmonizing compounds and metabolic reactions across various metabolic databases. The md_harmonize package utilizes a neighborhood-specific graph coloring method for generating a unique identifier for each compound via atom identifiers based on a compound’s chemical structure. The resulting harmonized compounds and reactions can be used for various downstream analyses, including the construction of atom-resolved metabolic networks and models for metabolic flux analysis. Parts of the md_harmonize package have been optimized using a variety of computational …

Design And Characterization Of A Novel Eef2k Degrader With Potent Therapeutic Efficacy Against Triple-Negative Breast Cancer, Changxin Zhong, Rongfeng Zhu, Ting Jiang, Sheng Tian, Xiaobao Zhao, Xiaoya Wan, Shilong Jiang, Zonglin Chen, Rong Gong, Linhao He, Jin-Ming Yang, Na Ye, Yan Cheng

Markey Cancer Center Faculty Publications

Dysregulated eEF2K expression is implicated in the pathogenesis of many human cancers, including triple-negative breast cancer (TNBC), making it a plausible therapeutic target. However, specific eEF2K inhibitors with potent anti-cancer activity have not been available so far. Targeted protein degradation has emerged as a new strategy for drug discovery. In this study, a novel small molecule chemical is designed and synthesized, named as compound C1, which shows potent activity in degrading eEF2K. C1 selectively binds to F8, L10, R144, C146, E229, and Y236 of the eEF2K protein and promotes its proteasomal degradation by increasing the interaction between eEF2K and the …

Cerebrospinal Fluid Biomarkers Not Associated With Neurologic Compromise Among Mild Cognitively Impaired Reverters With Parkinson's Disease, Cameron Ryczek

Electronic Theses, Projects, and Dissertations

Parkinson's Disease (PD) is a neurodegenerative disease characterized by motor (e.g. tremors) and non-motor symptoms (e.g. cognitive impairment). PD patients' change in cognitive functioning can be observed using the following classifications: cognitively intact, mild cognitive impairment (MCI), or dementia (PDD). MCI has many subtypes, one of which is MCI reversion which is defined as those with MCI at one time point reverting to cognitively intact later. While there is limited research into the utility of MCI reversion and its relationship with cerebrospinal fluid (CSF) biomarkers in PD, this study will begin to elucidate this relationship. To this end, data from …

Effect Of Macrophage Expressed Α7 Nicotinic Acetylcholine Receptor (Α7nachr) On Migration Of Macrophages During Inflammation, Kasey Keever

Electronic Theses and Dissertations

Sepsis is a life-threatening condition characterized by overwhelming inflammation, resulting in organ system damage, leading to a high mortality rate. Care in the clinical setting is supportive, and there are no approved sepsis-specific treatments. In septic mice, activation of the cholinergic anti-inflammatory pathway decreases cytokine secretion by leukocytes and improves survival. The cholinergic anti-inflammatory pathway is a reflex of the parasympathetic nervous system, converging on the α7 nicotinic acetylcholine (α7nAChR) at the surface of macrophages. Signaling through the receptor blocks NF-kB activation, thus cytokine secretion. Receptor activation has other effects on macrophages, including modulating their migration to …

Aicropcam: Deploying Classification, Segmentation, Detection, And Counting Deep-Learning Models For Crop Monitoring On The Edge, Nipuna Chamara, Geng (Frank) Bai, Yufeng Ge

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Precision Agriculture (PA) promises to meet the future demands for food, feed, fiber, and fuel while keeping their production sustainable and environmentally friendly. PA relies heavily on sensing technologies to inform site-specific decision supports for planting, irrigation, fertilization, spraying, and harvesting. Traditional point-based sensors enjoy small data sizes but are limited in their capacity to measure plant and canopy parameters. On the other hand, imaging sensors can be powerful in measuring a wide range of these parameters, especially when coupled with Artificial Intelligence. The challenge, however, is the lack of computing, electric power, and connectivity infrastructure in agricultural fields, preventing …

Analysis Of Mitochondrial Dna Sequence Data Demonstrates That Monophyly Of Myotis Occultus Is Complicated By Greater Sampling Of Myotis Lucifugus, Jeffrey M. Lorch, Daniel R. Taylor, Antoinette J. Piaggio

United States Department of Agriculture Wildlife Services: Staff Publications

Abstract

The validity of Myotis occultus as a species unique from Myotis lucifugus has been a source of debate. Most recently, many authorities treat M. occultus as a distinct species, at least in part because a previous study showed that M. occultus and M. l. carissima (the subspecies that occurs in closest geographic proximity to M. occultus) form separate monophyletic clades based on sequences of two mitochondrial genes (cytochrome-b [cytb] and cytochrome oxidase subunit II [COII]). We re-evaluated the phylogenetic relationship between M. occultus and M. lucifugus based on mitochondrial sequences …

Diet Induced Metabolic Alterations In The Brain Tissues Of Juvenile Pigs With Non-Alcoholic Fatty Liver Disease, Rhesa Lacanienta

Master's Theses

The objective of this study was to investigate the diet-induced metabolic changes that affect the brain tissue of juvenile pigs with NAFLD. This study explored the liver- brain axis and metabolic markers in the frontal cortex (FC) affected by liver damage. 18 male (M) and 20 female (F) Iberian pigs were randomly allocated to 1 of 3 high-fructose high-fat liquid diets (lard, olive oil, and coconut oil) and fed for 10 consecutive weeks. “Healthy” Iberian pigs were fed a eucaloric diet to establish a physiological baseline. Protein precipitation extraction using ultra-performance liquid chromatography-tandem quadrupole mass spectrometry was performed for primary …

First Draft Genome Of Thecaphora Frezii, Causal Agent Of Peanut Smut Disease, Renee S. Arias, Cinthia Conforto, Valerie A. Orner, Edgardo J. Carloni, Juan H. Soave, Alicia N. Massa, Marshall C. Lamb, Nelson Bernardi-Lima, Alejandro M. Rago

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Objectives: The fungal pathogen Thecaphora frezii Carranza & Lindquist causes peanut smut, a severe disease currently endemic in Argentina. To study the ecology of T. frezii and to understand the mechanisms of smut resistance in peanut plants, it is crucial to know the genetics of this pathogen. The objective of this work was to isolate the pathogen and generate the first draft genome of T. frezii that will be the basis for analyzing its potential genetic diversity and its interaction with peanut cultivars. Our research group is working to identify peanut germplasm with smut resistance and to understand the genetics …

Volunteers’ Stewardship Action-Taking Experiences During The Covid-19 Pandemic Predicted By Their Motivation Toward Engagement And Ability To Teach Others, Suzanna R. Windon, Olga Buchko, Linda Falcone

Journal of Human Sciences and Extension

The current study investigates the relationship between volunteer stewardship action-taking, motivation toward engagement in volunteer activities, and the ability to teach others during the COVID-19 pandemic. The final data set included 1,196 responses from the Penn State Extension Master Gardeners and Master Watershed volunteers, which provided a response rate of 39.9%. The results of this study showed that approximately 15.1% of the variation in volunteer stewardship action-taking experiences could be explained by volunteers’ motivation toward engagement in volunteer activities and their ability to teach others. Most findings are in line with previous research. Extension and outreach educators and volunteer coordinators …

Examining College Students’ Attitudes Toward Poverty During The Adult Role Of The Community Action Poverty Simulation, Jessica M. Parks, Portia Johnson, Diann C. Moorman, Sheri Worthy, Leigh Anne Aaron

Journal of Human Sciences and Extension

Family and Consumer Sciences (FCS) and Extension professionals need to understand the lived experience of poverty because it affects every aspect of an individual’s life. Poverty is related to inadequate nutrition and food insecurity, lack of access to health care, insufficient child care, unsafe neighborhoods, lack of affordable housing, under-resourced schools, and a lower quality of life. Attitudes toward poverty vary widely among Americans and can be categorized as either internal/individual attributions (e.g., laziness, welfare dependency, etc.) or systemic/structural attributions (e.g., unemployment, inflation, etc.). Individuals holding internal attributions toward poverty are more likely to have negative feelings toward impoverished individuals. …

Full Issue, Volume 11, Number 3, Donna J. Peterson, Scott Cummings

Journal of Human Sciences and Extension

No abstract provided.

A Study Of The Snd1/Prmt5 Axis In Liver Cancer By Genetic Mouse Models, Tanner Wright, Tanner Wright

Dissertations and Theses (Open Access)

Arginine methylation is an essential post-translational modification (PTM) in cells. Protein arginine methyltransferase 5 (PRMT5) is the primary enzyme that catalyzes symmetric dimethyl arginine (SDMA) and requires methylosome protein 50 (MEP50) for stability and enzymatic activity which are necessary for life and development. Effector proteins bind different types of PTM’s to facilitate signaling. Staphylococcal nuclease Tudor domain containing 1 (SND1) is an effector that specifically binds SDMA via its single C-terminal Tudor domain. Both SND1 and PRMT5 have been implicated in hepatocellular carcinoma (HCC). SND1 has been confirmed as a driver of HCC using genetically engineered mouse models (GEMMs), though, …

Re: Incidence Of Sars-Cov-2 Breakthrough Infections After Vaccination In Adults: A Population-Based Survey Through 1 March 2023, Stacia M Desantis, Ashraf Yaseen, Tianyao Hao, Luis León-Novelo, Yashar Talebi, Melissa A Valerio-Shewmaker, Cesar L Pinzon Gomez, Sarah E Messiah, Harold W Kohl, Steven H Kelder, Jessica A Ross, Lindsay N Padilla, Mark Silberman, Samantha Wylie, David Lakey, Jennifer A Shuford, Stephen J Pont, Eric Boerwinkle, Michael D Swartz

Faculty, Staff and Student Publications

No abstract provided.

Development Of Novel Methods To Study Host-Microbe Interactions In The Larval Zebrafish Gastrointestinal Tract, Anh K. Trinh Nguyen

Dissertations and Theses (Open Access)

The dynamic nature and inaccessible location of the intestine pose significant challenges to the study of intestinal physiology and pathology. Zebrafish larvae, possessing optical transparency and genetic tractability, offer an accessible and clinically relevant model for investigating dynamic events in the intestine via time-lapse imaging. In the first part of this work, I discuss our efforts to optimize the parameters of a foodborne infection assay using paramecia as a vehicle. This method provides an effective, high-throughput alternative to infection via immersion or oral gavage, and replicates the most common route of transmission of gastrointestinal (GI) infection in humans. The foodborne …

Deciphering The Role Of Huntingtin In Endosomal Functions, Yue Yu

Dissertations and Theses (Open Access)

Huntington's disease (HD), a neurodegenerative disorder, is a result of an abnormal expansion of CAG trinucleotide repeat encoding an extended polyglutamine (polyQ) tract in the coding region of Huntingtin (HTT) gene. While antisense oligonucleotide (ASO) strategies aimed at lowering mutant HTT levels seemed promising, recent clinical trials were unsuccessful due to worsening patient outcomes in the ASO treatment group compared to the placebo. This may be attributed to potential adverse effects resulting from decreased levels of normal HTT, which could play a pivotal role in brain functions and HD progression. The impact of reduced HTT levels on cellular functions and …