Life Sciences Commons^™

Impact Of Unconventional Gas Extraction On Tributaries Of Tenmile Creek, Greene County, Pennsylvania: A 12-Year Perspective, Christian L. Beall

Electronic Theses and Dissertations

Much of southwestern Pennsylvania has been central to a rapid increase in development for unconventional natural gas extraction in the past two decades. The continued monitoring of streams over their lifetime as extraction sites is pivotal to understanding the effects of fracking on local waterways and their ability to provide for wildlife and human use. Here, using multiple indices of biotic integrity (IBI), I perform analyses of fish and macroinvertebrate communities as well as water chemistry on two streams, Bates Fork (with shale wells) and Fonner Run (without), as part of a follow-up to work performed there from 2010-2012. Fish …

Impaired Dnajb2 Response To Heat Shock In Fibroblasts From A Neuropathy Patient With Dnajb2/Hsj1 Mutation: Cystamine As A Potential Therapeutic Intervention, Raj K. Pradhan, Nikolas G. Kinney, Brigid K. Jensen, Hristelina Ilieva

Farber Institute for Neuroscience Faculty Papers

Background and Objectives: Neuropathy is a debilitating disorder characterized by peripheral nerve dysfunction and damage to sensory, motor, and autonomic neurons and their axons. While homozygous mutations in DNAJB2/HSJ1 have been linked to early-onset neuropathy, a heterozygous DNAJB2 c.823+6C>T was discovered in an adult patient with severe sensory–motor polyneuropathy. This mutation is predicted to affect both isoforms of the protein. DNAJB2 (HSP40), a key member of the heat shock protein family, plays a critical role in cellular protection and stress, including response to heat shock. DNAJB2 traffics unfolded proteins to another heat shock protein, HSP70, and activates its ATPase …

Earthworms, Slugs, And Salamanders: Community Interactions In A Massachusetts Forest, Emmalee Bent

Honors Program Theses and Projects

Earthworms (Order: Opisthopora) have several important ecological interactions with eastern red-backed salamanders (Plethodon cinereus). For the salamanders, earthworms can be nutrient-rich, easy-to-digest prey, or ecosystem engineers of burrows. Indirectly, earthworms can be competition for other microinvertebrate prey species that salamanders prefer to eat. Red-backed salamanders are thought to be a critical player in forest food-webs and possible ecosystem indicator, as they are highly abundant, mid-level consumers that are very sensitive to their abiotic environment. These factors make understanding the interactions between earthworms and salamanders valuable for broader understanding of forest communities. To better understand the earthworm community present at a …

Sustainable Process Valorization For Bioactives From Invasive Plants Environmental Burden And Their Efficacy As Antimicrobial Agents, Shamprasad Br

Theses and Dissertations

Agri-food industries produce large quantities of fruit waste which are usually discarded and one such major beverage juice waste is Citrus waste. Likewise, invasive plants like Prosopis juliflora, which is richly distributed across Tamil Nadu, are underutilized for secondary metabolites/bioactives isolation. Halophytes are another rich source of bioactives present around mangrove forests and distributed in the salt rich marshy land.

1. Separation of phenylpropanoids from the Citrus waste through solvent extraction and pH-assisted precipitation was developed. The PPCM precipitated (phenylpropanoids form Citrus medica) were analysed by HPTLC and were found to contain Rutin, Naringin, Quercetin-3-beta-glycoside, Chlorogenic acid, Ferulic acid and optimization …

Biomarkers That Could Explain Parasite-Induced Behavioral Alterations In The Golden Shiner (Notemigonus Crysoleucas) – Posthodiplostomum System, Laura D. Nicolas

All HCAS Student Capstones, Theses, and Dissertations

Trophically transmitted parasites require an intermediate host to be consumed and often manipulate host phenotype (i.e., morphology, physiology, and/or behavior) to increase predation risk by definitive hosts. Posthodiplostomum is a trematode with a complex life cycle involving snails as first hosts, fish as second intermediate hosts, and piscivorous birds as definitive hosts. In fish hosts, Posthodiplostomum infection has been linked to increased predation, suggesting suppression of antipredator behaviors. However, the specific physiological pathways remained unexplored and changes in the host’s neural, endocrine, and immune systems could be involved. Thus, I examined whether Posthodiplostomum infection intensity was associated with brain serotonin …

Effects Of Foam Rolling With And Without Vibration On Contralateral Limb Range Of Motion And Jump Performance, Lawton P. Hawkins

Honors Theses

Recently, foam rolling with vibration (VFR) has gained popularity with having similar benefits to standard foam rolling (FR). VFR may induce a greater improvement in pain pressure threshold, which could lead to a greater improvement in range of motion (ROM). When applied to one limb, improvements in ROM occur in the non-rolled limb for both FR and VFR. Studies comparing the effects of FR and VFR in terms of acute changes in ROM and performance have reported mixed results. Using a larger dosage of VFR may provide a greater improvement in ROM for the non-rolled limb compared to FR. PURPOSE: …

Understanding Temporal Changes In Leaf Traits Of Native Smilax Rotundifolia And Invasive Lonicera Japonica Using Long-Term Herbarium Records From Kentucky, Claudia Ebbecke, Claudia Ebbecke

Honors College Theses

Herbarium specimens are the most valuable, verifiable, and sustainable records to study the impacts of climate change on natural ecosystems. Temporal herbarium data can provide critical information on how species respond to changes in habitat conditions by tracking changes in species’ morphological and phenological traits. This study aims to use Japanese honeysuckle (Lonicera japonica) and common greenbrier (Smilax rotundifolia) to assess the impact of climate change on invasive and native plants. Leaf traits, such as leaf size and stomatal density are good indicators of plant’s adaptation to the changing environment. By examining changes in leaf traits …

Household Point-Of-Use Faucet Filters For Lead Removal: Field Performance And User Experiences, Jeannie M. Purchase, Chantaly Villalona, Adrienne Katner, Kelsey Pieper, Marc Edwards

School of Public Health Faculty Publications

Lead certified point of use (POU) faucet filters were field tested in two Louisiana cities in a total of 21 occupied homes during normal use and in two unoccupied homes with very high risk of water lead (Pb) contamination. In an unoccupied home with a 28 m lead service line (LSL) with average lead of 17 μg/L in flushed water, treatment by POU filters generally produced water with < 5 μg/L Pb even when tested to 200% of rated capacity. In the unoccupied home with a disturbed LSL, the water had erratic influent particulate lead of 9-3053 μg/L, and the POUs did not consistently produce water with < 10 μg/L Pb despite very high percentage removals. When testing POUs in occupied homes known to occasionally have lead over 5 μg/L, POUs always reduced lead to < 1 μg/L. In addition, POUs were also effectively removing high levels of iron and manganese present in the water of one city, but this also caused clogging before reaching half of their rated capacity. Laboratory experiments confirmed POU susceptibility to iron clogging.

Developing Novel Radical Protein Footprinting Methods For Application In Living Systems, Lyle Tobin

Honors Theses

Radical protein footprinting (RPF) is a family of structural biology techniques that generate radicals in situ to label solvent-accessible amino acid residues. Coupled with liquid chromatography/mass spectrometry, RPF enables the characterization of protein higher order structure and sites of protein-protein and protein-ligand interactions. While traditionally performed in vitro, recent advancements have extended RPF to ex vivo and in vivo applications, including intact cells, nematodes, and 3D cell cultures. RPF in living systems allows the structural analysis of proteins and protein complexes in their native environment, preserving physiological interactions, dynamic conformational changes, and structural contexts that might otherwise be lost …

A Qualitative Evaluation Of Diabetes Solutions Telehealth Coaching Services, Caroline Brock

Honors Theses

Diabetes remains a growing public health concern, particularly in underserved regions such as rural Mississippi, where barriers to healthcare access and diabetes education contribute to poor disease management. This qualitative study explores the lived experiences of 27 participants enrolled in Diabetes Solutions, a telehealth-based diabetes self-management education and support (DSMES/T) program offered by the Mississippi Diabetes Network. Using a phenomenological approach and structured interviews, the study identifies four major themes: structural benefits of the program, knowledge gained, common changes by participants, and quality of life outcomes. Participants consistently emphasized the value of personalized coaching, emotional encouragement, and practical education on …

Behavioral And Neural Microstructures Of Dynamic Cue-Motivated Responses, Erica Townsend

Dartmouth College Ph.D Dissertations

Sign-tracking, a conditioned response in which animals are physically attracted to reward-predictive cues due to motivational value attribution, is known to be persistent but can be flexible under some circumstances. For example, during an omission paradigm, in which vigorous responses must be withheld to avoid reward cancellation, animals can quickly restructure their responses. However, sign-tracking does not cease entirely, and cue attraction persists. This dissertation explores the behavioral and neural mechanisms underlying the simultaneous persistence and flexibility of sign-tracking during omission procedures. First, a novel method for behavioral analysis is introduced to accurately depict sign-tracking animals in dynamic tasks such …

Student Perceptions Of Supports And Barriers For Transferring Quantitative Reasoning In Introductory Biology Lab Courses, Joelle Prate, Jeremy L. Hsu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Quantitative reasoning is a critical skill in biology and has been highlighted as a core competency by Vision and Change. Despite its importance, students often struggle to apply mathematical skills in new contexts in biology, a process called transfer of knowledge. However, the supports and barriers that students perceive for this process remain unclear. To explore this further, we interviewed undergraduate students in an introductory biology lab course about how they understand and report the transfer of quantitative skills in these courses. We then applied these themes to the Step Back, Translate, and Extend (SBTE) framework to examine student …

Ligand-Activated Egfr/Mapk Signaling But Not Pi3k, Are Key Resistance Mechanisms To Egfr-Therapy In Colorectal Cancer, Xueping Qu, Habib Hamidi, Radia M Johnson, Ethan S Sokol, Eva Lin, Cathy Eng, Tae Won Kim, Johanna Bendell, Smruthy Sivakumar, Benjamin Kaplan, Felipe De Sousa E Melo, Andrew Mancini, Matthew Wongchenko, Yi Shi, David Shames, Yibing Yan, Fortunato Ciardiello, Carlos Bais

Faculty, Staff and Student Publications

Understanding mechanisms of resistance to active therapies is crucial for developing more effective treatments. Here, we investigate resistance to anti-EGFR and anti-VEGF plus chemotherapy treatment in colorectal cancer (CRC) patients from the IMblaze370 trial (NCT02788279). While anti-VEGF does not select for secondary mutations, anti-EGFR leads to simultaneous mutations in EGFR and MAPK, but not PI3K pathway genes. Notably, we observe frequent acquired mutations in the EGFR extracellular but not intracellular domain and that patients with higher baseline expression of EGFR-ligands are prone to acquire resistant mutations. This data reveals a ligand-activated EGFR/MAPK-signaling dependency in CRC. We also observe enrichment for …

Mesoderm-Specific Transcript Has A Role In The Systemic Regulation Of Obesity, Maria J. Orellana Rosales

Thinking Matters Symposium

Mesoderm specific transcript (Mest) expression in white adipose tissue (WAT) is variable in genetically identical mice. Previous studies have shown a connection between Mest high expression and propensity for fat mass expansion. WAT and liver crosstalk has been well documented with hormone-like peptides signaling and regulating important metabolic pathways. The aim of this study is to investigate the correlation between these circulating factors and Mest expression in mice after exposure to a high fat diet (HFD). A group of 120 C57B6/J mice, males and females, were exposed to a HFD (Western Diet, 40 kcal% fat) for 4 weeks (8-12 weeks …

Comparative Three-Barcode Phylogenetics And Soil Microbiomes Of Planted And Wild Strawberry Trees., Flannery Mclamb, Armando Vazquez, Natalie Olander, Miguel F. Vasquez, Zuying Feng, Niharika Malhotra, Liisa Bozinovic, Karen Najera Ruiz, Katherine O'Connell, Joseph Stagg, Goran Bozinovic

Center for Life in Extreme Environments Publications

Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild plants across a large geographic range, we complemented three standard plastid barcodes , , and with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry …

Associations Of Muscular And Cardiovascular Fitness Variables With Cardiovascular Disease In Older Adult Athlete Populations, Lauren T. Zick

Honors Thesis

This data analysis examined associations between cardiovascular and muscular fitness indicators and the presence of cardiovascular disease (CVD) in older adult athletes. Using cross-sectional data from 1,110 participants aged 50 and older who completed the Sustained Athlete Fitness Exam (SAFE) at state-level Senior Games events, we evaluated both objective performance metrics and self-reported exercise behaviors. Cardiovascular measures included systolic blood pressure (SBP), waist circumference (WC), waist-to-hip ratio (WHR), and body mass index (BMI). Muscular fitness was assessed through grip strength, maximum walking speed, and chair stand time. CVD status was defined as the presence of two or more self-reported cardiovascular …

Sirt6 Deficiency Promotes Senescence And Age-Associated Intervertebral Disc Degeneration In Mice, Pranay Ramteke, Bahiyah Watson, Mallory Toci, Victoria Tran, Shira N Johnston, Maria Tsingas, Ruteja Barve, Ramkrishna Mitra, Richard Loeser, John Collins, Makarand Risbud

Department of Orthopaedic Surgery Faculty Papers

Intervertebral disc degeneration is a major risk factor contributing to chronic low back and neck pain. While the etiological factors for disc degeneration vary, age is still one of the most important risk factors. Recent studies have shown the promising role of SIRT6 in mammalian aging and skeletal tissue health, however its role in the intervertebral disc health remains unexplored. We investigated the contribution of SIRT6 to disc health by studying the age-dependent spinal phenotype of mice with conditional deletion of Sirt6 in the disc (Acan^CreERT2; Sirt6^fl/fl). Histological studies showed a degenerative phenotype in knockout mice …

Genomic Characterization Of Novel Bacteriophage: Bellis, Emmanauel Z. Gibbs

Honors Theses

Phages are the most abundant life-forms on the planet. Due to their unique ability to infect and lyse specific bacterial strains, phages have been proposed as a potential therapeutic agent to fight antibiotic resistance bacterial infections. Consequently, more research is required to further our understanding of phages. We were provided with an isolated, novel Mycobacterium bacteriophage: Bellis. Utilizing a bioinformatic approach, we successfully annotated Bellis’ genome using a variety of computer programs like GeneMark, Glimmer, HHpred, and PECAAN. We discovered that Bellis has 122 genes, including a RecB-like endonuclease and an AAA-ATPase, as well as 10 tRNAs. Through the genomic …

Genome Annotation Of Stargaze, Madison R. Murray

Honors Theses

Bacteriophages are viruses which solely infect bacteria. They are one of the most abundant and diverse biological entities, yet there is a limited amount of information on these viruses, including their gene functions. Several previously unknown phages have been discovered including Stargaze, whose bacterial host is Mycobacterium Smegmatis. Characterization of phage genes and their functions deepen our understanding of phages and potentially contribute to the broader biomedical effort associated with phages ability to combat bacterial infections. Stargaze is a G5 subcluster phage and it only has one other related phage in its cluster, that phage is from Madagascar. Using a …

Microplastics In Brachyurans: Comparing Contents Of The Atlantic Ghost Crab, Ocypode Quadrata, And Their Surrounding Sediments, Michael See

Honors Theses

The emergence of microplastics as a threat to physiological and environmental health has led to an increase in studies in recent years that aim to identify and quantify potential risks to marine ecosystems. Ocypode quadrata is a species that is a critical component of coastal ecology, leading this study to collect and analyze specimens regarding microplastics and their presence as a pollutant to the marine environment. Samples were collected from beaches along the Grand Strand of South Carolina. Microplastic density and diversity were recorded from investigating fecal pellets from the captive crab specimens to examine microplastic abundance. In addition to …

Depalmitoylation Regulates Metabolism And Mitochondrial Function, Sarah Lilly Speck

Arts & Sciences Graduate Student Theses and Dissertations

Tens of millions of Americans suffer from metabolic disorders, predisposing patients to cardiovascular disease, kidney disease, liver disease, infertility, and cancer. Unfortunately, the etiology of many of these diseases remains a mystery, limiting our ability to identify targets for pharmacologic therapies. Due to the relationship between altered lipid dynamics and metabolic dysfunction, we decided to study the effect of the posttranslational lipid modification, S-palmitoylation, on metabolism. S-palmitoylation is the only known reversible lipid modification for proteins, and this depalmitoylation process is catalyzed by acyl-protein thioesterases including APT1 and APT2. We hypothesized that APT deficiency in various tissues would predispose mammals …

Parental Guidance Suggested: Genetic, Epigenetic, And Environmental Factors Shape Allele-Specific Gene Regulation In Metabolic Traits, Celine Louise St. Pierre

Arts & Sciences Graduate Student Theses and Dissertations

Deciphering the “genotype to phenotype” map is a crucial goal of biology. We will not improve our ability to predict phenotypes from DNA sequences until we better incorporate epigenetic and environmental variation into our models of human health and disease. Genes are typically presumed to express both parental alleles equally, but genetic and epigenetic factors can cause one allele to function differently than the other (e.g. expressed or silenced more). These allele-specific imbalances can alter the final composition of a gene’s transcriptional product and ultimately shape phenotypes. Allele-specific effects have widespread impacts on complex traits, but how environmental signals contribute …

Client-Centered Food Distribution: An Analysis Of Patron Preferences At The Oxford Food Pantry, Ella Mann

Honors Theses

Food insecurity has long penetrated the rural South. This limits access to nutritious foods like fresh produce and contributes to chronic health conditions that may arise. Food pantries serve as a vital resource in addressing these disparities by providing free food to families in need. Many of these pantries incorporate strategies to increase consumption of nutrient dense options such as fruits as vegetables. These strategies can vary but the client choice model has proven to align with the self determination theory and promote greater autonomy in food selection. This study aimed to assess the food preferences of patrons at the …

Demography Of Alligator Snapping Turtles (Macrochelys Temminckii) Along A Fishing Pressure Gradient, Luke T. Micek

Electronic Theses and Dissertations

Passive fishing gear is a threat to the alligator snapping turtle (Macrochelys temminckii). The spatio-temporal persistence of this threat and its impacts on M. temminckii populations has not been quantified. I quantified the density of passive fishing gear and the demographic parameters of M. temminckii along a fishing pressure gradient in East Texas streams. Most gear was abandoned and illegally deployed, with densities varying seasonally. Detectability of passive fishing gear declined with increasing gear age, water depth, and volume, but increased with increasing precipitation. Macrochelys temminckii catch per unit effort, abundance, and survival was lower at sites with …

Monitoring Cellular Glycolysis Pathway Kinetics In The Extracellular Medium Using Label-Free, Raman Spectroscopy, Nitin Patil, Zohreh Mirveis, Hugh J. Byrne

Articles

This study explored the potential of Raman spectroscopy to holistically monitor the glycolysis pathway kinetics as a function of time through the extracellular medium. Initially, the collinearity of individual metabolites of interest- glucose and lactic acid as a function of their concentration was tested followed by the sensitivity analysis of the approach by elucidating the limits of detection (0.85 mM and 2.8 mM) and quantification (2.5 mM and 9.5 mM) for glucose and lactic acid respectively in the biological range. In the process several datamining approaches were also explored. Finally, the A549 cell culture was used for kinetic spectral acquisition …

A Search For Transcriptional Cofactors Of Gcm/Repo Involved In Determining Glia Cell Fate In Drosophila Melanogaster, Nivedha Kosalram

Honors Theses

In Drosophila melanogaster, the mechanism influencing the differentiation of glia and neurons is directed by a key transcription factor known as glial cells missing (gcm). gcm is a crucial regulator of cell fate decision, functioning as a binary switch to direct glial fate in gcm- positive cells and neuronal fate in gcm-negative cells (Jones, et.al, 1995; Hosoya, et.al, 1995; and Vincent, et.al, 1996). In addition to directing gliogenesis, gcm and its homolog gcm2 facilitate the determination of macrophages and tendon cells, highlighting that gcm acts with supplementary factors to induce various signaling pathways in different contexts (Jones, 2005; Johnson, et …

Swine Solutions: Enhancing Ffa Supervised Agricultural Experience Projects, Hannah M. Daily, Dr. John Michael Mehaffey, Dr. Candis Scallan, Dr. Amy Mehaffey, Dr. Joe Mask

Electronic Theses and Dissertations

Supervised Agricultural Experience (SAE) is a portion of the three-circle model of agriculture education, providing experiential learning opportunities for students. The immersion SAE encourages students to build upon foundational learning components in a real-world application. A popular area of the immersion SAE includes ownership of market swine being raised for exhibition. This study serves as a pilot mentorship program for agricultural science educators and students, creating an educational resource encouraging record-keeping techniques and skill development, leading to eventual independence from the student’s standpoint. The model for the Swine Solutions Program includes utilization of the provided handbook, completion of daily observation …

Evaluating Predictive Models For Predicting Total Score Of Beef Carcasses, Emmanuel Forson

Electronic Theses and Dissertations

The beef industry plays a vital role in global agriculture, with carcass quality and consumer preference being key determinants of market success. This thesis examines predictive modeling techniques for estimating the Total Score of beef carcasses, a composite measure representing yield and quality, primarily used by the Nebraska Cattlemen Association. Using data from the Nebraska Cattlemen’s Foundation Retail Value Steer Challenge (2000–2023), the study compares the performance of First Order Multiple Linear Regression (MLR) with three machine learning techniques: K-Nearest Neighbors (KNN), Random Forest, and Gradient Boosting Machine (GBM).

The analysis focuses on six key predictors: Hot Carcass Weight, Back …

Patterns Of Taxonomic, Functional, And Phylogenetic Diversity, And Ecological Drivers Of Stream Fish Assemblages In East Texas, Anastasia M. Umstott

Electronic Theses and Dissertations

Freshwater ecosystems in East Texas contain a rich freshwater biodiversity, with the Neches and Sabine River basins supporting some of the greatest freshwater fish diversity in the state. Given the heterogeneity of habitats and species diversity, these rivers serve as excellent natural systems for examining the ecological processes shaping biodiversity patterns and species distributions. In 2023-2024, 60 streams in the Neches and Sabine River basins were surveyed across three seasons to investigate the patterns and ecological drivers of taxonomic (TDβ), functional (FDβ), and phylogenetic β-diversity (PDβ) facets of freshwater fish assemblages. Additionally, I created two ecological niche models for a …

Pan-Cancer Universal Targets For Immunotherapy Resulted From Transposable Elements Activation, Yonghao Liang

Arts & Sciences Graduate Student Theses and Dissertations

Transposable elements (TEs) contribute to nearly half of the human genome yet have been overlooked in genomic medicines due to the stereotypic impression as “junk DNA” and technical challenges. However, studies in the last two decades demonstrated that dysregulation of the epigenome in cancer cells resurrects the cis-regulatory functions of TEs, including the promoter activities. The tumor-specific TE activation events along with the resulting tumor-specific RNA and protein molecules, provide a potential “gold mine” for identifying tumor-specific therapeutic targets for cancer treatments, including immunotherapy. Here, I present a series of works to investigate the potential of providing actionable, pan-cancer, and …