Notes On Patagium Morphology In The Gliding Flat-Tailed House Gecko (Hemidactylus Platyurus), Amber M. Petty, Tony Gamble, Aaron H. Griffing

Biological Sciences Faculty Research and Publications

Several species of geckos have independently evolved patagia, membranous features that facilitate gliding. Detailed morphological investigations of gecko patagia have largely been limited to gliding members of the genus Gekko (formerly in the genus Ptychozoon). Herein we describe the morphology of gliding patagia of the Flat-tailed House Gecko (Hemidactylus platyurus), a species with an independent evolutionary origin of gliding patagia from Gekko and an important species for researching gliding biomechanics. We compared morphology of H. platyurus with a closely related non-gliding species, the Common House Gecko (Hemidactylus frenatus). Using external examination and histological techniques, we …

Synthesis And Evaluation Of 1,3-Disubstituted Imidazolidine-2,4,5-Triones As Inhibitors Of Pyruvate Carboxylase, Nicholas O. Schneider, Keandra Gilreath, Niel M. Henriksen, William A. Donaldson, Subhabrata Chaudhury, Martin St. Maurice

Biological Sciences Faculty Research and Publications

Substituted imidazolidinetriones (IZTs) have been identified as potent inhibitors of pyruvate carboxylase (PC) through an in silico screening approach. Alkyl 2-(2,4,5-trioxo-3-substituted imidazolidin-1-yl)acetates (6i–6r) are the most potent of the series, with IC50 values between 3 and 12 μM, and several IZTs demonstrate high passive permeability across an artificial membrane. IZTs are mixed-type inhibitors with respect to pyruvate and noncompetitive with respect to ATP. This class of inhibitors appears to be selective for PC. Inhibitors in the IZT series do not inhibit the metalloenzymes human carbonic anhydrase II and matrix metalloprotease-12, and they do not inhibit the related biotin-dependent enzyme, guanidine …

Importance Of Conserved Hydrophobic Pocket Region In Yeast Mitoribosomal Ml44 Protein For Mitotranslation And Transcript Preference, Jodie M. Box, Margo E. Higgins, Rosemary A. Stuart

Biological Sciences Faculty Research and Publications

The mitochondrial ribosome (mitoribosome) is responsible for the synthesis of key oxidative phosphorylation subunits encoded by the mitochondrial genome. Defects in mitoribosomal function therefore can have serious consequences for the bioenergetic capacity of the cell. Mutation of the conserved mitoribosomal mL44 protein has been directly linked to childhood cardiomyopathy and progressive neurophysiology issues. To further explore the functional significance of the mL44 protein in supporting mitochondrial protein synthesis, we have performed a mutagenesis study of the yeast mL44 homolog, the MrpL3/mL44 protein. We specifically investigated the conserved hydrophobic pocket region of the MrpL3/mL44 protein, where the known disease-related residue …

In Vitro Assessment Of The Anti-Biofilm Effectiveness Of Copper And Zinc Enhanced Borate Bioactive Glass Using Processed Microscopic Images, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

The escalating burden of nosocomial infections presents a formidable challenge to healthcare systems worldwide, leading to increased morbidity, prolonged hospital stays, and elevated healthcare costs. These infections are often resistant to conventional antibiotic therapies due to their association with biofilms which contribute to the persistence and resistance of pathogens. In addressing the challenge of biofilm-associated nosocomial infections, borate bioactive glasses (BBGs) have emerged as promising biomaterials. Doping these glasses with antimicrobial metals could potentially harness their antibacterial properties to prevent biofilm formation. This study undertakes a rigorous evaluation of the anti-biofilm efficacy of copper and zinc-doped BBGs by employing processed …

Plasmid-Borne Biosynthetic Gene Clusters Within A Permanently Stratified Marine Water Column, Paraskevi Mara, David Geller-Mcgrath, Elizabeth A. Suter, Gordon T. Taylor, Maria G. Pachiadaki, Virginia P. Edgcomb

BCES: Faculty Publications

Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmidencoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpenesynthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are …

A Molecular-Informed Species Inventory Of The Order Ceramiales (Rhodophyta) In The Narragansett Bay Area (Rhode Island And Massachusetts), Usa, Thomas Irvine, Brian Wysor, Alicia Beauvais

Arts & Sciences Faculty Publications

Narragansett Bay is an estuarine system in the western North Atlantic Ocean that harbors a diverse marine flora, providing structure, habitat, and food for native biodiversity. This area has been the center of numerous environmental, biological, ecological, and oceanographic studies; however, marine macroalgae have not been extensively examined using modern molecular methods. Here, we document the biodiversity of the red algal order Ceramiales based on DNA sequence comparisons of the 3′ end of the RuBisCo large subunit (rbcL-3P) and the universal plastid amplicon (UPA). Thirty-seven distinct species of this order were identified and validated with molecular data, including five new …

Four-Dimensional Ecology Education (4dee) For Everyone: Teaching Ecology To Non-Majors, Vikki L. Rodgers, Sara E. Scanga, Justin R St Juliana, Erica S. Tietjen, Jon M. Honea, Loren B. Byrne, Zakiya H. Leggett, George Middendorf

Arts & Sciences Faculty Publications

Originally developed for application to ecology courses for undergraduate majors, the Four-Dimensional Ecology Education (4DEE) Framework offers possibilities for adaptation to courses with ecology content for many other audiences. Recognizing the extraordinary range of classroom contexts and constraints, we developed some general, flexible recommendations and approaches to guide instructors in adapting the 4DEE Framework for an array of non-major audiences and classroom context needs. Our hope is that 4DEE-aligned courses for non-majors will provide these students with greater appreciation of ecology and inspire them to use their knowledge to address many critical environmental issues in their personal and professional lives. …

Application Of Environmental Dna Metabarcoding To Differentiate Algal Communities By Littoral Zonation And Detect Unreported Algal Species, Sergei Bombin, Andrei Bombin, Brian Wysor, Juan M. Lopez-Bautista

Arts & Sciences Faculty Publications

Coastal areas are the most biologically productive and undoubtedly among the most complex ecosystems. Algae are responsible for most of the gross primary production in these coastal regions. However, despite the critical importance of algae for the global ecosystem, the biodiversity of many algal groups is understudied, partially due to the high complexity of morphologically identifying algal species. The current study aimed to take advantage of the recently developed technology for biotic community assessment through the high-throughput sequencing (HTS) of environmental DNA (eDNA), known as the “eDNA metabarcoding”, to characterize littoral algal communities in the Northern Gulf of Mexico (NGoM). …

Forty Years Of Inferential Methods In The Journals Of The Society For Molecular Biology And Evolution, Claudia A.M. Russo, Adam Eyre-Walker, Laura A. Katz, Brandon S. Gaut

Biological Sciences: Faculty Publications

We are launching a series to celebrate the 40th anniversary of the first issue of Molecular Biology and Evolution. In 2024, we will publish virtual issues containing selected papers published in the Society for Molecular Biology and Evolution journals, Molecular Biology and Evolution and Genome Biology and Evolution. Each virtual issue will be accompanied by a perspective that highlights the historic and contemporary contributions of our journals to a specific topic in molecular evolution. This perspective, the first in the series, presents an account of the broad array of methods that have been published in the Society for Molecular Biology …

Developing Cellular Systems To Elucidate Rna Structural Dynamics Of Cag Expansion Transcripts In Spinocerebellar Ataxias, Victoria Demeo

Electronic Theses & Dissertations (2024 - present)

Spinocerebellar ataxias (SCAs) are a diverse group of over 40 genetically heterogeneous neurodegenerative disorders, many of which are caused by a trinucleotide CAG repeat expansion in the coding region of specific genes. These expansions lead to the production of polyglutamine (polyQ) tracts that interfere with normal protein function, triggering cellular dysfunction and contributing to disease pathogenesis. The most well-known of these SCAs, such as SCA1, SCA2, and SCA3, exhibit progressive neurodegeneration, yet the precise mechanisms through which these mutations cause disease remain poorly understood.

A significant challenge in studying CAG repeat expansion disorders lies in the complexity of the disease …

Female Titin Mutant Mice Outperform Young And Old Males, Reese Ger

Scripps Senior Theses

Exercise performance is widely believed to generally be maximal among young males. However, little research has been conducted to investigate the impact of sex or age on muscle performance. This study investigated the effects of sex and age on forelimb and all limb grip strength performance in wildtype and titin mutant mice. Titin is the largest known protein, with known involvement in muscle function. The mice in this study were Ttn∆112-158 with a 75% deletion to the PEVK region of titin. Based on limited existing research, we hypothesized that wildtype mice would outperform all Ttn∆112-158 mice, males would outperform females …

Effect Of Bioactive Borate Glass On Printability And Physical Properties Of Hydrogels, Fateme Fayyazbakhsh, Mehedi H. Tusar, Yue-Wern Huang, Ming C. Leu

Mechanical and Aerospace Engineering Faculty Research & Creative Works

Hydrogels are a key component in bioinks and biomaterial inks for bioprinting due to their biocompatibility and printability at room temperature. The research described in the present paper contributes to the advancement of bioprinting by studying the effect of bioactive borate glass (BBG) incorporated into hydrogels on printability and physical properties. In this study, we fabricated 3D-printed hydrogel scaffolds using gelatin and alginate hydrogel mixture incorporated with various amounts of BBG, a bio ceramic rich in therapeutic ions including boron, calcium, copper, and zinc. We investigated the effect of incorporating BBG on the density, viscosity, physical interactions, chemical structure, and …

Characterization Of Tonneau1 Recruiting Motif Proteins And Ton2 Signaling Functions, Tyler Falk

Theses and Dissertations

Plants cells are fixed in place. As a result they have to carefully divide in order to function properly. Plants use a number of complex microtubule arrays to ensure proper division and orientation including the preprophase band (PPB) and the phragmoplast. The PPB orients the cell prior to division and marks the cortical division site, which is where the phragmoplast is guided to. The phragmoplast is a dynamic microtubule array that builds the cell plate which later becomes the cell wall that divides daughter cells. Proteins involved with PPB formation include Tonneau1 (TON1) and Tonneau2 (TON2) which localize to and …

Effects Of Glyphosate-Based Herbicide Exposure On Life History, Stress Tolerance, And Microbiome—From Plasticity To Evolution, Jacob R. Whitlock

University of the Pacific Theses and Dissertations

Glyphosate (GLY) is the most used pesticide worldwide, and GLY-based herbicides (GBHs) can affect animals’ microbiomes and, in turn, their physiology and morphology. Environmental stressors can be mitigated by flexibility in life-history strategies, which can also dictate animal physiology and morphology. However, we lack an understanding of how GBH influences life-history strategies and stress tolerance, in addition to its effects across generations. Thus, I exposed the variable field cricket, Gryllus lineaticeps, to GBH within- and across-generations to examine the role of GBH in developmental plasticity and evolution. Specifically, I measured its effects on life-history traits (e.g., developmental duration and a …

Effects Of Fetal Bovine Serum On The Proteome And Secretome Of Pichia Pastoris, Kenneth L. Nguyen

University of the Pacific Theses and Dissertations

Komagataella pastoris, formerly known as Pichia pastoris, and hereafter referred to as Pichia, is a methylotrophic yeast widely employed as a recombinant protein factory for biotechnical and industrial purposes. P. pastoris boasts the ability to thrive at high cell densities, executes numerous post-translational modifications, and exhibits minimal secretion of endogenous proteins, thus greatly facilitating the expression and purification of recombinant proteins. Despite these advantages, Pichia still presents certain challenges as an expression system. Occasionally, recombinant proteins are retained within the cell and subject to degradation. Furthermore, Pichia falls short in matching the production capabilities of more widely used systems like …

The Role Of The Unfolded Protein Response In Fatty Liver Disease, Anusha L. Murshed

University of the Pacific Theses and Dissertations

The unfolded protein response (UPR) is composed of three highly conserved pathways (ATF6, IRE1, PERK). Cellular stressors induce protein misfolding and aggregation in the endoplasmic reticulum (ER). This signaling pathway maintains protein homeostasis when there is stress in the ER. When the UPR is activated, the eukaryotic initiation factor 2 alpha (eIF2α) becomes phosphorylated, which inhibits global mRNA translation. If ER stress remains chronically unmitigated, the UPR induces apoptosis. GADD34 and CReP shift in expression when the UPR is activated and work as phosphatases and dephosphorylate eIF2α in a feedback loop, allowing protein synthesis to resume. Several human diseases, including …

Insight Into A Sexually Dimorphic Ostracod Crustacean By Mass Spectrometry And Microtomography, Cindy D. Davis

University of the Pacific Theses and Dissertations

The importance of the central nervous system cannot be understated. An array ofmolecules associated with the brain regulate basic behaviors as well as sex specific behaviors. Describing the molecular background is not the only way that I can learn more of the central nervous system. Describing the anatomy of the central nervous system can be crucial in understanding what regions of the brain is particularly key to the animal. Euphilomedes carcharodonta is a small marine crustacean native to the subtidal zone of the California coast. This ostracod makes for a compelling candidate to explore these research interests as this organism …

Plasticity In Response To Temperature Magnitude And Variation---From Life History To Thermal Tolerance And Coloration, Austin Rex Hoffman

University of the Pacific Theses and Dissertations

Warming associated with climate change has many direct and downstream effects on animals. For example, warmer developmental temperatures can improve heat tolerance and reduce insect melanization, which is related to coloration, thermoregulation, immunity, desiccation resistance, and potentially life-history traits, such as investment into reproduction and dispersal. Increased temperature variation is also a feature of climate change, and it may have a larger impact on animals than warming. However, I lack insight into the combined effects of temperature magnitude and variability on important traits of life history, thermal tolerance, and coloration. Thus, I integrated temperature variation into thermal performance using a …

Ecosystem Functions And Services​ Landscaping For Water Quality – April 30, 2024​ Sunapee, Nh​, Julia Peterson

UNH Cooperative Extension

No abstract provided.

Mammalian Biodiversity On Greenways Across An Urban-To-Rural Gradient, Brooklyn C. Zwinklis

College of Graduate Studies: Theses & Dissertations

Large-scale urbanization is one of the leading causes of biodiversity loss on a global scale due to habitat loss and fragmentation. This has created a need to investigate ways to mitigate the damage caused by urban development, such as studying whether green spaces in urban areas can serve as means of preserving mammalian biodiversity in cities. This study specifically focused on greenways as they are understudied when compared to other green spaces, such as parks and cemeteries. Greenways are linear tracts of paved land, usually designed for human recreational activities. However, their benefits to wildlife have not been well researched. …

Evaluating Reactive Gliosis In The Brain Of Adult Zebrafish Following The Ingestion Of Nanopolystyrene., Hannah A. Kelehear

College of Graduate Studies: Theses & Dissertations

Polystyrene nanoplastics are one of the most pervasive environmental contaminants and have been shown to infiltrate multiple organ systems following ingestion. Studies in several animal models and humans have demonstrated that nanoplastics can cross the blood-brain barrier. Additionally, there is evidence that plastics will induce an inflammatory response in the brain involving reactive gliosis of microglia and astrocytes. This process has yet to be thoroughly investigated in the zebrafish model system in the context of micro-/nanoplastic ingestion. In the current study, we examined microglial and astrocytic phenotypes in the adult zebrafish telencephalon after consuming food contaminated with 44 nm polystyrene …

Aberrant Lipid Accumulation And Retinal Pigment Epithelium Dysfunction In Prcd-Deficient Mice, Sree Indrani Motipally

Graduate Theses, Dissertations, and Problem Reports (ETD)

Progressive Rod-Cone Degeneration (PRCD) is a peripheral membrane protein predominantly expressed in photoreceptor outer segment (OS) disc membranes with an unknown function. Several mutations in Prcd are implicated in Retinitis pigmentosa (RP) in humans. The most common “cysteine to tyrosine” (C2Y) mutation in Prcd leads to progressive retinal atrophy in multiple dog breeds and RP in humans. Canine models harboring the C2Y mutation in Prcd show disorganized OS structure with greatly attenuated photoreceptor OS renewal rates. Recent studies show defects in the photoreceptor nascent disc flattening in the absence of Prcd. However, it is unclear how OS discs eventually …

Mortality Index Of Drosophila Melanogaster, Following Traumatic Brain Injury, Megan N. Ashworth

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Traumatic brain injuries (TBI) are associated with immediate and long-term consequences that can be divided into primary and secondary injuries. A primary injury results due to the direct damage inflicted on the brain by the hit, whereas a secondary injury takes more time to manifest due to the cascade of molecular events that lead to cellular damage and death within the brain. This study analyzes mortality as a secondary injury following traumatic brain injury in the presence of a human neurodegenerative genetic risk factor, APOE ε4. The High Impact Trauma (HIT) device developed by Katzenberger et al. (2013) was utilized …

The Effects Of Early Exposure To Prescription/Illicit Drugs And Drug Metabolites On Larval Zebrafish Behavioral And Motor Function Development, Jacob Thomas, Dena Weinberger, Bikram Subedi, Brandon Capps

Murray State Theses and Dissertations

THE EFFECTS OF EARLY EXPOSURE TO PRESCRIPTION/ILLICIT DRUGS AND DRUG METABOLITES ON LARVAL ZEBRAFISH BEHAVIORAL AND MOTOR FUNCTION DEVELOPMENT

A Thesis Presented to the Faculty of the Department of Biology

Murray State University

Murray, Kentucky

In Partial Fulfillment of the Requirements for the Degree of Masters In Science

By Jacob Thomas, B.S., Murray State University

December 2024

Acknowledgements

Brandon Capps, who pretty much did a whole third of the legwork on this project and saved me lots of headaches;

Chandler Maddox, one of the University of Kentucky’s finest undergrads who came in from the top rope with a folding chair …

Pseudomonas Mosselii Improves Cold Tolerance Of Asian Rice (Oryza Sativa L.) In A Genotype-Dependent Manner By Increasing Proline In Japonica And Reduced Glutathione In Indica Varieties, Nasim Maghboli Balasjin, James Maki, Michael Schläppi

Biological Sciences Faculty Research and Publications

Cold stress is an important factor limiting rice production and distribution. Identifying factors that contribute to cold tolerance in rice is of primary importance. While some plant specific genetic factors involved in cold tolerance have been identified, the role of the rice microbiome remains unexplored. In this study, we evaluated the influence of plant growth promoting bacteria (PGPB) with the ability of phosphate solubilization on rice cold tolerance and survival. To reach this goal, inoculated and uninoculated 2-week-old seedlings were cold stressed and evaluated for survival and other phenotypes such as electrolyte leakage (EL) and necessary elements for cold tolerance. …

Tarantula Toxin Transcripts And Toxin Structure Prediction By Alphafold, Christine Vega, Rebekkah Sepulveda, Ying Jia

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Tarantula venom predominantly comprises peptides and small proteins (venom toxins). To explore this further, we generated a combined gland cDNA library from five different tarantula species. Subsequently we randomly sequenced 752 clones, which led to the identification of sixteen distinct toxin groups, including one novel group. Each group consists of a minimum of three identical sequences. A comprehensive analysis of these toxin groups was carried out, and we simulated the 3D structures of certain predicted toxins. These transcripts can be used to the production of venom toxins through recombinant techniques, offering promising applications in various biomedical applications.

Stress Biology: Complexity And Multifariousness In Health And Disease, Emily M. Sontag

Biological Sciences Faculty Research and Publications

Preserving and regulating cellular homeostasis in the light of changing environmental conditions or developmental processes is of pivotal importance for single cellular and multicellular organisms alike. To counteract an imbalance in cellular homeostasis transcriptional programs evolved, called the heat shock response, unfolded protein response, and integrated stress response, that act cell-autonomously in most cells but in multicellular organisms are subjected to cell-nonautonomous regulation. These transcriptional programs downregulate the expression of most genes but increase the expression of heat shock genes, including genes encoding molecular chaperones and proteases, proteins involved in the repair of stress-induced damage to macromolecules and cellular structures. …

Exploring The Relative Contribution Of Humans On Genetic Differentiation Among Speyeria Callippe Populations In The California Coast Ranges, Laura K. Heller

University of the Pacific Theses and Dissertations

The distinction between populations due to environmental factors like climate and geography are well-known and expected, therefore it is not illogical to believe more disjunct habitats would also impact genetic structure. Through Restriction Site Associated DNA Sequencing (RADseq) and Mitochondrial DNA (mtDNA) analysis the genetic structure and differentiation (fixation index, Fst) of Speyeria callippe across four regions in California: the North Coast Ranges, Bay Area, Diablo Range, and South Coast Ranges were analyzed. The influence of geographic distance, human population density, and forest cover were explored as factors influencing the genetics of these populations. The combination of mtDNA and RADseq …