Biology Commons^™

Genome-Wide Snp Analyses Reveal High Gene Flow Of Endemic Smallscale Croaker (Boesemania Microlepsis) In The Lower Mekong Basin, Quyen Dang Ha Vu, Christopher E. Bird, Oanh Thi Truong, Sang Quang Tran, Ellen E. Biesack, Amanda S. Ackiss, Kent E. Carpenter, Binh Truy Dang

Biological Sciences Faculty Publications

The Smallscale Croaker, Boesemania microlepis, is a valuable fishery resource in the Mekong River basin that lacks clear biological data to understand its basic ecology and conservation management priorities. This species is common in the southernmost floodplain of the Mekong which extends from Tonlé Sap in Cambodia to the Mekong Delta in Vietnam. This floodplain is of particular biodiversity conservation concern because of the many upstream dams that restrict water flow in an ecology that relies heavily on a flood-pulse cycle. The literature regarding the biology B. microlepis in this region contains conflicting ideas that populations are both highly …

Intraspecific Variation In Plant–Fungal Interactions Across Tidal Elevation In A Salt Marsh, Torrie Hanley, Catherine Gehring, Ron Deckert, Behzad Mortazavi, Christina Richards, A. Randall Hughes

Biology Faculty Publications

Interspecific interactions vary depending on environmental and genetic factors, with intraspecific variation potentially altering these relationships. Specifically, intraspecific variation within host plants and their endosymbionts may affect above- and belowground interactions depending on environmental conditions. We examined how intraspecific variation within the salt marsh foundation species Spartina alterniflora and a common fungal root endosymbiont (Lulworthia sp.) affected their interactions. We conducted a glasshouse experiment comparing interactions between Spartina growth forms (tall-form from low marsh and short-form from high marsh) and Lulworthia isolates from different marsh locations, and a laboratory experiment exposing Lulworthia isolates from both endpoints of a tidal elevation …

Comparing The Development And Viability Of Horseshoe Crab Eggs Laid In Beach And Salt Marsh Habitats, Daniel A. Sasson, Christopher C. Chabot, Jo-Marie Kasinak, Jennifer Mattei Ph.D., Elizabeth U. Scott, Fletcher K. Hall, Michael R. Kendrick

Biology Faculty Publications

The horseshoe crab, Limulus polyphemus, has recently been found to spawn regularly in salt marshes, despite the long-held assumption that salt marsh sediments are not conducive for embryonic development. Here, we tested the prediction that eggs laid in the salt marsh would develop more slowly and be less viable than eggs laid on beaches. We flagged the nests of spawning horseshoe crabs in the marshes and beaches of three states—South Carolina, Connecticut, and New Hampshire—and then excavated those nests one or three weeks later. We staged the excavated embryos to compare developmental progress between marshes and beaches. We found …

Spectral Divergence Prioritizes Key Classes, Genes, And Pathways Shared Between Substance Use Disorders And Cardiovascular Disease, Everest Castaneda, Elissa Chesler, Erich J. Baker

Funded Scholarship

Substance use disorders (SUDs) are heterogeneous diseases with 

overlapping biological mechanisms and often present with co-occurring disease, 

such as cardiovascular disease (CVD). Gene networks associated with SUDs 

also implicate additional biological pathways and may be used to stratify 

disease subtypes. Node and edge arrangements within gene networks impact 

comparisons between classes of disease, and connectivity metrics, such as 

those focused on degrees, betweenness, and centrality, do not yield sufficient 

discernment of disease network classification. Comparatively, the graph 

spectrum’s use of comprehensive information facilitates hypothesis testing 

and inter-disease clustering by using a larger range of graph characteristics. 

By adding a connectivity-based …

Symbiodiniaceae Shifts Over The Last Decade On The Hottest Coral Reefs On Earth, Anna Fiesinger, Rachel Alderdice, Luigi Colin, Hannah Manns, Gabriela Perna, Kathryn H. Stankiewicz, Jacob J. Valenzuela, Line K. Bay, Daniel J. Barshis, Nitin S. Baliga, Iliana B. Baums, John A. Burt, Christian R. Voolstra

Biological Sciences Faculty Publications

Corals in the Persian/Arabian Gulf (PAG) are resilient to various stressors, whose levels exceed those of coral reefs globally. These corals thereby offer insight into mechanisms underlying thermal resilience, e.g., regarding the role of endosymbiotic microalgae in the family Symbiodiniaceae. Previous studies have identified the thermotolerant species Cladocopium thermophilum as broadly associated with corals in the southern PAG. However, algal-host specificity at the within-species level and the temporal stability of these associations are not well understood. Here we sampled two dominant stony corals (Porites harrisoni, n = 119 and Platygyra daedalea, n = 79) at three sites …

Patterns Of Kinship And Sociality In North American River Otters, Whitney E. Vickers

Cal Poly Humboldt theses and projects

Previous studies of river otters (Lontra canadensis) in coastal Humboldt County, California have documented varying social group compositions over the last four decades. It has been assumed that otters travel between coastal wetland sites, but the extent of movement has been unknown. Socially, river otters have been observed alone, in small family groups that consisted of an otter mom and pup(s), in larger helper groups that consisted of an otter mom, pup(s), and at least one additional adult or juvenile (helpers), and in all-adult social groups. Until now it was unknown whether the composition of social groups was …

Diversity, Genomics And Antimicrobial Resistance Of Coagulase-Negative Staphylococcus: A Literature Review, Kathleen Okeefe

Electronic Theses & Dissertations (2024 - present)

Members of the gram-positive bacterial genus Staphylococcus have historically been classified into coagulase-positive Staphylococcus (CoPS) and coagulase-negative Staphylococcus (CoNS). This classification is based on the ability of clotting of plasma by the coagulase enzyme, which converts fibrinogen to fibrin. CoNS species are ubiquitous commensals that frequently colonize the skin and mucosal surfaces. They are also opportunistic pathogens implicated in many human and animal infections. The evolutionary history of CoNS has generally been overlooked because of the historical lack of recognition for their clinical importance and poor taxonomic sampling. They are often perceived as being less or non-pathogenic, especially compared to …

Resources To Study The Isoforms Of The P53 Family Of Transcription Factors, Dana L. Woodstock

Electronic Theses & Dissertations (2024 - present)

The p53 family of transcription factors regulates diverse gene regulatory networks such as those involved in DNA damage repair, epidermal commitment, and neuronal development. As a result, dysfunction in these pathways lead to numerous human health conditions, including multiple types of cancer and craniofacial developmental disorders. Each family member regulates a distinct gene network leading to varied cellular and organismal phenotypes, but all are capable of regulating programmed cell death, likely due to considerable similarity between protein structure and binding sites in DNA. Analysis of these shared and distinct functions is complicated by each p53 family member gene (TP53, TP63, …

Loss Of Endogenous Circadian Clock Function In Mice Alters Respiratory Cycle Timing In A Time Of Day- And Sex-Specific Manner, Aaron A. Jones, Deanna M. Arble

Biological Sciences Faculty Research and Publications

Resting breathing and ventilatory chemoreflexes are regulated in a 24-hr manner by the endogenous circadian clock. However, it is unclear how circadian biology influences different phases of the breath-to-breath respiratory cycle which are predominantly controlled by pontomedullary regions of the brainstem. Here, we performed whole-body plethysmography during quiet wakefulness in young adult male and female mice lacking the core clock gene Brain and Muscle Arnt-like 1 (BMAL1) to determine the extent to which the molecular clock affects respiratory cycle timing and ventilatory airflow mechanics. Breath waveform analysis revealed that male BMAL1 knockout (KO) mice exhibit time of day-specific differences in …

Global Decoupling Of Functional And Phylogenetic Diversity In Plant Communities, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Plant communities are composed of species that differ both in functional traits and evolutionary histories. As species’ functional traits partly result from their individual evolutionary history, we expect the functional diversity of communities to increase with increasing phylogenetic diversity. This expectation has only been tested at local scales and generally for specific growth forms or specific habitat types, for example, grasslands. Here we compare standardized effect sizes for functional and phylogenetic diversity among 1,781,836 vegetation plots using the global sPlot database. In contrast to expectations, we find functional diversity and phylogenetic diversity to be only weakly and negatively correlated, implying …

Cumulative Effects Of H+ And PI On Force And Power Of Skeletal Muscle Fibres From Young And Older Adults, Christopher W. Sundberg, Laura E. Teigen, Sandra K. Hunter, Robert H. Fitts

Biological Sciences Faculty Research and Publications

The cellular causes of the age-related loss in power output and increased fatigability are unresolved. We previously observed that the depressive effects of hydrogen (H+) (pH 6.2) and inorganic phosphate (Pi) (30 mm) did not differ in muscle fibres from young and older men. However, the effects may have been saturated in the severe fatigue-mimicking condition, potentially masking age differences in the sensitivity of the cross-bridge to these metabolites. Thus, we compared the contractile mechanics of muscle fibres from the vastus lateralis of 13 young (20–32 years, seven women) and 12 older adults (70–90 years, six women) in conditions mimicking …

The Complex Development Of Psoralen-Interstrand Crosslink Resistance In Escherichia Coli Requires Acrr Inactivation, Retention Of A MarboxSequence, And One 3 Of Three Mara, Soxs, Or Rob Global Regulators, Travis K. Worley, Ayah H. Asal, Lo Cooper, Charmain T. Courcelle, Justin C. Courcelle

Biology Faculty Publications and Presentations

Crosslinking agents, such as psoralen and UVA radiation, can be effectively used as antimicrobials and for treating several dysplastic conditions in humans, including some cancers. Yet, both cancer cells and bacteria can become resistant to these compounds, making it important to understand how resistance develops. Recently, several mutants were isolated that developed high-levels of resistance to these compounds through upregulation of components of the AcrAB-TolC-efflux pump. Here, we characterized these mutants and found that resistance specifically requires inactivating mutations of the acrR transcriptional repressor which also retain the marbox sequence found within this coding region. In addition, the …

Heterospecific Coprophagy In The White-Tailed Deer Odocoileus Virginianus (Zimmermann, 1780) In Costa Rica, Mora Manuel Jose, Juan De Dios Astorga-Acuña

Biology Faculty Publications and Presentations

Animals may engage in coprophagy, including heterospecific coprophagy, where they consume the feces of other species. The white-tailed deer, Odocoileus virginianus, primarily feeds on plant material, such as tender forbs and shrub shoots. This report documents a case of heterospecific coprophagy by the white-tailed deer in Costa Rica, where two individuals were observed consuming domestic horse feces. The reasons for heterospecific coprophagy in ruminants like the white-tailed deer are unclear. Nutritional supplementation, microbial transfer, or other ecological factors may play a role in this behavior. However, such a behavior also poses risks, including the transmission of diseases and parasites from …

Identification Of Salt Tolerance And Stress Response In Us Department Of Agriculture Tomato Germplasm At The Seedling Stage, Ibtisam Alatawi, Haizheng Xiong, Kenani Chiwina, Hanan Alkabkabi, Qun Luo, Neelendra K. Joshi, Xiaolun Sun, Xuan Zhuang, Kai-Shi Ling, Ainong Shi

Horticulture Faculty Publications and Presentations

Soil salinity is a significant abiotic factor that impedes sustainable crop production in key agricultural regions worldwide. Saline cultivation adversely affects soil quality, whereas the use of saline water for irrigation disrupts the physiological and biochemical processes of plants. Continuous irrigation with high salt concentrations leads to a gradual buildup of soil salinity, thus hindering optimal plant growth and development. Consequently, there is a growing emphasis on breeding salinity-tolerant cultivars of various crops. In this study, 71 tomato accessions sourced from 20 countries and provided by the US Department of Agriculture were evaluated under controlled greenhouse conditions and subjected to …

Long-Term Increases In Wing Length Occur Independently Of Changes In Climate And Climate-Driven Shifts In Body Size, Tiffany Dias, Nathan P. Lemoine, Scott W. Yanco, Marketa Zimova, Rachael A. Bay, Brian C. Weeks

Biological Sciences Faculty Research and Publications

Recent widespread reductions in body size across species have been linked to increasing temperatures; simultaneous increases in wing length relative to body size have been broadly observed but remain unexplained. Size and shape may change independently of one another, or these morphological shifts may be linked, with body size mediating or directly driving the degree to which shape changes. Using hierarchical Bayesian models and a morphological time series of 27 366 specimens from five North American migratory passerine bird species, we tested the roles that climate and body size have played in shifting wing length allometry over four decades. We …

The Role Of Floodplain Complexity In Wood Turtle Habitat Use, Laura S. Deming

Antioch University Dissertations & Theses

Wood turtles occupy cold, low-gradient riverine habitat throughout the northeastern United State and southeastern Canada. Stream alterations, such as dams, channel straightening, and floodplain development have diminished the natural hydrologic and sedimentation regimes that result in complex channel and floodplain geomorphology. Studies throughout the species’ range have quantified many aspects of their habitat, but none have quantified components of geomorphology of wood turtle sites. The goal of this study was to explore the role of stream channel and floodplain geomorphology in wood turtle habitat use, with specific objectives to (1) quantify components of stream channel and floodplain geomorphic complexity, (2) …

Epithelial Responses And Remodeling In The Submandibular Gland Post-Irradiation, Victoria Gellatly

Electronic Theses & Dissertations (2024 - present)

Radiation therapy for head and neck cancer often causes irreversible salivary gland dysfunction, resulting in chronic xerostomia. Understanding the cellular and molecular mechanisms underlying this dysfunction is essential for developing regenerative therapies. Given the cellular complexity of the salivary gland single-cell RNA sequencing (scRNA-seq) provides a powerful approach to investigate cell-type-specific injury responses to ionizing radiation (IR) and uncover transcriptional changes that may be masked in bulk analyses. This study investigates the cellular and molecular responses of the murine submandibular gland (SMG) to irradiation, with a focus on epithelial loss and remodeling, and regenerative failure. In order to effectively use …

System And Method For Simulating A Respiratory System, Yang Wang, Weixing Hao, Yue-Wern Huang

Patents

A system and method for simulating a human respiratory system to facilitate investigating the functioning of the respiratory system, such as the generation and effects of secondhand smoke. An aerosol generator, which may include an atomizer, is configured to generate an aerosol. A series of filter media includes, in order, an inhaling extrathoracic filter media, an inhaling tracheobronchial filter media, an alveolar filter media, an exhaling tracheobronchial filter media, and an exhaling extrathoracic filter media. Each filter media includes one or more layers of a material having a fiber diameter and a weight that simulate the corresponding region of the …

Bakterielle Schutzmechanismen Gegen Hypochlorige Säure, Jan-Ulrik Dahl

Faculty Publications – Biological Sciences

Reactive chlorine species (RCS) are highly bactericidal and produced in large amounts during host defense to kill invading pathogens. More recent studies have investigated how bacteria respond to and defend RCS, which appear to elicit more multifaceted responses compared to reactive oxygen species. A comprehensive understanding of bacterial RCS responses has clear potential to devise strategies that increase the sensitivity of bacterial pathogens to host defenses without harming commensals.

Host-Associated Beneficial Gut Microbiota Boosts Induced Immunity And Limits Immune Deployment Costs In Bumblebees, Austin C. Calhoun, Teni Shosanya, Brenna K. Long, Jade K. Rehberger, Ben M. Sadd

Faculty Publications – Biological Sciences

1. Ecological immunology posits that variation in host resistance to infection may be attributed partly to the ecological and evolutionary costs of immunity. While the deployment of immune defence is necessary to combat pathogenic infection, hosts pay energetic and other costs for activation.
2. Host-associated beneficial microbiota have been shown to affect multiple host traits, including immunity, but how interactions with these microbial communities may mitigate the costs of immune activation remains an open question. For apid bees, including eusocial bumblebees, core members of the adult gut microbiota contribute to a variety of fitness-relevant traits and provide a key ecological and evolutionary …

Variation In The Timing And Duration Of Rough-Skinned Newt (Taricha Granulosa) Larval Period In The Center Of Their Geographic Range (Humboldt County, California), Emmery R. Parker

Cal Poly Humboldt theses and projects

Rough-skinned newts (Taricha granulosa) occur along the Pacific coast of the U.S. from central California to southwestern Alaska at elevations from zero to 2,800 m. Across that range, the timing and duration of various life history events (i.e., hatching, metamorphosis, breeding, and oviposition) are largely unknown, although general trends have been observed in a few locales. Larval life stages are particularly important for determining amphibian population persistence, but there have been no formal studies describing the larval period of rough-skinned newts. Using minnow-trap and dip net surveys at nine lentic sites in northern Humboldt County, California (elevations 400 …

Dna Methylation Variation In Eastern Diamondback Rattlesnakes (Crotalus Adamanteus) On A Georgia Barrier Island, Megan Hoog

College of Graduate Studies: Theses & Dissertations

The Eastern Diamondback Rattlesnake (Crotalus adamanteus, EDB) is the largest rattlesnake in the world and is thought to be declining in many portions of its range. Genetic venom studies in the Southeast United States have shown evidence of fine-scale differences within two main geographic groups on Jekyll Island. My objective is to expand on this finding to determine if epigenetic mechanisms, specifically DNA methylation, varies among different populations of EDB in similar environments, age classes, and sexes. I collected EDB blood samples through a partnership with the Jekyll Island Authority and screened 44 individuals for epigenetic variation from …

Using Algal Turf Scrubber Biomass As A Feed Source For Juvenile Eastern Oysters, Taofeek Saka Jimoh

College of Graduate Studies: Theses & Dissertations

Algal turf scrubber (ATS) is an engineered system that promotes natural wastewater treatment processes and improves water quality by passing a shallow stream of nutrient rich water over the surface of a gently sloped flow-way. Algae turf scrubber biomass is a combination of micro and macroalgae, as well as micro-invertebrates, ciliates, bacteria, and more. The overall aim of the study was to reduce the feeding cost of juvenile eastern oysters by replacing the commercial microalgae diet with ATS biomass. The experiment was designed to assess the viability of replacing commercial microalgal diet with ATS biomass at different substitution levels (0, …

Community And Decomposition Dynamics Along A Saltwater Intrusion Gradient On Sapelo Island, Georgia, Zach Gordon

College of Graduate Studies: Theses & Dissertations

Saltwater intrusion, the movement of ocean water into freshwater, is a significant global threat to coastal freshwater ecosystems linked to both climate change and anthropogenic influences. Alterations to coastal landscapes can increase intrusion. Sapelo Island has an extensive history of agricultural landscape alteration, but freshwater flow decline increased the movement of saltwater inland by tides. Intrusion is expected to increase in frequency and magnitude due to rising sea levels and storms. Salinization puts inland habitats and the humans relying on them at risk. As saltwater is denser than freshwater, more pressure is placed on benthic organisms (i.e., macroinvertebrates) that will …

Microbial Community Stabilization By Restored Oyster Reefs: Implications For Blue Carbon Storage, Natalie Boydstun

College of Graduate Studies: Theses & Dissertations

Coastal ecosystems provide critical carbon sequestration services, yet the microbial mechanisms underlying carbon storage remain poorly understood, particularly in non-vegetated habitats. This study investigated whether restored oyster reefs (Crassostrea virginica) enhance sediment carbon storage potential by stabilizing microbial communities and promoting efficient organic matter processing. I hypothesized that reef-mediated sediment stabilization and organic deposition would create conditions favoring microbial degradation of complex carbon compounds into stable soil organic matter, ultimately supporting anaerobic carbon storage. To test this, I compared sediment biogeochemistry, enzyme activity, and microbial community structure between three restored oyster reef sites and two unstructured control sites …

Investigating The Role And Expression Of Aquaporin 10 Paralogs In Spiny Dogfish (Squalus Acanthias), Esosa Omoregie

College of Graduate Studies: Theses & Dissertations

Aquaporins (AQPs) are integral membrane proteins that facilitate the selective transport of water and small solutes across cell membranes, playing essential roles in maintaining osmotic balance in vertebrates. Among them, aquaglyceroporins such as AQP10 are capable of transporting water, glycerol, and urea, contributing to osmoregulatory and metabolic processes. This study investigated the expression, localization, and potential physiological roles of two AQP10 paralogs, AQP10C1 and AQP10C2, in the spiny dogfish (Squalus acanthias), a marine elasmobranch that maintains osmotic equilibrium through urea retention and ion regulation. Using RT-PCR, quantitative PCR, Western blotting and immunohistochemistry the study identified tissue-specific expression patterns of …

Effects Of Increased Temperatures And Migratory Status On Passerine Chick Rearing Phenology And Caterpillar Prey Synchrony, Marissa Calvert

College of Graduate Studies: Theses & Dissertations

Many species across the globe have been observed to shift the seasonal timing of life history events in response to climate change-induced shifts in their local environments. However, individual species vary greatly in the direction and magnitude of these phenological shifts. Variation in phenological responsiveness to climate change among interacting species can lead to phenological asynchrony, with potential consequences for survival and population health. In years with increased spring temperatures, the timing of passerine chick rearing and of caterpillar activity may shift earlier or later in the year. Differences in the magnitude and/or direction of phenological shifts among passerines and …

Molecular Insights Into The Impact Of Bone Marrow Stroma, Cb-6644 Inhibition Of The Ruvbl1/2 Complex, And Cebpβ On Regulating Drug Sensitivity In Multiple Myeloma, Sebastian Adam Dziadowicz

Graduate Theses, Dissertations, and Problem Reports (ETD)

Multiple myeloma (MM), is a hematological cancer originating in plasma cells. Currently multiple myeloma represents a significant clinical challenge due its incurable nature mainly due to inevitable drug resistance. MM is characterized by abnormal plasma cell proliferation within the bone marrow and production of abnormal immunoglobulin resulting in a plethora of physiological abnormalities. Although a rare malignancy, MM accounts for 1% of all cancers and currently has five-year survival rate of around 50%. Utilizing a combination of laboratory experiments and bioinformatics techniques, this dissertation examines multiple layers of MM physiology in the context of regulating drug resistance or sensitivity. First, …

Genomic Differences And Parentage In West Virginia's Reintroduced Elk (Cervus Canadensis), Adam A.V. Cook

Graduate Theses, Dissertations, and Problem Reports (ETD)

Elk (Cervus canadensis) reintroductions have been common in the 20th and 21st centuries, yet 40% have failed to establish self-sustaining elk populations due to a lack of post-reintroduction demographic monitoring. Elk were reintroduced to West Virginia in 2016 following more than a century of absence after the species was extirpated in 1875. Elk were translocated to West Virginia from Land Between the Lakes National Recreation Area (LBL) in eastern Kentucky and from Arizona. The two groups of elk differ in their subspecies, physiology, reintroduction history, connectivity, and habitat. Reintroductions create genetic risks such as the founder effect and …

Investigating The Physiological, Metabolomic, And Transcriptomic Changes In Response To Telomerase Deletion In Saccharomyces Cerevisiae, Taizina Momtareen

Graduate Theses, Dissertations, and Problem Reports (ETD)

Telomerase is an enzyme found in rapidly dividing cells that maintains chromosome ends and prevents the loss of genetic information during cell division. When telomerase is inactive, cells gradually lose their telomeres and eventually stop dividing. In yeast, a rare subset of cells can bypass this growth arrest by switching to a recombination-based mechanism to maintain telomeres. Therefore, yeast provides a powerful system to study this adaptation, as telomerase-deficient strains can generate 'survivors' that mimic the Alternative Lengthening of Telomeres (ALT) pathway observed in some human tumors. In this work, my goal was to examine how a telomerase-null (TLC1 …