Biology Commons^™

Genomic And Metabolic Network Properties In Thermophiles And Psychrophiles Compared To Mesophiles, Amal Saeed Alblooshi

Theses

Thermophiles and psychrophiles are extremophilic microorganisms that thrive in harsh conditions. Thermophiles are mostly located in hot springs, prosper in high temperatures. Psychrophiles thrive in extremely cold environments, including polar regions and deep-sea habitats. Although they play a crucial role in biotechnology and environmental research, their mechanisms of adaptation are still not well understood. The main objective of this thesis is to understand the genomic characteristics and metabolic network features in thermophiles and psychrophiles compared to mesophiles. The genomes of 59 species among thermophiles, psychrophiles, and mesophiles were collected from the NCBI database. These genomes were used to analyze their …

Designing Tpack-Driven Mobile Learning With Digital Citizenship For Biology Education: Insights From Ngt And Ism Approaches, Cik Jamaliah Abd Manaf, Shakinaz Desa, Muhamad Ikhwan Mat Saad, Helen Crompton

STEMPS Faculty Publications

The rapid digitization of education and the complexity of scientific content demand the integration of digital citizenship in TPACK-based mobile learning for Biology. This study aimed to identify and prioritize relevant digital citizenship practices using a Design and Development Research approach. In Phase One, the Nominal Group Technique with 10 experts evaluated eight proposed practices. Phase Two employed Interpretive Structural Modeling with nine experts to structure hierarchical relationships. Seven practices were retained, with Ethical Use of Digital Resources as the top-level driver. The resulting framework supports ethical and discipline-specific mobile learning models, promoting responsible digital engagement in Biology education.

Environmental Pollutants: A Risk For Premature Aging And Transgenerational Toxicity, Alex Kathleen Daniels

Masters Theses

"This thesis aims to identify interactions between C. elegans’ reproductive system and global pollutants such as microplastics, HgCl₂, nicotine, and pesticides. Human exposure to these pollutants and their effect on reproduction can be analyzed using the C. elegans as a model organism. Systematic analysis of matricidal hatching, progeny production, germline apoptosis, and lifespan assays determined effects on reproduction and reproductive aging. Through my experiments, it was determined that no significant effects were produced from the selected polystyrene, polyethylene, vape juice, nicotine hemi sulfate salt, imidacloprid, or glyphosate regarding matricidal hatching or progeny production. I confirmed that HgCl₂ induced significant effects …

Evaluation Of The Impact Of Secondhand E-Cigarette Aerosols On Ros-Mediated Alterations Of Epigenetic Events: Implications For Copd Pathogenesis And Assessment Of The Efficacy Of Cold Atmospheric Plasma In Degrading Organophosphate Pesticides On Kevlar Materials, Ta-Chun Lin

Masters Theses

"We explored 1) the toxicological impacts of e-cigarette aerosols and 2) the decontamination efficacy of Cold Atmospheric Plasma (CAP) technology over organophosphates. In examining the effects of firsthand and secondhand e-cigarette aerosol exposure on A549 and BEAS-2B lung cells, we observed significant cytotoxicity, increased ROS levels, and epigenetic modifications, including heightened DNA methylation and downregulation of histone deacetylases (HDACs). These molecular alterations may contribute to chronic respiratory conditions, such as COPD, underscoring the health risks of e-cigarette exposure.

We investigated CAP’s effectiveness in degrading organophosphate pesticide (OP) residues on fabric surfaces, revealing that CAP treatment effectively decomposes OPs such as …

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 …

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 …

The Effect Of Sars-Cov-2 On Bacterial Diversity And Abundance In Community Wastewater, Joshua Lambert

Graduate Theses, Dissertations, and Problem Reports (ETD)

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) enters human respiratory cells through binding of its spike (S) protein to the ACE-2 receptor, which is highly expressed in lung cells, but is also found in over 150 other cell types encompassing major organs including GI enterocytes. SARS-CoV-2 causes gut dysbiosis in infected individuals and patients with COVID-19 and also coincides with lower alpha diversity of the individual’s gut microbiome. Certain gut microbiome-associated genera are lower in abundance in COVID-19 patients including Lachnospira, Prevetolla, Roseburia, Bifidobacterium, and Faecalibacterium while genera such as Bacteroides, Enterococcus and Proteobacteria are increased during a SARS-CoV-2 …

Spatial Analysis Of American Chestnut (Castanea Dentata) Distribution And Ecology In Kentucky’S Federal Lands, Jacob Raymond Pease

Murray State Theses and Dissertations

Anthropogenic factors have been the cause of the decline of tree species across the globe. From unsustainable logging and development to disease and improper management, threats to forests have taken their toll. The American chestnut (Castanea dentata) was once an integral basal tree species in Appalachian forests, but chestnut blight drove the species to functional extinction by the mid-1900s. The recent creation of genetically modified chestnuts gives hope for future restoration of the species throughout its historical range. Despite blight resistance, effective restoration will require optimal site selection for finding and planting chestnuts, which will maximize limited resources. …

Understanding Bird Diversity: A Modeling Approach In An Urban And Wetland Ecosystem, Clay Bliznick

Murray State Theses and Dissertations

The global increase in anthropogenically-driven shifts of land cover has resulted in losses to many natural communities such as prairies and wetlands. These ecosystems take on artificially-derived characteristics such as croplands, buildings, and roads to the extent that they no longer resemble the areas they once were. This process often results in the loss of biodiversity, ecological integrity, and valuable ecosystem services in these environments. Attempts to restore the condition and function of these disturbed areas are often implemented, but due to the complexity of factors driving these restorations, there is often a lack of practical insight needed to optimize …

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 …

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 …

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 …

Contactin2(Cntn2)Creert2 Mouse Line, A New Genetic Tool For Temporal Control To Trace The Developing Neurons In The Nose, Alexis M. Semon

Electronic Theses & Dissertations (2024 - present)

Neuronal migration is a vital process in embryonic development. In rodents, the very first neurons that originate from the olfactory placode migrate toward the developing brain as part of the migratory mass. This migratory mass includes Gonadotropin-releasing hormone-1 (GnRH-1) neurons, pioneer/terminal nerve (TN) neurons, and olfactory ensheathing cells—a type of glial cell.

Contactin-2 (Cntn2), also referred to as transiently expressed axonal surface glycoprotein-1 (TAG-1), belongs to the contactin family of proteins, which is part of the immunoglobulin superfamily of cell adhesion molecules. Cntn2 has been extensively utilized as a transient/stage-specific molecular marker for various neuronal populations, including commissural neurons of …

Larval Environments Affect The Implementation Of The Sterile Insect Technique On Aedes Mosquitoes, Katherine G. Evans

Theses and Dissertations

Sterile Insect Technique (SIT) is an effective method for controlling pests and has been increasing in popularity to control Aedes mosquitoes. SIT involves inundating an area with sterilized male mosquitoes to reduce egg hatch and ultimately the number of wild adults. Previous research indicates that enacting mortality early in the larval life of Aedes mosquitoes can result in counter-productive effects, due to reduced competition among developing larvae. I hypothesize that the effectiveness of SIT at reducing adult populations is modified by densitydependent mortality and density-dependent growth among larvae. I performed two field-to-lab studies and developed an individual-based model to test …

A Novel Silver-Ruthenium-Based Antimicrobial Kills Gram-Negative Bacteria Through Oxidative Stress-Induced Macromolecular Damage, Patrick O. Tawiah

Theses and Dissertations

The rise in drug-resistant bacteria, together with the decline in antibiotic development, requires new strategies for infectious disease control. Gram-negative pathogens are particularly challenging to combat due to their outer membrane. This study highlights the effectiveness of the silver-containing antimicrobial AGXX® against the Gram-negative bacterium Escherichia coli. AGXX® is a promising silver coating that presumably kills bacteria through the generation of reactive oxygen species (ROS). However, neither AGXX®’s mode of action is fully understood, nor have its effects on Gram-negative bacteria or bacterial response and defense mechanisms towards AGXX® been studied in detail. Here, I report that the bactericidal …

Accurate Body Weight Class Prediction From Mirna And Gene Expression In Blood And Saliva Samples, Kimberly Lettner

Master of Science in Forensic Science Directed Research Projects

miRNA interference on protein abundance related to glucose uptake and lipid production has been evaluated in biomedical research and linked to metabolic disorders like severe obesity. The direct regulation of protein abundance caused by miRNAs on a person’s metabolism can lead to an increased weight and overall size. Body size, measured by BMI, provides additional physical descriptions that can be combined with hair color, eye color, age, and skin pigment to aid investigations of unidentified remains or unknown suspects not found in a database. The purpose of this project was to evaluate the miRNA expression of target biomarkers in dried …

Comparative Semiotic Analysis Of Non-Verbal Communication: Apis Mellifera Waggle Dance And Human Kinesic Signaling Systems, Nishtha Tikalal

Honors Undergraduate Theses

There are many parallels between two seemingly disparate forms of non-verbal communication: the waggle dance of Apis mellifera (honeybees) and human kinesic signaling systems. Through a comparative semiotic analysis, this research aims to conduct a comparative semiotic analysis, investigating structural and functional similarities between these communication methods, challenging anthropocentric assumptions about meaning making in the natural world. This research employs a meta-synthesis approach, drawn from a methodological literature review to examine historical representations of bee-human relationships, semiotics of non-verbal communication, and the specific mechanisms of the waggle dance and human kinesics. This methodology involves systematic categorization and analysis of extracted …

Salinity Effects On Cu(Ii) Bioremediation By Chlamydomonas Reinhardtii Microalgae, Jennifer Hughes

Honors Undergraduate Theses

Microalgae offer a sustainable approach to wastewater treatment by removing pollutants such as excess nutrients, CO₂, and heavy metals. Among various species, Chlamydomonas reinhardtii shows strong potential in removing Cu(II) ions from wastewater. In addition, salinity stress in C. reinhardtii has been linked to morphological and metabolic changes that enhance lipid and phytochemical production. While salinity stress has been studied for enhancing biofuel production, its impact on microalgal removal of heavy metals, particularly Cu(II), remains largely unexplored. Understanding how varying salinity conditions affect both algal growth and the efficiency of Cu(II) remediation could provide critical insights for improving integrated wastewater …

Factors Influencing The Discovery And Use Of Carrion By Vertebrate Scavengers From Human-Induced Mass-Mortality Events, Samantha J. Leivers, Michael J. Bodenchuk, Tyler A. Campbell, John M. Tomeček

Human–Wildlife Interactions

Scavengers play critical roles in ecosystem health and stability, and both biotic and abiotic factors can influence scavenger guild dynamics. Carrion is often limited both temporally and spatially on the landscape, but mass mortality events (MMEs)—in which there is an influx of carrion biomass on the landscape—may result in different scavenger community dynamics compared to when carrion is scarcely distributed. In this study, we investigated factors affecting the discovery and use of carrion by a natural, unharrassed scavenger guild during wild pig (Sus scrofa) MMEs conducted at East Foundation’s San Antonio Viejo Ranch in South Texas, USA. We …

Enhancing Alfalfa Persistence In Rangelands: Evaluating Morphological Traits Of Medicago Sativa Subsp. Falcata Germplasm, Abdulallah Mohammed Alomair

Electronic Theses and Dissertations

Rangelands cover nearly half of the Earth’s surface, representing about 54% (79 million km2), and occur in different types and climates worldwide. Alfalfa (Medicago sativa L.) is a major component in rangelands and covers about (320 thousand km2), representing about 0.4% of total global rangeland area. As a critical perennial legume crop, alfalfa can improve soil health by fixing approximately 336 kg/ha/year of nitrogen and sequestering up to 614 kg/ha/year of carbon, while enhancing livestock production due to its high content level of vitamins, magnesium, minerals, fiber, and protein. However, environmental stresses such as drought, freezing, and grazing limit alfalfa …

Mechanisms Leading To Cell Survival Through Membrane Repair In Pyroptosis, Prafulla Shrestha

Electronic Theses and Dissertations

No abstract provided.

No Detected Signal Of The 2022 Epizootic From Multiannual Diadema Antillarum Settlement Data In The Florida Keys, Jason Albrecht

Theses, Dissertations and Culminating Projects

The sea urchin Diadema antillarum is a key coral reef grazer that remains functionally extinct on many Caribbean reefs following a mass mortality event in 1983–84. In 2022, another widespread mortality event, likely caused by a scuticociliate parasite, again decimated D. antillarum at reefs across the Caribbean. Understanding the population-level impacts of this recent epizootic will be important for coral reef conservation efforts. This study examines multi-year larval settlement data from the Florida Keys to determine if the 2022 mortality event reduced larval settlement. Larval settlement was assessed monthly at three long-term monitoring sites (Delta Shoal, Tennessee Reef, and Pickles …

Tricolored Bat (Perimyotis Subflavus) Population Genetic Structure In The Southeastern United States, Laura Henderson

Master's Theses

Tricolored bats (Perimyotis subflavus) have experienced substantial population losses from white-nose syndrome (WNS), a disease caused by the pathogenic fungus Pseudogymnoascus destructans (Pd) which infects hibernating bats. Determining population genetic structure helps assess genetic diversity and the impacts of wildlife threats to populations. Pre-WNS data shows weak-to-negligible structure and panmictic P. subflavus populations at core portions of their range. However, current genetic data from their southeastern U.S. range is lacking. I sought to determine whether recent genetic data help resolve genetic structure among southeastern populations and assess genetic differences at two stages of impact: post-WNS and …

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 …

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 …

Cultivation Of Winged Kelp (Alaria Marginata) In Humboldt Bay, Evan C. Simpson

Cal Poly Humboldt theses and projects

The cultivation potential of the winged kelp (Alaria marginata) was evaluated in Humboldt Bay, California, to further develop sustainable aquaculture in the region. Seasonality, depth, and system design were evaluated in regard to harvest biomass and quality. Results suggested that single-longline configurations at shallow depths (< 2 m) produced greater total biomass than a multi-longline system, suggesting enhanced water flow and reduced self-shading improved growth. Kelp grew best with a winter outplanting period (December-April), most likely due to environmental conditions (e.g., temperature, nutrients, and salinity) being within the kelp’s tolerable range, with as much as 2.24 kg/meter of kelp being harvested. These findings demonstrate that while the estuarine system has more variable conditions than predicted, A. marginata can be successfully cultivated in Humboldt Bay and highlight its potential as a viable crop for northern California’s emerging seaweed industry. Future work targeting the optimization of single-longline design and deployment timing may further improve yield and support regional goals for sustainable aquaculture and food security.