Biology Commons^™

Quantitative Shotgun Proteomic Analysis Of Bacteria After Overexpression Of Recombinant Spider Miniature Spidrion, Masp1, Kathryn P. Randene

University of the Pacific Theses and Dissertations

Spider silk has extraordinary mechanical properties, displaying high tensile strength, elasticity, and toughness. Given the high performance of natural fibers, one of the long-term goals of the silk community is to manufacture large-scale synthetic spider silk. This process requires vast quantities of recombinant proteins for wet-spinning applications. Attempts to synthesize large amounts of native size recombinant spidroins in diverse cell types have been unsuccessful. In these studies, we design and express recombinant miniature black widow (Latrodectus hesperus) MaSp1 spidroins in bacteria that incorporate the NTD and CTD, along with varying numbers of codon-optimized internal block repeats. Following spidroin overexpression, we …

Transgenerational Effects Of Stress On The Plasma Proteome Of A Marine Mammal, Emily Voelkner

University of the Pacific Theses and Dissertations

The physiological stress response enables animals to respond to changes in their environment, and is mediated by the hypothalamic-pituitary-adrenal (HPA) axis in mammals. Increased activation of the HPA axis by repeated stress during critical life stages like reproduction could affect fitness. Information about a stressor can be communicated to offspring via hormone signals prenatally, or postnatally via milk, and affect offspring development and stress reactivity. Experimentally activating the HPA axis by adrenocorticotropic hormone (ACTH) administration results in the synthesis of the major glucocorticoid hormone cortisol, which has well-studied far-reaching effects on growth, metabolism, and immunity. Beyond cortisol levels alone, biomarkers …

Investigating Changing Macronutrient Dynamics At A Plant, Microbe And Plant-Microbe Interactions Scale, Emel Kangi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nutrient limitation drives forest ecosystem processes by altering net primary production, belowground (C) investments, and microbial activity. As such, the availability of essential macronutrients, such as nitrogen (N) and phosphorus (P), can severely impact plant growth, microbial decomposition, and the strength of plant-microbial interactions. However, our understanding of plant and microbe responses to changing nutrient availability, and the extent to which nutrient availability affects plant-microbe interactions, remains somewhat limited. Therefore, in this dissertation, I aimed to investigate nutrient limitation on a plant, microbe, and plant-microbe interaction level. First, to connect the phenotypic responses of nutrient-limited plants to key molecular mechanisms, …

Building Better Biofuel Crops: A Field Evaluation Of Transgenic Populus Modified To Improve Feedstock Performance For Bioenergy Use, Molli Elisabeth Coombs

Graduate Theses, Dissertations, and Problem Reports (ETD)

A transition away from fossil fuel use is necessary for the future of energy production, and biofuels are a renewable energy option that can mitigate the impacts of fossil fuels through lowered carbon emissions and possible carbon sequestration. In order to successfully compete with fossil fuels, the production of biofuels must be sustainable and cost effective. Populus species are a biofuel crop used for bioenergy conversion from lignocellulosic biomass that have been proposed for use in feedstock plantations on marginal lands, which would avoid competition with agricultural production. Two challenges of feedstock production being faced are recalcitrance to chemical processing, …

Better Understanding The Barred Owl, Adam Lee Potts

Graduate Student Theses, Dissertations, & Professional Papers

This thesis research presents an analysis of barred owl nest site selection in an understudied region of their expanded range. The barred owl has dramatically expanded its range westwards over the last 150 years, prompting multiple conflicting reinterpretations of their species account. Hypotheses of range expansion are reviewed to provide context for this study’s research. This study gathers empirical data on nest site selection in the mixed conifer forests of Montana’s Seeley-Swan and Mission Valleys. Eight barred owl nests were located following extensive territory surveys. Field measurements of tree height and diameter using USFS Forest Inventory and Analysis (FIA) plot …

Abundance And Habitat Associations Of Bivalves In Mosquito Lagoon, A Preliminary Survey, Mariam Sonbol

Honors Undergraduate Theses

This study investigates the understudied abundance and habitat associations of bivalves in Mosquito Lagoon. Seagrass habitats were found to support the highest diversity of mollusks in earlier surveys (Mikkelsen et al., 1995). Twelve sites, including seagrass-vegetated, unvegetated, and seagrass-restored areas, were sampled in March and May 2024. Habitat characteristics, such as sediment composition and seagrass cover, were analyzed alongside bivalve populations. Across all sites, 6 genera were identified among 44 individuals. Overall abundance and diversity of bivalves collected were low in all sites, and most individuals were juveniles. Sediment characteristics influenced differences in diversity across site types, with restored sites …

Role Of Interferon Induced Transmembrane Protein 3 (Ifitm3) And Neural Precursor Cell Expressed Developmentally Down Regulated Protein 4 (Nedd4) In Seneca Virus A (Sva) Replication, Shamiq Aftab

Electronic Theses and Dissertations

In this study, we studied the role of IFITM3 in SVA replication in vitro by silencing the endogenous IFITM3 in NCI-H1299 cells. An average of 1.94-fold increase in SVA VP2 expression and an average of 4.4-fold increase in supernatant virus titer was observed after 24h SVA isolate SD15-26 infection. We have indeed observed an increase in viral mRNA copies by an average of 5-fold in IFITM3 silenced NCI-H1299 cells at 8 hpi indicating that IFITM3 restricts SVA replication post virus attachment and entry. A positive correlation between interferon-alpha induced IFITM3 upregulation and reduced SVA replication was observed. To further confirm …

Dynamic Genomic Evolution Via Active Ltr Transposable Elements In Maize, Taylor Isles

Theses, Dissertations and Culminating Projects

Long terminal repeats (LTR) retrotransposons, found across eukaryotes, are transposable elements which can copy and insert themselves into other loci within a genome. These transposable elements are similar to retroviruses in that they rely on reverse transcriptase to “copy and paste” themselves elsewhere in the genome. From the RNA transcript they are able to use reverse transcriptase to make another DNA copy of themselves. This initially gave them the moniker, selfish genes. However, in the decades after the discovery of reverse transcriptase and LTR retrotransposons, it became known that non-genic DNA could have other functions. LTR retrotransposons are sources of …

The Blackfeet Nation’S Bison Conservation Herd Management Plan, Brandon Kittson

Graduate Student Theses, Dissertations, & Professional Papers

This document is meant to act as a guide to understanding Bison reintroduction on the Blackfeet reservation and serve as a resource for bison management. This report and plan will: 1) review bison ecology and the history of reintroduction efforts on the reservation; 2) identify potential issues and barriers to successful reintroduction; 3) present a summary of current land policies and patterns of land use on the reservation; and 4) provide recommendations for dealing with those potential issues. Recommendations will be based on analyses of previous knowledge of bison and bison behavior.

Csn-5: A Tumor's Friend Or Foe In The C. Elegans Germline?, Kellie C. Kuch

Graduate Student Theses, Dissertations, & Professional Papers

The COP9 signalosome is a highly conserved eukaryotic complex regulating protein degradation via deneddylation of Cullin-RING E3 ligases. CSN5, the COP9’s fifth component, contains the catalytically active domain for CSN deneddylation. The complex is inactive without CSN5; however, CSN5 engages in COP9-independent binding with several other proteins, typically promoting either destruction or stabilization of its partners. Many of its confirmed interaction partners are also implicated in tumorigenesis (prominent examples being p27 and p53) and a complex cancer interactome has been established for CSN5. Additionally, CSN5 overexpression has been documented in a staggering array of cancers of diverse origins. This discovery …

Understanding Cellular Dynamics: Investigating A Yeast-Two Hybrid Protein-Protein Interaction, Riok3:Cse1l; Also By Investigating Trogocytosis Of Cd4+ T Cells From Rhog-/- Mice, Brittnee N. Crane

Graduate Student Theses, Dissertations, & Professional Papers

Rift Valley fever virus (RVFV) is a negative-sense virus that was first described in 1930 when it was isolated from sheep during an outbreak. In the last 25 years there has been a spread in the geographical range into the Middle East. The most susceptible animals are cattle, goats, sheep, and camels. The most overt symptom of livestock infection is that infected pregnant animals experience spontaneous abortion. Humans are susceptible as well and symptoms range from mild febrile illness to liver necrosis, blindness, hemorrhagic fever, and death. An important player in the cellular innate response to RVFV infections is the …

Repatriation And A Biological Profile Of Indigenous Remains Of West Texas, Haley P. Rebardi

Graduate Student Theses, Dissertations, & Professional Papers

The Native American Graves Protection and Repatriation Act (NAGPRA) was created in response to the injustice, mishandling, looting, and trafficking of Native American remains and cultural artifacts. However, even with the latest amendment in December of 2023, there are still gray areas in the context and language. Notably, an issue with NAGPRA is the act only includes institutions and organizations that receive and are supported by Federal funding. Consequently, the act does not cover private collections. The main concern in these contexts is the lack of communication, awareness, and/or permission with and from descendant tribes or potential descendants when it …

Bird Predation On Coho Salmon (Oncorhynchus Kisutch) In Humboldt Bay, Colton J. Dixon

Cal Poly Humboldt theses and projects

Coho Salmon (Oncorhynchus kisutch) populations along the west coast of the United States are declining. In Humboldt County, located in northwestern California, Coho Salmon have been in decline since their federal listing as threatened in 1997, primarily due to habitat loss from logging, agriculture, and urban development. Although these anthropogenic factors caused salmon populations to decline, bird predation may also be hindering population recovery, as evidenced by the recovery of Passive Integrated Transponder (PIT) tags, originally implanted in Coho Salmon, from bird colonies in Humboldt Bay. This study examines predation by Double-crested Cormorants (Phalacrocorax auritus), Caspian …

The Larval Preference Of An Invasive Bryozoan (Watersipora 'New Species') For Copper-Based Antifouling Paints, Alexander K. Strawhand

Cal Poly Humboldt theses and projects

The bryozoan Watersipora subtorquata and its cryptic congener Watersipora ‘new species’ are now globally invasive species. Previous studies have found this species complex to have a high tolerance to copper-based antifouling paints, which represent a large portion of the mitigation effort toward preventing hull fouling by invasive invertebrates. Tolerance alone, however, is unlikely to explain the full extent of Watersipora’s massive and rapid worldwide invasion success. The aim of this research was to move beyond tolerance, and test whether larvae of Watersipora ‘new species’ exhibit a preference for copper-coated settlement surfaces in both laboratory and field settings. For the laboratory …

Characterizing The Habitat Use Of Pacific Coast Feeding Group Gray Whales (Eschrichtius Robustus) And The Spatial And Temporal Variability Of Their Benthic And Planktonic Invertebrate Prey In Northern California, Robyn E. Norman

Cal Poly Humboldt theses and projects

As opportunistic foragers, the Eastern North Pacific population (~20,000) of gray whales (Eschrichtius robustus) feed on diverse benthic and planktonic invertebrates in northern Alaska foraging grounds before they undertake one of the largest yearly migrations of any mammal to breed in Baja California, Mexico. While most of the population travels to the summer foraging grounds in Alaska, a sub-group of whales (~230) called the Pacific Coast Feeding Group (PCFG) summer between British Columbia, Canada, and northern California. The diet of PCFG whales typically includes high-density and/or high-caloric prey items like mysids and diverse species of amphipods, yet a …

Protein Turnover Rate And Life History As An Explanation Of The Extreme Difference In Cost Of Biosynthesis In Cockroach Nymphs And Painted Lady Butterfly Larva, Kyara Nicole Holloway

Masters Theses

The cost of biosynthesis in painted lady caterpillars is far lower than that of a red runner cockroach. A promising explanation for this phenomenon is the protein turnover rate for the animal during biosynthesis and tissue maintenance. Previous research has shown that, per gram of body weight, the painted lady butterfly can synthesize a biomass using up to 15x less energy and resources than the cockroach, even under similar conditions. The resulting ratios, especially in respect to growth rate, show a wide disparity between species in such a manner that does support a protein synthesis and degradation rates as a …

Functional Investigation Of Shaggy, An Inhibitor Of Canonical Wnt Signaling, In The Tardigrade Hypsibius Exemplaris, Raul A. Chavarria

UNF Graduate Theses and Dissertations

Tardigrades have a highly simplified anteroposterior (AP) axis. The mechanisms that regulate the development of this secondarily simplified AP axis are not known. In many animals, the canonical Wnt (cWnt) signaling pathway regulates primary axis establishment through antagonistic interactions with inhibitors of cWnt signaling. This study investigated the roles of shaggy, an inhibitor of cWnt signaling, in regulating development in the tardigrade Hypsibius exemplaris. Gene expression patterns of shaggy and other components of the cWnt signaling pathway were analyzed alongside markers of anterior and posterior identity using Hybridization Chain Reaction in situ in H. exemplaris. RNA interference …

Endophytic Fungi Associated With Galls And Host Plants Of Asphondylia Borrichiae (Diptera: Cecidomyiidae), Shannon Lynn Sharpe

UNF Graduate Theses and Dissertations

Asphondylia borrichiae, like other gall-forming gnats, are obligate symbionts to the endophytic fungi (EF) they deposit when laying eggs. Asphondylia spp. and EF are important biocontrol agents, yet details surrounding their diversity, life cycles, and host interactions remain poorly understood. Galls and leaf-stem tissues from two host plants were surveyed to identify and compare EF diversity between the host tissues and species of A. borrichiae. Identification of 114 isolates was carried out by sequencing the internal transcribed spacer (ITS 1/4 primers). Pairwise alignments in multiple genetic databases were bolstered by phylogenetic analyses using maximum parsimony and maximum likelihood …

High-Quality Dietary Protein (Essential Amino Acids Matched To Reproductive Needs) Partially Breaks The Lifespan And Reproduction Trade-Off In Lubber Grasshoppers, Emma Kordek

UNF Graduate Theses and Dissertations

Finding interventions to break the trade-off between reproduction and lifespan can provide insight into physiological limitations of animals. Effects of dietary protein quality on the trade-off are currently unclear, but clarity could lead to better designed diets that match animal needs. Dietary amino acid blends matching yolk proteins support reproduction and extend lifespan in fruit flies. To test if this is conserved across species, we matched dietary amino acids to vitellogenin to test reproduction and lifespan in adult females of the lubber grasshopper. Specifically, we compared varying degrees of protein quality by manipulating dietary essential amino acids. We identified a …

Evaluating The Use Of Baited Remote Underwater Video (Bruv) In Assessing Shark And Fish Populations In A Low Visibility Estuarine System, The Tolomato River, Fl, Usa, Sarah Worthington

UNF Graduate Theses and Dissertations

Recently, there has been increasing use of baited remote underwater video (BRUV) surveys for assessing shark and fish populations in marine ecosystems. This approach can be useful because it may provide a non-destructive, non-extractive, and cost-effective alternative to traditional fishing-based methods. However, to date, most studies using BRUVs have focused on their use in high-visibility ecosystems, such as tropical reefs. Furthermore, few studies have compared results from BRUV surveys with those obtained using traditional methods to evaluate the efficacy of this approach. Therefore, the goal of this study was to evaluate the effectiveness of using BRUV surveys to assess shark …

Examining Genome Size And Nutrient Influence On Damage Patterns, And Plant-Invertebrate Community Dynamics, Hailee B. Petosky

Dissertations, Master's Theses and Master's Reports

Genome size (GS) varies widely among angiosperms and has been shown to mediate plant responses to nutrients. Variations of GS drastically impact plant growth, fitness, and competitive responses, influencing plant functioning, nutrient requirements, and potentially, consumptive interactions. Specifically, plants with larger genomes vary in their cellular nutrient requirements, affecting tissue quality, nutrient constraints, and invertebrate interactions. Furthermore, environmental nutrient enrichments are a key driver affecting ecosystem functioning and species interactions. Plant communities are impacted by both top-down and bottom-up controls of herbivores and nutrients, respectively, and alterations to these interactions may cause cascading trophic level effects to influence damage patterns …

Acidophile Microbiology: From Extreme Environments To Biotechnological Applications, Elizabeth L.J. Watkin, Ivan Nancucheo, Axel Schippers

Research outputs 2022 to 2026

No abstract provided.

Effects Of Subchronic Oral Pfos Exposure Via Drinking Water On Gut Microbiota Composition, Emma Ann Loder

Graduate Theses/Dissertations

Perfluorooctanesulfonic acid (PFOS) has been phased out of production in the United States, but because of its resistance to degradation and its persistence in the environment, PFOS can be found in drinking water across America. Oral exposure to PFOS has been linked to adverse developmental, immunological, hepatic, and endocrine health. Oral PFOS exposure may alter the gut microbiota and cause dysbiosis, which is implicated in the pathology of inflammatory diseases like Crohn’s disease, diabetes, and ulcerative colitis. The goal of the study was to investigate the effects of subchronic oral PFOS exposure on the composition of the gut microbiota. Adult …

Valorization Of Spent Vetiver Roots For Biochar Generation, Sameer Neve, Dibyendu Sarkar, Manas Warke, Teresa Bandosz, Rupali Datta

Michigan Tech Publications

Vetiver root is widely used to produce essential oils in the aromatherapy industry. After the extraction of oil, the roots are disposed of as waste. The central objective of this research was to explore the conversion of this waste into a resource using a circular economy framework. To generate biochar, vetiver roots were pyrolyzed at different temperatures (300, 500, and 700 °C) and residence times (30, 60, and 120 min). Analysis showed the root biochar generated at 500 °C and held for 60 min had the highest surface area of 308.15 m2/g and a yield of 53.76%, in addition to …

Quantum Dot Effect On Endocytic Pathways And Eisosome Organization, Onyinye Dorathy Okafor

Graduate Theses/Dissertations

Despite the promising applications of Quantum Dots (QDs) in the biomedical field, the long-lasting effects of QDs on the cell remain poorly understood. To comprehend the mechanisms underlying the toxic effects of QDs in yeast, I characterized defects associated with receptor-mediated endocytosis (RME) as well as on pinocytosis using Saccharomyces cerevisiae as a model in the presence of CdSe/ZnS QDs. My findings revealed that QDs led to an inefficient RME at the early, intermediate, and late stage of endocytic patch maturation at the endocytic site, with the prolonged lifespan of GFP-fused yeast fimbrin (Sac6-GFP), a late marker of endocytosis. The …

Effect Of Rare Earth Element Mixtures On Daphnia Magna, Celine Do

Theses and Dissertations (Comprehensive)

Rare earth elements (REEs) are increasingly being used in modern technologies and as such, there is an increasing concern for the potential environmental risk associated with anthropogenic contamination. In addition to there being very little data available for individual REEs, there is also a lack of knowledge concerning mixtures. The objective of my study was to investigate the chronic effects of lanthanum (La) and yttrium (Y) as well as the acute effects of neodymium (Nd), praseodymium (Pr) and Y as a single metal and as a mixture to Daphnia magna. Standard 21-d chronic tests and 48-h single metal acute …

Evaluating The Risk Posed By Gadolinium In The Grand River Watershed, Johann Memmel

Theses and Dissertations (Comprehensive)

Gadolinium (Gd) is a rare earth element (REE), primarily used in contrast agents for magnetic resonance imaging (MRI), with additional applications in metallurgy, phosphors, neutron shielding, and other niche applications. Both Gd and Gd-based contrast agents (GBCAs, the form used for MRIs) have been detected downstream of wastewater effluent discharges and there is currently little research into the risk this poses to aquatic ecosystems. This study investigated the potential environmental risks of Gd and GBCAs using the Grand River watershed (GRW) in southwestern Ontario as a model ecosystem due to it containing a variety of land uses (urban, industrial, agricultural) …

The Effects Of Warmer Temperatures On The Physiology Of Invasive Sea Lamprey And Imperiled Populations Of Lake Sturgeon In The Laurentian Great Lakes, Milica Koledin

Theses and Dissertations (Comprehensive)

Invasive sea lamprey (Petromyzon marinus) contributed to massive declines in fisheries in the Laurentian Great Lakes due to their parasitism of large-bodied salmonid fishes in the 20^th century. Chemical control measures, which involve the application of 3-trifluoromethyl-4-nitrophenol (TFM) into rivers containing larval sea lamprey, were successfully implemented approximately 60 years ago to control populations. Recently, however, it was discovered that TFM tolerance increases in sea lamprey with a rise in temperature for reasons which are incompletely understood. Nor is it understood how sea lamprey will respond to warmer temperatures due to climate change, which could affect their …

Comparing Ionoregulation And Modes Of Nitrogen Excretion Across The Life Cycle Of Parasitic And Non-Parasitic Lamprey Species, Shannon Davidson

Theses and Dissertations (Comprehensive)

Abstract

Ionoregulation and nitrogenous waste (N-waste) metabolism in fishes has been extensively documented in teleosts and elasmobranchs, but less so in lampreys (Petromizontiformes). All lamprey species undergo metamorphosis which drastically changes their physiology and modes of feeding. However, differences in ionoregulatory mechanisms due to anadromous versus non anadromous life history strategies emerge following metamorphosis in different lamprey species. Furthermore, some species, such as anadromous juvenile sea lamprey (Petromyzon marinus), are parasitic and migrate to seawater (SW) to ingest blood protein from host fishes, while juveniles of freshwater (FW), non-parasitic species, such as the American brook lamprey …

Impacts Of Environmental Stressors On Mummichog (Fundulus Heteroclitus) Growth And The Gh-Igf1 Pathway Using A Laboratory Bioassay, Olena Kuntyj

Theses and Dissertations (Comprehensive)

Using a flow-through laboratory bioassay, experiments investigated the effects of limited feeding, increased temperature, ammonium chloride (NH₄Cl), and 17α-ethinylestradiol (EE₂) on juvenile mummichog (Fundulus heteroclitus) growth. Weight measurements were taken every three days as the apical growth endpoint. Gene expression was examined by qPCR for genes in the GH (growth hormone)-IGF1 (insulin-like growth factor 1) pathway, including gh, igf1, and their receptors (ghra, ghrb, igf1ra, igf1rb). In Experiment 1, juvenile mummichog were exposed to excess or limited feed for 21 days. The limited-fed mummichog weighed less, were …