Biology Commons^™

Fine Characterization Of Leafing Phenology In The Brazilian Atlantic Forest By Optical And Microwave Remote Sensing, James B. Bell

Dissertations and Theses

Tropical forests provide important ecosystem functions in the global biosphere, but they remain among the most poorly understood elements of land surface models, especially with regard to their seasonal dynamics. For instance, in seasonally dry forests, the pattern of the annual green-up in their canopies closely follows annual patterns of rainfall. The same, however, does not occur in wet forest canopies which are dominated by evergreen trees. In the latter, water is not scarce enough to limit leaf photosynthetic function. Canopy leafing phenology in these forests is therefore poorly characterized by optical remote sensing methods which are not sensitive to …

Human Fatalities Resulting From Wild Pig Attacks Worldwide: 2000–2019, John J. Mayer, James E. Garabedian, John C. Kilgo

Human–Wildlife Interactions

Although reported to be rare, human fatalities resulting from wild pig (Sus scrofa) attacks do occur. Toward a better understanding of patterns in fatal wild pig attacks, we synthesized worldwide reports of wild pig attacks on humans between 2000 and 2019. We documented 163 separate reports of fatal wild pig attacks that resulted in 172 human deaths. On average, 8.6 human deaths occurred annually due to wild pig attacks during those 2 decades. The majority of fatal attacks resulted in a single human death; however, there were 6 cases in which an individual fatal attack resulted in 2–4 …

Grizzly Bears And Humans At Alpine Moth Sites In Wyoming, Usa, Erika A. Nunlist, Dan Tyers, Andrew Pils, Bok F. Sowell

Human–Wildlife Interactions

Army cutworm moths (Euxoa auxiliaris; moths) are an important seasonal higher elevational food source for grizzly bears (Ursus arctos horribilis; bears) in the Greater Yellowstone Ecosystem (Wyoming, Montana, and Idaho, USA). Increased human interaction with bears at moth sites is an important management issue because of the potential for displacing bears and the concern for human safety. Managers will need better information regarding human–bear interactions at high-density moth sites that are also accessible to humans to mitigate potential conflicts. In the summers of 2017 and 2018, we studied human–bear interactions at 2 of the most human …

Dune Building Dynamics Impact Cross-Island Connectivity And Barrier Island Characteristics, Alexander Sabo

Theses and Dissertations

Located at the land-sea interface, barrier islands are important protective features that reduce wave energy and erosion from mainland areas. Further, barrier islands provide habitat for many different organisms and serve as popular areas for recreation and tourism. As sandy landforms, barrier islands are easily disturbed, but often recover after disturbance as a result of island plant communities, specifically dune building grasses. Disturbance on barrier islands is driven by storms, tides, and overwash events. After disturbance has occurred, dune grasses colonize the dunes allowing for dune building and habitat restoration. On the Virginia barrier islands, there are three dominant dune …

Pre-Clinical Trials With Precision-Medicine Based Therapeutics In Basal-Like Patient-Derived Xenografts, David C. Boyd

Theses and Dissertations

Breast cancer treatments have improved over time, but the diseases seeing the most benefit from these improvements have the estrogen receptor, progesterone receptor, or are positive for HER2. Basal-like breast cancer tends to not have these biomarkers, which necessitates their treatment to be traditional, untargeted therapeutics which are less effective and tend to have harsh adverse effect profiles – this is an important unmet need. These studies utilize a variety of techniques, including tissue culture, viability assays, high-throughput screening, in vivo drug treatments and imaging, pathway analyses, molecular techniques such as Western blot, antibody arrays, RNA sequencing, sc RNA sequencing, …

Plant Trait Effects On Tidal Wetland Methane Emission, Adam M. Dunn

Theses and Dissertations

High rates of carbon (C) sequestration exhibited by coastal wetlands is an important natural climate solution to global environmental change. At the same time, however, wetlands are the largest natural source of methane (CH₄) to Earth’s atmosphere, a potent greenhouse gas that influences the global climate. Wetland CH₄ emissions display high degrees of uncertainty in accounting for spatial and temporal variations in emissions due to the complex interactions between biotic and abiotic factors that influence methane production and transport, in addition to simultaneous influences from climate-driven effects on wetlands such as rapid sea level rise and increased …

Epithelial Membrane Protein 3 (Emp3b) Is A Novel Regulator Of Sympathetic Nervous System Development In Zebrafish., Jessica M. White

Theses and Dissertations

Notable progress has been made in understanding the development of the neural crest (NC). Neural crest cells (NCCs) can be divided into 4-5 subpopulations. A major lineage among trunk NC derivatives are sympathoadrenal (SA) cells, which give rise to the sympathetic nervous system (SNS). Trunk NCCs follow a ventromedial migration pathway where signals derived from the dorsal aorta instruct migrating NCCs to a SA cell fate. Defects in NC development can result in syndromes known as neurocristopathies. Neuroblastoma is one of the most common forms of pediatric cancer affecting nearly 800 infants each year in the United States (Takita et …

Salinization Impacts On Heterotrophic Respiration, Ecosystem Respiration, And Plant Productivity In Tidal Freshwater Marshes, Kelsie J. Moses

Theses and Dissertations

Tidal freshwater marshes have preserved substantial stocks of soil carbon, which represents carbon dioxide that is no longer in the atmosphere. There is conflicting evidence in the literature about how disturbances such as sea level rise and associated wetland salinization impact the accumulation and long-term stability of this stored carbon. The goal of this experiment was to quantify how salinization impacts total ecosystem respiration and its component parts, autotrophic and heterotrophic respiration. This was a microcosm experiment using a C4 plant (Spartina cynosuroides) grown in soil derived from C3 plant matter and exposed to different salinities (0 to …

Wolbachia Infection In Gall Associated Insect Communities In Illinois And Indiana, Jakeb Watts

Masters Theses

Wolbachia is a maternally inherited, gram-negative bacterium and has been found to be associated with up to 60% of all insects, frequently resulting in male-killing, feminization, and cytoplasmic incompatibility in the hosts. Gall wasps and other gall-forming insects induce on various host plants abnormal tissue growths, or plant galls, with distinct morphology. They are considered as obligatory parasites to their host plant. The presence of Wolbachia infection in gall wasp populations in North America has not been extensively documented. Given the strong influence on host reproduction, not knowing Wolbachia infection in insect populations prevents the understanding of how populations are …

Identifying Microdebris In Biodeposits Of The Eastern Oyster, Crassostrea Virginica, Elizabeth E. Hieb, Sadie Snow, Ruth H. Carmichael

Gulf and Caribbean Research

No abstract provided.

Application Of Crispr/Cas9 Whole Genome Screens To Advance Macrophage Biology, Kevin Wanniarachchi

Electronic Theses and Dissertations

Advances in CRISPR/Cas9 gene editing technologies present opportunities to better understand the contribution of individual genes to complex eukaryotic cellular processes. I have applied CRISPR whole genome screen technologies to inform further mechanistic understanding of macrophage fitness and neutral lipid metabolism. This work is important because macrophages play critical roles in immune function and are implicated as causative agents in disease states. Chapter One of this dissertation provides insights into how CRISPR genome screening technologies have improved biological discovery and key findings from their application and discusses how this technology can be implemented to advance the discovery of novel macrophage …

Application Of Hierarchical Species Distribution Models To Avian Species Of South Dakota And The Upper Missouri River Basin, Reza Goljani Amirkhiz

Dissertations and Theses

Recognizing the distributional patterns of species can inform management actions and increase scientific knowledge about species. Habitat Suitability Models (HSMs) are valuable tools in modeling species’ niches and effects of climate change and anthropogenic and natural disturbances on species’ distributions and abundances. In this dissertation, I expanded the application of hierarchical HSMs for a rare bird (Virginia’s warbler) and an economically valuable bird (ring-necked pheasant) in South Dakota. Also, we developed multiscale HSMs for grassland birds in the Upper Missouri River Basin (UMRB) to quantify current habitat associations and predict the influences of climate and landcover change associated with the …

Variation In Carapace Damage Within And Among Loggerhead Musk Turtle (Sternotherus Minor) Populations In Florida Spring-Fed Ecosystems, Joseph J. Pignatelli Iii, Katrina Campbell, Brian P. Butterfield, Gerald R. Johnston, Joseph C. Mitchell, Grover J. Brown, J. Brian Hauge, Andrew D. Walde, Eric C. Munscher

Research, Publications & Creative Work

Damage to a turtle’s shell can provide evidence of past events such as vehicle collisions, disease, predator encounters, or even a behavioural interaction between members of the same species. Documenting shell damage as part of long-term mark and recapture studies enables researchers to determine population trends, intraspecific interactions and identify potential issues within turtle populations. This paper analyses shell damage in populations of the Loggerhead Musk Turtle (Sternotherus minor) (Agassiz, 1857). We examined carapace shell damage frequency and severity in 2701 individual S. minor (1468 males and 1233 females) captured in spring-fed habitats in one state preserve and five state …

Dna Barcoding Indicates Multiple Invasions Of The Freshwater Snail Melanoides Tuberculata Sensu Lato In Florida, Lori Tolley-Jordan, Michael A. Chadwick, Jimmy K. Triplett

Research, Publications & Creative Work

Melanoides tuberculata sensu lato (Thiaridae) are polymorphic female-clonal snails of Asian and African origins that have invaded freshwaters worldwide, including those in Florida. Although the snails have been documented in Florida for at least 70 years, no studies have investigated whether the observed distribution is due to a single introduction or multiple independent invasions. Here, cytochrome oxidase I was used to measure genetic diversity within and among sites in Florida and compare genetic diversity between Florida and other regions of the world. We also examined the relationship between shell morphology and haplotype diversity to determine if shell morphs can serve …

Genetic Selection For Improved Production Efficiency In The Mature Dairy Herd, Maeve Williams

Theses

Improving dairy cow production efficiency is highly desirable because of its well-documented impact on profitability and sustainability. Long-term gains in dairy cow production efficiency have already been delivered through genetic selection. Nonetheless, achieving further improvements in production efficiency could cement the economic and environmental efficiency of the dairy industry, globally. To date, several components contributing to production efficiency have been overlooked, with many studies focusing on dairy cow production efficiency over short periods rather than lifetime efficiency. Therefore, the objectives of this thesis were to quantify the genetic variance components of complementary dairy cow efficiency metrics; including dry matter intake, …

Identification And Creation Of Novel Bacteriocins With Potential Food And Clinical Applications, David Lynch

Theses

Bacteriocins represent a heterogeneous group of small, ribosomal-synthesized, potent antibacterial peptides produced by bacteria, capable of inhibiting bacteria both closely related or indeed those from other genera than the producer. In addition to their role as food preservatives, bacteriocins have potent activity against medically significant pathogens and are considered attractive alternatives to antibiotics, due to their inherent heat stability, potency at nanomolar scale, resistance to proteases and low levels of acquired resistance in commercial applications. The aim of this thesis was to identify, purify and bioengineer novel bacteriocins from Staphylococcus and Lactic Acid Bacteria (LAB), with a view to expanding …

Survival In Common Snapping Turtles, Chelydra Serpentina (Testudines: Chelydridae), In Western Nebraska, John B. Iverson, Geoffrey R. Smith

Faculty Publications

Annual estimates of survival for Common Snapping Turtles (Chelydra serpentina) in western Nebraska USA were generated from mark-recapture data from nesting females encountered in 2005–2017. Our population models suggested no annual variation in either adult annual survival (0.947 ± 0.017 SE) or annual capture probability (0.294 ± 0.027 SE). However, there was a tendency toward higher survival in larger females. High annual survival (e.g. > 90%) characterises populations of Chelydra from Ontario to Texas.

Unraveling The Regulatory Basis Of The Desiccation Tolerance Trait In Selaginella Lepidophylla, Madhavi Anuradha Ariyarathne Hewa Babarandhage

Dissertations and Theses

Desiccation tolerance was a crucial adaptation for plants during their transition to terrestrial environments. Some spike mosses, including S. lepidophylla, have evolved the remarkable ability to tolerate extreme desiccation, enabling survival in arid regions of the world. However, the regulatory basis of this trait remains unknown. This dissertation aims to unravel the genetic basis of desiccation tolerance in Selaginella lepidophylla and its potential for improving crop abiotic stress tolerance. To achieve this goal, three objectives were pursued. Objective 1 focused on determining the regulatory role of the SlbHLH transcription factor (TF) by overexpressing it in Arabidopsis thaliana to assess its …

Host-Microbe Interactions In Non-Native Estuarine Anemones: Biogeography And Temperature, Parker K. Lund

Cal Poly Humboldt theses and projects

Non-native species are increasing in prevalence around the world, resulting in negative economic and ecological impacts. However, the broad distributions of non-native species also offer a system for investigating the response of host-associated microbial communities to environmental factors across a range of ecological scales. At the broadest scale, I investigated the geography of microbial communities in the non-native estuarine anemone Diadumene lineata on the west coast of the United States of America. Across latitudes, microbial community composition was very similar and displayed a high percentage of Klebsiella spp. at all sites. However, the communities in California tended to exhibit higher …

Prevalence Of Batrachochytrium And Ranavirus In Southern Torrent Salamanders (Rhyacotriton Variegatus) In Northern California, Marilyn Violeta Sandoval

Cal Poly Humboldt theses and projects

Amphibian population declines around the world have been attributed in part to the emergence of deadly pathogens. However, the severity of the effects of pathogens on amphibian communities can vary by species and location. This study focuses on assessing the prevalence of Batrachochytrium dendrobatidis (Bd), Batrachochytrium salamandrivorans (Bsal), and ranaviruses in populations of southern torrent salamanders (Rhyacotriton variegatus). I also tested for association between environmental factors and the prevalence and viral load of the three pathogens in Northern California. A total of 309 skin swab samples were collected from salamanders in nine sites in …

A Year At The Forefront Of Bacterial Defense Systems Against Neutrophilic Oxidants, Sadia Sultana, Jan-Ulrik Dahl

Faculty Publications – Biological Sciences

One challenge for invading pathogens represents the exposure to highly microbicidal hypohalous acids (HOX), such as hypochlorous acid (HOCl) and hypothiocyanous acid (HOSCN). Generated at high concentrations by innate immune cells during phagocytosis, HOX kills the engulfed microbes through extensive macromolecular damage. However, microorganisms have evolved strategies to detoxify the oxidants and/or alleviate HOX-mediated damage, which improves their survival during HOX exposure. Many of these defense systems are bacteria-specific and therefore considered potential drug targets. Our minireview highlights recent (July 2021 to November 2022) advances in the field of microbial HOX defense systems and how these systems are regulated. We …

The Use Of A Habitat Quality Stress Index To Evaluate Stress As An Analog For Proximate Fitness In The American Crow Within A Matrix Of Landcover Characteristics To Assess Its Potential Contribution To Disease Etiologies, Theodore Lee Grabarz

Antioch University Dissertations & Theses

All organisms occur within spatial and temporal environments to maximize proximate fitness (health) and thus life history outcomes. Previous work has examined the temporal and behavioral aspects of proximate fitness on life history outcomes particularly regarding highly perturbed environments (i.e., climate and land use change, resource extraction, agricultural erosion, etc.). My work focuses on the less examined spatial aspect of these perturbed environments. More specifically, this dissertation examines habitat selection and quality as the basis for understanding stress response (negative and positive feedback mechanisms) to environmental stressors within the larger context of regional or gamma (ɣ) biodiversity. Through the lens …

White Matter Hyperintensity Longitudinal Morphometric Analysis In Association With Alzheimer Disease, Jeremy Fuller Strain, Chia Ling Phuah, Babatunde Adeyemo, Kathleen Cheng, Kyle B. Womack, John Mccarthy, Manu Goyal, Yasheng Chen, Aristeidis Sotiras, Hongyu An, Chengjie Xiong, Andrea Scharf, Catherine Newsom-Stewart, John Carl Morris

Biological Sciences Faculty Research & Creative Works

INTRODUCTION: Vascular damage in Alzheimer's disease (AD) has shown conflicting findings particularly when analyzing longitudinal data. We introduce white matter hyperintensity (WMH) longitudinal morphometric analysis (WLMA) that quantifies WMH expansion as the distance from lesion voxels to a region of interest boundary. METHODS: WMH segmentation maps were derived from 270 longitudinal fluid-attenuated inversion recovery (FLAIR) ADNI images. WLMA was performed on five data driven WMH patterns with distinct spatial distributions. Amyloid accumulation was evaluated with WMH expansion across the five WMH patterns. RESULTS: The preclinical group had significantly greater expansion in the posterior ventricular WM compared to controls. Amyloid significantly …

Temperature Regulation Of Pipecolic Acid-Mediated Plant Systemic Immunity In Arabidopsis Thaliana, Alyssa Shields

Theses and Dissertations (Comprehensive)

Significant crop losses are caused by pathogenic infections annually, which are exacerbated by increasing global temperatures due to climate change. One way by which plants respond to pathogenic attacks is through the activation of pattern-triggered immunity (PTI), effector-triggered immunity (ETI), and systemic acquired resistance (SAR), which lead to production of the central defence phytohormone salicylic acid (SA). Accompanying SA release is the putative mobilization of pipecolic acid (Pip), which acts as an immune regulatory plant metabolite that works with and independently from SA. As demonstrated in the model plant Arabidopsis thaliana following infection with the model bacterial pathogen Pseudomonas syringae …

Potential Effects Of Road Proximity On Zooplankton Communities And Water Quality In Lakes In The Northwest Territories, Marie N. Hannan

Theses and Dissertations (Comprehensive)

Studies conducted along Canada’s Dempster Highway in the Northwest Territories have shown that road dust can affect water quality in roadside lakes, leading to higher calcium, conductivity, and pH levels. These water quality changes have the potential to affect important members of the lower aquatic food web, such as zooplankton.

For my thesis research, I had two main objectives: 1) To determine if changes in water chemistry caused by deposition of road dust affects zooplankton communities; and 2) To examine if the type of roadside vegetation influences the effects of road dust on aquatic habitats. To achieve these objectives, I …

The Effect Of Alkalinity On Lampricide Effectiveness And Gill Physiology In Invasive Sea Lamprey (Petromyzon Marinus), Alexandre J. Walsh

Theses and Dissertations (Comprehensive)

The pesticides, 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide are used to control populations of invasive sea lamprey (Petromyzon marinus) in the Laurentian Great Lakes of North America. Added to streams infested with larval sea lamprey, the effectiveness of these pesticides, commonly called lampricides, are strongly influenced by water pH, with greater toxicity for both TFM and niclosamide in lower pH than higher pH water. However, the TFM and niclosamide sensitivity of sea lamprey are also greater in poorly buffered, low alkalinity water than in high alkalinity water but it is unclear why. One goal of my thesis was to propose …

Characterization Of The Clostridioides Difficile Glycosyl Hydrolase Ccsz, Brian Lowrance

Theses and Dissertations (Comprehensive)

Bacteria inhabit many of the harshest environments on Earth; persisting and thriving in conditions thought to be unsuitable for life. One common strategy to withstand these environments is the formation of a biofilm. Biofilm composition varies greatly, depending on the underlying community that produces it. Cellulose, a polymer consistently prevalent in biofilms, has been identified as a virulence factor in many pathogens and is suspected to be involved in pathogenesis by Clostridioides difficile. C. difficile is the #1 cause of hospital acquired diarrhea, which can range from mild to life-threatening infections. Biofilm formation is hypothesized to be involved in …

Winter Dynamics Of Storm Water Management Ponds And Winter Tolerance In Three Aquatic Plant Species, Patrick Strzalkowski

Theses and Dissertations (Comprehensive)

The vast majority of the research into the performance of stormwater management ponds (SWMPs) has been performed in warm regions or during the warmer seasons in temperate regions. It is presumed that SWMPs are inactive in the winter as any potential stormwater is trapped in snow and ice. The main goal of this thesis was to test this presumption and to study the dynamics and performance of three SWMPs during the winter. Remote water level loggers were installed into the three SWMPs and daily grab samples from the influents and effluents were taken and analyzed for total phosphorus (TP), chloride, …

Updated Virophage Taxonomy And Distinction From Polinton-Like Viruses, Simon Roux, Matthias G. Fischer, Thomas Hackl, Laura A. Katz, Frederik Schulz, Natalya Yutin

Biological Sciences: Faculty Publications

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of “hyperparasitism” in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and …

Endogenous Antioxidant Response And Lipid Peroxidation Levels In Muscle Tissue Of The Cownose Ray (Rhinoptera Bonasus), Bailey Berry

College of Graduate Studies: Theses & Dissertations

Oxidative stress is the result of an imbalance between reactive oxygen species (ROS) and antioxidant response within cells. ROS generation is a natural consequence of ETC activity within the mitochondria and is associated with aerobic metabolism. Oxidative stress data on elasmobranch muscle is limited, with previous studies primarily focusing on mammalian and teleost muscle. Elasmobranch skeletal muscle is generally composed of large proportions of white muscle fibers (anaerobic), low proportions of red muscle fibers (aerobic), and low proportions of pink muscle fibers (anaerobic). The cownose ray, a benthopelagic batoid species, presents an interesting model of study because it contains relatively …