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Species Responses To Habitat Edges And Fragmentation Per Se: A Cross Taxa Meta-Analysis, Rachel Snyder Jan 2023

Species Responses To Habitat Edges And Fragmentation Per Se: A Cross Taxa Meta-Analysis, Rachel Snyder

Masters Theses

Aim We examined the scale equivalency of fragmentation effects at the patch scale and landscape scale to determine if patch level effects scale up to landscape level effects. First, we examined species responses to fragmentation effects at the patch scale and landscape scale. Second, we evaluated whether there is a difference in response between taxonomic groups and across latitudes. Finally, we analyzed the data at the level of individual species in order to determine how species respond to edge effects and fragmentation effects. Location Data for 71 studies were gathered from the BioFrag database. Studies used were located in 48 …

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The Effect Of Larval Competition On Adult Life History Traits And The Immune Response Of Adult Cat Fleas (Ctenocephalides Felis), Piper N. Zellner, Lisa D. Brown Jan 2023

The Effect Of Larval Competition On Adult Life History Traits And The Immune Response Of Adult Cat Fleas (Ctenocephalides Felis), Piper N. Zellner, Lisa D. Brown

Honors College Theses

In holometabolous insects, conditions during the larval stage can affect the adult stage. For instance, in mosquitoes, reduced larval food and high density can make adults more susceptible to infection. Fleas (Siphonaptera), like mosquitoes, go through complete metamorphosis and have adult stages that exclusively feed on the blood of vertebrates, including humans. However, flea larvae have chewing mandibles and rely on nutrients from dried fecal matter containing vertebrate blood proteins. Their limited mobility and unique nutritional needs confine their development to specific areas, likely leading to frequent larval competition in natural conditions. Yet, the influence of larval density on the …

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Application Of Hierarchical Species Distribution Models To Avian Species Of South Dakota And The Upper Missouri River Basin, Reza Goljani Amirkhiz Jan 2023

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 …

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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 Jan 2023

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 …

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Dna Barcoding Indicates Multiple Invasions Of The Freshwater Snail Melanoides Tuberculata Sensu Lato In Florida, Lori Tolley-Jordan, Michael A. Chadwick, Jimmy K. Triplett Jan 2023

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 …

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Genetic Selection For Improved Production Efficiency In The Mature Dairy Herd, Maeve Williams Jan 2023

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, …

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Identification And Creation Of Novel Bacteriocins With Potential Food And Clinical Applications, David Lynch Jan 2023

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 …

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Survival In Common Snapping Turtles, Chelydra Serpentina (Testudines: Chelydridae), In Western Nebraska, John B. Iverson, Geoffrey R. Smith Jan 2023

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.

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The Foxo1 Inhibitor As1842856 Triggers Apoptosis In Glioblastoma Multiforme And Basal-Like Breast Cancer Cells, David Flores, Alma Lopez, Shreya Udawant, Bonnie Gunn, Megan Keniry Jan 2023

The Foxo1 Inhibitor As1842856 Triggers Apoptosis In Glioblastoma Multiforme And Basal-Like Breast Cancer Cells, David Flores, Alma Lopez, Shreya Udawant, Bonnie Gunn, Megan Keniry

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

Basal-like breast cancer (BBC) and glioblastoma multiforme (GBM) are poor-prognosis cancers that lack effective targeted therapies and harbor embryonic stem gene expression signatures. Recently, our group and others found that forkhead box transcription factor FOXO1 promotes stem gene expression in BBC and GBM cell lines. Given the critical role of cancer stem cells in promoting cancer progression, we examined the impact of FOXO1 inhibition with AS1842856 (a cell-permeable small molecule that directly binds to unphosphorylated FOXO1 protein to block transcriptional regulation) on BBC and GBM cell viability. We treated a set of BBC and GBM cancer cell lines with increasing …

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Nilgai, Boselaphus Tragocamelus And White-Tailed Deer, Odocoileus Virginianus Use Of Water Troughs With And Without Remotely Operated Field Sprayers For Potential Treatment Of Cattle Fever Ticks, John A. Goolsby, Mauricio Cruz, Reyes Garcia Iii, Lauren P. Maestas, Teresa Patricia Feria-Arroyo Jan 2023

Nilgai, Boselaphus Tragocamelus And White-Tailed Deer, Odocoileus Virginianus Use Of Water Troughs With And Without Remotely Operated Field Sprayers For Potential Treatment Of Cattle Fever Ticks, John A. Goolsby, Mauricio Cruz, Reyes Garcia Iii, Lauren P. Maestas, Teresa Patricia Feria-Arroyo

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

Nilgai antelope, Boselaphus tragocamelus and white-tailed deer (WTD), Odocoileus virginianus are hosts of cattle fever ticks, Rhipicephalus (=Boophilus) microplus, in the Lower Rio Grande Valley of South Texas. Daily use of water troughs and ponds were observed to determine if these locations could be used for field treatment methods for cattle fever ticks using remotely operated field sprayers. Game cameras (n=16) were deployed between June 2020 and September 2022 at two private ranches in Cameron County, TX. Both nilgai and WTD visited water troughs equipped with motion detecting sprayers in similar numbers to ponds, but numbers of animal visits were …

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Unraveling The Regulatory Basis Of The Desiccation Tolerance Trait In Selaginella Lepidophylla, Madhavi Anuradha Ariyarathne Hewa Babarandhage Jan 2023

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 …

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Updated Virophage Taxonomy And Distinction From Polinton-Like Viruses, Simon Roux, Matthias G. Fischer, Thomas Hackl, Laura A. Katz, Frederik Schulz, Natalya Yutin Jan 2023

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 …

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Host-Microbe Interactions In Non-Native Estuarine Anemones: Biogeography And Temperature, Parker K. Lund Jan 2023

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 …

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Use Of Foreign Edna Tracers To Resolve Site- And Time-Specific Edna Distributions In Natural Streams, Braden A. Herman Jan 2023

Use Of Foreign Edna Tracers To Resolve Site- And Time-Specific Edna Distributions In Natural Streams, Braden A. Herman

Cal Poly Humboldt theses and projects

Substantial uncertainty in how to interpret eDNA observations motivates a need for a technique to effectively and efficiently measure of system- and time-specific eDNA distributions. Using a technique to robustly calibrate eDNA dynamics in a given system would improve established eDNA methods such as presence and absence and has the potential to refine estimates of organism abundance using eDNA concentration that are less well understood. Particles of eDNA are present in a wide variety of size and type resulting in varying transport dynamics, persistence, decay, among others. This variation likely makes eDNA transport more complex than that of conservative tracers …

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Prevalence Of Batrachochytrium And Ranavirus In Southern Torrent Salamanders (Rhyacotriton Variegatus) In Northern California, Marilyn Violeta Sandoval Jan 2023

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 …

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Assessing The Recovery Of Forest Understory Vegetation After Clearcut Logging Across A 445-Year Chronosequence, Molly Smith Metok Jan 2023

Assessing The Recovery Of Forest Understory Vegetation After Clearcut Logging Across A 445-Year Chronosequence, Molly Smith Metok

Cal Poly Humboldt theses and projects

The conversion of natural forested lands to managed forests has reduced the amount of older, structurally diverse forests worldwide. In conifer forests of the Pacific Northwest (USA) – where the understory plant communities comprise only 1% of forest biomass but represent 90% of the plant species richness – the long-term impacts of timber harvesting are not fully understood. I used a chronosequence of forests in southwestern Oregon that ranged from 25 to 445 years of age to compare changes in plant communities in logged (i.e., managed) stands with that of stands in late succession and old growth conditions. The chronosequence …

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C3 And C4 Grass Dominated Plant Communities Differ In Response To Future Larger And Less Frequent Rainfall, Zigeng Chen Jan 2023

C3 And C4 Grass Dominated Plant Communities Differ In Response To Future Larger And Less Frequent Rainfall, Zigeng Chen

Electronic Theses and Dissertations

Climate change is leading to larger and less frequent rainfall in the Northern Great Plains (NGP). We ask if this change in rainfall would influence carbon (C) and nitrogen (N) cycling in the NGP. First, we collected soils from C3 and C4 grass dominated plant communities from western South Dakota and conducted an incubation experiment to explore the effects of soil water content (SWC) and temperature on soil respiration (Rs) and N mineralization rate (ΔIN). Second, we conducted a three-year rainfallmanipulation (RaMP) experiment with two distinct rainfall regimes (frequent/small and infrequent/large events with constant total monthly precipitation) and two grasses …

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Effects Of Pregnancy And Lactation On Muscle-Tendon Morphology, Nicole Danos, Marjorie Patrick, Jacob Barretto, Francesca Bilotta, Megan Lee Jan 2023

Effects Of Pregnancy And Lactation On Muscle-Tendon Morphology, Nicole Danos, Marjorie Patrick, Jacob Barretto, Francesca Bilotta, Megan Lee

Biology: Faculty Scholarship

Pregnancy and lactation hormones have been shown to mediate anatomical changes to the musculoskeletal system that generates animal movement. In this study, we characterize changes in the medial gastrocnemius muscle, its tendon and aponeuroses that are likely to have an effect on whole animal movement and energy expenditure, using the rat model system, Rattus norvegicus. We quantified muscle architecture (mass, cross-sectional area, and pennation angle), muscle fiber type and diameter, and Young's modulus of stiffness for the medial gastrocnemius aponeuroses as well as its contribution to Achilles tendon in three groups of three-month-old female rats: virgin, primiparous pregnant, and primiparous …

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Mutational Analysis Of Mechanosensitive Ion Channels In The Carnivorous Venus Flytrap Plant, Carl Procko, Wen Mai Wong, Janki Patel, Seyed Ali Reza Mousavi, Tsegaye Dabi, Marc Duque, Lisa Baird, Sreekanth H. Chalasani, Joanne Chory Jan 2023

Mutational Analysis Of Mechanosensitive Ion Channels In The Carnivorous Venus Flytrap Plant, Carl Procko, Wen Mai Wong, Janki Patel, Seyed Ali Reza Mousavi, Tsegaye Dabi, Marc Duque, Lisa Baird, Sreekanth H. Chalasani, Joanne Chory

Biology: Faculty Scholarship

How the Venus flytrap (Dionaea muscipula) evolved the remarkable ability to sense, capture, and digest animal prey for nutrients has long puzzled the scientific community.1 Recent genome and transcriptome sequencing studies have provided clues to the genes thought to play a role in these tasks.2,3,4,5 However, proving a causal link between these and any aspect of the plant’s hunting behavior has been challenging due to the genetic intractability of this non-model organism. Here, we use CRISPR-Cas9 methods to generate targeted modifications in the Venus flytrap genome. The plant detects prey …

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Building Consensus Around The Assessment And Interpretation Of Symbiodiniaceae Diversity, Cawa Tran, Et Al. Jan 2023

Building Consensus Around The Assessment And Interpretation Of Symbiodiniaceae Diversity, Cawa Tran, Et Al.

Biology: Faculty Scholarship

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic …

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Changes In The Microbiome Of The Sea Anemone Exaiptasia Diaphana During Bleaching From Short-Term Thermal Elevation, Jamison R. Sydnor, Jamie Lopez, Gordon V. Wolfe, Lisa Ott, Cawa Tran Jan 2023

Changes In The Microbiome Of The Sea Anemone Exaiptasia Diaphana During Bleaching From Short-Term Thermal Elevation, Jamison R. Sydnor, Jamie Lopez, Gordon V. Wolfe, Lisa Ott, Cawa Tran

Biology: Faculty Scholarship

We examined the response of microbial communities in the model sea anemone Exaiptasia diaphana (Aiptasia) to short-term thermal elevation. Through 16S rRNA gene sequencing, we characterized the microbiomes of symbiotic (with algal symbionts) and aposymbiotic (bleached) anemones under ambient (27°C) and heat-stressed (34°C) conditions for 8-10 days, using both replicated endpoint and non-replicated time-course approaches. Consistent with prior studies, we observed a stable abundance of bacteria from the families Alteromonadaceae and Rhodobacteraceae, though with wide variation among individual anemones. We observed that symbiotic state conferred a larger impact on the microbiome than heat stress, implying the microbiome may play a …

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Proposing An Rna Interference (Rnai)-Based Treatment For Human Immunodeficiency Virus (Hiv) By Analyzing The Post-Transcriptional Gene Targeting Of Sars-Cov-2, Hepatitis C Virus, And A549 Lung Cancer Cells, Arjun Jagdeesh Jan 2023

Proposing An Rna Interference (Rnai)-Based Treatment For Human Immunodeficiency Virus (Hiv) By Analyzing The Post-Transcriptional Gene Targeting Of Sars-Cov-2, Hepatitis C Virus, And A549 Lung Cancer Cells, Arjun Jagdeesh

UROP Posters

Human Immunodeficiency Virus (HIV) is a retrovirus that infects CD4+ T cell lymphocytes in humans, leading to the development of Acquired Immunodeficiency Syndrome (AIDS) if left untreated. While current treatment methods, including antiretroviral combination treatments, effectively limit HIV replication, HIV can evade these treatments due to its high mutation rate. Long-term antiretroviral treatment can also be toxic to patients, meaning patients would benefit from a new mechanism of HIV treatment. RNA interference (RNAi) is an antiviral pathway found in mammals, plants, and insects that involves a small-interfering RNA that is incorporated into a protein complex called the RNA-induced Silencing Complex …

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Sense And Sensitivity: Spatial Structure Of Conspecific Signals During Social Interaction, Keshav Ramachandra Jan 2023

Sense And Sensitivity: Spatial Structure Of Conspecific Signals During Social Interaction, Keshav Ramachandra

Graduate Theses, Dissertations, and Problem Reports (ETD)

Organisms rely on sensory systems to gather information about their environment. Localizing the source of a signal is key in guiding the behavior of the animal successfully. Localization mechanisms must cope with the challenges of representing the spatial information of weak, noisy signals. In this dissertation, I investigate the spatial dynamics of natural stimuli and explore how the electrosensory system of weakly electric fish encodes these realistic spatial signals. To do so In Chapter 2, I develop a model that examines the strength of the signal as it reaches the sensory array and simulates the responses of the receptors. The …

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Morphological, Physiological, And Transcriptional Responses Of Populus Trichocarpa To Water Deficit Stress, Kristin Justine Ratliff Jan 2023

Morphological, Physiological, And Transcriptional Responses Of Populus Trichocarpa To Water Deficit Stress, Kristin Justine Ratliff

Graduate Theses, Dissertations, and Problem Reports (ETD)

Under the threat of climate change with continued fossil fuel use, investment in developing renewable energies is increasingly important. One category of renewable energy sources, biofuels, is well suited to industries that require a liquid fuel source. However, producing biofuel feedstocks is challenging from a sustainability perspective, as they require extensive land area and resource input to grow on marginal lands. The identification of strategies that feedstock species use to maintain productivity with limited to no resource inputs could aid in the selection of optimal genotypes or targets of breeding or engineering efforts to maximize productivity in feedstock plantations. Some …

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Assessment Of Conservation Reserve Program Enhancements At Contract Renewal: Impact On Monarch Butterfly (Danaus Plexippus) Habitat, Tristan L. Murphy Jan 2023

Assessment Of Conservation Reserve Program Enhancements At Contract Renewal: Impact On Monarch Butterfly (Danaus Plexippus) Habitat, Tristan L. Murphy

Dissertations and Theses @ UNI

The monarch butterfly (Danaus plexippus) is a migratory species whose primary breeding range is the upper Midwestern United States. In 2022, the International Union for the Conservation of Nature listed the monarch as endangered due to milkweed and migratory habitat loss. One of the most promising opportunities for monarch recovery is to enhance habitat quality on private land currently enrolled in the USDA Conservation Reserve Program (CRP). In order to qualify for re-enrollment in the program and continuation of annual government payments, farmers must show adequate habitat quality or enhance their site by overseeding after burning, herbicide application, …

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Endogenous Antioxidant Response And Lipid Peroxidation Levels In Muscle Tissue Of The Cownose Ray (Rhinoptera Bonasus), Bailey Berry Jan 2023

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 …

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Loggerhead Sea Turtle (Caretta Caretta) Nesting Experience, Seasonal Variation, And Hatching Success On A Georgia Barrier Island, Luke Sundquist Jan 2023

Loggerhead Sea Turtle (Caretta Caretta) Nesting Experience, Seasonal Variation, And Hatching Success On A Georgia Barrier Island, Luke Sundquist

College of Graduate Studies: Theses & Dissertations

Loggerhead sea turtles nest commonly on the Georgia barrier islands and serve critical roles in human cultures, coastal economies, and multiple ecosystems. However, their global populations are declining and dependent on conservation efforts and informed management of natural and anthropogenic threats. Nesting offers a unique opportunity to research and protect this valuable marine species in terrestrial habitats. Microsatellite DNA sampling from eggshells can consistently identify nesting females from eggshells, allowing tracking of nesting behaviors for large populations over multiple years. Using this novel technology, we compared maternal investment and nest site-selection between first-time nesting neophytes and experienced remigrants. We sampled …

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Dna Methylation And The Response To Infection In Introduced House Sparrows, Melanie Gibson Jan 2023

Dna Methylation And The Response To Infection In Introduced House Sparrows, Melanie Gibson

College of Graduate Studies: Theses & Dissertations

Epigenetics is the study of molecular modification of a genome without changing its base pairs. The most studied type of epigenetic mechanism is DNA methylation, which is capable of turning a gene “on” or “off.” Epigenetic potential is the capacity to which an individual can have methylation on its genome. The more CpGs available, the greater the epigenetic potential. In invasive species, genetic variation has been observed to be paradoxical: not much of it exists on a genomic level, but epigenetically, phenotypic variation can occur. The focus on shift in gene expression in this study is on Toll-Like Receptor 4 …

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Quantitative Measurement Of Protac Intracellular Accumulation, Xin Yu, Jin Wang Jan 2023

Quantitative Measurement Of Protac Intracellular Accumulation, Xin Yu, Jin Wang

Faculty, Staff and Students Publications

In recent years, Proteolysis Targeting Chimera (PROTAC) technology has emerged as one of the most promising approaches to remove disease-associated proteins by utilizing cells' own destruction machinery. To achieve successful degradation of a protein of interest (POI), the heterobifunctional PROTAC molecules must penetrate into the cells first, followed by target engagement and formation of the POI-PROTAC-E3 ligase complex. Based on this understanding, the assessment of cell permeability and in cell target engagement are of great importance to evaluate the efficacy of PROTAC candidates. PROTAC molecules can be classified as non-covalent and covalent, and covalent PROTACs can be further divided into …

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Room-Temperature Crystallography Reveals Altered Binding Of Small-Molecule Fragments To Ptp1b, Tamar Skaist Mehlman, Justin T. Biel, Syeda Maryam Azeem, Elliot R. Nelson, Sakib Hossain, Louise Dunnett, Neil G. Paterson, Alice Douangamath, Romain Talon, Danny Axford, Helen Orins, Frank Von Delft, Daniel A. Keedy Jan 2023

Room-Temperature Crystallography Reveals Altered Binding Of Small-Molecule Fragments To Ptp1b, Tamar Skaist Mehlman, Justin T. Biel, Syeda Maryam Azeem, Elliot R. Nelson, Sakib Hossain, Louise Dunnett, Neil G. Paterson, Alice Douangamath, Romain Talon, Danny Axford, Helen Orins, Frank Von Delft, Daniel A. Keedy

Advanced Science Research Center

Much of our current understanding of how small-molecule ligands interact with proteins stems from X-ray crystal structures determined at cryogenic (cryo) temperature. For proteins alone, room-temperature (RT) crystallography can reveal previously hidden, biologically relevant alternate conformations. However, less is understood about how RT crystallography may impact the conformational landscapes of protein-ligand complexes. Previously, we showed that small-molecule fragments cluster in putative allosteric sites using a cryo crystallographic screen of the therapeutic target PTP1B (Keedy et al., 2018). Here, we have performed two RT crystallographic screens of PTP1B using many of the same fragments, representing the largest RT crystallographic screens of …

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