Life Sciences Commons^™

Bridging The Gap Between Plot-Level And Landscape-Scale Analysis For Wildfire Risk Assessment, Vanessa Leigh Niemczyk

Graduate Student Theses, Dissertations, & Professional Papers

Remote sensing technology has advanced greatly over the past couple of decades proving its ability to aid in wildfire risk assessment and improve our understanding of forest structure and fuel inventory across the landscape. While some aerial and satellite sensors perform better than others, they all have a common weakness, their reduced ability to capture understory fuels with high detail. Terrestrial laser scanning is an emerging solution due to its understory perspective. This research leverages the beneficial aspects of both terrestrial laser scanning and various aerial- or satellite-based remote sensing platforms (aerial laser scanning, digital aerial photogrammetry, and Sentinel-2) to …

Spatial And Temporal Patterns Of Nutrient Limitation In A Western Montana River, Matthew T. Nichols

Graduate Student Theses, Dissertations, & Professional Papers

Enhanced loading of nitrogen (N) and phosphorus (P) is pervasive in rivers around the world. As a consequence of nutrient-rich conditions, many well-lit rivers experience severe algal blooms, which threaten water quality and aquatic habitats. Nutrient enrichment in the upper Clark Fork River, located in western Montana, has increased the productivity of benthic algae, Cladophora glomerata, which routinely forms extensive blooms during summer growing seasons (July – September). Addressing eutrophication in rivers begins with identifying the nutrients that contribute toward algal productivity. I deployed nutrient diffusing substrates (NDS), collected bi-weekly surface water samples, and conducted algal surveys at four …

Better Together: Leveraging Existing Research To Evaluate Population Trends, Habitat Selection, And Species Interactions Of Mesocarnivores, Jordan Lee Heiman

Graduate Student Theses, Dissertations, & Professional Papers

Whether from human impacts, climate change, or extreme fires, landscapes around the world are rapidly changing (Foley et al. 2005, Grimm et al. 2008, Bowman et al. 2020). As these landscapes change, it is clear that many ecosystems and species are being negatively affected (Laliberte and Ripple 2004, Butchart et al. 2010, Freeman et al. 2018, Li et al. 2022). With an expanding number of species facing extinction risks, it is critical for agencies to know when and where to focus their limited resources and conservation efforts (Martin et al. 2012, Auerbach et al. 2014, Bal et al. 2018). To …

Penta Ef-Hand Protein Alg-2 Regulates Copii Activity At Eres In Response To Calcium Signaling, Jacob Ryan Lapka

Graduate Student Theses, Dissertations, & Professional Papers

Intracellular protein trafficking is critical for maintaining cellular homeostasis, relying on highly regulated vesicular transport pathways originating from the endoplasmic reticulum (ER). Central to this process is the COPII coat complex, which governs cargo export at ER exit sites (ERES) by selectively packaging secretory proteins into transport vesicles. Recent studies highlight the regulatory role of calcium (Ca²⁺) signaling at ERES, where the Ca²⁺-binding Penta EF-hand proteins ALG-2 and peflin modulate COPII coat dynamics and cargo sorting in a context-dependent manner. In Chapter 2, we show that knockdown of the Inositol 1,4,5-trisphosphate receptor-3 (IP3R-3) in normal rat …

Linking Empirical Data And Numerical Simulation To Characterize Dynamic Fire Behavior Associated With Interacting Firelines, Marta Sergeevna Jerebets

Graduate Student Theses, Dissertations, & Professional Papers

Understanding fuel pattern-fire process relationships is key for predicting fire behavior and effects with follow-on benefits to proactive fire management and model validation. To characterize dynamic fire behavior, this thesis leverages empirical data and numerical simulation through two complementary studies.

In the first study, longwave thermal sensors aboard unmanned aerial systems (UAS) were used to capture fine-scale fire behavior in two experimental grass burns. A novel paired design was used to quantify the effects of fuel arrangement on fire behavior with 3.66 m diameter treatments cut to a height of 0.15 m. The treatments ephemerally reduced fire rate of spread …

Water Scarcity In The Bitterroot Valley, August W. Guenthner

Graduate Student Theses, Dissertations, & Professional Papers

Water scarcity in Montana’s Bitterroot Valley is an increasingly urgent issue, driven by the dual pressures of climate change and rapid population growth. Since 1970, the Bitterroot has been the fastest-growing region in the state, with much of this growth occurring in low-density rural subdivisions that rely on individual groundwater wells. Simultaneously, climate change has reduced snowpack levels, leading to diminished springtime recharge of surface water systems that are vital for both ecological and agricultural needs. For the Valley’s agricultural producers, adapting to decreasing water availability will be essential for sustaining their operations. This research project was designed to better …

Ineligible Partners: Tribal Nations And Cooperative Federalism In The Historical Development Of National Forest Law And Policy, James H. Baker

Graduate Student Theses, Dissertations, & Professional Papers

Lands within the National Forest System (NFS), like all federal public lands, are rooted in Aboriginal Title and were once exclusively inhabited by Indigenous peoples and communities. Through the process of treaty-making, the federal government amassed millions of acres of ceded Tribal lands, many of which are now managed by federal public land agencies, including 194 million acres managed by the U.S. Forest Service (USFS). Several Tribes reserved various use and property rights on these lands that are protected by the U.S. Constitution’s Treaty and Supremacy Clauses. The federal government also has an overarching trust obligation to Tribes – a …

A Novel Positive Allosteric Modulator Of Glun1/3 Nmda Receptors, Samuel A. Galindo

Graduate Student Theses, Dissertations, & Professional Papers

The GluN3-containing (GluN1/3) N-methyl-D-aspartate (NMDA) receptors are glycine activated ligand-gated ion channels that are members of the family of excitatory ionotropic glutamate receptors. Compared to the glycine/glutamate-activated GluN2- containing NMDA receptors (GluN1/2), which have been extensively studied, the GluN1/3 receptors are poorly understood, but are implicated in neuronal processes related to synaptic maturation and plasticity. GluN1/3 receptors are also implicated in a variety of neurological diseases. In addition to their poor understanding, we lack proper pharmacological tools for the study and modulation of these GluN1/3 receptors. In this study, we evaluate the activity and mechanism of action for AIMS-129 as …

Whole Genome Sequencing From Snowshoe Hare Fecal Samples, Jessica J. Powell

Graduate Student Theses, Dissertations, & Professional Papers

Genomic analyses can provide powerful insights into important issues in conservation biology, including rapid estimates of overall genetic diversity and related population genetic parameters. Noninvasive DNA sampling from fecal samples is an affordable, efficient, and broadly applicable sampling method that has been used in many targeted genetic analyses. However, the efficacy of whole genome sequencing from fecal samples remains relatively unexplored in most taxa. Here, we present results from two experiments designed to test the quantity and quality of whole genome resequencing data obtained from snowshoe hare (Lepus americanus) fecal pellets. Extensive previous research has used genetic analyses …

A Retrospective Assessment Of Post-Fire Planting In The Us: Aligning Actual And Optimal Planting Sites To Address The Reforestation Gap, Lewis Faller

Graduate Student Theses, Dissertations, & Professional Papers

The natural regeneration processes that maintain semi-arid North American conifer forests are being disrupted. Increasingly, large wildfires burn core areas beyond the typical seed dispersal range of surviving adult trees and even when seeds are present, climate conditions increasingly are unsuitable for conifer recruitment, establishment, and survival. The USDA Forest Service (USFS), mandated to maintain forest cover in response to harvest or disturbance, now faces a planting backlog of over 3.8 million acres. Here, we conduct a retrospective assessment (1986–2023) of USFS post-fire reforestation to evaluate (1) whether historical planting patterns align with the goal to close the national reforestation …

An Assessment Of The California Logging Workforce, Kendra Jean Gerstenberg

Cal Poly Humboldt theses and projects

There is limited literature describing the capacity and capabilities of the logging workforce in California. This study examines the logging workforce in California to quantify the number of logging crews, assess demographic diversity, and evaluate capacity and capabilities. The target population was California Licensed Timber Operators (LTOs) who have the legal right to harvest timber. A survey was developed and distributed to LTOs on the CAL FIRE database. Surveys were also distributed at regional logging conferences or collected by phone. Data were analyzed using Statistical Package for the Social Sciences (SPSS) and emergent coding for follow-up interviews was conducted. There …

An Evaluation Of Fuel Model Accuracy And Multi-Scale Mitigation Strategies In The Wildland-Urban Interface Of Southern Humboldt County, Julia I. Cavalli

Cal Poly Humboldt theses and projects

Strategic placement of fuel treatments is critical for mitigating wildfire risk and reducing potential structure losses in wildland-urban interface (WUI) communities. As wildfire activity accelerates across the western United States, the need to identify high-impact fuel treatment locations grows increasingly urgent. Concurrently, housing development in the WUI is expanding, intensifying the exposure of homes and infrastructure to wildfire threats. In response, many communities are looking to mitigate the likelihood and severity of losses during wildfire events. The success of these efforts depends, in part, on robust data to support strategic placement of effective treatments that reduce fuel availability.

This study …

Place-Based Learning Practices: A Diptych Case Study Of Human And More-Than-Human Relationality At The Tribal And Western Academic Institutional Interface, Karley M. Rojas-Vienneau

Cal Poly Humboldt theses and projects

The ‘Place-Based Learning Practices Project’ is a graduate project under the Native American Studies Department Rou Dalagurr Food Sovereignty Lab and Traditional Ecological Knowledges Institute (FSL). Making contributions at the intersection of Western academia and Indigenous science, it imagines and realizes content, policies, and protocols surrounding two case studies and the larger cal poly humboldt (cph) institution which respect, honor, and uplift Indigenous sovereignty and resurgence in partnership with the Blue Lake Rancheria Tribe and the greater regional tribal community. Encompassing two projects internal and external to the institution, I aim to address the construction of controlled and protective environments …

An Economic And Production Analysis Of Seaweed Farms In California And The Pacific Northwest, Brian Donovan

Cal Poly Humboldt theses and projects

Since the early 2010s, the seaweed aquaculture industry has steadily expanded in the United States, with states like Alaska, Maine, Hawaii, and Connecticut leading the way in the development of this emerging sector. However, information gaps remain concerning certain aspects of the domestic seaweed aquaculture industry. The purpose of this study was to examine the status of the seaweed aquaculture industry along the West Coast of the United States; specifically in the states of California, Oregon, and Washington. Seaweed farmers in these states were invited to voluntarily complete surveys asking important production, economic, and commercial questions regarding their operations. Data …

Can We Help Coast Redwood Adapt To Climate Change? A Provenance Study On Genetic Variation And Climate Transfer Distance, Aidan J. Murphy

Cal Poly Humboldt theses and projects

The climate is changing more rapidly than many species can adapt or migrate. Coast redwood (Sequoia sempervirens) is a unique, long-lived conifer and remains California’s most valuable and economically important timber species. The species is threatened in its natural range due to anthropogenic climate change and human activity. Redwood favors asexual reproduction which restricts its ability to migrate naturally. The consequences of asexual reproduction when faced with a rapidly changing climate may make some form of assisted migration necessary for long-lived organisms like redwood.

This study evaluates drivers of variation in redwood growth and the influence of climate …

Associational Seaweed Defense Reduces Sea Urchin Grazing On Bull Kelp: Potential Use In Restoration, Brayden Tate Wiley

Cal Poly Humboldt theses and projects

Kelp forests are declining globally under warming seas, altered predator–prey dynamics, and intensified herbivory, with sea urchins often driving shifts from canopy-dominated forests to persistent urchin barrens. Management commonly relies on labor-intensive urchin removals, with variable success, underscoring the need for complementary, ecosystem-based tools that directly reduce urchin grazing pressure. Focusing on far northern California kelp forests, we combined subtidal surveys, field experiments, and laboratory feeding assays to assess whether the understory alga Desmarestia cf. herbacea can provide associational defense for bull kelp (Nereocystis luetkeana) by physically deterring purple sea urchin (Strongylocentrotus purpuratus) grazing and offering low …

Environmental And Spatial Drivers Of Quillback Rockfish (Sebastes Maliger) Growth In The Northeast Pacific Ocean From California To Alaska, Claire E. Stuart

Cal Poly Humboldt theses and projects

Quillback rockfish (Sebastes maliger) are a nearshore fishery species found across the Northeast Pacific Ocean, but recent stock assessments have identified a research gap for biological growth parameters, particularly for the southern end of their range. Age-length data compiled from California to Alaska (n=34,396) was used to generate extended von Bertalanffy models with spatial, biological, and environmental covariates, specifically region, sex, depth, and an upwelling index. The objectives of this study were to explore how 1) spatial and 2) environmental covariates affect model parameters L_∞, k, and t₀. Four total models were developed: …

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.

Turbo Fladry Fencing To Mitigate Short-Term Agricultural Damage Caused By Wild Pigs, Michael P. Glow, Jesse A. Tussing, Johnathan G. Walls, Robert B. Hyle, Joseph M. Halseth, Nathan P. Snow, Kurt C. Vercauteren

Human–Wildlife Interactions

Wild pigs (Sus scrofa) are a destructive invasive species that damage agricultural crops in many regions of the world. Lethal techniques to reduce populations are most often used to mitigate damage, but additional techniques are also needed in conjunction with lethal tools to protect resources in some settings (e.g., where lethal control is not practical or possible to achieve population elimination). While additional tools such as deterrents or temporary fencing may provide short-term relief, few effective options are currently available because habituation by wild pigs often reduces long-term effectiveness. Turbo fladry, a type of electric fence, is an …

Effect Of Implementing An Educational Program About Post Kidney Transplant Care On Critical Care Nurses' Knowledge, Marwa Abdo, Asmaa Ibrahim Aboseda

Nursing

Background: Critical care nurses (CCNs) play a pivotal role in post-kidney transplant care, necessitating a comprehensive understanding of transplantation procedures, complications, and patient management. So, any knowledge gaps among CCNs may impact the quality of care provide to kidney transplant program. Aim: This study aimed to assess the effect of implementing an educational program about post-kidney transplant care on critical care nurses’ knowledge. Methods: A quasi-experimental study was conducted among 50 critical care nurses. A structured educational program was implemented, and nurses’ knowledge was assessed pre- program, post- program, and three months follow-up. Data was collected using a kidney transplantation …

Effects Of Climate Change On Fungal Diversity And Function In Streams, Syeda Tasfia Imam

Masters Theses

"This study investigated the impact of climate change, particularly drought, on leaf decomposition and associated fungal and macroinvertebrate communities in freshwater ecosystems. With climate change, streams may experience altered hydrology, leading to shifts in community composition and biogeochemical processes. Fungi decompose organic matter, facilitate nutrient cycling, and support food webs. However, drought can disrupt these processes by reducing water availability, causing declines in fungal diversity and activity. I examined leaf breakdown and associated biota in 13 stream sites across varying hydrologic conditions, from perennial to ephemeral flow patterns. Flow duration varied during the 8-week study. Leaf breakdown was significantly related …

Integrated Multi-Omics Analyses Of Synaptosomes Revealed Synapse-Associated Novel Targets In Alzheimer’S Disease, Subodh Kumar, Enrique Ramos, Axel Hidalgo, Daniela Rodarte, Bhupender Sharma, Melissa M. Torres, Davin Devara, Shrikanth Gadad

School of Medicine Publications

Synapse dysfunction is an early event in Alzheimer’s disease (AD) caused by various factors, including amyloid beta, p-tau, inflammation, and aging. However, the precise molecular mechanism underlying synapse dysfunction in AD remains largely unknown. To understand this, we comprehensively analyzed the synaptosomes fraction in post-mortem brain samples from AD patients and cognitively normal individuals. We conducted high-throughput transcriptomic analyses to identify changes in microRNA (miRNA) and mRNA levels in synaptosomes extracted from the brains of unaffected individuals and those with AD. Additionally, we performed mass spectrometry analysis of synaptosomal proteins in the same sample group. These analyses revealed significant differences …

General Kernel Machine Methods For Multi-Omics Integration And Genome-Wide Association Testing With Related Individuals, Amarise Little, Ni Zhao, Anna Mikhaylova, Angela Zhang, Wodan Ling, Florian Thibord, Andrew D. Johnson, Laura M. Raffield, Joanne E. Curran, John Blangero

School of Medicine Publications

Integrating multi-omics data may help researchers understand the genetic underpinnings of complex traits and diseases. However, the best ways to integrate multi-omics data and use them to address pressing scientific questions remain a challenge. One important and topical problem is how to assess the aggregate effect of multiple genomic data types (e.g. genotypes and gene expression levels) on a phenotype, particularly while accommodating routine issues, such as having related subjects' data in analyses. In this paper, we extend an existing composite kernel machine regression model to integrate two multi-omics data types, while accommodating for general correlation structures amongst outcomes. Due …

The Role Of Horizontal Gene Transfer In Antibiotic Resistance Amidst Prevalent Community And Healthcare-Associated Mrsa Rates, Gabrielle Nascimento

Honors College Theses

In recent decades, cases of community-acquired MRSA (CA-MRSA) and healthcare-associated MRSA (HA-MRSA) have been on the rise. The ability of antibiotic resistance to transfer between microorganisms greatly expands its threat to the effective treatment and containment of bacterial infections. The mecA gene is found on a mobile cassette within the Staphylococcal cell and encodes for PBP2a, an alternate version of penicillin-binding protein (PBP) with less binding affinity for β-lactam antibiotics, increasing resistance to the effects of antibiotics. The goal of this research is to investigate the horizontal transfer of the mecA gene between various Staphylococcus species as well as to …

Rice Plants Response To Modulation Of The Erecta Signaling, Yasmin Vasques Berchembrock, Flavia Barbos Silva Botelho, Bhuvan Pathak, Shan Zhao, Vibha Srivastava

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

The ERECTA family of receptors (ERfs), encoding leucine-rich repeat receptor-like kinases (LRR-RLKs), can regulate multiple aspects of plant development and abiotic stress responses. The rice (Oryza sativa) genome contains three ERfs, namely ERECTA 1 (OsER1), ERECTA 2 (OsER2), and ERECTA-LIKE (OsERL). However, there is limited information currently available on their expression pattern during the plant developmental stages. The expression pattern of OsERfs genes at reproductive stages from the booting (R2) to milk (R6) stage in Nipponbare cultivar and the transgenic plants expressing a truncated Arabidopsis ERECTA (ER) lacking the kinase domain (triangle Kinase) were studied. The triangle Kinase functions as …

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.

Effects Of Fiber Concentrations And Fermentation Rates On Reproductive Performance, Nutrient Digestibility, Immune Response, And Microbiota Of Lactating Sows, Tao Wang, Pieter Langendijk, Paula Azevedo, Lluis Faba, Bin Zuo, Jiangchao Zhao, Chengbo Yang

Animal Science Faculty Publications and Presentations

Certain types of fiber inclusion in sow diets can offer benefits such as promoting a healthy microbiome, improving intestinal health, and enhancing welfare through satiety mechanisms. While most research has focused on gestating sows, studies on lactating sows, especially regarding fiber types, levels, and fermentation rates, are limited. This study explored how fiber inclusion and fermentation rate affect lactation performance, nutrient digestibility, immune response, and microbiota. The study involved 136 lactating sows (Landrace x Large White) assigned to four dietary treatments with varying total dietary fiber (TDF) levels and proportions of fast-fermentable fiber. Diets 1 and 2 had low TDF …

Restored Wetlands Show Rapid Vegetation Recovery And Substantial Surface-Water Expansion, Thilina D. Surasinghe, Yin-Hsuen Chen, Kunwar K. Singh

Center for Geospatial Science, Education & Analytics Faculty Publications

Ecological restoration is essential for improving the ecological integrity of degraded ecosystems to enhance ecosystem services and biodiversity. In this study, we assessed the effectiveness of wetland restoration on retired cranberry farms by analyzing vegetation recovery and surface-water dynamics using the enhanced vegetation index (EVI) and normalized difference water index (NDWI) derived from Sentinel-2 satellite imagery. To quantify temporal dynamics of both vegetation recovery and surface-water cover, we identified the spectral distinctions among restored wetland plant communities. Our results indicated the emergence of distinct plant communities upon restoration. Restored wetlands in general showed significant and progressive vegetation recovery and expanding …

Wasting Disease Of A Marine Foundation Species Links Community Interactions To Disease Dynamics, Lillian R. Aoki, Olivia J. Graham, Reyn M. Yoshioka, Rebecca Maher, Lindsay Alma, Eileen E. Hofmann, Colleen A. Burge, Drew Harvell, Maya L. Groner

CCPO Publications

Infectious disease plays a key role in shaping marine communities, including in seagrass meadows, which form biodiverse coastal habitats. Eelgrass (Zostera marina) is the most widespread seagrass species and is susceptible to seagrass wasting disease, caused by the protist Labyrinthula zosterae. As a foundation species, eelgrass strongly influences ecosystem structure, function and services; recent work has begun to explore the links between critical community interactions and seagrass wasting disease. Here, we highlight recent advances about how the eelgrass community regulates and responds to seagrass wasting disease, from the microbiome to herbivores and filter feeders. We further show …

Tailwater Trout Population Dynamics, Connor Dylan Cunningham

Graduate Theses/Dissertations

Dams have been constructed throughout the world and provide several resources for humans (e.g., flood control, hydropower). These structures heavily alter the upstream and downstream environment. One consequence of these alterations is the creation of “tailwaters”, which can create cold-water habitat via hypolimnetic releases. In the southeast United States these tailwater environments are often managed for the recreational use of nonnative salmonids. The unnatural flow regimes of tailwaters affect the biotic and abiotic conditions and ultimately the dynamic rate functions (i.e., recruitment, growth, mortality) of the fish inhabiting them. As such, the goal of this research is to provide fisheries …