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Application Of Computational Biophysics Techniques To Characterize Cell Membrane-Associated Events, Kyle Billings

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell membranes are crowded environments which can modulate protein structure-function relationships through interaction with lipids, other proteins, carbohydrate structures and so on. This work focuses the impact of the membrane environment on two varieties of peptides: Microbial rhodopsin proteins, and cyclic peptides.

Life on Earth is dependent on the ability of plants and microbes to harness sunlight for energy production. Their ability to transform light into carbohydrates requires tailor-made machinery, and for a wealth of microorganisms, microbial rhodopsin proteins (MR) are critical for maintaining the concentration gradients used to produce the energy molecule Adenosine triphosphate (ATP). The central retinal molecule …

Using Machine Learning Classification And Esa Sentinel 2 Multispectral Imager Data To Delineate Marsh Vegetation And Measure Ecotone Movement In Coastal Georgia, Thomas A. Pudil

College of Graduate Studies: Theses & Dissertations

Tidal marshes are unique communities that are subjected to environmental stressors including sea level rise, salinity change, and drought, resulting in constant change. It is important to monitor these changing areas because of the ecosystem services they provide to us, such as protection from storms and carbon sequestration. The proposed work for this thesis project is focused on the study of tidal marshes and the dynamics between the vegetation species within them. The aim of this project is to use geospatial technology and analyses, along with machine learning classification methods, to monitor change in these valuable ecosystems. The Georgia coast …

Social Vulnerability And The Prevalence Of Opioid Use Disorder Among Older Medicare Beneficiaries In U.S. Counties, Tse-Chuan Yang, Seulki Kim, Stephen A. Matthews, Carla Shoff

Department of Sociology: Faculty Publications

Objectives: Recent research has investigated the factors associated with the prevalence of opioid use disorder (OUD) among older adults (65+), which has rapidly increased in the past decade. However, little is known about the relationship between social vulnerability and the prevalence of OUD, and even less about whether the correlates of the prevalence of OUD vary across the social vulnerability spectrum. This study aims to fill these gaps. Methods: We assemble a county-level data set in the contiguous United States (U.S.) by merging 2021 Medicare claims with the CDC’s social vulnerability index and other covariates. Using the total number of …

Exploratory Analyses Of American Lobster Habitat Preferences And Catchability In Ventless Trap Surveys, Annabelle Leahy

Open Access Master's Theses

Numerous factors must be considered in efforts to rebuild sustainable stock levels of the Southern New England (SNE) lobster stock including changing uses of marine space, such as the growth of the offshore wind industry, and stressors such as rising ocean temperatures. These factors may change the species’ habitat use and could further impact the ability of the region to support a healthy lobster population. This work uses data from pre-wind farm construction ventless trap surveys to further characterize the suitable habitat of the SNE lobster stock and to examine the effects of survey design, namely trap position and trap …

An Ecological Study Of The Spatiotemporal Dynamics And Drivers Of Domestically Acquired Campylobacteriosis In Ireland, 2011–2018, Martin Boudou, Coilín Ó Haiseadha, Patricia Garvey, Jean O'Dwyer, Paul Hynds

Articles

In 2021, Campylobacteriosis was the main gastrointestinal disease in the European Union since 2007 according to the European Centre for Disease Prevention and Control. In the Republic of Ireland, the incidence of the disease is particularly high with approximately 3,000 cases per annum, raising significant concerns for national health authorities with an expected increase in the number of cases in the light of climate change. The current study sought to assess the spatio-temporal patterns of campylobacteriosis in the Republic of Ireland using 20,391 cases from January 2011 to December 2018. An ensemble of spatial statistics techniques including seasonal decomposition, spatial …

The Environmental Cellular Stress Response: The Intertidal As A Multistressor Model, Michael Collins, Melody S. Clark, Manuela Truebano

School of Biological and Marine Sciences

The wild poses a multifaceted challenge to the maintenance of cellular function. Therefore, a multistressor approach is essential to predict the cellular mechanisms which promote homeostasis and underpin whole-organism tolerance. The intertidal zone is particularly dynamic, and thus, its inhabitants provide excellent models to assess mechanisms underpinning multistressor tolerance. Here, we critically review our current understanding of the regulation of the cellular stress response (CSR) under multiple abiotic stressors in intertidal organisms and consider to what extent a multistressor approach brings us closer to understanding responses in the wild. The function of the CSR has been well documented in laboratory …

Externalizing Traits: Shared Causalities For Covid-19 And Alzheimer's Dementia Using Mendelian Randomization Analysis, Haotian Wang, Mingyang Cao, Yingjun Xi, Weijie Cao, Xiaoyu Zhang, Xiaoni Meng, Deqiang Zheng, Lijuan Wu, Wei Wang, Di Liu, Youxin Wang

Research outputs 2022 to 2026

Externalizing traits have been related with the outcomes of coronavirus disease 2019 (COVID-19) and Alzheimer's dementia (AD); however, whether these associations are causal remains unknown. We used the two-sample Mendelian randomization (MR) approach with more than 200 single-nucleotide polymorphisms (SNPs) for externalizing traits to explore the causal associations of externalizing traits with the risk of COVID-19 (infected COVID-19, hospitalized COVID-19, and severe COVID-19) or AD based on the summary data. The inverse variance–weighted method (IVW) was used to estimate the main effect, followed by several sensitivity analyses. IVW analysis showed significant associations of externalizing traits with COVID-19 infection (odds ratio …

Abmr: An R Package For Agent-Based Model Analysis Of Large-Scale Movements Across Taxa, Benjamin Gochanour, Javier Fernández-López, Andrea Contina

School of Integrative Biological & Chemical Sciences Faculty Publications

1. Agent-based modelling (ABM) shows promise for animal movement studies. However, a robust, open-source and spatially explicit ABM coding platform is currently lacking.
2. We present abmR, an R package for conducting continental-scale ABM simulations across animal taxa. The package features two movement functions, each of which relies on the Ornstein–Uhlenbeck (OU) process.
3. The theoretical background for abmR is discussed and the main functionalities are illustrated using example populations.
4. Potential future additions to this open-source package may include the ability to specify multiple environmental variables or to model interactions between agents. Additionally, updates may offer opportunities for disease ecology and integration with …

Trophic Ecology And Mercury Concentrations Of Canary Rockfish (Sebastes Pinniger) In The California Current System, Michaela M. Melanson

Master's Theses

Canary rockfish are a profitable fishery resource that has failed and successfully recovered in the 21st century. This study aimed to evaluate their trophic ecology through stomach content and stable isotope analysis and relate these to their mercury concentrations, biological traits, and environmental conditions. Canary rockfish consume mostly krill and teleosts with their geographic location affecting the proportion of prey items, suggesting regional environmental effects: chlorophyll-a, relief, port, and depth impact dietary choices. Mean ??13C values (-17.18 ± 0.54) significantly increased in individuals residing in deeper depths, higher latitudes, higher productivity, and higher temperatures, and in sexually mature individuals. Mean …

Neighborhood Market Potentials For Alcohol Use And Rates Of Child Abuse And Neglect, Bridget Freisthler, Christiana Kranich, Jennifer Price Wolf, Reiko Boyd, Paul J. Gruenewald

Faculty Research, Scholarly, and Creative Activity

Background: Alcohol use can lead to child abuse and neglect even if the person using alcohol does not use heavily. Yet relatively few measures that reflect alcohol use are available at smaller geographic units. We assess whether the estimated level of total alcohol use per capita is related to measures of child abuse and neglect that include substantiated reports of maltreatment, total entries into foster care, and alcohol-related entries into foster care. Methods: Our sample consists of 326 Census block groups in Sacramento, California over three time points (978 space–time units). Administrative data for substantiations of child abuse and neglect …

Community Ecology And Disease Dynamics In Pacific Oysters: Unraveling Microbiome-Pathogen Interactions In The Wild, Victoria E. Cifelli

Cal Poly Humboldt theses and projects

In the context of multispecies microbial assemblages, disruptions can occur when there are alterations in host conditions, such as the onset of a disease. Notably, viruses have the potential to reshape a host's microbial community. However, the role of the host's habitat and environment, which could be pivotal in communities with shifting niche space and habitat filters, is often overlooked in host-microbe-pathogen interactions. Recognizing the importance of these factors, I employed a field-based approach to understand microbial community dynamics in the presence of disease. To address the influence of geographical location, I conducted an analysis involving healthy and infected oysters …

Factors Associated With Nonsyndromic Anotia And Microtia, Texas, 1999–2014, Jeremy M Schraw, J P Woodhouse, Renata H Benjamin, Charles J Shumate, Joanne Nguyen, Mark A Canfield, A J Agopian, Philip J Lupo

Faculty, Staff and Students Publications

BACKGROUND: Few risk factors have been identified for nonsyndromic anotia/microtia (A/M).

METHODS: We obtained data on cases and a reference population of all livebirths in Texas for 1999-2014 from the Texas Birth Defects Registry (TBDR) and Texas vital records. We estimated prevalence ratios (PRs) and 95% confidence intervals (CIs) for A/M (any, isolated, nonisolated, unilateral, and bilateral) using Poisson regression. We evaluated trends in prevalence rates using Joinpoint regression.

RESULTS: We identified 1,322 cases, of whom 982 (74.3%) had isolated and 1,175 (88.9%) had unilateral A/M. Prevalence was increased among males (PR: 1.3, 95% CI: 1.2-1.4), offspring of women with …

Restoring Human And More-Than-Human Relations In Toxic Riskscapes: “In Perpetuity” Within Lake Superior’S Keweenaw Bay Indian Community, Sand Point, Valoree Gagnon, Evelyn H. Ravindran

Michigan Tech Publications, Part 1

Lake Superior’s Keweenaw Bay is the ancestral and contemporary homeland of the Anishinaabe Ojibwa and their relatives. It is also a toxic riskscape: Its waters, shorelines, and fish beings are polluted by an unknown tonnage of legacy mining waste rock called “stamp sands,” which contain unsafe levels of toxic compounds. This paper describes Ojibwa stewardship principles and reciprocal obligations, illustrating First Treaty With Gichi-Manitou practices of restoring relations within a toxic riskscape. Defined here, riskscapes are places and spaces where pollution/toxicity relations are continually reconfigured in literal, symbolic, and systemic ways. We share a story from Keweenaw Bay’s Sand Point …

Use Of Artificial Nest Boxes By Two Species Of Small, Arboreal Mammals In Ecuadorian Tropical Dry Forest, Gabriel A. Brito Vera, Jaime A. Salas, George E. Heimpel, Mariana Bulgarella

Neotropical Biodiversity

The nest structure of two species of small mammals, Marmosa simonsi and Rhipidomys latimanus were recorded for the first time. Nests were found inside artificial nest boxes in a tropical dry forest remnant ecosystem in Western Ecuador. We described the nests and categorized them as rearing nest, permanent resting nest and transient refuge, depending on their intended use. Artificial nest boxes provide an optimal place for pup rearing and resting for these small mammals. These nest sites can be useful for ecological studies of behavior and habits of elusive, poorly-known mammalian species.

The Burrowing Crayfish Parastacus Pugnax (Decapoda: Parastacidae) In The Semiarid Region Of Chile: Findings Of A Naturalized Or Threatened Population?, Carlos Velásquez, Erich Rudolph, Alejandra Oyanedel, Yeriko Alanís, Luis A. Henríquez-Antipa

Neotropical Biodiversity

Parastacus pugnax is an endemic burrowing crayfish from the basins of the Mediterranean and Temperate Wet regions of Chile. For the first time, specimens were found incidentally in the Semiarid Region of Chile (Choapa River Basin). In these regions, hydrological changes derived from global warming and the intensive use of water for irrigation have resulted in highly fragmented habitats, where the effects of the dry season are exacerbated by periods of permanent drought. Unfortunately, in the Semiarid Region there are not regulatory measures for the conservation of the native biota. The aims of this study were to determine the spatial …

Home Range And Movement Patterns Of Male Dwarf Caimans (Paleosuchus Palpebrosus And Paleosuchus Trigonatus) Living In Sympatry In Amazonian Floodplain Streams, Boris Marioni, William Ernest Magnusson, Richard Carl Vogt, Francisco Villamarín

Neotropical Biodiversity

Dwarf caimans (Alligatoridae: Paleosuchus palpebrosus and Paleosuchus trigonatus), are small crocodilians exhibiting cryptic behaviour and complex habitat use that occur throughout the Amazon region. Our goals were to evaluate individual home range, habitat occupancy and movement patterns where they occur in sympatry in relation to seasonal water-level variation. We tracked five P. palpebrosus and seven P. trigonatus using VHS radio transmitters along the shores of two streams directly influenced by the flooding pulse of the Purus River. Paleosuchus palpebrosus individuals moved greater distances on a daily basis and had larger home ranges than P. trigonatus, and the species had different …

Macroinvertebrates’ Response To Different Land Use In Lowland Streams From Uruguay: Use Of Artificial Substrates For Biomonitoring, Bárbara Suárez, Margenny Barrios, Franco Teixeira De Mello

Neotropical Biodiversity

The use of macroinvertebrates as indicators of water quality is an effective and low-cost tool, which is widely implemented in biomonitoring programmes. Certain taxa are characteristic of impaired watercourses (e.g. Oligochaeta, Chironomidae and Amphipoda), while others are characteristic of good-quality watercourses (e.g. Ephemeroptera, Plecoptera and Trichoptera; EPT). In this work, we evaluated the response of the macroinvertebrate assemblages to different land uses. For this purpose, artificial substrate colonization experiments were conducted in streams including urban (U, n = 3), intensive agriculture and dairy production (AD, n = 4) and extensive cattle ranching (CR, n = 4) land uses. Because in …

Influence Of Predator Density In Foraging Behavior And Microhabitat Choice On Litter-Dwelling Scorpions, Vinicius B. Pessoa, Geraldo J. B. Moura, André F. A. Lira

Neotropical Biodiversity

The presence of a predator can cause behavioral changes in its prey, such as decreased foraging activity. Previous studies have indicated that the scorpion Ananteris mauryi has the ability to identify the chemical traces of its intraguild predator Tityus pusillus, causing it to reduce its exploratory activity. In this study, the foraging activities of A. mauryi in a natural environment with different densities of T. pusillus were compared. The study was carried out through active searches from 19:00 to 22:00 in five fragments of the Atlantic Forest in Pernambuco, Brazil, one having a low density of T. pusillus and four …

Risk Factors For Emergency Medical Care Or Hospitalization Due To Heat-Related Illness Or Injury: A Systematic Review, Blair Litwiller, Amber N. Barnes

Florida Public Health Review

Background: Temperatures globally have been predicted to increase due to changes in the climate. As the earth gets warmer, it is expected that heat-related illness will also increase worldwide. An effective and appropriate public health response will be critical. Purpose: The aim of this review was to identify risk factors associated with heat-related illness and injury to provide target areas for future interventions. Methods: A review of existing literature was analyzed for risk factors that may increase the likelihood of being admitted to an emergency department for a heat related illness or injury. Results: Of the …

Seaweeds Across Ecosystem Boundaries: From Habitat Formation To Harvest Implications, Brian P. Ulaski

Marine Biology

This dissertation broadly investigates the response of wild stock seaweeds to harvesting, and their role as biogenic habitat formers when cast ashore. Seaweeds are important primary producers and foundation species that maintain their functional roles across coastal ecosystem boundaries. Climate-driven loss of seaweed biomass, including that of kelp forests, is exacerbated by other human-related activities that directly impact their persistence, such as overharvesting. Attached rockweeds and kelps are commonly harvested for food, while diverse assemblages of beach-cast seaweed wrack are collected for fertilizer. The importance of wrack habitat in Alaska has not been extensively explored, especially in regions where there …

Phytoplankton Community Of Boalia Khal Tributary Of The Halda River, Chattogram, Bangladesh, Md. Shafiqul Islam, M.A. Azadi, Munira Nasiruddin

Journal of Bioresource Management

Boalia Khal is one of the important tributaries of the River Halda. The productivity of the Boalia Khal tributary of the Halda River mainly depends on the phytoplankton diversity. A study was conducted for two years period from January 2017 to December 2018 to identify the phytoplankton community of the Boalia Khal tributary. A total of 61 species of phytoplankton under 37 genera belonging to 8 classes were recorded. The dominant group of phytoplankton was 25 species of Diatoms (40.98 %) followed by 18 species of Green Algae (29.5 %), 9 species of Euglenophytes (14.75 %), 7 species of Blue …

Revelations In The Blood: Determination Of Biomarkers And Analytes, Jeremiah Jamrom

Electronic Theses and Dissertations

Changes in body chemistry have long been utilized as a tool for medical diagnosis. Whether blood panel, toxin level, antigen testing or any of the myriad other tests performed annually, searching for molecules which confer health status is a long-established practice. These tests give physicians more information and allow them to make a more accurate diagnosis, from which appropriate treatment can stem. Awareness of, and the subsequent search for, biomarkers for disease states have grown substantially in the past years as analytical, biochemical, and instrumental techniques have become more precises and powerful. In an era of increasingly personalized medicine, novel …

Assessing The Mental Health Of Women At The Intersection Of Intimate Partner Violence And Animal Cruelty: Personal And Population Level Risk Factors For Co-Victimization, Alaina M. Beauchamp

Dissertations and Theses (Open Access)

One predictor of intimate partner violence (IPV) occurring in the home is pet abuse. The high prevalence of pet cruelty among IPV relationship can create a significant barrier to seeking help due to the inability to bring the pet or concern for the pet’s wellbeing. This human-animal bond is a more common source of emotional support among victims with experiences of pet abuse, as opposed to women whose pets had not been abused. This study 1) explored the relationship between victims of IPV and their pets, the dynamics and characteristics of situations of co-victimization (i.e., abuse of both a human …

Socio‑Economic Inequalities In Minimum Dietary Diversity Among Bangladeshi Children Aged 6–23 Months: A Decomposition Analysis, Satyajit Kundu, Pranta Das, Ashfikur Rahman, Hasan Al Banna, Kaniz Fatema, Akhtarul Islam, Shobhit Srivastava, T. Muhammad, Rakhi Dey, Ahmed Hossain

Department of Statistics: Faculty Publications

This study aimed to measure the socio-economic inequalities in having minimum dietary diversity (MDD) among Bangladeshi children aged 6–23 months as well as to determine the factors that potentially contribute to the inequity. The Bangladesh Demographic and Health Survey (BDHS) 2017–2018 data were used in this study. A sample of 2405 (weighted) children aged 6–23 months was included. The overall weighted prevalence of MDD was 37.47%. The concentration index (CIX) value for inequalities in MDD due to wealth status was positive and the concentration curve lay below the line of equality (CIX: 0.1211, p < 0.001), where 49.47% inequality was contributed by wealth status, 25.06% contributed by the education level of mother, and 20.41% contributed by the number of ante-natal care (ANC) visits. Similarly, the CIX value due to the education level of mothers was also positive and the concentration curve lay below the line of equality (CIX: 0.1341, p < 0.001), where 52.68% inequality was contributed by the education level of mother, 18.07% contributed by wealth status, and 14.69% contributed by the number of ANC visits. MDD was higher among higher socioeconomic status (SES) groups. Appropriate intervention design should prioritize minimizing socioeconomic inequities in MDD, especially targeting the contributing factors of these inequities.

System Shock: Using -Omics Data To Characterize Biological Remodeling In The Microbiome, Resistome, And Transcriptome Of Bacteria, Winston Eugene Anthony

Arts & Sciences Graduate Student Theses and Dissertations

The human experience is indelibly linked to microbial life. So much so, that the holobiont theory has been coined to define the assemblage of host and microbe as a discrete ecological unit. Perturbation of the commensal microbiome can create niche space for pathogens, which through the concomitant rise of antimicrobial resistance represent an ever-evolving danger. In Chapter 2 of this dissertation, I describe the results of an interventional study designed to directly perturb the healthy gut microbiome and observe the dynamics of taxonomic composition and functional recovery. I observe significant decreases after 5 days of antibiotic treatment in the gold …

The Restoration Potential Of Offshore Mussel Farming On Degraded Seabed Habitat, D Bridger, Mj Attrill, Bfr Davies, La Holmes, A Cartwright, Se Rees, Lm Cabre, Ev Sheehan

School of Biological and Marine Sciences

The United Kingdom's first large-scale, offshore, long-line mussel farm deployed its first ropes in 2013 in Lyme Bay, southwest United Kingdom, located in an area of seabed that was heavily degraded due to historic bottom-towed fishing. It was hypothesised that due to the artificial structures that accumulate mussels and exclude destructive fishing practices, the seabed could be restored. To assess the restoration potential of the farm and its ecosystem interactions over time, a multi-method, annual monitoring approach was undertaken. Here, we tested the effects of the farm trial stations on the seabed habitat, epifauna and demersal species over 5 years. …

Diet And Disturbance: Seaside Sparrow Resource Use Driven By Oiling And Hurricane Isaac, Allison M. Snider, Andrea Bonisoli-Alquati, Anna A. Pérez-Umphrey, Stefan Woltmann, Philip C. Stouffer, Sabrina S. Taylor

Faculty Publications

The 2010 Deepwater Horizon (DWH) disaster led to extensive oil deposition in Louisiana’s coastal wetlands, followed two years later by Hurricane Isaac. These disturbances led to changes in saltmarsh invertebrate communities, potentially affecting higher-level predators and the saltmarsh food web. Seaside Sparrows (Ammospiza maritima) are ubiquitous, year-round residents of the coastal saltmarsh affected by the DWH spill, where they consume diverse invertebrates and may be considered an indicator species for the ecosystem’s integrity. We used DNA metabarcoding to evaluate prey consumed by Seaside Sparrows to understand how sparrows responded to residual contamination from the DWH oil spill and ecosystem disturbance …

Urban Green Roofs Can Support A Diversity Of Parasitoid Wasps, Aramee C. Diethelm, Susan Masta

Biology Faculty Publications and Presentations

Green roofs are often installed atop buildings to provide ecological services such as mitigating storm water runoff and cooling air within urban heat islands. We found that green roofs in Portland, Oregon, also can support biodiversity, including a diverse assemblage of parasitoid wasps, with 20 morphospecies from 10 families present on the four roofs we surveyed. The roofs with greater plant diversity and structural complexity harbored comparatively more parasitoid morphospecies than the structurally simpler Sedum-dominated roofs. The oldest green roof supported much greater diversity than the younger roofs, including a comparably planted roof three times its size. Parasitoid wasps from …

Larval Ecology Of Atlantic Bluefin Tuna (Thunnus Thynnus): New Insights From Otolith Microstructure, Biotic, And Abiotic Analyses From The Gulf Of Mexico And Mediterranean Sea, Estrella Malca

All HCAS Student Capstones, Theses, and Dissertations

Atlantic bluefin tuna (ABT), Thunnus thynnus, spawn in the Gulf of Mexico (GoM) and the Mediterranean Sea (MED). Spawning occurs within narrow temporal and environmental parameters. Efforts to characterize growth of ABT in wild conditions revealed a wide range of growth variability during the early life stages. This series of studies examined potential biotic and abiotic influences of larval growth from seven ABT cohorts, and identified several key drivers of growth for this commercially valuable species. A detailed investigation of larval dynamics using otolith microstructure was conducted as follows. First, companion growth curves and stable isotope analysis from the same …

Remote Reef Cryptobenthic Diversity: Integrating Autonomous Reef Monitoring Structures And In Situ Environmental Parameters, M Steyaert, M Lindhart, A Khrizman, Rb Dunbar, Mb Bonsall, Da Mucciarone, E Ransome, N Santodomingo, P Winslade, Cei Head

School of Biological and Marine Sciences

Coral reef sessile organisms inhabiting cryptic spaces and cavities of the reef matrix perform vital and varied functional roles but are often understudied in comparison to those on exposed surfaces. Here, we assess the composition of cryptobenthic taxa from three remote tropical reef sites (Central Indian Ocean) alongside a suite of in situ environmental parameters to determine if, or how, significant patterns of diversity are shaped by local abiotic factors. To achieve this, we carried out a point-count analysis of autonomous reef monitoring structure (ARMS) plate images and employed in situ instrumentation to recover long-term (12 months) profiles of flow …