Bioinformatics Commons^™

Microbial Community Dynamics Of A Microcystis Bloom, Helena Pound

Doctoral Dissertations

Harmful algal bloom events are notoriously associated with massive economic and environmental consequences, causing wildlife and human health risks. As these blooms increase in occurrence, duration, and severity around the world, it is essential to understand conditions leading to bloom formation and why they persist. Abiotic factors such as nutrients are commonly considered in bloom dynamics, but biotic interactions with co-occurring microbial species and viruses must also be taken into account. Harmful algal blooms dominated by the cyanobacterial genus Microcystis occur in bodies of water around the world and provide an ideal system in which to study top-down controls on …

Effects Of Habitat Disturbances On Reptiles In Sagebrush Steppe, Kristina Joan Parker

Boise State University Theses and Dissertations

Reptiles inhabiting shrub-steppe ecosystems of the Intermountain West have adapted to harsh, unpredictable desert conditions, yet recent changes in disturbance regimes may put species at risk. In southwest Idaho, cheatgrass (Bromus tectorum) has altered the fire regime resulting in a vast conversion of shrub-steppe to mostly annual grasslands that burn too frequently to allow shrublands to recover. Southwest Idaho has the highest reptile diversity in the Pacific Northwest, yet we know little about reptile community dynamics in response to the cheatgrass-fire cycle. We hypothesized that wildfires and cheatgrass negatively affect reptile communities directly (i.e., mortality during fires) and …

The Evolutionary Origins Of Autism Associated Genes And Their Role In Great Ape Socio-Communicative Behavior, Azeeza Abdulrauf

Master of Science in Integrative Biology Theses

Autism Spectrum Disorder (ASD) is a set of neurological disorders characterized by reduced social interactions and deficits in verbal and nonverbal communication. Although there are no clear genetic markers for ASD, studies have found associations between gene single nucleotide polymorphisms (SNPs) and patients diagnosed with ASD. For this study, the focus is on OXTR, AVPR1A, and FOXP2. OXTR is reported to regulate empathy and stress reactivity while AVPR1A is reported to regulate stress management and territorial aggression, as well as social bonding and recognition. FOXP2 is one of the first genes to be associated with both speech and language recognition …

The Effect Of Disturbance And Invasion On Fungal And Plant Communities Over An Elevational Gradient, Adam N. Trautwig

Doctoral Dissertations

High-elevation ecosystems are at risk of disruption from the future effects of climate change. Sub-alpine meadows are a source of unique plant populations, intraspecific variation of elevationally extreme populations, and vital sources of fresh water resources. We evaluated the whole fungal communities, arbuscular mycorrhizal fungal (AMF) communities, plant communities, and edaphic variables of sub-alpine meadows in undisturbed, disturbed, and disturbed with a non-native member of the Brassicaceae (Thlaspi arvense) plots. In conjunction with measuring the effects of disturbance on native communities we conducted potting experiments on a dominant grass of sub-alpine meadows (Festuca thurberi). We also …

Monitoring Mammals At Multiple Scales: Case Studies From Carnivore Communities, Kadambari Devarajan

Doctoral Dissertations

Carnivores are distributed widely and threatened by habitat loss, poaching, climate change, and disease. They are considered integral to ecosystem function through their direct and indirect interactions with species at different trophic levels. Given the importance of carnivores, it is of high conservation priority to understand the processes driving carnivore assemblages in different systems. It is thus essential to determine the abiotic and biotic drivers of carnivore community composition at different spatial scales and address the following questions: (i) What factors influence carnivore community composition and diversity? (ii) How do the factors influencing carnivore communities vary across spatial and temporal …

Discovering Mechanisms Driving Adaptive Evolution In The Cross-Kingdom Fungal Pathogen Fusarium Oxysporum, Dilay Hazal Ayhan

Doctoral Dissertations

Fusarium oxysporum is a cross-kingdom pathogenic fungus that can cause vascular wilt disease in many economically important plants and local or disseminated infections in humans. Although it lacks a sexual stage in its life cycle, F. oxysporum can adapt to a wide range of hosts because of accessory chromosomes (ACs) which are enriched in host-specific genes and repeat content. This dissertation investigates the mechanisms that drive the adaptive evolution in the cross-kingdom pathogen F. oxysporum using comparative genomics and an experimental evolution approach. The first chapter compares phenotypes and genomes of a plant pathogenic isolate F. oxysporum f. sp. lycopersici …

Phenotype Bias Determines How Natural Rna Structures Occupy The Morphospace Of All Possible Shapes, Fatme Ghaddar, Dr Kamaludin Dingle, Dr Petr Sulc, Prof Ard A. Louis

Undergraduate Research Symposium

The relative prominence of developmental bias versus natural selection is a long standing controversy in evolutionary biology. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. By using the RNAshapes method to define coarse-grained SS classes, we can measure the frequencies that non-coding RNA SS shapes appear in nature. Our main findings are firstly that only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored. Secondly, and perhaps more surprisingly, these frequencies are accurately …

The Evolutionary Origins Of Autism Associated Genes And Their Role In Great Ape Socio-Communication, Azeeza Abdulrauf, Martin Hudson, Susan M.E. Smith, Jared P. Taglialatela

Symposium of Student Scholars

Single nucleotide polymorphisms (SNPs) play a major role in socio-communicative behavior. For this study, the focus is on autism associated OXTR, AVPR1A, and FOXP2 SNPs, and the role they play in great apes. Prior research on the OXTR, AVPR1A, and FOXP2 SNPs show that they affect behavior skills such as understanding and controlling emotion, understanding the emotions of others, and communications skills. Great apes, such as bonobos, chimpanzees, and gorillas are the model, since they are our closest relatives in the animal kingdom capable of understanding complex communication. Each gene has at least two SNPS that are investigated in the …

Analyzing Genetic Variation Of The Tussock Cottongrass Among Ecotypes Along A Latitudinal Gradient Through Transcriptomics, Carmen Webster

Open Access Theses & Dissertations

The Arctic is seeing some of the most extreme effects of climate change that induce environmental pressures, including warmer temperatures and longer growing seasons. Due to this, taxa may need to adapt or migrate in order to survive. The long-lived tussock cottongrass, Eriophorum vaginatum, is a foundation species in the Arctic, and little is currently known about the genetic constraints that could be playing a role in how this species will respond to the changing climate. Specific gene families that play an important role in signaling genetic pathways related to plant phenology and response to environmental stress are likely to …

Nematode Biodiversity In Lincoln, Nebraska's Tallgrass Prairie Corridor, Abigail Borgmeier

Department of Plant Pathology: Dissertations, Theses, and Student Research

The tallgrass prairie was once one of the most diverse grasslands on the planet, however over 95% has been converted to agriculture in the past 150 years. The remaining prairie is still host to a wide variety of plants, insects, mammals, and soil-dwelling microorganisms, creating an incredibly complex ecosystem. The first aim of this study is to compare three approaches for the measurement of nematode diversity within a 10-mile-long protected prairie habitat corridor near Lincoln, Nebraska. The methods are 1) a traditional morphological analysis of 150 nematodes per study site, 2) a metabarcoding analysis using the 18S genetic marker of …

Investigation Into The Evolution Of Heterogeneity Within Secondary Replicons And Their Maintenance In Genus Variovorax, Christopher Ne Ville

Electronic Theses, Projects, and Dissertations

Approximately 10% of all bacterial genomes sequenced thus far contain a secondary replicon. This considerable genetic reservoir contains many potentially mobilizable elements, allowing for the formation of many unique secondary replicons. This property of bacterial populations vastly increases the genomic diversity available to species that effectively take up and maintain these replicons. Members of the genus Variovorax have extensive heterogeneity in genome architecture, including sequenced isolates containing plasmids, megaplasmids, and chromids. Using available Illumina data on the NCBI database, we have completed these assemblies using 3^rd generation sequencing methods on 17 members of this genus. We have sequenced, assembled, …

Using Bioenergetics To Model The Effects Of Climate Change On Bluntnose Minnows Pimephales Notatus In A Western Kentucky Stream, Christian Slone, Christian Slone

Student Scholarship & Creative Works

Bioenergetics considers a variety of factors like consumption, excretion, and metabolism to quantify the energy use of an organism. A common use of bioenergetics modeling is to help solve fish stock problems. This project looks to develop a bioenergetics model for Bluntnose Minnows Pimephales notatus to help predict effects of climate change on the biodiversity of western Kentucky streams. We used R and NetLogo to create an agent-based bioenergetics model to simulate the size distribution of Bluntnose Minnows under various temperature regimes. Bluntnose Minnow metabolism increases, and consumption decreases with an increase in water temperature. Fish growth seems to be …

Comparative Genomics Methods And Applications, Emily N. Alden

Biomedical Sciences ETDs

Virtually all fields of biology have benefited from the advancements in comparative genomics technologies, specifically in the study of evolution. In this dissertation I develop and use comparative genomic technologies to investigate the novel SARS-CoV-2 virus, assembly the first genome of the black lace domestic angelfish and identify germline genetic variants associated with altered breast cancer-specific survival. Our genome tiling array for the novel coronavirus presents a rapid and cost-effective method to sequence the entire viral genome and can be used to track the rapid evolution of viral variants in the population. The domestic angelfish is a member of the …

Dynamic Observers For Unknown Populations, Chris Guiver, Nathan Poppelreiter, Richard Rebarber, Brigitte Tenhumberg, Stuart Townley

Brigitte Tenhumberg Papers

Dynamic observers are considered in the context of structuredpopulation modeling and management. Roughly, observers combine a known measured variable of some process with a model of that process to asymptotically reconstruct the unknown state variable of the model. We investigate the potential use of observers for reconstructing population distributions described by density-independent (linear) models and a class of density-dependent (nonlinear) models. In both the density-dependent and -independent cases, we show, in several ecologically reasonable circumstances, that there is a natural, optimal construction of these observers. Further, we describe the robustness these observers exhibit with respect to disturbances and uncertainty in …

Applications Of Comparative Genomics And Data Science To Agricultural And Clinical Research, Katrina A. Schlum

Doctoral Dissertations

The advent of inexpensive, high-throughput whole genome sequencing (WGS) technologies has led to the generation of thousands of related genomes, even from a single study. Large-scale genome analysis has resulted in hypothesis-generating approaches in the fields of clinical, human and agriculture genomics. Additionally, population-level genomic sampling has resulted in a decrease in false positives in genotype-phenotype associations and an increase in understanding of the basis of disease, antibiotic and pesticide resistance. Deeper understanding of migration, genetic divergence and evolution has also been made possible due to WGS. This research applies comparative genomics, population genomics and data science approaches to whole …

A Test Of Rad Capture Sequencing On Ethanol-Preserved Centennial And Contemporary Specimens Of Philippine Fishes, Madeleine I. Kenton

Biological Sciences Theses & Dissertations

Understanding the relationship between ecological characteristics and genetic change in natural populations in different time scales can reveal how anthropogenic stressors affect natural populations and can improve the success of conservation strategies. The purpose of the Philippines Partnerships for International Research and Education (PIRE) project is to examine levels of genetic change between historical fish samples collected by the USS Albatross expedition in the early 1900s in the Philippines and contemporary populations collected at the same localities. This study tests genetic protocols to process historical and contemporary DNA for simultaneous comparison. Two DNA library preparation methods, single digest RADseq (“un-baited” …

Assessing And Mapping The Spatial-Temporal Change In Forest Phenology Of Arabuko-Sokoke Forest Using Moderate Resolution Satellite, Bailey Ytterdahl

Independent Study Project (ISP) Collection

This study focuses on coastal forests in Kenya that have some of the highest variety of flora and fauna, specifically Arabuko Sokoke Forest. Arabuko Sokoke Forest is located 110 miles north of Mombasa and 18 kilometers south of Malindi. This forest is known to be a worldwide biodiversity hotspot that is home to endemic and rare plants and animals. Within the Arabuko Sokoke Forest ecosystem, there are two main issues that challenge the conservation of the area. First, there has been more competition for land, primarily for agriculture and development. Second, there is an increase demand for forest resources due …

The Feasibility Of Renewable Natural Gas In New Jersey, Anneliese Dyer, Amelia Christine Miller, Brianna Chandra, Juan Galindo Maza, Carley Tran, Justin Bates, Vicky Olivier, Amy Tuininga

Publications

With traditional natural gas being one of the top options for heating in the United States and the present threat of climate change, there is a demand for an alternative clean fuel source. A Renewable Natural Gas Implementation Decision-Making Conceptual Model was created to provide a framework for considering the feasibility of renewable natural gas (RNG) projects and applied to New Jersey, specifically investigating landfills and wastewater treatment plants (WWTPs). Data from the US EPA’s Landfill Methane Outreach Program and New Jersey’s Department of Environmental Protection Sewage Sludge databases were used to identify seven landfills and 22 WWTPs as possible …

Characterizing Patterns Of Genomic Variation In The Threatened Utah Prairie Dog: Implications For Conservation And Management, Rachael M. Giglio, Tonie E. Rocke, Jorge E. Osorio, Emily Latch

Biological Sciences Faculty Articles

Utah prairie dogs (Cynomys parvidens) are federally threatened due to eradication campaigns, habitat destruction, and outbreaks of plague. Today, Utah prairie dogs exist in small, isolated populations, making them less demographically stable and more susceptible to erosion of genetic variation by genetic drift. We characterized patterns of genetic structure at neutral and putatively adaptive loci in order to evaluate the relative effects of genetic drift and local adaptation on population divergence. We sampled individuals across the Utah prairie dog species range and generated 2,955 single nucleotide polymorphisms (SNPs) using double digest restriction site associated DNA sequencing (ddRAD). Genetic …

Climate Niche Evolution In C4+Cam Portulaca And Closely Related C3+Cam Lineages, Nora M. Heaphy

Library Map Prize

With at least a hundred independent origins among land plants, the CAM and C4 photosynthetic pathways represent one of the most notable examples of global convergent evolution of a complex trait. While biochemically similar, CAM and C4 are generally understood to be two distinct ecological adaptations evolving along separate trajectories. However, the purslanes (Portulaca), a globally widespread clade of around 100 species of annual and perennial succulents, are able to operate both CAM and C4 cycles in the same leaf. Portulaca likely originated from a facultative CAM ancestor and then evolved a C4 system at least three times …

Metagenomic Identification And Classification Of The Mercury-Methylating Gene Hgca In Response To Water Table And Plant Functional Group Manipulations In Peat Soil, Madeline Peterson

Dissertations, Master's Theses and Master's Reports

Methyl-mercury (MeHg) is a potent neurotoxin that threatens the health of humans and wildlife alike. Climate warming threatens to shift regional precipitation and climate regimes in peatland environments, which could destabilize northern peatlands and accelerate both Hg release from soil and MeHg production. Peatlands are among the leading hotspots for MeHg, yet little is known about the community composition or functional relationship of mercury-methylating microbes in response to varying environmental conditions. The recognized mercury-methylating genes responsible for this activity are the obligatory gene pair hgcA and hgcB. Metagenomic data from the full-factorial peatland mesocosm experiment PEATcosm was obtained to …

Applications Of Machine Learning In Microbial Forensics, Ryan B. Ghannam

Dissertations, Master's Theses and Master's Reports

Microbial ecosystems are complex, with hundreds of members interacting with each other and the environment. The intricate and hidden behaviors underlying these interactions make research questions challenging – but can be better understood through machine learning. However, most machine learning that is used in microbiome work is a black box form of investigation, where accurate predictions can be made, but the inner logic behind what is driving prediction is hidden behind nontransparent layers of complexity.

Accordingly, the goal of this dissertation is to provide an interpretable and in-depth machine learning approach to investigate microbial biogeography and to use micro-organisms as …

Red Drum And Spotted Seatrout Live-Release Tournament Mortality And Dispersal, T. Reid Nelson, Crystal Hightower, Sean P. Powers

University Faculty and Staff Publications

Although catch-and-release fishing tournaments undoubtedly reduce mortality of target species, postrelease mortality and fish stockpiling at release sites remain common concerns related to these tournaments. The impacts of liverelease tournaments on freshwater species have been widely studied. However, research on estuarine sport fishes is lacking even though catch-and-release tournaments targeting these species are prevalent and popular recreational fisheries exist. Therefore, we estimated the post-weigh-in mortality and dispersal of Red Drum Sciaenops ocellatus and Spotted Seatrout Cynoscion nebulosus released from the 2016–2018 Alabama Deep Sea Fishing Rodeo live-weigh-in categories using acoustic telemetry. To concurrently estimate overall post-weigh-in mortality and dispersal, we …

Comparison Of Standard And Environmental Dna Methods For Estimating Chinook Salmon Smolt Abundance In The Klamath River, California, Doyle Joseph Coyne

Cal Poly Humboldt theses and projects

Evaluating abundance of juvenile salmonids is critical to conservation and management. Current abundance estimation involves use of rotary screw traps and mark-recapture studies. Use of environmental DNA (eDNA) in water samples offers a noninvasive and less expensive approach that may potentially improve or eventually replace traditional monitoring. Here I evaluate the utility of eDNA to predict weekly abundance estimates of outmigrating Chinook salmon (Oncorhynchus tshawytscha) smolts in the Klamath River, California. A total of 15 water samples were collected per week over the 17-week smolt outmigration in both 2019 and 2020. Chinook salmon eDNA concentration in each water …

Population Genetics Of A Reintroduced Fisher (Pekania Pennanti) Population In West Virginia, Caroline E. Harms

Graduate Theses, Dissertations, and Problem Reports

Fishers (Pekania pennanti) were reintroduced in West Virginia in 1969 with no population wide genetic analysis ever having been conducted. Genetic analysis of reintroduced populations is vital to assess genetic diversity as an indicative of population viability. My objective was to collect fisher samples throughout West Virginia, nearby states where fisher may be migrating (PA and NY), and the New Hampshire source population to provide a full genetic interpretation of the reintroduced West Virginia population. Genetic analysis was used to measure genetic diversity, admixture or delineation of subpopulations, and effective population size. Sample location and genetic data were …