Biology Commons^™

Connecting Environment And Phenotype: Deciphering Mechanisms Of Diapause Entry And Exit In The Annual Killifish Austrofundulus Limnaeus, Erin Monica Davis

Dissertations and Theses

Embryonic development is complex, dynamic, and dependent on environmental factors. Mechanisms of sensing and integrating environmental stimuli are diverse, and understanding these mechanisms in extant species can elucidate how complex phenotypes emerge from genomic information expressed in an environmental context. In Austrofundulus limnaeus, an annual killifish with alternative developmental trajectories, light and temperature are vital factors that determine if an embryo will enter a state of diapause. We hypothesize that embryos of A. limnaeus use the vitamin D₃ signaling pathway as a vehicle to incorporate these ecological signals into their developmental programing. Here we provide evidence of …

Characterizing The Cellular Dynamics Of Nup155 And A Clinically Identified Variant, Emily Storm

Dissertations and Theses

The nuclear pore complex (NPC) is a highly conserved, yet dynamic structure within the cell. As the sole point of communication between the nucleus and cytoplasm, maintenance of its function and composition is essential. Recent studies have shown that both NPCs and their constitutive components, nucleoporins (NUPs), can have diverse roles separate from canonical transport. In addition, mutations in individual NUPs have been linked to a wide variety of clinical diseases, however, the exact mechanism by which they cause pathology is often unclear. Recently, a point mutation in NUP155, R391H, was identified specifically in patients with familial atrial fibrillation. We …

There’S More Than One Way To Beat The Heat: What Anal Probes Reveal About Thermal Responses In Neotropical Beetles (Coleoptera: Cerambycidae)., Emilie I. Dion

Dissertations and Theses

Increasing global temperatures have been linked to shifts in the distributions and preferred microhabitats of terrestrial species. This trend is predicted to impact tropical forest insects, which may already be exposed to conditions that bring them close to their thermal maxima. Tropical microhabitats are linked to vertical stratification, because the canopy is hotter, winder, and less humid than the ground. In ectothermic organisms, such as beetles, thermoregulation is dependent on morphological and behavioral traits. This study investigates woodboring cerambycid beetles, to determine how behavioral thermoregulation through microhabitat selection (vertical stratification) is correlated to morphological attributes (color lightness, size, and pubescence) …

Analyzing Ultrastructural Characteristics Of Post-Synaptic Targets Of Pre-Identified Presynaptic Boutons In Layer 3 And Layer 4 Of The Ferret Primary Visual Cortex, Donia Shehab

Dissertations and Theses

The purpose of this study was to analyze the size and ultrastructural characteristics of post-synaptic elements apposed to previously characterized pre-synaptic elements in layers 3 and 4 of the primary visual cortex (PVC). We are aiming to quantify a range of values for synaptic element morphologies as well as to correlate pre- and post-synaptic elements to find a set of rules that is prevalent in the visual cortex that can also be upheld in other mammals. We hypothesize that bigger pre-synaptic elements correlate to bigger synapses and bigger post-synaptic elements. We compared these two different layers because they receive synaptic …

Investigating Dose-Dependent, Multi-Generational, And Strain-Specific Effects Of 17Α-Ethynylestradiol Exposure In Zebrafish (Danio Rerio), Decatur Mitochondria Foster

Dissertations and Theses

Endocrine disrupting chemicals (EDCs) pose a threat to biodiversity at the individual, population, and ecosystem level, as they can interfere with processes that are responsible for regulating metabolism, development, behavior, and reproduction in living organisms. 17α-ethynylestradiol (EE2) is a synthetic estrogen and EDC utilized in pharmaceutical and livestock industries, and contaminates waterways worldwide. This research explores the effects of dose-dependent and multi-generational exposure of EE2 in three strains of zebrafish. High dose (10-25 ng/L EE2) exposure led to complete reproductive failure, as well as significantly decreased survival and growth. A period in clean water (depuration) after exposure allowed for some …

Battle Of The Buttercups: Investigating Hybrid Zone Dynamics In A Ranunculus Species Complex, Jessica Persinger

Dissertations and Theses

Plants pose a well-known challenge to the biological species concept because hybridization is a common occurrence. Range dynamics have a crucial role in determining whether species are given the opportunity to interbreed or not. Successful hybridization can be of particular concern when considering range-limited species and their persistence. In my thesis research, I examine the apparent hybrid zone between the southern Oregon endemic Ranunculus austro-oreganus, a candidate threatened species due to its limited range, and its widespread congener, Ranunculus occidentalis, whose range spans from California to Alaska. The discovered contact zone was recognized in populations which contained apparent …

Assessing Well-Being Of Asian Elephants (Elephas Maximus) Through Major Events And Transitions, With Development And Aging, And Husbandry Changes, Sharon Stuart Glaeser

Dissertations and Theses

In this body of research, reproductive and adrenal hormones and behavior were used to evaluate individual and group responses to physiological, social, and environmental changes in zoo-housed Asian elephants, considering factors of sex, age, and life stage. Animals experience physiological, social, and environmental changes as part of their natural history and individual life experience. Measures of both positive and negative states are needed to assess the impact of these changes at the individual and group level. Such measures can help us better understand how animals cope with a changing environment, and can help inform management decisions. Through longitudinal analyses of …

Energy Stores And Life-History Transitions In Red-Sided Garter Snakes (Thamnophis Sirtalis Parietalis), Rachel Catharine Wilson

Dissertations and Theses

All organisms must prioritize investment in either reproductive or self-maintenance activities. Despite this established paradigm, our understanding of how organisms choose to prioritize certain behaviors and physiologies over others remains limited. It is likely that an organism's energy status not only influences variation in reproductive effort, but also transitions to and from reproductive activities. My dissertation aims to investigate how energy metrics (body condition index, adipocyte follicle size, and liver glycogen) relate to reproduction and associated life-history stages in red-sided garter snakes (Thamnophis sirtalis parietalis). Chapter two examines if energy metrics differ with migratory status and sex in …

No Oxygen, No Water: The Unique Physiology Of Annual Killifish Embryos Across Development, Daniel Erik Zajic

Dissertations and Theses

For most vertebrates, an abundance of oxygen is necessary for the production of ATP and the maintenance of cellular homeostasis. The absence of oxygen, even for brief periods, quickly leads to ATP depletion which can lead to irreparable damages to sensitive organs, such as the brain and heart. However, certain vertebrates demonstrate an extraordinary ability to thrive and recover fully from periods of no oxygen (anoxia). The annual killifish (Austrofundulus limnaeus) lives in ephemeral ponds in the Maracaibo basin of Venezuela and their embryos have the remarkable ability to not only survive anoxic periods for months, but also …

Short- And Long-Term Impacts Of A Deliberative Pedagogy In Introductory Biology And Chemistry Courses, Liz Rain-Griffith

Dissertations and Theses

There have been multiple national calls for curricular reform in college-level science, technology, engineering, and mathematics (STEM), including a need to instill democratic skills in students. Democratic skill building can be embedded in STEM classrooms through intentional "deliberative pedagogies" which include skills in: communication, collaboration, and application. We developed and implemented a deliberative pedagogy, Deliberative Democracy (DD), across introductory majors and non-majors biology courses and a majors chemistry course. In two separate studies, I took a longitudinal, qualitative research approach to understand introductory biology and chemistry students' experiences and perceptions of DD. For the first study, I tracked a cohort …

Morphology, Taxonomy, And Ecological Niche Modeling Of The Cochabamba Grass Mouse, Akodon Siberiae Myers & Patton, 1989, James George Dunn

Dissertations and Theses

The Cochabamba Grass Mouse, Akodon siberiae, is a small mouse (mean head+body length: 103 mm, N = 22) that occurs in a spatially restricted range in the Bolivian Yungas forests, the cloud forest transition zone between lowland Amazonia and the Andean Altiplano. Like many species in the genus, their appearance is very similar to that of other species in the genus: they are difficult to distinguish from their congeners, and are challenging to identify. In the absence of molecular data, A. siberiae specimens require a thorough and careful analysis of external and cranial features for identification. Furthermore, Akodon …

Sensing Malignancy: Expanding Upon The Nematode Scent Detection Test, Morgan Alexandra Thompson

Dissertations and Theses

With the growing prevalence of cancer worldwide, research has increasingly focused on methods of early detection since the early detection of cancer can dramatically improve health outcomes for affected individuals. Ideally, early detection systems would be highly reliable yet cost-effective and easy to use. Toward development of such a system, Hirotsu et al. (2015), developed a "Nematode Scent Detection Test" (NSDT) that capitalizes upon the attraction of Caenorhabditis elegans nematodes to various tissue samples from cancer patients to detect multiple types and stages of cancer. However, it is currently unknown which G-protein coupled receptors (GPCRs), and/or ligands interacting with theses …

Biogeography, Morphology, And Systematics Of The Mountain Cottontail, Sylvilagus Nuttallii (Bachman, 1837), Mammalia: Lagomorpha: Leporidae, Johnnie H. French

Dissertations and Theses

Widespread species often present taxonomic conundrums: are they truly a single panmictic species, or, is the widespread species in fact a polytypic species complex constituted by independently evolving, morphologically or otherwise cryptic species? One such broadly distributed taxon is Sylvilagus nuttallii, with distribution across the western United States, ranging from South Dakota to California, and from Canada to Arizona. The three subspecies constituting S. nuttallii are, however, geographically isolated and it has been hypothesized that they likely constitute independent, species level taxa. However, that study examined only two of the three holotypes, rather than broader geographic and non-geographic variation. …

From Theory To Practice: Interdisciplinary Science In Undergraduate Education, Brie Tripp

Dissertations and Theses

Science has undergone a major transformation in the 20th and 21st centuries with new fields emerging at the intersection of disciplines, such as bioethics, bioinformatics, and chemical ecology. Yet, opportunities to engage with interdisciplinary science, and the skills needed to work in these fields, are largely absent from undergraduate biology classrooms. As a consequence, students are potentially deprived of opportunities to think interdisciplinarily and engage with real-world issues that often necessitate interdisciplinary efforts. To be informed citizens in society and forward-thinking scientists in the workforce, undergraduate students will undoubtedly benefit from exposure to these interdisciplinary science experiences.

Given these considerations, …

Bone Mineral Density Of The Common Bottlenose Dolphin, Tursiops Truncatus: A Proposed Model For Monitoring Osteological And Ecosystem Health, James Wright Burrus Powell

Dissertations and Theses

Bone mineral density (BMD) in the pectoral flipper of the common bottlenose dolphin, Tursiops truncatus, was examined to address the need to define a comprehensive target site for clinical osteodensitometric assessment and to establish ranges of observed bone density values for this species. Radii were analyzed using dual energy X-ray absorptiometry (DXA), the accepted standard in human medical studies. Multiple loci within the radius were identified and assessed for their correlation to BMD of the entire bone. Radii BMD were also examined for differences based on sex, age, total body length, handedness, geographical affinity, and nutritional status at time …

Avian Dispersal Networks, Metacommunity Structure, And Bryophyte Community Assemblages, Matthew Wojciech Chmielewski

Dissertations and Theses

Spatial processes have a profound influence on the structure and function of community assemblages. The dispersal of organisms from their place of origin to the location in which they live out their reproductive life is particularly important for plant communities, which generally cannot adjust their location post-germination. Connection between communities at a landscape scale can also influence species persistence, local and regional diversity, and functional turnover at the metacommunity scale. Animals have been shown to disproportionately deposit propagules in particular microsites in many plant species, facilitating the arrival of plants to appropriate niche-space. Birds are particularly notable seed dispersers, given …

Parr Going The Distance: How Migratory Difficulty Influences Red Muscle Lipid Storage In Juvenile Oncorhynchus Mykiss, Emily Jean Morse

Dissertations and Theses

Adult salmonid populations embarking on difficult migrations have evolved to store more somatic energy prior to river entry. While it is known that lipids are the primary fuel for endurance swimming in fish, uncertainty still surrounds how these mechanisms are utilized by juvenile fish during seaward migration. A key phase in salmonid migration is the preparatory season of feeding and growth before swimming downstream. During this period, juvenile fish build somatic fuel stores through dietary uptake. Intestinal microbiota of steelhead trout (Oncorhynchus mykiss) vary drastically across their geographic range, with significant differences in the coastal and inland subspecies' …

Use Of Two-Replisome Plasmids To Characterize How Chromosome Replication Completes, Nicklas Alexander Hamilton

Dissertations and Theses

All living organisms need to accurately replicate their genome to survive. Genomic replication occurs in three phases; initiation, elongation, and completion. While initiation and elongation have been extensively characterized, less is known about how replication completes. In Escherichia coli completion occurs at sites where two replication forks converge and is proposed to involve the transiently bypass of the forks, before the overlapping sequences are resected and joined. The reaction requires RecBCD, and involves several other gene products including RecG, ExoI, and SbcDC but can occur independent of recombination or RecA. While several proteins are known to be involved, how they …

Snowy Plover Demography In Oregon, Eleanor Prindiville Gaines

Dissertations and Theses

A thorough understanding of demographic parameters and their contribution to overall population growth is fundamental to effective conservation of small populations, but this information is often lacking. The Pacific Coast population of the Western Snowy Plover (Charadrius nivosus nivosus) is listed as threatened and has been the target of long-term, multi-pronged management in Oregon. The Oregon coastal population has been intensively monitored since 1990, and over 80% of the population is color banded, but a comprehensive analysis of demographic parameters and the effect of management on vital rates and population growth has been unavailable until now. Here, the …

Isoprene Emission In Polytrichaceae Mosses, Timea Deakova

Dissertations and Theses

Our first aim was to identify and quantify Biological Volatile Organic Compound (BVOC) emissions, specifically emissions of isoprene, from the moss Polytrichum juniperinum during its earliest stage of life. Isoprene emission from mosses could be a significant component of the total global budget of BVOC emissions. Data concerning the spatial and temporal variability of these emissions are lacking due to poor characterization of the physical and biological factors controlling isoprene synthesis in both vascular and non-vascular plants. We found that P. juniperinum in its early life stage (protonema) can emit isoprene at detectable levels at day five after spore germination. …

The Interactive Effect Of Temperature And Salinity In The Nile Tilapia (Oreochromis Niloticus), Rachel Marie Palmer

Dissertations and Theses

Frequent measures that aim to identify the tolerance of an organism to various environmental conditions rely on the mortality of said organism. However, the effects of sub-lethal stress can be just as important to consider as they may give rise to how an organism may live in such an environment (growth, reproduction, etc.). Coping with changes in environmental conditions can have a high energy cost. Even starting a cellular stress response alone has proven to be costly. It is therefore reasonable that organisms in stressful situations will dedicate energy sources to survival mechanisms, and downregulate non-necessary activities like growth, and …

The Influence Of Hibernation Temperature On Deiodinase 2 In Red-Sided Garter Snakes (Thamnophis Sirtalis Parietalis), Kalera Stratton

Dissertations and Theses

Environmental cues such as day length and temperature contribute to timing of biological rhythms in seasonal breeders. Life-history transitions such as spring emergence from hibernation, migration, or mating must be coordinated with environmental conditions or survival is compromised. Therefore, there must be chemical signaling pathways in the brain that transduce seasonally-changing sensory inputs into signals that initiate a hormonal cascade, culminating in reproductive behavior. The relative importance of environmental cues to reproductive timing varies with species, time of year, and sex, and the mechanisms driving these differences remain unknown. The role of photoperiod in regulating reproductive behavior has been explored …

Symbiosis In Archaea: Functional And Phylogenetic Diversity Of Marine And Terrestrial Nanoarchaeota And Their Hosts, Emily Joyce St. John

Dissertations and Theses

The Nanoarchaeota are an enigmatic lineage of Archaea found in deep-sea hydrothermal vents and geothermal springs across the globe. These small (~100-400 nm) hyperthermophiles live ectosymbiotically with diverse hosts from the Crenarchaeota. Despite their broad distribution in high-temperature environments, very few Nanoarchaeota have been successfully isolated in co-culture with their hosts and nanoarchaeote genomes are poorly represented in public databases. However, the Nanoarchaeota provide unique insights into the structure and function of symbiosis in the archaeal domain. This study describes novel nanoarchaeotes from multiple geothermal habitats, using a combination of direct cultivation techniques and genomic analysis. A new nanoarchaeote …

Optimizing Crispr/Cas9 Gene Targeting To Investigate Cone Photoreceptor Development In The Chick Retina, Diana Y. Kim

Dissertations and Theses

Many human eye conditions result in the loss of vision, due to the degeneration of cone photoreceptors in the retina. Thus, the development of methods to regenerate these cone photoreceptors is an active area of study. In order to find ways to regenerate cones, the molecular pathways and gene regulatory networks that a retinal progenitor cell takes to develop into a postmitotic cone photoreceptor needs to be well understood. In an attempt to answer this question, this paper studies the effect of CRISPR/Cas9-mediated mutagenesis of two key transcription factors, Otx2 and Nr2e3, on retinal progenitor cells and cone photoreceptors throughout …

Role Of Moa-1, An Anti-Phosphatase, And Apl-1, An App-Related Protein, In Morphogenesis And Mating Behavior In Caenorhabditis Elegans, Valerie C. Moscoso

Dissertations and Theses

Alzheimer's disease is a neurodegenerative disease that affects more than 30 million people globally. The disease is characterized by an accumulation of extracellular beta-amyloid peptide plaques and intracellular neurofibrillary tangles in the brain. The beta-amyloid peptide is derived from a larger precursor protein, the amyloid precursor protein (APP). Mutations in APP have been correlated with Alzheimer's disease. Due to the presence of two paralogues, APLP1 and APLP2, which have overlapping functions, the normal function of APP is difficult to elucidate. Knockout of the entire APP gene family in mice results in lethality and developmental defects, indicating that the APP gene …

Small Rna Mgrr Regulates Sensitivity Of Escherichia Fergusonii To Oxidative Stress, Austin Paul Wright

Dissertations and Theses

Non-coding small RNAs (sRNAs) are integral to post-transcriptional gene regulation in bacteria. The function of an sRNA is dependent on both secondary structure and the sequence of its unstructured seed region. The sRNA seed region typically base-pairs with target mRNAs to down-regulate the expression of target genes by blocking the ribosome-binding site or by promoting RNase-mediated degradation of the sRNA-mRNA complex. sRNAs have also been shown to increase expression of target genes by releasing RNA secondary structures that block ribosome-binding sites. Selective pressure to maintain sRNA function conserves the sequence of the sRNA seed region, but mutations in mRNA sequences …

Accumulation And Transmission Dynamics Of A Naturally-Occurring Mtdna Deletion In Caenorhabditis Briggsae, Jennifer Anne Sullins

Dissertations and Theses

Maintaining mitochondrial genome sequence integrity is essential for preserving normal mitochondrial function. Several human diseases have been associated with heteroplasmic mitochondrial genome mutations, but few genetic systems can simultaneously represent pathogenic mitochondrial genome evolution and inheritance. The nematode Caenorhabditis briggsae is one such model. Natural C. briggsae isolates are globally-distributed and phylogenetically grouped into three distinct clades, with isolates exhibiting varying levels of a large-scale mtDNA deletion, nad5∆. Furthermore, a small subset of clade II isolates exhibits putative compensatory mutations that may reduce the risk of deletion formation and accumulation in those populations. In this thesis, the author characterizes the …

Impact Of Suburban Landscape Features On Gene Flow Of The Model Invasive Grass, Brachypodium Sylvaticum, Tina Marie Arredondo

Dissertations and Theses

Rapid range expansion of newly invasive species provides a unique opportunity for studying patterns of dispersal and gene flow. In this thesis, I examined the effect of landscape features on gene flow in the invasive grass Brachypodium sylvaticum at the edge of its expanding range. I used genome-wide Single Nucleotide Polymorphism (SNP) surveys of individuals from 22 locations in the Clackamas Watershed in the Portland, Oregon metropolitan region to assess genetic diversity and structure, to identify putative source populations, and to conduct landscape genetic analyses. Resistance surfaces were created for each landscape feature, using ResistanceGA to optimize resistance parameters. My …

The Limitations Of Dna Interstrand Cross-Link Repair In Escherichia Coli, Jessica Michelle Cole

Dissertations and Theses

DNA interstrand cross-links are a form of genomic damage that cause a block to replication and transcription of DNA in cells and cause lethality if unrepaired. Chemical agents that induce cross-links are particularly effective at inactivating rapidly dividing cells and, because of this, have been used to treat hyperproliferative skin disorders such as psoriasis as well as a variety of cancers. However, evidence for the removal of cross-links from DNA as well as resistance to cross-link-based chemotherapy suggests the existence of a cellular repair mechanism. Characterizing the pathways involved in DNA interstrand cross-link repair has been challenging due to the …

Comparative Genetic And Genomic Analysis Of The Novel Fusellovirus Sulfolobus Spindle-Shaped Virus 10, David Andrew Goodman

Dissertations and Theses

Viruses that infect thermophilic Archaea are unique in both their structure and genetic makeup. The lemon-shaped fuselloviruses - which infect members of the order Sulfolobales, growing optimally at 80º C and pH 3 - are some of the most ubiquitous and best studied viruses of the thermoacidophilic Archaea. They provide a malleable and useful genetic tool for probing into the functions of their host, as well as the host responses to infection. Nonetheless, much about these viruses remains to be learned to further understand their morphological, genetic, and life cycle characteristics.

In order to investigate these aspects of these …