Life Sciences Commons^™

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 …

The Effect Of Styrene-Maleic Acid (Sma) Copolymers On Solubilizing Lipid Bilayers And Forming Nanodiscs, Ghada Alramadan

Dissertations and Theses

Cell membranes, or plasma membranes, play an essential role in the structure and the function of living cells. In 1972, the fluid mosaic membrane model was the first unifying paradigm of membrane structure. It is no longer considered adequate because evidence of many non-homogeneous lipid structures in both natural and model membranes have been discovered over the past thirty years. The field of membrane biophysics now uses updated versions of the mosaic model, which consists of the complex mixture of different lipid species. The lipid species found in natural membranes produce a range of dynamic, laterally segregated, non-homogeneous domains, which …

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 …

Ecology And Population Dynamics Of Salmonids In The Columbia River: Response Of Fishes To Anthropogenic Change In A Large Riverscape, Timothy Sean Elder

Dissertations and Theses

Freshwater ecosystems and the species that reside therein are disproportionately imperiled compared to terrestrial systems. Over the past 150 years, the Columbia River basin in the western United States has gone from one of the most productive and abundant salmon watersheds in the world, to having just a small fraction of its former salmon abundance. The cause of declines in salmon productivity and abundance are related to overlapping and confounding stressors including changes in large-scale climatic patterns and anthropogenic alterations within and adjacent to the Columbia River. Four main anthropogenic stressors have been identified as the leading causes of salmonid …

Delphinids On Display: The Capture, Care, And Exhibition Of Cetaceans At Marineland Of The Pacific, 1954-1967, Taylor Michael Bailey

Dissertations and Theses

When Marineland of the Pacific opened in 1954 on the Palos Verdes Peninsula in greater Los Angeles, it was the second oceanarium in the world and the first on the West Coast. An initial investment of $3 million by Oceanarium Inc., owners of the popular Marine Studios park located near St. Augustine, Florida, ensured that Marineland was built with the same state of the art facilities needed to produce an authentic representation of the ocean floor on land. Building on Marine Studios' success exhibiting bottlenose dolphins (Tursiops truncatus), Marineland's central draw was its performing cetaceans. During the park's …

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 …

Framing Physical Activity: Weight Control Frames And Physical Activity Motivation, Kristin Spurkland

Dissertations and Theses

Public health institutions and popular media frequently frame weight loss and weight control as primary benefits of physical activity. This exploratory, descriptive study examined how respondents rated statements exemplifying three physical activity frames: a weight control frame, a medical frame, and an active embodiment frame. An anonymous, online survey was conducted in March 2018; respondents rated frame statements in terms of inspiring motivation to engage in physical activity, and in terms of perceived credibility. They also provided anthropometric data and physical activity data. Data were analyzed for the entire sample as well as stratified by multiple variables, including body mass …

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 …

Mooring Impacts On Zostera Marina Meadows And Associated Epifauna In Nantucket Harbor, Massachusetts, Usa, Andrew Wright Mccandless

Dissertations and Theses

Seagrass ecosystems are some of the most productive in the world and provide a variety of ecosystem services but are facing global decline chiefly due to anthropogenic disturbance. Mechanical disturbances to seagrass meadows from anchoring, propeller scars, and mooring scars result in losses or damage to both shoots and the underlying rhizome. I conducted a literature synthesis on the extent of, recovery from, and ecological impacts of these mechanical disturbances to seagrass meadows. The literature suggests that anchoring damage tends to be worst in deeper water where larger vessels anchor and can cause large (>100m²) loss per …

Biomimetic Design And Construction Of A Bipedal Walking Robot, Alexander Gabriel Steele

Dissertations and Theses

Human balance and locomotion control is highly complex and not well understood. To understand how the nervous system controls balance and locomotion works, we test how the body responds to controlled perturbations, the results are analyzed, and control models are developed. However, to recreate this system of control there is a need for a robot with human-like kinematics. Unfortunately, such a robotic testbed does not exist despite the numerous applications such a design would have in mobile robotics, healthcare, and prosthetics.

This thesis presents a robotic testbed model of human lower legs. By using MRI and CT scans, I designed …

Composition And Dispersal Dynamics Of Vegetation Communities In Urban Riparian Forests, Christa Von Behren

Dissertations and Theses

In urban riparian areas, vegetation composition may be affected by urban land use changes at both the stream reach and the watershed scale. Moreover, the mechanisms by which seeds disperse may be affected both by reduction in seed sources due to vegetation removal and by the urban stream syndrome that produces flashier hydrographs and incised channels. I hypothesized that vegetation communities with high cover of native and hydrophilic species would be found in watersheds with high forest cover, while more limited cover of these species would be found in highly developed watersheds. Additionally, to examine the dispersal mechanisms contributing to …

Woodpeckers In The City: Habitat Use And Minimum Area Requirements Of Woodpeckers In Urban Parks And Natural Areas In Portland, Oregon, Adam Baz

Dissertations and Theses

Urbanization has contributed to the fragmentation and alteration of natural habitats around the globe, and is rapidly increasing. In this context, forested parks play a critical role for many species by providing patches of usable habitat within the urban matrix. Such patches may be particularly valuable to forest-specialists like woodpeckers (Picidae). Yet many woodpeckers require large forest patches, which are limited in fragmented landscapes. Despite their recognized value as ecosystem engineers and keystone species, almost no research exists on woodpecker ecology or space-use in urban settings. What habitat components influence woodpecker abundance and what are their functional minimum area requirements …

Maternal Angiotensinogen Genotype And Fetal Sex Impact Uteroplacental Function And The Developmental Origins Of Stress-Induced Hypertension, Jessica Faith Hebert

Dissertations and Theses

Fetal growth restriction (FGR) is a common and potentially life-threatening complication that affects 5-10% of human pregnancies. Maternal genetic predisposition and fetal male sex are known risk factors, but the underlying mechanisms are unknown. To study a known maternal genetic risk factor and the impact of fetal sex, we employed a published transgenic (TG) mouse model, which was designed to mimic a common human angiotensinogen (AGT) promoter variant associated with a 20% increase in circulating AGT levels. We hypothesized that TG dams would deliver growth restricted pups and that the underlying mechanism would be related to differences in maternal uterine …

Completion Of Dna Replication In Escherichia Coli, Brian Michael Wendel

Dissertations and Theses

To maintain genomic integrity, all cells must accurately duplicate their genetic material in order to provide intact and complete copies to each daughter cell following cell division. Successful inheritance of chromosomal information without changing even a single nucleotide requires accurate and robust DNA replication. This requires that cells tightly control replication initiation from the origin(s), processive elongation of the replisome, and the completion of DNA replication by resolving convergent replication forks ensuring that each sequence is duplicated without alteration. Unlike initiation and elongation, the process by which replication forks converge and are resolved into two discrete, inheritable DNA molecules is …

Interplay Of Transcription Factor E And Spt4/5 During Transcription Initiation In Pyrococcus Furiosus, Kimberly Kay Sheffield

Dissertations and Theses

Transcription, the first step in gene expression, is a highly regulated process which relies on a multi-protein complex to occur. Among these proteins are transcription factors, including initiation and elongation factors, which play differing roles in early and late stages of transcription. The mechanisms of transition from transcription initiation to elongation are not well understood in archaea, nor are the structures of the transcription factors involved. For transcription to occur in vitro, transcription factors TATA binding protein (TBP) and Transcription Factor B (TFB) are sufficient to allow RNA polymerase (RNAP) to synthesize RNA from template DNA. Another factor, Transcription …

Fungal Endophytes In A Seed-Free Host: New Species That Demonstrate Unique Community Dynamics, Brett Steven Younginger

Dissertations and Theses

Fungal endophytes are highly diverse, cryptic plant endosymbionts that form asymptomatic infections within host tissue. They represent a large fraction of the millions of undescribed fungal taxa on our planet with some demonstrating mutualistic benefits to their hosts including herbivore and pathogen defense and abiotic stress tolerance. Other endophytes are latent saprotrophs or pathogens, awaiting host plant senescence to begin alternative stages of their life cycles. Most, however, are likely plant commensals with no observable benefits to their hosts while under study. Yet, when considering the context-dependence that may determine plant resistance to pathogen attack, the consortium of endophytes present …

Understanding The Impacts Of Urbanization On The Avian Community Of Portland Oregon And Evaluation Of The Portland Oregon Backyard Habitat Certification Program, Andrew Daniel Gibbs

Dissertations and Theses

Over fifty percent of humans live in cities. The environmental cost of this is massive, as is the potential for utilizing privately held yards as an integral part of conservation in urban areas. The Backyard Habitat Certification Program (BHCP) in Portland, Oregon, was established to reduce invasive plants, support wildlife, and promote conservation. The program involves > 3000 yards certified at three tiers. While onsite inspections are required to verify compliance, there has never been an assessment of the value of these yards to wildlife. Chapter 1 examined the relationships between the urban landscape and bird distributions outside of yards. Chapter …

Investigating The Role Of Genomic Variation In Susceptibility To Environmental Chemicals Across Populations, Lindsay Adrian Holden

Dissertations and Theses

No two individuals are identical. This is true at the genetic level and at the phenotypic level. One of the traits that varies between populations is toxicant susceptibility: some individuals are sensitive to the effects of environmental chemical exposure, and others are resistant. This body of work aims to address the impact of genomic copy number variants (CNV)--large (>1 Kb) duplications or deletions across the genome--on the toxicant-susceptibility phenotype.

Herein copy number variants were characterized across three commonly used laboratory strains of zebrafish (Danio rerio) and mRNA expression phenotypes were identified in the same strains. It was found that …

Food Waste Diversion Programming In Post-Secondary Education, Manar Arica Alattar

Dissertations and Theses

The urgent need for reform of USA and global food systems is evident in the pervasiveness of both food waste and food insecurity. Such an inefficient system strains the environmental, social, and economic systems on which it relies. Although policy and infrastructure changes are essential, consumers can play a significant role by decreasing their food waste, given that consumer waste represents 60% of the waste along the food cycle in developed countries. Incorporation of food literacy and food waste education in school curricula may provide a meaningful entry point for promoting food waste reduction skills.

This dissertation presents context on …

Effect Of Microbes On The Growth And Physiology Of The Dioecious Moss, Ceratodon Purpureus, Caitlin Ann Maraist

Dissertations and Theses

The microorganisms colonizing plants can have a significant effect on host phenotype, mediating such processes as pathogen resistance, stress tolerance, nutrient acquisition, growth, and reproduction. Research regarding plant-microbe interactions has focused almost exclusively on vascular plants, and we know comparatively little about how bryophytes -- including mosses, liverworts, and hornworts -- are influenced by their microbiomes. Ceratodon purpureus is a dioecious, cosmopolitan moss species that exhibits sex-specific fungal communities, yet we do not know whether these microbes have a differential effect on the growth and physiology of male and female genotypes. Using a common-garden design, we reared ten axenic genotypes …

Assessing The Effects Of Climate Change And Fuel Treatments On Forest Dynamics And Wildfire In Dry Mixed-Conifer Forests Of The Inland West: Linking Landscape And Social Perspectives, Brooke Alyce Cassell

Dissertations and Theses

Over the past century in the western United States, warming has produced larger and more severe wildfires than previously recorded. General circulation models and their ensembles project continued increases in temperature and the proportion of precipitation falling as rain. Warmer and wetter conditions may change forest successional trajectories by modifying rates of vegetation establishment, competition, growth, reproduction, and mortality. Many questions remain regarding how these changes will occur across landscapes and how disturbances, such as wildfire, may interact with changes to climate and vegetation. Forest management is used to proactively modify forest structure and composition to improve fire resilience. Yet, …

Whence And Whither: Acoustic Variability And Biogeography Of Tarsiers In North Sulawesi, Olivia Clare Kulander

Dissertations and Theses

The morning duet calls of eastern tarsiers (Tarsius spp.) in North Sulawesi were recorded and analyzed to examine the effects of geography and geologic history on their call structure. Tarsius species exhibit interspecifically variable duet calls shown to correlate with species differentiation and distribution. They are distributed across Sulawesi, a biogeographically complex island in the Indonesian archipelago, where tectonic activity and multiple glaciations during the Pleistocene generated and modified barriers to their dispersal and gene flow.

Recordings were made at ten locations from November of 2012 through June of 2014. Two locations were categorized as mainland, while eight island …

Recovery Of Zooplankton Communities To Whole-Lake Disturbance, Brian Newton Mcgann

Dissertations and Theses

Community assembly following disturbance is a key process in determining the composition and function of the future community. However, replicated studies of community assembly at whole ecosystem scales are rare. Here is described a series of whole-lake experiments in which the recovery of zooplankton communities is tracked following an ecosystem-scale disturbance. Fourteen lakes in eastern Washington were chosen: seven lakes were treated with rotenone, while the remaining seven were reference. Each lake was monitored up to six months before and one to two years after the rotenone treatments. Zooplankton tows were taken monthly, at a shallow, intermediate, and deep site …

Morphological Correlates And Behavioral Functions Of Sound Production In Loricariid Catfish, With A Focus On Pterygoplichthys Pardalis (Castelnau, 1855), Monique Renee Slusher

Dissertations and Theses

The Neotropical catfish Pterygoplichthys pardalis produces a harsh stridulation sound upon manual capture. This stridulation sound is made on the abduction of the pectoral fin spine, and is accomplished by friction of a ridged dorsal condyle against a rough spinal fossa of the cleithrum in the pectoral girdle. The sound produced has an average frequency of 121 Hz, and is used with other anti-predator adaptations such as bony subdermal armor and defensive fin-spreading. Pterygoplichthys pardalis does not display behavioral modification in response to conspecific stridulation sound, and therefore it is likely that stridulation sound in P. pardalis is being used …

Water Transport In The Lateral Line Canal Of The Intertidal Fish Xiphister Mucosus (Girard 1858) And Its Significance To Evaporative Water With Preliminary Observations Of The Metabolic Consequences Of Water Loss, Whitney Anne Gayer

Dissertations and Theses

The lateral line canal system is a sensory organ found in all teleost fish that has a wide range of morphological variation. Variation in morphology may often be the result of evolutionary necessity where the need for function dictates form. Xiphister mucosus is an amphibious Stichaeid fish that inhabits the rocky intertidal zone of the northeastern Pacific Ocean. The rocky intertidal is considered an extreme environment where crashing waves and ebbing tides may require the specialization of adaptations for surviving the many abiotic stressors encountered there.

The lateral line trunk canal of Xiphister is regarded as unique among teleosts with …

The Effect Of Stress Induced Premature Senescence On The Expression Of Heterogeneous Ribonucleoieoprotein, Yuriy Pechenyy

Dissertations and Theses

The role of heterogeneous nuclear ribonucleoproteins (hnRNP) in cellular senescence is yet to be defined. Cellular senescence is a terminal growth arrest in somatic cells. It is thought to be the consequence of telomeric shortening that acts as a DNA damage signal. Conversely, cells induced into premature senescence (SIPS) by oxidative stress, is independent of telomere attrition. Premature senescence has been proposed to be physiologically relevant as it can be induced by treatment with chemotherapeutic agents. In particular, we are studying the roles of hnRNP A1 and A2 in the maintenance of the senescence phenotype. hnRNPs are a family of …

Wnt Secretion Proteins Modulate Rankl-Induced Expression Of Aire In Thymic Epithelial Cells, Daniel Pollack

Dissertations and Theses

Thymic epithelial cells (TEC) are essential for a proper adaptive immune response by regulating thymocyte development and establishing central tolerance. In the thymus, TECs differentially express Wnt proteins, which activate canonical and non-canonical Wnt signaling pathways. Wnt signaling is thought to regulate cell survival, proliferation, and development although the direct molecular mechanisms in TECs have yet to be elucidated. The inducible inhibition of canonical Wnt signaling with Dkk1 leads to a rapid loss of TEC progenitors as well as a decline in mature Aire-expressing mTECs. Therefore, we explore the role of Wnt ligands potentially responsible for stimulating and/or regulating Wnt …

Evolution Of Floral Morphology And Symmetry In The Miconieae (Melastomataceae), Maria Gavrutenko

Dissertations and Theses

Analyses of evolution of floral morphology and symmetry broaden our understanding of the drivers of angiosperm diversification. Integrated within a flower, labile floral characters produce different phenotypes that promote variable interactions with pollinators. Thus, investigation of floral evolution may help infer potential historic transitions in pollinator modes and ecological pressures that generated present diversity. This study aims to explore morphological evolution of flowers in Miconieae, a species-rich Neotropical tribe within family Melastomataceae. Despite a constrained floral plan, Melastomataceae manage to achieve a variety of floral traits appealing to diverse pollinator types, with majority of the species requiring specialized “buzz pollination” …

Bone Marrow Derived Progenitor Cells And Their Contributions To The Thymic Stroma, Mohammed Hoque

Dissertations and Theses

The thymus serves as the primary lymphoid organ responsible for the development and selection of a self-tolerant T cell repertoire. In paradox to its critical functions for the adaptive immune response, the thymus undergoes a profound age associated decline beginning in early adult life resulting in significant decline in T-cell function.Thymic epithelial cells (TECs) are the most critical component of the thymic microenvironment and undergo rapid turn-over, so understanding the cellular mechanisms responsible for the maintenance of TEC number and organization will be critical in counteracting age associated involution, particularly in cancer patients, due to enhanced degeneration in response to …