Biology Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

Investigating The Role Of Small Noncoding Rnas In Vertebrate Anoxia Tolerance, Claire Louise Riggs

Dissertations and Theses

Very few vertebrates survive extended periods of time without oxygen. Entry into metabolic depression is central to surviving anoxia, which is supported by overall suppression of protein synthesis, yet requires increased expression of specific proteins. Studying the rapid and complex regulation of gene expression associated with survival of anoxia may uncover new mechanisms of cellular biology and transform our understanding of cells, as well as inform prevention and treatment of heart attack and stroke in humans. Small non-coding RNAs (sncRNAs) have emerged as regulators of gene expression that can be rapidly employed, can target individual genes or suites of genes, …

Transcriptomic Regulation Of Alternative Phenotypic Trajectories In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Amie L. Romney

Dissertations and Theses

The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of two developmental phenotypes. Alternatively, individuals can "escape" entry into diapause and develop continuously until hatching. The alternative phenotypes of A. limnaeus are a form of developmental plasticity that provides this species with a physiological adaption for surviving stressful environments. The developmental trajectory of an embryo is not distinguishable morphologically upon fertilization and phenotype is believed to be influenced by maternal provisioning within the egg based on observations of offspring phenotype …

Expanding Metabolic Diversity Of Two Archaeal Phyla: Nanoarchaeota And Korarchaeota, John Forad Kelley

Dissertations and Theses

Culture independent studies have revealed a greater diversity of Archaea than the two kingdoms initially defined by Carl Woese. Culturing species from the newly discovered archaeal lineages, as with the majority of microbes, has been difficult. To overcome the culturing dilemma, metagenomics is being used to reconstruct environmental genomes. Two metagenomic studies are presented in this thesis, with the aim of recovering newly proposed archaeal genomes from the Nanoarchaeota and Korarchaeota.

In the first study, a sediment sample, NZ13, was collected from a terrestrial New Zealand hot spring. Along with the sediment sample, two complex enrichments were sequenced on an …

Evolution And Metabolic Potential Of Francisella-Like Endosymbionts Of Ticks, Jonathan Graham Gerhart

Dissertations and Theses

Endosymbiosis in arthropods involves intracellular bacteria that supply an array of benefits to the host. Endosymbionts likely enhance the health of ticks by provisioning amino acids such as cysteine and tyrosine, and cofactors such as biotin and folic acid that are not available in blood--the sole nutrient source of ticks. Endosymbionts of ticks are of special interest due to their close evolutionary relationship with tick-vectored pathogens that impact livestock and human health. For example, ticks typically contain Coxiella-like endosymbionts (CLEs) that are the closest relatives of the human pathogen Coxiella burnetii. In order to understand the evolutionary relationship …

The Cul3 Ubiquitin Ligase: An Essential Regulator Of Diverse Cellular Processes, Brittney Marie Davidge

Dissertations and Theses

Cul3 forms E3 ubiquitin ligase complexes that regulate a variety of cellular processes. This dissertation describes Cul3's role in several of these pathways and provides new mechanistic details regarding the role of Cul3 in eukaryotic cells. Cyclin E is an example of a protein that is regulated in a Cul3-dependent manner. Cyclin E is a cell cycle regulator that controls the beginning of DNA replication in mammalian cells. Increased levels of cyclin E are found in some cancers, in addition, proteolytic removal of the cyclin E N-terminus occurs in some cancers and is associated with tumorigenesis. Cyclin E levels are …

Intestinal Microbiota Diversity Of Pre-Smolt Steelhead (Oncorhynchus Mykiss) Across Six Oregon And Washington Hatcheries, Christina Carrell Yildirimer

Dissertations and Theses

The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess …

Symbiosis With Nitrogen-Fixing Rhizobia Influences Plant Defense Strategy And Plant-Predator Interactions, Adrienne Louise Godschalx

Dissertations and Theses

As sessile organisms, plants evolved a plethora of defenses against their attackers. Given the role of plants as a primary food source for many organisms, plant defense has important implications for community ecology. Surprisingly, despite the potential to alter entire food webs and communities, the factors determining plant investment in defense are not well-understood, and are even less understood considering the numerous symbiotic interactions in the same plant. Legume-rhizobia symbioses engineer ecosystems by fixing nitrogen from the atmosphere in trade for plant photosynthates, yet connecting symbiotic resource exchange to food web interactions has yet to be established. Here I test …

Predicting Parturition In A Long-Gestating Species: Behavioral And Hormonal Indicators In The Asian Elephant (Elephas Maximus), Heather Kelly Velonis

Dissertations and Theses

Captive populations of Asian elephants (Elephas maximus) in North America are not self-sustaining, and increasing reproductive success within captive populations is a high priority. The ability to accurately predict parturition can have a direct impact on elephant welfare. Elephants in captivity often require significant preparation and management throughout the birthing process, and complications during labor and delivery can necessitate immediate intervention, including stillbirth, protracted labor, maternal aggression towards a newborn calf, and dystocia. Being able to predict when parturition will commence can ensure appropriate staff is available and adequate monitoring is performed. Routine endocrine sampling can be used …

Examination Of Human Impacts On The Biodiversity And Ecology Of Lichen And Moss Communities, Hannah Marie Prather

Dissertations and Theses

Globally, more than half of the world's population is living in urban areas and it is well accepted that human activities (e.g. climate warming, pollution, landscape homogenization) pose a multitude of threats to ecosystems. Largely, human-related impacts on biodiversity will hold consequences for larger ecological processes and research looking into human impacts on sensitive epiphytic lichen and moss communities is an emerging area of research. While seemingly small, lichen and moss communities exist on nearly every terrestrial ecosystem on Earth and contribute to whole-system processes (e.g. hydrology, mineral cycling, food web energetics) worldwide. To further examine human impacts on epiphytic …

An Efficient Pipeline For Assaying Whole-Genome Plastid Variation For Population Genetics And Phylogeography, Brendan F. Kohrn

Dissertations and Theses

Tracking seed dispersal using traditional, direct measurement approaches is difficult and generally underestimates dispersal distances. Variation in chloroplast haplotypes (cpDNA) offers a way to trace past seed dispersal and to make inferences about factors contributing to present patterns of dispersal. Although cpDNA generally has low levels of intraspecific variation, this can be overcome by assaying the whole chloroplast genome. Whole-genome sequencing is more expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among SNPs are lost in pooled samples and treating SNP frequencies as independent estimates of variation provides biased estimates of genetic distance. I have developed …

Why Do Animals Do What They Do, When They Do It? Characterizing The Role Of The Hypothalamus-Pituitary-Adrenal Axis In Seasonal Life-History Transitions, Catherine Anne Dayger Forbes

Dissertations and Theses

Resource availability follows seasonal cycles in environmental conditions. To align physiology and behavior with prevailing environmental conditions, seasonal animals integrate cues from the environment with their internal state. One of the systems animals use to integrate those cues is the hypothalamus-pituitary-adrenal (HPA) axis and its primary effector, glucocorticoid hormones. The HPA axis has wide-ranging effects on physiology and behavior and, in the context of a glucocorticoid stress response, is known to mediate tradeoffs between immediate survival and future fitness. The HPA axis also plays an important role in facilitating predictable life-history events. Variation in HPA axis activity has been reported …

Let The Seeds Fall Where They May: Investigating The Effect Of Landscape Features On Fine-Scale Seed Dispersal, Monica R. Grasty

Dissertations and Theses

Seed dispersal is a crucial ecological and evolutionary process that allows plants to colonize sites and expand their ranges, while also reducing inbreeding depression and facilitating the spread of adaptive genetic variation. However, our fundamental understanding of seed dispersal is limited due to the difficulty of directly observing dispersal events. In recent years, genetic marker methods have furthered our understanding of colonization and range expansion due to seed dispersal. Most investigations focus on regional scales of dispersal, due to low levels of variation in the chloroplast genome (cpDNA), which can serve as an indirect measure of seed dispersal. Here, I …

Adaptive Evolution Under Favorable And Unfavorable Population Genetic Conditions In Caenorhabditis Elegans Nematodes, Stephen Fuller Christy

Dissertations and Theses

Mutation is a fundamental process that drives evolutionary change; however, most new mutations are deleterious for organismal fitness and can readily propagate within populations under a broad range of conditions. Mutational processes able to counteract deleterious mutation accumulation include: 1) reversion mutation back to wildtype, 2) acquisition of generally beneficial mutations, and 3) compensatory mutations that specifically mitigate the effects of previously-acquired deleterious mutations through epistasis. The potential for any of these mutation types alters our expectations for the impact of deleterious mutation in populations, but since the fitness effects of individual mutations are rarely characterized, the relative importance of …

Quantifying The Impacts Of A Novel Predator: The Distinctive Case Of The Oregon Spotted Frog (Rana Pretiosa) And The Invasive American Bullfrog (Rana (Aquarana) Catesbeiana), Kyle Scott Tidwell

Dissertations and Theses

The decline of the Oregon Spotted Frog (Rana pretiosa), a Pacific Northwest endemic now federally listed as threatened, has been attributed to several aspects of ecosystem alteration, primarily habitat degradation and loss. The introduced American Bullfrog (Rana (Aquarana) catesbeiana) has been widely implicated in those declines, but the basis of that contention has been difficult to characterize. The bullfrog occurring at every site of recent Oregon Spotted Frog extirpation has focused concern about its impact.

Here, I present a suite of interconnected studies that examine the behavioral ecology of both species to better understand the potential …

Defining The Relationship Between Maternal Care Behavior And Hearing Development In Wistar Rats, Jingyun Qiu

Dissertations and Theses

Previous studies in rodents have demonstrated the profound effects that variations in maternal care play during the postnatal development of the brain. However, much less is known about how maternal care affects hearing development. Recently, manipulations of maternal care have been investigated to accelerate hearing onset. We hypothesized that accelerated hearing development results from changes in maternal care behavior. To test this hypothesis, we used a selection model in which natural variations in maternal care were identified in a large cohort of dams by measuring the frequency of different behaviors including LG followed by selection of dams with LG scores …

Surviving Catastrophe: Resource Allocation And Plant Interactions Among The Mosses Of Mount St. Helens Volcano, Trevor David Williams

Dissertations and Theses

Mosses are some of the first colonizers to disturbed sites, yet their roles in early plant community structuring are not well understood. The primary succession zones of volcanoes provide opportunities to conduct natural experiments into how mosses contribute to early plant community formation, as well as how the unique environments found in such zones affect plant traits, particularly those associated with stress tolerance. Though plant community changes have been well-documented since Mount St. Helens (MSH) volcano erupted in 1980, the volcano's moss assemblages, their influence on other plants, and their potential roles in chemical-mediated competition and biogeochemical cycling have garnered …

Investigating The Origin And Functions Of A Novel Small Rna In Escherichia Coli, Fenil Rashmin Kacharia

Dissertations and Theses

Non-coding small RNAs (sRNAs) regulate various cellular processes in bacteria. They bind to a chaperone protein Hfq for stability and regulate gene expression by base-pairing with target mRNAs. Although the importance of sRNAs in bacteria has been well established, the mode of origination of novel sRNA genes is still elusive, mainly because the rapid rate of evolution of sRNAs obscures their original sources. To overcome this impediment, we identified a recently formed sRNA (EcsR2) in E. coli, and show that it evolved from a degraded bacteriophage gene. Our analyses also revealed that young sRNAs such as EcsR2 are expressed …

Stranding Mortality Patterns In California Sea Lions And Steller Sea Lions In Oregon And Southern Washington, 2006 To 2014, Kessina Lee

Dissertations and Theses

As changing ocean conditions lead to declining fish stocks and movement of forage fish, sea lions on the Oregon coast are subject to the pressures of declining prey availability and increasing conflicts with commercial and recreational fisheries. An analysis of strandings of California sea lions, Zalophus californianus, and Steller sea lions, Eumetopias jubatus, from 2006 to 2014, included cause of death, changing ocean conditions, and anthropogenic activity. Causes of death included disease, injury, and human interaction, such as gunshot wounds, fisheries net entanglements and boat strikes.

Oregon and Washington strandings of California sea lions are primarily adult and …

Investigating The Effects Of 17Α-Ethynylestradiol On Mitochondrial Genome Stability, Alicia M. Chivers

Dissertations and Theses

Environmental toxicants are ubiquitous throughout the environment as a result of human activity. Among these toxicants, environmental estrogens are a category of particular concern due to their environmental prevalence and potency in altering reproductive traits. While many studies have addressed the detrimental effects of environmental estrogens on both aquatic and terrestrial organisms, few have analyzed the potential for these compounds to alter mitochondrial function. Mitochondria are the primary energy-generating system for all eukaryotic life, supporting all aspects of development, metabolism, and growth. Each cell within the body contains many mitochondria which in turn contain multiple copies of their own DNA …

Sex-Specific Fungal Communities Of The Dioicous Moss Ceratodon Purpureus, Mehmet Ali Balkan

Dissertations and Theses

Mosses display a number of hallmark life history traits that influence their ecology at the population and community level. The long lived separation of sexes observed in the haploid gametophyte (dioicy) is one such feature of particular importance, as it is observed in the majority of bryophytes and creates intraspecific specialization of male and female individuals.

The prevalence of sexually dimorphic mosses raises the possibility of sex-specific interactions with fungi as observed in some vascular plants. Here I investigated how moss sex shapes fungal communities associated with gametophytic tissues of the ubiquitous moss, Ceratodon purpureus. Using greenhouse populations of …