Life Sciences Commons^™

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, …

Genetic Analysis Of The Major Capsid Protein Of The Archaeal Fusellovirus Ssv1: Mutational Flexibility And Conformational Change, Eric A. Iverson, David A. Goodman, Madeline E. Gorchels, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Viruses with spindle or lemon-shaped virions are rare in the world of viruses, but are common in viruses of archaeal extremophiles, possibly due to the extreme conditions in which they thrive. However, the structural and genetic basis for the unique spindle shape is unknown. The best-studied spindle-shaped virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), is composed mostly of the major capsid protein VP1. Similar to many other viruses, proteolytic cleavage of VP1 is thought to be critical for virion formation. Unlike half of the genes in SSV1, including the minor capsid protein gene VP3, the VP1 gene does not tolerate …

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 …

Dynamics Of Prochlorococcus And Synechococcus At Station Aloha Revealed Through Flow Cytometry And High-Resolution Vertical Sampling, Ger J. Van Den Engh, Joseph K. Doggett, Anne W. Thompson, Martina A. Doblin, Carla N.G. Gimpel, David M. Karl

Biology Faculty Publications and Presentations

The fluorescence and scattering properties of Prochlorococcus and Synechococcus at Station ALOHA as measured by flow cytometry (termed the FCM phenotype) vary with depth and over a variety of time scales. The variation in FCM phenotypes may reflect population selection or physiological acclimation to local conditions. Observations before, during, and after a storm with deep water mixing show a short-term homogenization of the FCM phenotypes with depth, followed by a return to the stable pattern over the time span of a few days. These dynamics indicate that, within the upper mixed-layer, the FCM phenotype distribution represents acclimation to ambient light. …

A Metabolic Hypothesis For The Evolution Of Temperature Effects On The Arterial Pco2 And Ph Of Vertebrate Ectotherms, Stanley S. Hillman, Michael Scott Hedrick

Biology Faculty Publications and Presentations

Body temperature increases in ectothermic vertebrates characteristically lead to both increases in arterial PCO2 (PaCO2) and declines in resting arterial pH (pHa) of about 0.017 pH units/°C increase in temperature. This ‘alphastat’ pH pattern has previously been interpreted as being evolutionarily-driven by the maintenance of a constant protonation state on the imidazole moiety of histidine protein residues, hence stabilizing protein structure-function. Analysis of the existing data for interclass responses of ectothermic vertebrates show different degrees of PaCO2 increases and pH declines with temperature between the classes with reptiles>amphibians>fish. The PaCO2 at the temperature where maximal aerobic metabolism (VO2max) …

An Efficient Pipeline To Generate Data For Studies In Plastid Population Genomics And Phylogeography, Brendan F. Kohrn, Jessica M. Persinger, Mitchell B. Cruzan

Biology Faculty Publications and Presentations

Premise of the study: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole‐genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single‐nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure.

Methods: We developed sampling methodologies and an application, CallHap, that uses a least‐squares algorithm to evaluate the fit between …

Plasma Cell Survival In The Absence Of B Cell Memory, Erika Hammarlund, Archana Thomas, Ian J. Amanna, Lindsay Holden, Ov D. Slayden, Byung S. Park, Lina Gao, Mark K. Slifka

Biology Faculty Publications and Presentations

Pre-existing serum antibodies play an important role in vaccine-mediated protection against infection but the underlying mechanisms of immune memory are unclear. Clinical studies indicate that antigen-specific antibody responses can be maintained for many years, leading to theories that reactivation/differentiation of memory B cells into plasma cells is required to sustain long-term antibody production. Here, we present a decade-long study in which we demonstrate site-specific survival of bone marrow-derived plasma cells and durable antibody responses to multiple virus and vaccine antigens in rhesus macaques for years after sustained memory B cell depletion. Moreover, BrdU+ cells with plasma cell morphology can be …

Adaptive Evolution Under Extreme Genetic Drift In Oxidatively Stressed Caenorhabditis Elegans, Stephen Fuller Christy, Riana I. Wernick, Michael James Lue, Griselda Velasco, Dana K. Howe, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1. The original intent of the study was to assess the effect of electron transport chain dysfunction involving elevated reactive oxygen species production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared with their ancestor. Likewise, the gas-1 MA lines experienced partial recovery to wildtype reactive oxygen species levels. Whole-genome sequencing and analysis revealed that …

Use Of Gene Editing In Usda Research, Mark R. Mclellan, Patsy Brannon, Adriana Campa, Carrie Castille, Steven Daley-Laursen, Roch Gaussoin, Govind Kannan, Mark Lawrence, Dawn Thilmany

Biology Faculty Publications and Presentations

The Science Advisory Council was established in FY2016 as a subcommittee of the National Agricultural Research, Extension, Education, and Economics (NAREEE) Advisory Board by the Chief Scientist as a result of recommendations from the 2012 report on Agricultural Preparedness by the President’s Council of Advisors on Science and Technology. The Council's charge is to provide advice and guidance, on a scientific basis, on the overall strength, practicality, and direction of agricultural research, including emerging technology and scientific issues and report any findings publicly to the NAREEE Advisory Board.

The USDA Chief Scientist first asked the Council to examine rigor and …

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 …

Winter Diet Of Bobolink, A Long-Distance Migratory Grassland Bird, Inferred From Feather Isotopes, Rosalind B. Renfrew, Jason M. Hill, Daniel H. Kim, Christopher Romanek, Noah G. Perlut

Biology Faculty Publications and Presentations

Effective conservation of migratory bird populations depends on advancements in our understanding of processes throughout the life cycle. Fundamental information about wintering ecology (e.g., habitat use and diet composition) remains limited, which limits assessment of threats to populations during winter. Bobolink (Dolichonyx oryzivorus) is a year-round grassland obligate and Nearctic-Neotropical migrant that undergoes 2 complete molts each year, including a complete prealternate molt on the South American wintering grounds. This unusual winter molt provides a rare opportunity to examine, using stable isotope analysis, the timing and contribution of foraging resources in the Bobolink diet prior to northbound migration from disparate …

Arginine Vasotocin And Neuropeptide Y Vary With Seasonal Life-History Transitions In Garter Snakes, Ashley R. Lucas, Daelyn Y. Richards, Lucy M. Ramirez, Deborah Lutterschmidt

Biology Faculty Publications and Presentations

Transitions between life-history stages are often accompanied by dramatic behavioral switches that result from a shift in motivation to pursue one resource over another. While the neuroendocrine mechanisms that regulate such behavioral transitions are poorly understood, arginine vasotocin (AVT) and neuropeptide Y (NPY) are excellent candidates because they modulate reproductive and feeding behavior, respectively. We asked if seasonal changes in AVT and NPY are concomitant with the seasonal migration to and from the feeding grounds in red-sided garter snakes (Thamnophis sirtalis parietalis). Male and female snakes were collected in different migratory states during both the spring and fall. The total …

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 …

Assessing The Potential Of Land Use Modification To Mitigate Ambient No2 And Its Consequences For Respiratory Health, Meenakshi Rao, Linda A. George, Vivek Shandas, Todd N. Rosenstiel

Urban Studies and Planning Faculty Publications and Presentations

Understanding how local land use and land cover (LULC) shapes intra-urban concentrations of atmospheric pollutants—and thus human health—is a key component in designing healthier cities. Here, NO₂ is modeled based on spatially dense summer and winter NO₂ observations in Portland-Hillsboro-Vancouver (USA), and the spatial variation of NO₂ with LULC investigated using random forest, an ensemble data learning technique. The NO₂ random forest model, together with BenMAP, is further used to develop a better understanding of the relationship among LULC, ambient NO₂ and respiratory health. The impact of land use modifications on ambient NO₂, …

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 …

Experimental Evolution With Caenorhabditis Nematodes, Henrique Teotónio, Suzanne Estes, Patrick C. Phillips, Charles F. Baer

Biology Faculty Publications and Presentations

The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic …

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 …

Horizontally Acquired Biosynthesis Genes Boost Coxiella Burnetii's Physiology, Abraham S. Moses, Jess A. Millar, Matteo Bonazzi, Paul A. Beare, Rahul Raghavan

Biology Faculty Publications and Presentations

Coxiella burnetii, the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such an hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella's intracellular growth. Recent studies indicate that C. burnetii evolved from a tick-associated ancestor and that the metabolic capabilities of C. burnetii are different from that of Coxiella-like bacteria found in ticks. Horizontally acquired genes that …

Females Are The Brighter Sex: Differences In External Fluorescence Across Sexes And Life Stages Of A Crab Spider, Erin E. Brandt, Susan E. Masta

Biology Faculty Publications and Presentations

Fluorescence is increasingly recognized to be widespread in nature. In particular, some arachnids fluoresce externally, and in spiders the hemolymph fluoresces. In this study, we examined the external fluorescence and the fluorophores of different sexes and life stages of the crab spider Misumena vatia (Clerk 1757), a sit-and-wait predator that feeds on insects as they visit flowers. We designed novel instrumentation to measure external fluorescence in whole specimens. We found that although males and females possess internal fluorophores with similar properties, the external expression of fluorescence varies across sexes and life stages. Spiders fluoresce brightly as immatures. Females maintain their …

The Aerodynamic Effects On Flight Patterns And The Evolutionary Changes In Pterosaurs, Johnathan D. Talik

Undergraduate Research & Mentoring Program

Early pterosaurs were the first vertebrates to achieve powered flight, and remained small-to-medium sized from the Triassic Period to the end of the Jurassic Period. During that interval, lasting from 210 million years ago to 66 million years ago, pterosaurs underwent a notable changes at the end of the Jurassic Period and through the Cretaceous Period. They were abruptly replaced by much larger forms, characterized by great size and peculiar head ornamentation, among other unique and notable morphological features. While many different explanations theorize why and how the features of the pterosaurs changed over the Cretaceous Period, the aerodynamic influences …

Accumulation And Expression Of Multiple Antibiotic Resistance Genes In Arcobacter Cryaerophilus That Thrives In Sewage, Jess A. Millar, Rahul Raghavan

Biology Faculty Publications and Presentations

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also …

Transcriptomic Analysis Of Maternally Provisioned Cues For Phenotypic Plasticity In The Annual Killifish, Austrofundulus Limnaeus, Amie L. Romney, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Background: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifsh Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause. Alternately, embryos can be programmed to “escape” from diapause and develop directly by both maternal …

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 …

Each To Their Own Cure: Faculty Who Teach Course-Based Undergraduate Research Experiences Report Why You Too Should Teach A Cure, Erin E. Shortlidge, Gita Bangera, Sara Brownell

Biology Faculty Publications and Presentations

Course-based undergraduate research experiences (CUREs) meet national recommendations for integrating research experiences into life science curricula. As such, CUREs have grown in popularity and many research studies have focused on student outcomes from CUREs. Institutional change literature highlights that understanding faculty is also key to new pedagogies succeeding. To begin to understand faculty perspectives on CUREs, we conducted semi-structured interviews with 61 faculty who teach CUREs regarding why they teach CUREs, what the outcomes are, and how they would discuss a CURE with a colleague. Using grounded theory, participant responses were coded and categorized as tangible or intangible, related to …