Index Catalog // ScholarsArchive@OSU

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

Creator:: Quandt, C. Alisha, Di, Yanming, Elser, Justin, Jaiswal, Pankaj, and Spatafora, Joseph W.
Abstract:: This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045
Resource Type:: Article
Full Text:: infection that is not solely involved in changes in growth morphology. The upregulation of Mad1 on EMP and

De Novo Assembly and Characterization of Four Anthozoan (Phylum Cnidaria) Transcriptomes

Creator:: Kitchen, Sheila A., Crowder, Camerron M., Poole, Angela Z., Weis, Virginia M., and Meyer, Eli
Abstract:: Many nonmodel species exemplify important biological questions but lack the sequence resources required to study the genes and genomic regions underlying traits of interest. Reef-building corals are famously sensitive to rising seawater temperatures, motivating ongoing research into their stress responses and long-term prospects in a changing climate. A comprehensive understanding...
Resource Type:: Article
Full Text:: , furthering studies of gene evolution and func- tion across basal metazoans (Poole andWeis 2014; Putnam et al

Genome Organization in the Ectomycorrhizal Truffle Rhizopogon vesiculosus

Creator:: Lu, Dabao Sun
Abstract:: Rhizopogon vesiculosus is a common ectomycorrhizal (EM) symbiont of Pseudotusga menziesii (Douglas-fir) in the coast range of the Pacific Northwest. The species has been studied for its systematics, genet size, population structure, and competitive ability in several field and experimental studies. This thesis seeks to provide a more thorough characterization...
Resource Type:: Masters Thesis
Full Text:: vesiculosus………….…..………………………..5 Population genetic structure and patterns of genet distribution in R

Origins and evolution of plant microRNA genes

Creator:: Fahlgren, Noah
Abstract:: Eukaryotic small RNA (~20-30 nucleotides) are diverse regulatory molecules that repress gene expression at the transcriptional and post-transcriptional levels, defend hosts against invading viruses and defend genomes against selfish DNA elements. Small RNA populations are studied by high-throughput sequencing of the total small RNA fraction isolated from cells, however, the...
Resource Type:: Dissertation
Full Text:: presented on December 6, 2010. Title: Origins and Evolution of Plant MicroRNA Genes. Abstract

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Creator:: Manning, Viola A., Pandelova, Iovanna, Dhillon, Braham, Wilhelm, Larry J., Goodwin, Stephen B., Berlin, Aaron M., Figueroa, Melania, Freitag, Michael, Hane, James K., Henrissat, Bernard, Holman, Wade H., Kodira, Chinnappa D., Martin, Joel, Oliver, Richard P., Robbertse, Barbara, Schackwitz, Wendy, Schwartz, David C., Spatafora, Joseph W., Turgeon, B. Gillian, Yandava, Chandri, Young, Sarah, Zhou, Shiguo, Zeng, Qiandong, Grigoriev, Igor V., Ma, Li-Jun, and Ciuffetti, Lynda M.
Abstract:: Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins ( HST), which are recognized by their host in a genotype-specific...
Resource Type:: Article
Full Text:: . 2008; Singh and Hughes 2006). Studies on population genetics have failed to find genetic groupings

The genus Caenorhabditis : a system for testing evolutionary questions

Creator:: Raboin, Michael J.
Abstract:: Caenorhabditis elegans is arguably the best understood animal on the planet. Used for over 50 years to study development, we have a vast amount of knowledge of the inner workings of this worm. Our knowledge is incomplete, however, without placing this organism in its evolutionary and ecological context. In this...
Resource Type:: Dissertation
Full Text:: , and the population genetic analyses. Statistical tests of evolution were conducted at several levels

Development of a 10,000 Locus Genetic Map of the Sunflower Genome Based on Multiple Crosses

Creator:: Bowers, John E., Bachlava, Eleni, Brunick, Robert L., Rieseberg, Loren H., Knapp, Steven J., and Burke, John M.
Abstract:: Genetic linkage maps have the potential to facilitate the genetic dissection of complex traits and comparative analyses of genome structure, as well as molecular breeding efforts in species of agronomic importance. Until recently, the majority of such maps was based on relatively low-throughput marker technologies, which limited marker density across...
Resource Type:: Article
Full Text:: . J. Knapp, and L. H. Rieseberg, 2002 Genetic analysis of sunflower domestication. Genetics 161: 1257

Genome of Drosophila suzukii, the Spotted Wing Drosophila

Creator:: Chiu, Joanna C., Jiang, Xuanting, Zhao, Li, Hamm, Christopher A., Cridland, Julie M., Saelao, Perot, Hamby, Kelly A., Lee, Ernest K., Kwok, Rosanna S., Zhang, Guojie, Zalom, Frank G., Walton, Vaughn M., and Begun, David J.
Abstract:: Drosophila suzukii Matsumura (spotted wing drosophila) has recently become a serious pest of a wide variety of fruit crops in the United States as well as in Europe, leading to substantial yearly crop losses. To enable basic and applied research of this important pest, we sequenced the D. suzukii genome...
Resource Type:: Article
Full Text:: - scriptome and describe patterns of genome evolution in D. suzukii and its close relatives. Our analyses and

Multilocus Sex Determination Revealed in Two Populations of Gynodioecious Wild Strawberry, Fragaria vesca subsp bracteata

Creator:: Ashman, Tia-Lynn, Tennessen, Jacob A., Dalton, Rebecca M., Govindarajulu, Rajanikanth, Koski, Matthew H., and Liston, Aaron
Abstract:: Gynodioecy, the coexistence of females and hermaphrodites, occurs in 20% of angiosperm families and often enables transitions between hermaphroditism and dioecy. Clarifying mechanisms of sex determination in gynodioecious species can thus illuminate sexual system evolution. Genetic determination of gynodioecy, however, can be complex and is not fully characterized in any...
Resource Type:: Article
Full Text:: illuminate sexual system evolution. Genetic determina- tion of gynodioecy, however, can be complex and is not

Targeted Sequence Capture Provides Insight into Genome Structure and Genetics of Male Sterility in a Gynodioecious Diploid Strawberry, Fragaria vesca ssp. bracteata (Rosaceae)

Creator:: Tennessen, Jacob A., Govindarajulu, Rajanikanth, Liston, Aaron, and Ashman, Tia-Lynn
Abstract:: Gynodioecy is a sexual system wherein females coexist with hermaphrodites. It is of interest not only because male-sterile plants are advantageous in plant breeding but also because it can be a crucial step in the evolutionary transition to entirely separate sexes (dioecy) from a hermaphroditic ancestor. The gynodioecious diploid wild...
Resource Type:: Article
Full Text:: North America (Staudt 1989), is an ideal model for studying the genetic basis and evolution of male

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon

Creator:: Wang, Yizhou, Smith, Kristina M., Taylor, John W., Freitag, Michael, and Stajich, Jason E.
Abstract:: Genome defense likely evolved to curtail the spread of transposable elements and invading viruses. A combination of effective defense mechanisms has been shown to limit colonization of the Neurospora crassa genome by transposable elements. A novel DNA transposon named Sly1-1 was discovered in the genome of the most widely used...
Resource Type:: Article
Full Text:: Genetics Stock Center and P01GM068087 “Functional analysis of a Model Filamentous Fungus.” We thank

Functional Analyses of Trichoderma reesei LAE1 Reveal Conserved and Contrasting Roles of This Regulator

Creator:: Karimi-Aghcheh, Razieh, Bok, Jin Woo, Phatale, Pallavi A., Smith, Kristina M., Baker, Scott E., Lichius, Alexander, Omann, Markus, Zeilinger, Susanne, Seiboth, Bernhard, Rhee, Catherine, Keller, Nancy P., Freitag, Michael, and Kubicek, Christian P.
Abstract:: The putative methyltransferase LaeA is a global regulator that affects the expression of multiple secondary metabolite gene clusters in several fungi, and it can modify heterochromatin structure in Aspergillus nidulans. We have recently shown that the LaeA ortholog of Trichoderma reesei (LAE1), a fungus that is an industrial producer of...
Resource Type:: Article
Full Text:: Trichoderma reesei LAE1 Reveal Conserved and Contrasting Roles of This Regulator Razieh Karimi-Aghcheh,* Jin

SNP data for 295 snap bean genotypes utilized in a study of snap bean genetic diversity published in Genes

Creator:: Wallace, Lyle, Arkwazee, Haidar, Vining, Kelly, and Myers, James R.
Abstract:: The accessions used in this study were comprised of 246 snap bean and 49 dry bean genotypes. Of these, 150 snap bean accessions came from the Common Bean Coordinated Agriculture Project Snap Bean Diversity panel, an assemblage of 59 Chinese snap bean genotypes obtained from a trip to China in...
Resource Type:: Dataset

Cost to Biomphalaria glabrata of Resisting Infection by Schistosoma mansoni

Creator:: Sergi, Clint
Abstract:: Schistosomiasis is a neglected tropical disease caused by parasitic trematodes in the genus Schistosoma. 200 million people are infected with schistosomes. Schistosomiasis causes acute and chronic disease, and may lead to death in chronic infections. Schistosomes have a complex life cycle that requires passage through a snail intermediate host. Understanding...
Resource Type:: Masters Thesis
Full Text:: . Snail resistance to infection by S. mansoni and mortality. 95% confidence.……27 intervals for

Genomic characterization of a novel leporid Herpes simplex virus

Creator:: Babra, Bobby A.
Abstract:: The viral family Herpesviridae consists of large double stranded DNA viruses including eight species that infect humans with varying pathology from benign rashes to cancerous cell transformation. From three subfamilies, alpha-, beta- and gammaherpes, the alphaherpes contains the genera iltovirus, mardivirus, varicellovirus and simplex, two of which, the human simplex...
Resource Type:: Dissertation
Full Text:: within the host’s nucleus without integration. Reviewing the basic molecular and genetic

Systematic, genomic, and transcriptomic analysis of mycoparasitic Tolypocladium species and their Elaphomyces hosts

Creator:: Quandt, C. Alisha
Abstract:: Fungi in the genus Tolypocladium are diverse in their host associations, but the predominant ecologies include parasites of the ectomycorrhizal genus Elaphomyces and pathogens of insects. The aim of this dissertation research is to examine the evolution of these fungi and their host associations. To accomplish this several lines of...
Resource Type:: Dissertation
Full Text:: and clusters, including three, large peptaibiotic genes. The evolution of these genes, which have

Symbiosis in the Pacific Ring of Fire : evolutionary-biology of Rhizopogon subgenus Villosuli as mutualists of Pseudotsuga

Creator:: Mujic, Alija Bajro
Abstract:: Rhizopogon is a large genus of ectomycorrhizal (EM) fungi that grows in association with host trees of the family Pinaceae. We have conducted a series of studies investigating the ecology and evolutionary biology of the EM symbiosis shared between R. subgenus Villosuli and trees of the genus Pseudotsuga. Two members...
Resource Type:: Dissertation
Full Text:: Rhizopogon vinicolor and Rhizopogon vesiculosus: Ecology and population genetics

Adaptation to long-term osmotic stress in a domesticated Saccharomyces cerevisiae strain

Creator:: Holman, Douglas S.
Abstract:: Osmotic stress is a common challenge faced by organisms in environments with variable salinity or aridity. Understanding the evolutionary mechanisms underlying adaptation to osmotic stress may have wide applications, including management of populations experiencing climate change, or engineering industrial organisms involved in processes such as fermentation. While Saccharomyces cerevisiae is...
Resource Type:: Honors College Thesis
Full Text:: genes. This work verifies that genetic changes arose over the course of a previous long-term evolution

Evolution of a streamlined cooperator in Pseudomonas aeruginosa quorum sensing

Creator:: Huie, Jessica L.
Abstract:: Social behavior leading to the production of common goods is prone to exploitation. One such behavior in Pseudomonas aeruginosa is quorum sensing (QS), by which the bacteria produce signals to regulate extracellular common goods. Exploitation comes in the form of cheaters which have a mutation in the central quorum sensing...
Resource Type:: Masters Thesis
Full Text:: will be an excellent model for the evolution of regulators and their specificity

Metabolomic Profiling of Natural Products from Two Tolypocladium Fungal Species as Part of An Evolutionary Genomics Study

Creator:: Dickey, Bailey J.
Abstract:: This thesis describes an investigation of the natural products chemistry of two fungal species of the genus Tolypocladium. Natural products are small organic molecules that are considered non-essential for cell growth and reproduction, and thus part of secondary metabolism. Chemical profiling of these secondary metabolites using a combination of high-performance...
Resource Type:: Masters Thesis
Full Text:: enzyme that is transcribed by DNA, and synthesizes peptides for which the genetic sequence is not coded

Evolutionary Genomic Responses to Mitochondrial Dysfunction in Caenorhabditis elegans

Creator:: Wernick, Riana I.
Abstract:: Understanding the impact of mitochondrial dysfunction on genome evolution has the potential not only to provide new insights on the basic evolutionary processes influencing mitochondrial and nuclear genomes, but may also reveal novel avenues for evolutionary adaptive recovery from harmful mutations. Aberrant mitochondrial activity is fundamental to the pathology of...
Resource Type:: Dissertation
Full Text:: known about their impact on genome evolution and potential target mechanisms for ameliorating the

Quantitative and molecular genetics of larval susceptibility to Vibrio tubiashii in Pacific oysters (Crassostrea gigas)

Creator:: Chen, Chao
Abstract:: Vibriosis caused by the bacterial pathogen Vibrio tubiashii is one of several factors contributing to mass larval mortalities of the Pacific oyster (Crassostrea gigas) in Pacific Northwest shellfish hatcheries in recent years. Genetically improved strains of the Pacific oyster resistant to V. tubiashii would be highly desirable. This study investigates...
Resource Type:: Dissertation
Full Text:: Quantitative and molecular genetics of larval susceptibility

The influence of social structure and molecular evolution on genetic diversity in the sperm whale (Physeter macrocephalus)

Creator:: Alexander, Alana
Abstract:: The sperm whale (Physeter macrocephalus) shows some of the most derived characteristics of any mammal: a large body size, large brain, complex social organization and a capacity for deep foraging dives that few other marine mammals can match. Despite a history of exploitation that removed hundreds of thousands of individuals,...
Resource Type:: Dissertation
Full Text:: Rights Reserved The Influence of Social Structure and Molecular Evolution on Genetic

Rapid evolution of post-transcriptionally regulated RESTORER OF FERTILITY-LIKE genes in the genus Arabidopsis

Creator:: Jogdeo, Sanjuro
Abstract:: The Pentatricopeptide Repeat (PPR) gene family produces RNA-binding proteins that target organellar transcripts. The PPR family is expanded in land plants, with nearly 450 genes identified in Arabidopsis thaliana. In plants with a Cytoplasmic Male Sterility (CMS) phenotype, members of the PPR family can act as a RESTORER OF FERTILITY...
Resource Type:: Masters Thesis
Full Text:: (Bentolila et al., 2002) and the genetic basis of CMS has been identified in several other species

Investigating variation in immunity and infection risk in wild ungulates

Creator:: Dugovich, Brian S.
Abstract:: In the midst of the sixth mass extinction, understanding wildlife disease spillover is critical to maintaining protected wildlife areas. Studying ecoimmunology and wildlife disease ecology helps to understand immune and disease traits in an ecological context, which is invaluable in preventing pathogen spillover between livestock and wildlife. To investigate this...
Resource Type:: Dissertation
Full Text:: : Investigating Variation in Immunity and Infection Risk in Wild Ungulates. Abstract approved

Phylogeography and Evolution of Effector Genes in Phytophthora Species

Creator:: Shakya, Shankar K.
Abstract:: Plant pathogens in the genus Phytophthora are known to cause disease on field crops, nursery plants, and forest trees. The best known example probably is Phytophthora infestans, which triggered the infamous Irish potato famine. Other important Phytophthora species include: P. ramorum (sudden oak death pathogen), P. sojae (soybean root rot...
Resource Type:: Dissertation
Full Text:: , 2019. Title: Phylogeography and Evolution of Effector Genes in Phytophthora Species

Phylogeny and Evolution of Gall-Associated Plant Pathogenic Bacteria

Creator:: Davis, Edward W., II
Abstract:: Gall-associated phytopathogens have unique evolutionary histories that haveshaped both their modes of infection and genomic structures. Pathogenicity of the gall-associated plant pathogens of the Rhodococcus, Agrobacterium, and Rathayibactergenera is mediated by horizontally acquired virulence loci. The relative ease of gainand loss of the virulence loci has confounded accurate characterization of...
Resource Type:: Dissertation
Full Text:: , especially in light of Darwin’s theory of evolution. Selective pressure and genetic drift shape the

Disease models and infectious phenotypes of Mycobacterium avium subspecies paratuberculosis

Creator:: Everman, Jamie L.
Abstract:: Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic inflammatory bowel disease that affects ruminant populations worldwide. The characteristic stages of the disease make diagnosis difficult, resulting in silent transmission among animals in a herd for years before proper detection of the infection. The extensive...
Resource Type:: Dissertation
Full Text:: opsonization affects cell infection, and to study the metabolic interaction between MAP and the host

Pseudoloma neurophilia in the Zebrafish (Danio rerio) : Consequences of Infection on Neurobehavioral and Biomedical Research using a Burgeoning Model Organism

Creator:: Spagnoli, Sean
Abstract:: Since its inception as a laboratory animal in the early 1970s, the zebrafish has proven itself a rising star in the world of comparative biomedical sciences due to its short generation time, ease of care, external fertilization, and transparent larvae. In a very few decades, the zebrafish has been utilized...
Resource Type:: Dissertation
Full Text:: rerio): Consequences of Infection on Neurobehavioral and Biomedical Research using a Burgeoning Model

The Effects of Prostaglandin F2α on Reproductive Performance in the Postpartum Dairy Cow and the Mechanism Behind its Benefits

Creator:: Younger, Kathryn Genevieve
Abstract:: During the beginning of the postpartum period, 80 to 100% of lactating dairy cows have bacterial contamination within their uteri. Presence of uterine bacteria may contribute to increased number of days open and services per conception within these cows. Expulsion of uterine contamination is crucial for uterine involution and reproductive...
Resource Type:: Masters Thesis
Full Text:: ramifications, and uterine infection is one of the most expensive impediments of conception for dairy cattle

Seasonal distribution and environmental associations among late larval and juvenile rockfish (Sebastes spp.) off Oregon and Washington: new insights based on genetics

Creator:: Johansson, Mattias L., Litz, Marisa N. C., Brodeur, Richard D., Britt, Tristan A., Vanegas, Camilo A., Hyde, John R., and Banks, Michael A.
Abstract:: Cytochrome B sequence data (FASTA format) from the paper “Seasonal distribution and environmental associations among late larval and juvenile rockfish (Sebastes spp.) off Oregon and Washington: new insights based on genetics”. The data was generated from a sample of 2534 unknown, field collected late-larval and juvenile rockfishes from the Pacific...
Resource Type:: Dataset

Origins and evolution of viruses of eukaryotes: The ultimate modularity

Creator:: Koonin, Eugene V., Dolja, Valerian V., and Krupovic, Mart
Abstract:: Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority...
Resource Type:: Article
Full Text:: Origins and evolution of viruses of eukaryotes: The

Characterization of microaggregate formation by Mycobacterium avium subspecies hominissuis

Creator:: Babrak, Lmar
Abstract:: Mycobacterium avium subsp hominissuis (MAH) is an opportunistic environmental pathogen that causes respiratory and gastrointestinal illness in immunocompromised persons such as those with chronic respiratory diseases or AIDs, respectively. In recent years, there has been a significant increase in the incidence of nontuberculous mycobacterial (NTM) lung infections, including in cystic...
Resource Type:: Dissertation
Full Text:: differences in the host response to microaggregate and planktonic infection. In Chapter 4, the bacteria-host

Secondary Metabolism in Tolypocladium : Characterization, Ecology, Evolution and Regulation

Creator:: Blount, Rheannon Rua
Abstract:: An increased understanding of secondary metabolism in fungi is important for both biological and societal reasons. The ascomycete genus, Tolypocladium, is an ideal system to explore secondary metabolism characterization, ecology, evolution and regulation. The genus produces and has the genomic potential to produce a wide array of metabolites. Paired with...
Resource Type:: Dissertation
Full Text:: : Characterization, Ecology, Evolution and Regulation Abstract approved

Genetic characterization of a reptilian calicivirus (Cro1)

Creator:: Sandoval-Jaime, Carlos, Parra, Gabriel I., Smith, Alvin W., Green, Kim Y., and Sosnovtsev, Stanislav V.
Abstract:: Background: Vesiviruses in the family Caliciviridae infect a broad range of animal hosts including mammals, birds, fish, amphibians and reptiles. The vesivirus Cro1 strains were isolated from diseased snakes in the San Diego zoo in 1978 and reported as the first caliciviruses found in reptiles. The goal of this study...
Resource Type:: Article
Full Text:: should facilitate investigation of the molecular mechanisms involved in Cro1 virus evolution and host

Using Culture-independent Genomics as a Means for Understanding Chlamydial Biology

Creator:: Putman, Timothy E.
Abstract:: The chlamydiae are a family of obligate intracellular bacteria that have a unique bi-phasic developmental cycle, unique cellular properties, and a unique set of challenges to studying its biology. While genetic manipulation is becoming routine in Chlamydia, there are significant challenges to working with this intracellular parasite. The body of...
Resource Type:: Dissertation
Full Text:: include data on the host microbiome and host genetic background. We

The Economic Repercussions of Fisheries-induced Evolution

Creator:: Eikeset, Anne Maria, Richter, Andries, Dunlop, Erin, Dieckmann, Ulf, and Stenseth, Nils Chr.
Abstract:: Human-induced changes in life-history traits have been observed for many harvested populations, with a component of those changes being attributed to an evolutionary (i.e., genetic) response. Most notably, fish stocks that experience high fishing mortality show a tendency to mature earlier and at a smaller size. Some have suggested that...
Resource Type:: Other
Full Text:: fisheries-induced evolution could affect the fishery’s yield and therefore have economic repercussions for

Pseudoloma neurophilia : progression of infection and transmission characteristics of a microsporidian parasite in a model vertebrate, Danio rerio

Creator:: Sanders, Justin L.
Abstract:: The microsporidian parasite, Pseudoloma neurophilia, is the most commonly diagnosed infectious disease in laboratory populations of the zebrafish, Danio rerio. Infections by P. neurophilia are generally subclinical, however, they can become acute either incidentally or due to experimental immune suppression. Non-protocol induced variation can confound results in laboratory experiments using...
Resource Type:: Dissertation
Full Text:: of Infection and Transmission Characteristics of a Microsporidian Parasite in a Model Vertebrate

A virocentric perspective on the evolution of life

Creator:: Koonin, Eugene V. and Dolja, Valerian V.
Abstract:: Viruses and/or virus-like selfish elements are associated with all cellular life forms and are the most abundant biological entities on Earth, with the number of virus particles in many environments exceeding the number of cells by one to two orders of magnitude. The genetic diversity of viruses is commensurately enormous...
Resource Type:: Article
Full Text:: cellular evolution The history of life is a story of coevolution of selfish genetic elements and their

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

Creator:: Bushley, Kathryn E., Raja, Rajani, Jaiswal, Pankaj, Cumbie, Jason S., Nonogaki, Mariko, Boyd, Alexander E., Owensby, C. Alisha, Knaus, Brian J., Elser, Justin, Miller, Daniel, Di, Yanming, McPhail, Kerry L., and Spatafora, Joseph W.
Abstract:: The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of...
Resource Type:: Article
Full Text:: : Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster Kathryn E. Bushley1

Evolutionary relationships and an investigation of sympatric speciation within Limnanthaceae

Creator:: Meyers, Stephen C.
Abstract:: Limnanthes floccosa ssp. floccosa and L. floccosa ssp. grandiflora are two of five subspecies of Limnanthes floccosa endemic to vernal pools in southern Oregon and northern California. Three seasons of monitoring natural populations have quantified that L. floccosa ssp. grandiflora is always found growing sympatrically with L. floccosa ssp. floccosa...
Resource Type:: Dissertation
Full Text:: population can result in the evolution of new species, remains an intensely debated issue (Coyne and Orr

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

Creator:: Traeger, Stefanie, Altegoer, Florian, Freitag, Michael, Gabaldon, Toni, Kempken, Frank, Kumar, Abhishek, Marcet-Houben, Marina, Poggeler, Stefanie, Stajich, Jason E., and Nowrousian, Minou
Abstract:: Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely...
Resource Type:: Article
Full Text:: -Albrechts- Universität zu Kiel, Kiel, Germany, 6 Institute of Microbiology and Genetics, Department of

Understanding chlamydial biology through genome sequencing and comparative genomics

Creator:: Jeffrey, Brendan
Abstract:: The human pathogen Chlamydia trachomatis displays different phenotypes between serovars both in vivo and in vitro. The study of chlamydial biology has been hampered by the lack of a tractable genetic system. Here, chlamydial isolates with known phenotypes as well as strains generated though recombination were fully sequenced to address...
Resource Type:: Dissertation
Full Text:: Chlamydia Genetics: Progress and Challenges .................................................... 2

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

Creator:: Kimbrel, Jeffrey A., Thomas, William J., Jiang, Yuan, Creason, Allison L., Thireault, Caitlin A., Sachs, Joel L., and Chang, Jeff H.
Abstract:: Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing...
Resource Type:: Article
Full Text:: frameworks of mutualist-host co-evolution (Figures 2 and 3; Table S2). Rhizobial T3E genes show genetic

Population genetics of ranid frogs : investigating effective population size and gene flow

Creator:: Phillipsen, Ivan C.
Abstract:: This dissertation focuses on the evolutionary forces of genetic drift and gene flow in frog populations. The balance of these two forces and the force of mutation largely determine the amount of neutral genetic variation within populations as well as the degree of genetic similarity among populations. The stochastic evolutionary...
Resource Type:: Dissertation
Full Text:: , 2010. Title: Population Genetics of Ranid Frogs: Investigating Effective Population Size and

Social Evolution and Regulatory Architecture of Pseudomonas aeruginosa Quorum Sensing

Creator:: Asfahl, Kyle L.
Abstract:: Cell-cell communication in bacteria is understood to facilitate the coordination of population-wide cooperative behavior in the form of concerted gene expression. The opportunistic pathogen Pseudomonas aeruginosa uses such a communication mechanism to regulate a large group of genes important to virulence strategies in this bacterium. This general mechanism of communication...
Resource Type:: Dissertation
Full Text:: . Title: Social Evolution and Regulatory Architecture of Pseudomonas aeruginosa Quorum Sensing

Breeding and genetics of lilacs and hardy hibiscus

Creator:: Lattier, Jason D.
Abstract:: Lilacs are a group of ornamental trees and shrubs in the Oleaceae family consisting of 22 to 30 species. There are six series within genus Syringa: Pubescentes, Villosae, Ligustrae, Ligustrina, Pinnatifoliae, and Syringa. Fertility and cross-compatibility among cultivars, species, and series have yet to be formally investigated. Over three years,...
Resource Type:: Dissertation
Full Text:: : Breeding and Genetics of Lilacs and Hardy Hibiscus Abstract approved

Hidden dynamics : community ecology and costs of parasite infection in African buffalo (Syncerus caffer)

Creator:: Henrichs, Brian
Abstract:: Most wild animals are concurrently infected with multiple parasite species for most of their lives. These parasite species assemble into rich and diverse communities, with parasites using host tissues for growth and reproduction as well as evolving strategies to evade the host immune system. The net effect of these ecological...
Resource Type:: Masters Thesis
Full Text:: : Community Ecology and Costs of Parasite Infection in African Buffalo (Syncerus caffer

Tempo and Mode of Diversification in the Neotropical Fish Superfamily Anostomoidea (Ostariophysi: Characiformes)

Creator:: Frable, Benjamin W.
Abstract:: Neotropical characiform fishes form one of the most diverse freshwater ichthyofauna in the world. Knowledge of evolutionary processes that generated and maintain the immense characiform lineage and morphological diversity is still poorly understood. When did characiform lineages diversify? How have major geological and environmental changes affected diversification? Why are some...
Resource Type:: Masters Thesis
Full Text:: .!..........................!55! ! 2.3!!Partitioning!schemes!and!substitution!models!used!for!molecular!evolution! priors!in

Viability and infective potential of Phytophthora pini zoospores in a recirculating irrigation system

Creator:: Shay, Sarah D.
Abstract:: Phytophthora pini Leonian, recently re-established from P. citricola I, is a pathogen with a wide range of forest and nursery hosts. It causes foliar infections in horticultural nurseries in Oregon, where recirculating irrigation systems are common. Increased use of recirculating irrigation systems may contribute to disease caused by waterborne plant...
Resource Type:: Masters Thesis
Full Text:: affected foliar infection of Rhododendron. Wounded and nonwounded leaves were dipped into suspensions

Chlamydiae Enhance Self-Antigen Presentation in a Mechanism that is Dependent on Biosynthesis of Lipooligosaccharide

Creator:: Cram, Erik D.
Abstract:: Chlamydia is a genus of obligate intracellular bacteria that undergo a unique, biphasic developmental cycle. The infectious and metabolically inert Elementary Bodies (EBs) begin the cycle of infection by attaching and invading a host cells. Once inside, the EBs differentiate into the metabolically active, dividing Reticulate Bodies (RBs) within their...
Resource Type:: Dissertation
Full Text:: infection by attaching and invading a host cells. Once inside, the EBs differentiate into the

Modern Wheat Breeding: Next Generation Sequencing and CRISPR Transformation

Creator:: Brandt, Kali M.
Abstract:: Wheat (Tritium aestivum) is an extremely important crop worldwide. It accounts for almost one quarter of the calories consumed each day by more than one third of the world’s population, and is grown over more land area than any other crop. Wheat breeding programs constantly strive to increase or maintain...
Resource Type:: Dissertation
Full Text:: temperatures, and the integration of new traits with genetic editing. This study found novel, useful markers

Alternative splicing in the obligate biotrophic oomycete pathogen, Pseudoperonospora cubensis

Creator:: Cumbie, Jason S.
Abstract:: Oomycetes are some of the most devastating pathogens, causing upwards of billions of dollars of damage each year to plants. They also diminish ecological diversity and health through the destruction of trees and shrubs. The genome sequence of Pseudoperonospora cubensis, an obligate plant pathogen and causative agent of downy mildew...
Resource Type:: Dissertation
Full Text:: disease severity on watermelon, squash, and/or pumpkin, suggesting that the genetic basis of host-range

Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

Creator:: Bassil, Nahla, Boccacci, Paolo, Botta, Roberto, Postman, Joseph, and Mehlenbacher, Shawn
Abstract:: The US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus), including C. avellana cultivars and representatives of 10 other recognized shrub and tree species. Characterization and study of genetic diversity in this collection require cross-transferable markers, such...
Resource Type:: Article
Full Text:: microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

Reproductive implications of parasitic infections and immune challenges in garter snakes

Creator:: Uhrig, Emily J.
Abstract:: Parasitic infections and immune challenges can affect host reproductive fitness and, ultimately, the evolution of host populations in a myriad of ways. The fitness implications of parasitic infections range from increased host mortality to subtle changes in reproductive investment. From alterations of behaviors, sexual signaling, and competitive ability to changes...
Resource Type:: Dissertation
Full Text:: fitness and, ultimately, the evolution of host populations in a myriad of ways. The fitness

Further Understanding Mycobacterial Biofilms and Their Interaction with the Host

Creator:: Rose, Sasha J.
Abstract:: Respiratory infections caused by nontuberculous mycobacteria (NTM), especially Mycobacterium avium, can lead to progressive, recurrent disease that is refractory to therapy. Bacterial biofilms are intrinsically resistant to a variety of stressors and pressures, including host killing mechanisms and antibiotic therapy. Though it is becoming increasingly evident that NTM biofilms are...
Resource Type:: Dissertation
Full Text:: between NTM biofilms and respiratory infection, the more we can learn about the physiology of these

Genetic and phenotypic variation associated with the resistance gene SOD1 in Biomphalaria glabrata, an important intermediate host of Schistosomiasis

Creator:: Bonner, Kaitlin M.
Abstract:: Schistosomiasis afflicts 200 million people and is responsible for 200,000 deaths per year. The infection is caused by a digenean trematode in the genus Schistosoma. The parasite must cycle through both a vertebrate (human) and invertebrate (snail) host to complete the life cycle. My dissertation focuses on the genetic mechanisms...
Resource Type:: Dissertation
Full Text:: , Michael S. Blouin Infection, Genetics, and Evolution To be submitted – awaiting coauthor comments

Phenotypic Evolution: The Ongoing Synthesis

Creator:: Arnold, Stevan J.
Abstract:: I explore the proposition that evolutionary biology is currently in the midst of its greatest period of synthesis. This period, which I call the Ongoing Synthesis, began in 1963 and continues at the present time. I use analysis of citations, conduct, and content to compare the Ongoing Synthesis to widely...
Resource Type:: Article
Full Text:: centuries. To compare content, I focus on phenotypic evolution and compare current efforts with George

Physiological, Chemical and Genetic Studies in Meadowfoam (Limnanthes alba)

Creator:: Zhang, Jun
Abstract:: Meadowfoam (Limnanthes alba) is an oilseed crop with unique chemical characteristics. The ability to identify physiological maturity (PM) and harvest maturity HM of the crop would permit timely harvest of high quality seeds. However, changes of oil contents, fatty acid profile and glucosinolate contents, as well as seed quality during...
Resource Type:: Dissertation
Full Text:: . Title: Physiological, Chemical and Genetic Studies in Meadowfoam (Limnanthes alba) Abstract

Examining Evidence-based Intervention Sustainability and De-adoption in the Context of HIV Prevention

Creator:: McKay, Virginia R.
Abstract:: Evidence-based interventions (EBIs), which demonstrate efficacy in research settings, are rarely sustained when implemented in public health organizations. Rather, EBIs are often de-adopted - potentially undermining the positive benefits of the EBIs for the communities that access them. The lack of sustainability is particularly troubling among public health organizations that...
Resource Type:: Dissertation
Full Text:: presented on November 13, 2015. Title: Examining Evidence-based Intervention Sustainability and De

Sensory Analysis and Genetic Mapping of Green Bean Flavor

Creator:: Wallace, Lyle T.
Abstract:: Green bean flavor has been studied since the 1960’s to better understand Blue Lake flavor in processed green beans in Oregon. Research by Stevens and colleagues showed that Blue Lake flavor could be reconstituted in a bland bean by adding 0.4ppm of 1-octen-3-ol and 1.6ppm of 3-hexen-1-ol. These two volatile...
Resource Type:: Dissertation
Full Text:: : Sensory Analysis and Genetic Mapping of Green Bean Flavor. Abstract approved

The Effects of Host and Pathogen Variation on Infection Dynamics in the Amphibian-Chytrid System

Creator:: Dang, Trang D.
Abstract:: This dissertation uses manipulative experiments to explore amphibian-Bd infection dynamics. Although there has been almost two decades research since the discovery of Bd, many questions still remain regarding what conditions mediate chytridiomycosis virulence. My research shows how certain host and pathogen factors can influence disease virulence. Identifying how host and...
Resource Type:: Dissertation
Full Text:: Biology presented on June 9, 2017. Title: The Effects of Host and Pathogen Variation on Infection

Recombination, resistance, and drug discovery in Chlamydia

Creator:: Sandoz, Kelsi
Abstract:: The intracellular life cycle of Chlamydia has been difficult to study due to the inability to genetically manipulate the bacteria. As a result, indirect methods have been employed to study the pathogen and the aspects that contribute to its unique intracellular life cycle. A wide variety of laboratory adapted strains,...
Resource Type:: Dissertation
Full Text:: chlamydial system, and with the aid of high through put technologies, to develop genetic tools in a system

The Dynamic Field of Genetic Counseling and How Students Can Best Prepare Themselves

Creator:: Bauder, Malia V.
Abstract:: Genetic counseling, a healthcare profession centered on communicating genetic information to patients and helping them understand it, has been rapidly evolving with the development of genetic sequencing and editing technology over the past decades. Consequently, future and current genetic counselors must address societal and ethical implications, as well as historical...
Resource Type:: Honors College Thesis
Full Text:: future genetic counselors who are passionate about genetics and their patients. There are two primary

Role of Transcriptional Factor COUP-TF-interacting Proteins in Skin Permeability Barrier Development, and in Skin Carcinogenesis, and Role of Lipids in Atopic Dermatitis

Creator:: Li, Shan
Abstract:: Mammalian skin is the largest organ of the body and serves as a barrier to protect the body against chemical, mechanical and pathogenic insults as well as water loss. The epidermis is formed from the primitive ectoderm into a multilayered stratified epithelium, consisting of basal, spinous, granular and outermost cornified...
Resource Type:: Dissertation
Full Text:: colonized by S.aureus. S.aureus colonization and infection is an important trigger of AD and aggravates

The ecology of parasite interactions within Chinook salmon

Creator:: Hurst, Charlene N.
Abstract:: The within-host interactions that can occur as a result of mixed infections in wildlife likely influence the outcome of an infection. We investigated the infection frequency and outcome as well as the potential mechanisms regulating mixed infections with two Ceratonova shasta genotypes within the Chinook salmon host. Previous research in...
Resource Type:: Dissertation
Full Text:: mediated the mixed infection interaction. The immune response to each genotype alone was specific and

Advances in molecular systematics of clavicipitaceous fungi (Sordariomycetes: Hypocreales)

Creator:: Kepler, Ryan M.
Abstract:: Historical concepts of Clavicipitaceae have included a broad range of species that display diverse morphologies, ecological modes and host associations. When subjected to multigene phylogenetic investigation of evolutionary history, the family was found to be polyphyletic, largely driven by diversity in the genus Cordyceps, previously containing over 400 taxa. The...
Resource Type:: Dissertation
Full Text:: explore the evolution of host association, morphology and ecology with ancestral character-state

Infection of Brachypodium distachyon by Formae Speciales of Puccinia graminis: Early Infection Events and Host-Pathogen Incompatibility

Creator:: Figueroa, Melania, Alderman, Stephen, Garvin, David F., and Pfender, William F.
Abstract:: Puccinia graminis causes stem rust, a serious disease of cereals and forage grasses. Important formae speciales of P. graminis and their typical hosts are P. graminis f. sp. tritici (Pg-tr) in wheat and barley, P. graminis f. sp. lolii (Pg-lo) in perennial ryegrass and tall fescue, and P. graminis f....
Resource Type:: Article
Full Text:: Speciales of Puccinia graminis: Early Infection Events and Host-Pathogen Incompatibility Melania Figueroa1

Roles and Programming of Arabidopsis ARGONAUTE Proteins during Turnip Mosaic Virus Infection

Creator:: Garcia-Ruiz, Hernan, Carbonell, Alberto, Hoyer, J. Steen, Fahlgren, Noah, Gilbert, Kerrigan B., Takeda, Atsushi, Giampetruzzi, Annalisa, Garcia Ruiz, Mayra T., McGinn, Michaela G., Lowery, Nicholas, Martinez Baladejo, Maria T., and Carrington, James C.
Abstract:: In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has...
Resource Type:: Article

Genomic Resource Development for European Hazelnut (Corylus avellana L.)

Creator:: Rowley, Erik R.
Abstract:: European hazelnut (Corylus avellana L.) is an important crop Oregon's Willamette Valley, producing 99% of the hazelnuts grown in North America and brings over US $60 million dollars to the region annually. Hazelnuts are rich in fiber and vitamins, as well in demand by consumers due to their popularity as...
Resource Type:: Dissertation
Full Text:: been developed for hazelnut and placed on a genetic linkage map, linking DNA marker sequences that

Effects of genetic drift, natural selection, and population connectivity on adaptive-linked genetic diversity of desert bighorn sheep

Creator:: Nickerson, Brandon Scott
Abstract:: The amount and distribution of neutral and adaptive genetic diversity are often assumed to follow similar patterns. However, natural selection on adaptive loci may cause divergence from patterns observed for loci which are only influenced by selectively neutral processes such as genetic drift. The interaction between selection and neutral processes...
Resource Type:: Masters Thesis
Full Text:: Science presented on September 10, 2014 Title: Effects of Genetic Drift, Natural Selection, and

Deoxyribonucleotides as Genetic and Metabolic Regulators

Creator:: Mathews, Christopher K.
Abstract:: For more than 35 years we have known that the accuracy of DNA replication is controlled in large part by the relative concentrations of the four canonical deoxyribonucleoside 5'-triphosphates (dNTPs) at the replisome. Since this field was last reviewed, about eight years ago, there has been increased understanding of the...
Resource Type:: Article
Full Text:: Deoxyribonucleotides as Genetic and Metabolic Regulators

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP

Creator:: Dugas, Diana V., Hernandez, David, Koenen, Erik J. M., Schwarz, Erika, Straub, Shannon, Hughes, Colin E., Jansen, Robert K., Nageswara-Rao, Madhugiri, Staats, Martijn, Trujillo, Joshua T., Hajrah, Nahid H., Alharbi, Njud S., Al-Malki, Abdulrahman L., Sabir, Jamal S. M., and Bailey, C. Donovan
Abstract:: The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily...
Resource Type:: Article

Characterization of the response mediated by the plant disease susceptibility gene LOV1

Creator:: Gilbert, Brian M.
Abstract:: Victoria blight, caused by fungus Cochliobolus victoriae, is a disease originally described on oats and recapitulated on Arabidopsis. Victoria blight is used as a model plant disease that conforms to an inverse gene-for-gene interaction. C. victoriae virulence is dependent upon its production of victorin, a host-specific toxin that induces programmed...
Resource Type:: Dissertation
Full Text:: , ethylene evolution, extracellular alkalization, phytoalexin synthesis, and K+ efflux – all documented

The effects of single and multiple pathogen and parasite infections on juvenile chinook and coho salmon during early marine residency

Creator:: Sandell, Todd A.
Abstract:: Nearly 3000 juvenile Chinook (Oncorhynchus tshawytscha) and coho (O. kisutch) salmon captured in nearshore waters off the coasts of Washington and Oregon from 1999-2004 were tested for infection by Renibacterium salmoninarum, Nanophyetus salmincola, and skin metacercariae. First, three quantitative PCR primer/probe sets were compared for detection of R. salmoninarum; amplification...
Resource Type:: Dissertation
Full Text:: 1999-2004 were tested for infection by Renibacterium salmoninarum, Nanophyetus salmincola, and skin

Thirty-four Kilometers and Fifteen Years : Rapid Adaptation at a Novel Chromosomal Inversion in Recently Introduced Deschutes River Three-spined Stickleback

Creator:: Hemstrom, William
Abstract:: Rapid adaptation and evolution based on standing genetic variation and novel mutations is likely to be one of the primary ways that species survive the widespread anthropogenic environmental changes expected of the next century. Three-spined stickleback (Gasterosteus aculeatus) are known to be capable of extremely quick, dramatic adaptation in response...
Resource Type:: Masters Thesis
Full Text:: : ______________________________________________________ Michael A. Banks Rapid adaptation and evolution based on standing genetic variation

Stress Physiology in Free-ranging Female African Buffalo (Syncerus caffer) : Environmental Drivers, and Immunological and Infection Consequences

Creator:: Spaan, Johannie M.
Abstract:: Fecal glucocorticoid metabolites (FGMs) are commonly used as indicators of an animal’s stress response in behavioral and eco-physiological studies. Stress in wild animals represents an immediate measure of the physiological response to changes in the environment, and, potentially, a prospective assessment of the animal’s health and well-being. In wild mammals,...
Resource Type:: Dissertation
Full Text:: ): Environmental Drivers, and Immunological and Infection Consequences. Abstract approved

Characterization of novel exopolysaccharide producing lactic acid bacteria

Creator:: Garcia, Roberto A., III
Abstract:: Lactic Acid Bacteria (LAB), an important group of organisms in modern food production, are known to secrete a unique compound called exopolysaccharide (EPS). EPS is economically important because it enhances functional properties in food and may confer beneficial health effects to consumers. Novel strains of Lactococcus lactis, Streptococcus thermophilus, and...
Resource Type:: Masters Thesis
Full Text:: ). Phage infection of Lactococcus lactis during production of cheese and yogurt is a common problem

Quorum sensing gene regulation in Pseudomonas aeruginosa

Creator:: Gupta, Rashmi
Abstract:: Pseudomonas aeruginosa is an opportunistic human pathogen that infects immunocompromised individuals such as those suffering from burns or the genetic disorder cystic fibrosis. This organism utilizes a cell-cell communication mechanism known as quorum sensing (QS) to coordinate virulence gene expression and biofilm formation. It has three interconnected QS systems, namely...
Resource Type:: Dissertation
Full Text:: ......................................................................13 Evolution and maintenance of QS in P. aeruginosa .........................................17

The Role of the Mucosal Immunoglobulin IgT and Inflammatory Cytokines in Ceratonova shasta Infections in Rainbow Trout

Creator:: Taggart-Murphy, Laura M.
Abstract:: The myxozoan parasite Ceratonova shasta threatens both juvenile and adult salmonid populations in the Pacific Northwest region of the United States, causing intestine necrosis and hemorrhaging, along with high mortality in some fish strains. It induces an inflammatory tissue response in susceptible strains of fish; understanding the interactions between C....
Resource Type:: Masters Thesis
Full Text:: infection, and so the disease is of concern for management agencies in the Pacific Northwest. Fish

Molecular and genetic assessment of selected antiporters and methyl-accepting chemotaxis proteins in Vibrio cholerae

Creator:: Quinn, Matthew J.
Abstract:: The pathogen Vibrio cholerae uses cations as a primary currency of virulence and environmental persistence, using gradients of those cations to move, acquire nutrients, and control virulence gene expression. An understanding of the overlapping roles of bioenergetics and chemotaxis in the virulence and environmental survival of V. cholerae issues from...
Resource Type:: Dissertation
Full Text:: Microbiology presented on December 5, 2011. Title: Molecular and Genetic Assessment of Selected

Trade-offs in a pathogen-rich world : genetic and maternal drivers of variation in costly resistance and immunity in African buffalo (Syncerus caffer)

Creator:: Tavalire, Hannah F.
Abstract:: Disease acts as a powerful selective force in natural systems, driving the rapid evolution of resistance in the host. In the face of a myriad of pathogenic challenges in natural systems, hosts must balance the energetic needs of maintenance and reproduction with costly resistance mechanisms. In this dissertation I will...
Resource Type:: Dissertation
Full Text:: of phagocytosis. Infection and Immunity 64, 2523-2531. Gandon, S., Vale, P.F., 2014. The evolution

The Evolution of Scleractinian Microbial Symbionts

Creator:: McMinds, Ryan C.
Abstract:: The modern world has presented many threats to the health and stability of ecosystems worldwide. One of the most biodiverse ecosystems, coral reefs, faces particularly strong pressures, and is already declining rapidly in complexity and area. Although the stressors that affect reefs are diverse, ranging from nutrient pollution to overfishing,...
Resource Type:: Dissertation
Full Text:: both the recent and less-recent past. Since I was little, my interest and skills in genetics and

Bacteriophages Significantly Reduce Mortality of Larval Pacific Oysters Crassostrea gigas from Infection by the Pathogenic Bacterium Vibrio coralliilyticus RE98

Creator:: Madison, David B.
Abstract:: Vibrio coralliilyticus (Vcor) is a bacterial pathogen that is well adapted to shellfish hatcheries and is very pathogenic to the larvae of the Pacific oyster Crassostrea gigas. Vcor has been associated with several large scale larval mortality events in the Pacific Northwest that interrupt the supply of seed oysters available...
Resource Type:: Masters Thesis
Full Text:: al., 2005). The broad distribution and host range of Vcor may be due to the genetic diversity

Middle Jurassic evidence for the origin of Cupressaceae: A paleobotanical context for the roles of regulatory genetics and development in the evolution of conifer seed cones

Creator:: Spencer, Alan R. T., Mapes, Gene, Bateman, Richard M., Hilton, Jason, and Rothwell, Gar W.
Abstract:: Premise of the study: Triassic and Jurassic fossils record structural changes in conifer seed cones through time, provide the earliest evidence for crown-group conifer clades, and further clarify sister-group relationships of modern conifer families. A new and distinct seed-cone from the Isle of Skye in western Scotland provides the oldest...
Resource Type:: Article
Full Text:: paleobotanical context for the roles of regulatory genetics and development in the evolution of conifer seed

Fungal endophytes as source to combat bacterial infections

Creator:: Green, Jaimie R
Abstract:: Endophytes, foliage inhabiting fungi, are an unexplored source of fungal biodiversity and a potential resource for the production of bioactive natural products. In this research, leaf tissues from the species Arbutus menziesii, Rhododendron macrophyllum and the genus, Ilex and Salix were collected for the isolation of endophytic fungi. Fungal extracts...
Resource Type:: Presentation and Undergraduate Thesis
Full Text:: . Current clinical and agricultural practices provide strong selection for evolution of drug resistance

Genomic Investigations of Diversity within the Milkweed Genus Asclepias, at Multiple Scales

Creator:: Weitemier, Kevin A.
Abstract:: At a time when the biodiversity on Earth is being rapidly lost, new technologies and methods in genomic analysis are fortunately allowing scientists to catalog and explore the diversity that remains more efficiently and precisely. The studies in this dissertation investigate genomic diversity within the milkweed genus, Asclepias, at multiple...
Resource Type:: Dissertation
Full Text:: for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies

Development and Application of Tools for Genetic Analysis of Clonal Populations

Creator:: Kamvar, Zhian N.
Abstract:: Research on the population genetics of microbial organisms requires the use of specialized analyses designed for clonal organisms to avoid violating the assumptions of traditional population genetic models. The tools necessary for performing these analyses existed as a set of unrelated software with non-overlapping capabilities and did not cover all...
Resource Type:: Dissertation
Full Text:: . Title: Development and Application of Tools for Genetic Analysis of Clonal Populations Abstract

Genetic Structure in Populations of the Douglas-fir Swiss Needle Cast Fungus Nothophaeocryptopus gaeumannii

Creator:: Bennett, Patrick I.
Abstract:: The fungus Nothophaeocryptopus gaeumannii is the causative agent of Swiss needle cast (SNC), a foliar disease of Douglas-fir. Disease is characterized by premature loss of foliage and reduced growth resulting from the inhibition of photosynthesis due to the occlusion of stomata by the ascocarps of N. gaeumannii. Although the disease...
Resource Type:: Dissertation
Full Text:: Botany and Plant Pathology presented on May 10, 2018. Title: Genetic Structure in Populations of the

Analysis of Genome Sequences from Plant Pathogenic Rhodococcus Reveals Genetic Novelties in Virulence Loci

Creator:: Creason, Allison L., Vandeputte, Olivier M., Savory, Elizabeth A., Davis, Edward W., II, Putnam, Melodie L., Hu, Erdong, Swader-Hines, David, Mol, Adeline, Baucher, Marie, Prinsen, Els, Zdanowska, Magdalena, Givan, Scott A., El Jaziri, Mondher, Loper, Joyce E., Mahmud, Taifo, and Chang, Jeff H.
Abstract:: Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus, some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with...
Resource Type:: Article

DNA markers and characterization of novel sources of eastern filbert blight resistance in European hazelnut (Corylus avellana L.)

Creator:: Peterschmidt, Brooke C.
Abstract:: European hazelnut is a significant crop in the Pacific Northwest, and the US ranks 4th internationally for hazelnut production. Production in the Pacific Northwest is threatened, however, by the disease eastern filbert blight (EFB) caused by the fungus Anisogramma anomala (Peck) E. Müller. To meet the challenges faced by the...
Resource Type:: Masters Thesis
Full Text:: that provide information about the genetic characteristics of an organism, and their use has become

The conservation genetics juggling act: integrating genetics and ecology, science and policy

Creator:: Haig, Susan M., Miller, Mark. P., Bellinger, Renee, Draheim, Hope M., Mercer, Dacey M., and Mullins, Thomas D.
Abstract:: The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980s following the development of polymerase chain reaction and now...
Resource Type:: Article
Full Text:: The conservation genetics juggling act: integrating genetics and

Surface-exposed proteins in the pathogenesis of Mycobacterium avium subsp. hominissuis

Creator:: McNamara, Michael J.
Abstract:: Mycobacterium avium subsp. hominissuis (MAH) is a pervasive environmental bacterium that can cause opportunistic infections in humans. Among the most robust and hardy members of the Mycobacterium genus, M. avium can persist and thrive in a range of challenging environments, including many which place it in direct contact with humans....
Resource Type:: Dissertation
Full Text:: context of early infection, we then developed a method, based on selective biotinylation and affinity

Identification and distribution of the mating-type locus and development of cleistothecia of Podosphaera macularis

Creator:: Wolfenbarger, Sierra N.
Abstract:: Podosphaera macularis, causal agent of hop powdery mildew, is known to produce cleistothecia (syn. chasmothecia) in eastern North America and Europe, but ascocarps are not reported from the Pacific Northwestern region of North America. Reasons for the apparent absence of cleistothecia in the Pacific Northwest are unknown. We established that...
Resource Type:: Masters Thesis
Full Text:: ascocarp ontogeny, maturation, dehiscence, and ascopore infection proceeds similarly to other powdery

Evolution and Expression of TSR-domain proteins in cnidarian-dinoflagellate symbiosis

Creator:: Tan, Kenneth
Abstract:: The symbiotic relationship between cnidarians, such as corals and sea anemones, and dinoflagellates plays a crucial role in supporting the diversity and productivity of coral reefs. Critical to the symbiosis is the recognition process between host and symbiont at the onset of symbiosis, which involves the host innate immune system....
Resource Type:: Poster
Full Text:: Slide 1 v Evolution and Expression of TSR-domain proteins

The Economic Cost of Ignoring Fishery Induced Evolution

Creator:: Faig, Amanda D.
Abstract:: Ecologists warn that the rapid evolution occurring as a result of high-intensity commercial fishing could have potentially disastrous economic and ecological effects. The evolution of economically relevant life-history traits in fish, which can occur due to the harvesting pressure from commercial fisheries, can irreversibly diminish fisheries yields and ecological services....
Resource Type:: Presentation
Full Text:: Considering Fishery Induced Evolution Amanda Faig – University of California, Davis Introduction and

The conserved biology of herpesvirus latency : a study in cyprinid herpesvirus 3

Creator:: Reed, Aimee N.
Abstract:: Cyprinid herpesvirus 3 (CyHV-3), commonly known as koi herpesvirus (KHV), is a member of the Alloherpesviridae and is a deadly pathogen for koi and common carp, Cyprinus carpio. It causes severe gill necrosis and nephritis, dermal ulceration and hemorrhage, and mass mortality of up to 100% of affected fish. Fish...
Resource Type:: Dissertation
Full Text:: infection begins -127 bp upstream of the ATG and ends +188 bp downstream of the stop codon, +20 bp

Selfish Little Circles: Transmission Bias and Evolution of Large Deletion-Bearing Mitochondrial DNA in Caenorhabditis briggsae Nematodes

Creator:: Clark, Katie A., Howe, Dana K., Gafner, Kristin, Kusuma, Danika, Ping, Sita, Estes, Suzanne, and Denver, Dee R.
Abstract:: Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals...
Resource Type:: Article
Full Text:: common. We analyzed the inheritance and evolution of mitochondrial DNA bearing large heteroplasmic

Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus

Creator:: Inglis, Diane O., Skrzypek, Marek S., Liaw, Edward, Moktali, Venkatesh, Sherlock, Gavin, and Stajich, Jason E.
Abstract:: Cryptococcus, a major cause of disseminated infections in immunocompromised patients, kills over 600,000 people per year worldwide. Genes involved in the virulence of the meningitis-causing fungus are being characterized at an increasing rate, and to date, at least 648 Cryptococcus gene names have been published. However, these data are scattered...
Resource Type:: Article

Re-examining Ceratomyxa shasta in the Pacific Northwest

Creator:: Stinson, Matthew E. T.
Abstract:: Ceratomyxa shasta infects salmonids in the Pacific Northwest (PNW) of North America, occasionally causing losses in wild and captive populations. Host-specific parasite genotypes (O, I, II, III) were previously characterized molecularly using markers in the ribosomal DNA and phenotypically by type host in the Klamath River, CA/OR. This thesis sough...
Resource Type:: Masters Thesis
Full Text:: structure the Ceratomyxa shasta (Myxozoa) population in the Klamath River basin. Infection, Genetics and

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