Reintroduction programs are increasingly being used to save animals from extinction and aid in their recovery. The California Condor (Gymnogyps californianus), one of the most endangered birds in the world, is a remarkable example of how reintroduction programs can help rapidly increase a species' population numbers and range following a...
Forest fires contribute a significant amount of CO₂ to the atmosphere each year, and CO₂ emissions from fires are likely to increase under projected conditions of global climate change. In addition to volatilizing aboveground biomass and litter layers, forest fires have a profound effect on belowground carbon (C) pools and...
Five varieties of industrial hemp (Cannabis sativa) were grown in the field in Imperial Valley, CA, USA in order to determine whether light conditions or harvest times influence cannabinoid content. A total of 16 cannabinoids were investigated in this study: Delta-9-tetrahydrocannibinol (THC-d9), Delta-9-tetrahydrocannibinolic acid (THC-a), Cannabidiol (CBD), Cannabidiolic acid (CBD-a),...
Hybridization, polyploidy, and apomixis have made phylogenetic estimation in Rubus challenging. I used target capture to sequence approximately 1000 low copy nuclear loci and the chloroplast genome for 94 accessions representing the genus Rubus and distributed worldwide. Species phylogenies were estimated using two coalescent based methods, ASTRAL-II and SVDQuartets, and...
Oomycetes are an important group of organisms with a variety of ecological roles similar to fungi. Although many are well-studied plant pathogens known for their devastating effects on agricultural systems, most are little-studied saprobes and parasites of plants and animals in nearly every ecosystem on earth. The advent of affordable...
The essential oil from two Lantana species (Lantana lucida Schauer and Lantana salzmannii Schauer) were evaluated for their chemical composition by GC-MS. Results showed 17 predominant compounds for L. lucida, among which β-caryophyllene (19.0%) and α- caryophyllene (or humuleno, 33.0%) were the major components. L. salzmannii showed the presence of...
This book is based on a project to completely annotate what is known about the function of the ~150 genes encoded by the genome of the most commonly investigated baculovirus, AcMNPV. Once the annotation was completed (summarized in Chapter 11), the material was organized into a series of chapters integrating...
This is the third edition of a book that was initiated with the annotation of the function of all the genes in the most commonly studied baculovirus, AcMNPV. The second and third editions involved the update of this information and its integration into chapters covering the major processes central to...
This book is based on a project to completely annotate what is known about the function of the ~150 genes encoded by the genome of the most commonly investigated baculovirus, AcMNPV. Once the annotation was completed (summarized in Chapter 12), the material was organized into a series of chapters integrating...
This is the 4th edition of a book that was initiated with the annotation of the function of all the genes in the most commonly studied baculovirus, AcMNPV. It has been almost six years since I reviewed this literature. As a measure of the research that has occurred over this...
Contaminants used at low elevation, such as pesticides on crops, can be transported tens of kilometers and deposited in adjacent mountains in many parts of the world. Atmospherically deposited organic contaminants in the Sierra Nevada Mountains of California, USA, have exceeded some thresholds of concern, but the spatial and temporal...
Perfluorooctanesulphonicacid (PFOS) is an organic contaminant that is ubiquitous in the environment, wildlife, and humans. Few studies have assessed the effects of chronic PFOS exposure on central nervous system function in aquatic organisms. The present study defined the behavioral effects of varying life span chronic exposures to low dose PFOS...
Parasites are unique study organisms for evolutionary ecologists. Yet, molecular ecology studies on parasites have lagged far behind those on free-living organisms. The goal of the review in Chapter 2 was to illustrate areas of research that may be of particular interest in relation to the parasitic life style and...
Rhizopogon is a hypogeous fungal genus that forms ectomycorrhizae
with genera of the Pinaceae. The greatest number and species of
Rhizopogon are found in coniferous forests of the Pacific Northwestern
United States, where members of the Pinaceae are also concentrated.
Rhizopogon spp. are host-specific primarily with Pinus spp. and
Pseudotsuga...
In this dissertation, I present the results from three studies: (1) a phylogeny of Tenebrionoidea (Coleoptera) inferred from a seven-gene dataset derived from PCR and Sanger sequencing; (2) a phylogeny of Tenebrionidae, the largest family in Tenebrionoidea, inferred from a four-gene dataset also derived from PCR and Sanger sequencing; (3)...
Species conservation depends on robust population assessment. Data on population abundance, distribution, and connectivity are critical for effective management, especially as baseline information for newly documented populations. I describe a pygmy blue whale (Balaenoptera musculus brevicauda) population in New Zealand waters with year-round presence that overlaps with industrial activities. This...
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...
Many of Earth’s terrestrial large carnivore species are threatened with extinction. As a result, some of the ecological effects associated with these species may be lost. With the goal of furthering large carnivore conservation research, I conduct three global scale analyses involving these species. First, I explore prey depletion as...
1,1,1-Tricholorethane (1,1,1-TCA), a widely used industrial solvents, is one of the most common subsurface contaminants. Transformation processes in the subsurface can result in the production of 1,1-dichioroethane (1,1-DCA) and 1,1- dichioroethene (l,1-DCE) from 1,1,1-TCA contamination, resulting in plumes of mixed chlorinated aliphatic hydrocarbons (CAHs). A butane-utilizing microorganism, strain 1 83BP,...
OmniGen-AF® (OG; Prince Agri Products, Inc., Quincy, IL) is a feed additive containing brewers dehydrated yeast and B-vitamins that supports immune function in ruminant livestock. Targeted profiling of immune-associated genes in whole blood is an effective platform for identification of a) novel molecular pathways and b) immune response markers to...
Pre-existing Expressed Sequence Tag (EST) libraries (1,305 sequences) and a newly constructed microsatellite-enriched genomic library (136 clones) from the V. corymbosum cultivar 'Bluecrop' were screened for unique Simple Sequence Repeat (SSR)-containing sequences. Our goal was to develop a set of robust SSR markers for use in managing the National Clonal...
This thesis summarizes work completed over the previous four years primarily focusing on chloroplast phylogenomic inquiry into the genus Pinus and related Pinaceae outgroups using next-generation sequencing on Illumina platforms. During the time of our work, Illumina sequence read lengths have essentially been limited to 25 to 100 base pairs,...
We studied genetic polymorphism and phylogeny using nuclear random amplified polymorphic DNA markers (RAPDs) and mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs) in the three California Closed-Cone Pines: Pinus attenuata Lemm., P. muricata D. Don, and P. radiata D. Don. A total of 343 to 384 trees derived from...
Craterellus tubaeformis is a small to medium-sized forest mushroom that is fairly common in the Douglas-fir/western hemlock forests of the Pacific Northwestern United States and is most often associated with decayed coarse woody debris. In this study, the mycorrhizae of Craterellus tubaeformis in western Oregon is identified by DNA analysis...
Many streams in eastern Oregon are listed as water quality impaired on the basis of water temperature. However, it is often difficult to predict water temperature for these streams even if there are no anthropogenic impacts. We measured air and water temperature and stream characteristics on three Type C and...
A case study examining the relationship between stream temperatures and the thermal environment through which streams flow was conducted on the headwaters of 4 tributaries of the Burnt River (Barney, Elk, Greenhorn, and Stevens Creeks) in northeastern Oregon during July through August 1998 and 1999. Barney Creek and Stevens Creek...
Two tributaries of the south fork of the Burnt River, near Unity Oregon were studied
during the summers of 2000 and 2001 to determine water heating and cooling
patterns. Hourly temperature data were recorded for air, water, and soil parameters
at four elevations 150m apart on Barney and Stevens Creeks....
Gymnomyces is an ectomycorrhizal basidiomycete genus in the family Russulaceae estimated to contain less than 50 species worldwide, with 23 species known to occur in the Pacific Northwest. Gymnomyces species are common in Pacific Northwest forests that include Pseudotsuga, Abies, Tsuga, and Quercus. They produce sequestrate (truffle-like) sporocarps with ornamented...
Plant pathogenic Rhodococcus species are persistent pathogens able to cause severe growth deformities on a large range of hosts. The most well studied species, R. fascians is predicted by current models to synthesize a mixture of cytokinins that act to directly perturb the hosts' hormone balances, which results in abnormal...
Proteins are the metabolic machines of the cell and as such, the study of proteins could illuminate the dominant biological activities that are occurring within cells and reveal how an organism interacts with its environment. Here, we used proteomic techniques to study the abundant marine bacterium SAR11 both as an...
Riparian zones of Pacific Northwest forests have high species diversity and abundance and act as an important interface between the aquatic and terrestrial ecosystems. In addition, riparian zones comprise a significant portion of the total buffer zone established during commercial forest production to protect aquatic ecosystems from adjacent management activities....
Pollutant body burdens, ability to tolerate supplementary stressors, and biomarkers of physiological stress were investigated in the ground beetle, Pterostichus oblongopunctatus (Coleoptera: Carabidae), inhabiting a gradient of heavy metal contamination in Poland. The central question was to determine if beetles inhabiting polluted habitats incurred costs compared with beetles in less...
There have been many studies that describe the protective degradation or metabolism of potentially harmful plant toxins, such as, mimosine from Leucaena leuconcephala, pyrrolizidine alkaloids from tansy ragwort (Senecio jacobaea), oxalate and some mycotoxins by rumen microbes. There are many cases of plant-related toxicoses suffered by ruminant animals where there...
Arbuscular mycorrhizal fungi (AMF) are plant symbionts that associate with the vast majority of terrestrial plants species. The AMF colonizes the plant roots by penetrating the root cortical cells, where the fungi exchanges mineral nutrients with the host plant for photosynthates. This association exists as a complex system in which...
This dissertation describes the application and development of molecular tools that have great potential for use in studying variation in strawberry germplasm. The first study evaluated 91 microsatellite (simple sequence repeat, SSR) markers for transferability in 22 Fragaria species and their utility in fingerprinting octoploid strawberries. Out of the transferable...
Pallidosis is a disease of strawberry identified in 1957 with an unknown etiology. Two previously uncharacterized viruses in strawberry, Strawberry pallidosis associated virus (SPaV) and Beet pseudo-yellows virus (BPYV), have been found associated with disease symptoms. The complete nucleotide sequence of both viruses was determined and molecular detection protocols developed....
Biological plant invasions are diminishing the ecological integrity and function of ecosystems worldwide. A primary example of this is in the Great Basin of the United States, where invasive annual grasses, like cheatgrass (Bromus tectorum L.) and medusahead (Taeniatherum caput-medusae L. Nevski), are dominating many sagebrush-steppe ecosystems. In these invaded...
Infrageneric classification in Ribes has previously relied on a few, often
conflicting, morphological markers, such as spines, glands, and inflorescence
morphology. Suggestions that hybridization drives the evolution of the genus have
not been tested using phylogenetic methods. To assess the validity of infrageneric
classifications and the importance of hybridization to...
Grasslands in the Pacific Northwest are characterized by seasonally wet, acidic soils that mainly support cool season grasses and a limited number of legume species. A major limitation to efficient animal production in grass-dominant pastures is the decline in the herbage growth rate and nutritional quality of forage from late...
Arbuscular mycorrhizal fungi (AMF) may exert profound influences on ecosystem resilience and invasion resistance in western North American sagebrush steppe and other arid rangeland plant communities. Maintenance of plant community structure through ecological feedbacks such as facilitation of nutrient cycling and uptake by host plants, physical and chemical contributions to...
Quaking aspen, Populus tremuloides, has experienced severe declines in recent years in part due to the effects of changing climate and extreme drought. As the dominant deciduous tree in Western North American forests, aspen plays a critical role in forest biodiversity and ecosystem function. Therefore, the persistence of this species...
In the area that is now Saguaro National Park East, grazing began in the 1880's. Because of the impact to the iconic saguaro cactus as well as all palatable plant species in the area, ecological damage in the park were determined to be so great that anti-grazing conservationists challenged the...
Reestablishing native perennial vegetation in annual grass-invaded rangelands is critical to restoring ecosystems, especially following wildfires. Controlling invasive annual grasses is essential to increasing revegetation success; however, pre-emergent herbicides used to control annual grasses prohibit immediate seeding due to non-target herbicide damage. Thus, seeding is often delayed one year following...
Intracellular symbioses between cnidarians and dinoflagellates from the genus Symbiodinium are widespread throughout the marine environment. These associations are ecologically significant, especially in tropical waters where symbiotic interactions between corals and Symbiodinium culminate in the formation of limestone reefs. This thesis focuses on cellular and molecular aspects of the symbiosis,...