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...
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., Koenen, E. J., Schwarz, E., Straub, S., Hughes, C.
E., ... & Hajrah, N. H. (2015). Mimosoid legume
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...
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Koenen, Erika Schwarz, ShannonStraub, Colin E. Hughes, Robert K. Jansen, Madhugiri Nageswara-Rao
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
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, K., Straub, S. C. K., Fishbein, M., & Liston, A. (2015). Intragenomic
polymorphisms among high-copy
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common
phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT.
We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
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(Apocynaceae)
Shannon C.K. Straub1,*, Richard C. Cronn2, Christopher Edwards1, Mark Fishbein3, and Aaron
Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common
phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT.
We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common
phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT.
We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common
phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT.
We sequenced the 158 kb plastome and the 690 kb mitochondrial genome...
PREMISE OF THE STUDY: Hyb-Seq, the combination of target enrichment and genome skimming
allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets
for plant systematics and evolution studies.
METHODS AND RESULTS: Genome and transcriptome assemblies for milkweed (Asclepias syriaca)
were utilized to design enrichment probes for 3385...
This dataset contains a draft assembly of the common milkweed (Asclepias syriaca) nuclear genome, linkage group information, and gene family counts for Asclepias and related species. The genome assembly is accompanied by annotation of gene models, repeat models, transfer RNAs, and open reading frames, and mapping information of Asclepias transcripts,...
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to...
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...
Few plant mitochondrial genomes have been published to date
because of their structural complexity and difficulties in their physical
isolation. Plant mitochondrial genomes are known to have a high level
of heteroplasmy and can exist as several different circular or linear
strands. Sequencing additional mitochondrial genomes will help to
understand...
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...
The taste qualities of acidulants have not been studied in detail despite
the fact that they are widely used by the food industry. Studies on
characterizing the sensory properties of organic and inorganic acids are very
limited. Reported studies are commonly on threshold, equi-sour and the time
intensity values of...
• Premise of the study: The dramatic advances offered by modern DNA sequencers continue to redefine the limits of what can be accomplished in comparative plant biology. Even with recent achievements, however, plant genomes present obstacles that can make it difficult to execute large-scale population and phylogenetic studies on next-generation...
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Sundholm, and
Jennifer Swanson for laboratory assistance. Tara Jennings and ShannonStraub provided
Acidulants can contribute considerably to the flavor of food.
However, limited research on differences in acid flavor exists. While
numerous researchers have studied acids, most have focused on sourness
exclusively. Acids have been shown previously to differ in non-sour
components, such as bitterness and astringency. A series of experiments
were...
Marine heatwaves (“MHWs”) are discrete periods of anomalously warm ocean conditions that can lead to shifts in the distribution and abundance of marine organisms. Low-trophic level, pelagic forage species are frequently among those affected by MHWs, often resulting in considerable impacts upon their predators. In the North Atlantic Ocean, Atlantic...
Acidulants are an important functional ingredient group in the food industry, providing sourness, lowering pH, ensuring safe processing, and extending shelf life. Hence, understanding the effect of acids on sensory characteristics of foods is critical. Of the many topics dealing with acidulants, sourness is a topic where considerable research has...
Cheese is a fermented dairy product that is made from animal milk and is considered to be healthy food due to its available nutrients and potential probiotic characteristics. Since the microbes in the cheese matrix directly contribute to the quality and physicochemical properties of cheese, it is important to understand...
Predators are fundamentally important for regulating and driving prey population dynamics as well as structuring ecological communities. Over-exploitation of marine resources has caused dramatic depletions of predatory fish species and shifts in marine community composition, with attendant declines in productivity and diversity of marine ecosystems. Despite the important ramifications of...
Assembly and genotyping of polyploid genomes poses many problems due to the complex nature of polyploid data, including the inability to determine allelic dosage and mixed inheritance patterns. This study was the first application of POLiMAPS genotyping on whole genome sequences without using cross information. In this study, whole genome...
Freshwater cyanobacterial blooms are a nuisance and health threat in the Pacific Northwest. The accepted methods of characterizing these blooms by microscopic cell counts cannot differentiate between toxic and non-toxic strains of the cyanobacterium Microcystis. Also, there is limited understanding of freshwater cyanophage that may control bloom dynamics. In order...
Marine heat waves are forecasted to increase in frequency and intensity under future climate scenarios, but little is known about the impact of these events on the one of the most commonly used proxies of ocean temperature - foraminiferal assemblages. This research explores the planktic foraminifera community along the Newport...
Pinot noir has a reputation for lower color stability than other red wine varieties. Because it has relatively low anthocyanin and phenolic content and lacks acylated anthocyanin pigments compared to other red vinifera varieties, color extraction and stability are particularly important. Varying the processing during fermentation of red wine can...
The California Current Large Marine Ecosystem (CCLME), located on the eastern boundary of the North Pacific Ocean, is highly dynamic, with variable conditions driven by seasonal upwelling, regional oceanography, and broad scale climate patterns. In the last decade, the northeast Pacific Ocean has experienced several marine heatwaves (MHWs), prolonged periods...
With congressional passage of the BEACH Act in October of 2000, Coastal and Great Lakes states were mandated to assess coastal recreation waters for the application of ambient water quality standards. This research encompasses two components involved in applying the BEACH Act statues to Oregon. The first component was to...
The global water crisis is defined as one of the major threats facing humankind over the next decade with over 1 in 10 people lacking access to clean drinking water worldwide. An estimated 1.2 million people pasteurize their drinking water by using boiling as an indicator. Pasteurization is the process...
Herbs have been used for many centuries in diverse civilizations for the treatment of heart disease. Only a few natural supplements claim to have direct cardiovascular actions including hawthorn (Crataegus spp.) and berberine derived from the Berberidaceae family. Several different studies indicate important cardiovascular effects of hawthorn and berberine. For...
Environmental DNA (eDNA) is an emerging biological monitoring tool that can aid in assessing the effects of forestry and forest manufacturing activities on biota. Monitoring taxa across broad spatial and temporal scales is necessary to ensure forest management and forest manufacturing activities meet their environmental goals of maintaining biodiversity. Our...
Ovarian cancer, “the silent killer,” is one of the deadliest gynecological diseases due to delayed diagnosis, leading to a heavily disseminated and aggressive metastatic cancer. Therapeutic options are limited at stages III-IV of ovarian cancer, in which debulking surgery and cytotoxic chemotherapy remain the mainstays of
intervention. However, these therapeutic...
Rapid rates of biodiversity loss have supported the notion that Earth is experiencing a sixth major extinction event. The causes of worldwide biodiversity loss are multifaceted and context dependent. One of the most prominent groups experiencing population declines and extinctions are amphibians. Several pathogens and their associated diseases are especially...
The purpose of this investigation was to obtain a broad view of the development
and structure of the program of college education conducted at the Oregon
State Penitentiary (OSP) in Salem, Oregon to arrive at a means to explicate program
effectiveness. This research problem encompassed the compilation and interpretation
of...
Hydrogen cyanamide (CY) induced earlier budbreak, more
uniform and a higher percentage of budbreak in resting
poplar (Populus alba x P. gradidentata, NC 5339) plants.
However, it was phytotoxic to poplar when applied at 0.5 M
or higher concentrations. Percent budbreak increased and
percent dieback decreased when poplar plants were...
Translation of efficacious programs into real-world settings is an important step in ensuring improved public health outcomes. Yet, the process of translating evidence-based interventions (EBIs) according to fidelity is fraught with challenges. Organizational factors, specifically organizational communication, have been shown to influence translation processes.
To date, there is limited research...
The testimonios of three Canadian women athletes and the 1980 Olympic boycott are presented. The Latin American method of testimonio is adapted as a framework for understanding personal stories. Testimonios written in a series of interpretive narratives and poems--poetic testimonios--represent three women's voices. This study includes three journeys: the research...
Kelps are large brown algae in the order Laminariales and are foundation species that form the basis of kelp forests. Present across a quarter of the world’s coastlines, kelp forests provide diverse services to coastal communities, as habitat for commercially and culturally important species, as a food source for humans...
The climate of the Pacific Northwest is in flux, and existing forest ecosystems are stressed and poised to shift in fundamental ways, with or without human intervention. This dissertation probes the nature of forest responses to environmental change through investigations of morphology and genetics of three species of alder co-occurring...
The portability and reduced price of unmanned aerial systems (UAS) in recent years has led to a broad range of new UAS-enabled scientific inquiries, including for forestry. Small, consumer-grade UAS are advantageous for forest measurements due to their portability, ease and safety of deployment, and notably, they are currently the...
The atomic solid state energy (SSE) scale is introduced as a tool for inorganic materials design. The SSE scale is obtained by assessing an average electron affinity (EA) (for a cation) or an average ionization potential (IP) (for an anion) for each atom using data from compounds having that specific...
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...
This dissertation has two objectives. The first objective is to determine where best to situate the study of mentoring (i.e. the 'making of scientists') on the landscape of the history of science and science studies. This task is accomplished by establishing mentoring studies as a link between the robust body...
The Forest Service and the Bureau of Land Management propose to adopt coordinated ecosystem management direction for the lands they administer within the range of the northern spotted owl. This Supplemental Environmental Impact Statement (SETS) presents as alternatives the options, with slight modifications, developed by the Forest Ecosystem Management Assessment...
