Background: Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Evidence also suggests that many pre-mRNAs undergo unproductive alternative splicing resulting in incorporation of in-frame premature termination codons (PTCs). The destinies and potential functions...
Background:
Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. While this method was...
In 1964, Zarantonello published a constructive method for
the solution of certain nonlinear problems in a Hilbert space. We
extend the method in various directions including a generalization
to a Banach space setting. A revealing geometric interpretation of
the method yields guidelines for the analysis.
BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental
changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a
substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day.
Synchronized...
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and cis-Regulatory Modules
SergeiA. Filichkin1, Ghislain Breton2¤a, Henry D. Priest1, Palitha
BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental
changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a
substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day.
Synchronized...
BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental
changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a
substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day.
Synchronized...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
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, SergeiA. Filichkin, Samuel E. Fox, Pankaj Jaiswal, Kira S. Makarova,
Eugene V. Koonin, and Valerian V
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
G. F. Drukarev has given a method for solving the Fredholm
equations which arise in the study of collisions between electrons
and atoms. He transforms the Fredholm equations into Volterra
equations plus finite algebraic systems. H. Brysk observes that
Drukarev's method applies generally to a Fredholm integral equation
(I-λ G)u...
One-electron oxidation of the μ-oxo dimer
(cis,cis-[Ruᴵᴵᴵ(bpy)₂(OH₂)]₂O⁴⁺, {3,3}) to {3,4} by S₂O₈²⁻ can
be described by three concurrent reaction pathways corresponding
to the three protic forms of {3,3}. Free energy
correlations of the rate constants, transient species dynamics
determined by pulse radiolysis, and medium and temperature
dependencies of the alkaline...
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(bpy)2(OH2)]2O4+ “Blue Dimer”
James K. Hurst,† Margo Roemeling,‡ and Sergei V. Lymar
One-electron oxidation of the μ-oxo dimer
(cis,cis-[Ruᴵᴵᴵ(bpy)₂(OH₂)]₂O⁴⁺, {3,3}) to {3,4} by S₂O₈²⁻ can
be described by three concurrent reaction pathways corresponding
to the three protic forms of {3,3}. Free energy
correlations of the rate constants, transient species dynamics
determined by pulse radiolysis, and medium and temperature
dependencies of the alkaline...
Full Text:
-[Ru(bpy)2(OH2)]2O
4+ “Blue Dimer”
James K. Hurst,† Margo D. Roemeling,‡ and Sergei V. Lymar
One-electron oxidation of the μ-oxo dimer
(cis,cis-[Ruᴵᴵᴵ(bpy)₂(OH₂)]₂O⁴⁺, {3,3}) to {3,4} by S₂O₈²⁻ can
be described by three concurrent reaction pathways corresponding
to the three protic forms of {3,3}. Free energy
correlations of the rate constants, transient species dynamics
determined by pulse radiolysis, and medium and temperature
dependencies of the alkaline...
Facultative/winter six-row malting barley is a distinct elite germplasm pool and a valuable resource that may prove useful in meeting the challenges of climate change. To preserve its diversity and make it accessible to the research and agricultural communities, the Oregon State University and University of Minnesota barley breeding programs...
New seafloor mapping and sampling demonstrates that the eruption of the high-Ca boninites is clearly associated with rifting of the northern Tonga ridge and the northern Lau Basin at the northern termination of the Tonga Trench. There is very strong evidence for OIB plume related mantle sources involved in the...
We report new geochemical data for boninites and backarc basin-type basalts recovered from the northern termination of the Tonga trench and Lau Basin. Boninitic pillow lavas, ranging from high-Mg compositions to andesites and dacites, have been erupted within large submarine volcanic edifices (calderas and volcanoes) associated with active rifting of...
Barley (Hordeum vulgare) is an important component of heart-healthy
whole grain diets because it contains β-glucan. All current US barley
varieties with high β-glucan are spring habit and have waxy starch. Winter
varieties have agronomic advantages but require low-temperature tolerance
(LTT). Vernalization sensitivity (VS) is associated with higher
levels of...
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. Cereal Chem. 79, 596—599.
Cuesta-Marcos, A., P. Szucs, T. J. Close, T. Filichkin, G. J. Muehlbauer,
K. P
Barley (Hordeum vulgare) is an important component of heart-healthy
whole grain diets because it contains β-glucan. All current US barley
varieties with high β-glucan are spring habit and have waxy starch. Winter
varieties have agronomic advantages but require low-temperature tolerance
(LTT). Vernalization sensitivity (VS) is associated with higher
levels of...
Barley (Hordeum vulgare) is an important component of heart-healthy whole grain diets because it contains β-glucan. All current US barley varieties with high β-glucan are spring habit and have waxy starch. Winter varieties have agronomic advantages but require low-temperature tolerance (LTT). Vernalization sensitivity (VS) is associated with higher levels of...
Thermoelectric materials are playing a larger role in the global effort to
develop diverse, efficient, and sustainable energy technologies: primarily through
power-generating thermoelectric modules. The principal components of
thermoelectric modules are solid-state thermoelectric materials – typically heavily
doped semiconductors – that convert heat directly into electricity. However, this
conversion efficiency...
Hop (Humulus lupulus L. var. lupulus) is a diploid, dioecious plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. Hop is prized for its ability to produce a variety of aromatic and flavor compounds, as well as compounds with anti-microbial...
The success of NIKE, Inc. is deemed miracle by professionals on both Wall
Street and Madison Avenue. Research done in the past tends to credit the growth
of NIKE, Inc. to its marketing strategies. By placing the achievement of the
company in the postmodern context, this study analyzes the cultural...
Creeping bentgrass (Agrostis stolonifera L.) is an outcrossing, small- seeded, perennial grass that can establish outside of cultivation and has several compatible relatives. Glyphosate is a nonselective, broad spectrum, herbicide. Transgenic glyphosate-resistant (GR) creeping bentgrass (GRCB) was developed by The Scotts Company and Monsanto, but is still under USDA-APHIS regulated...
European hazelnut, Corylus avellana L., is the only economically important nut crop
in the family Betulaceae. One of the threats to the hazelnut industry in the Pacific
Northwest is the fungal disease eastern filbert blight (EFB) caused by the
pyrenomycete Anisogramma anomala. Host genetic resistance to EFB identified in the...
In this dissertation we study the electromagnetic properties of planar waveguides
with non-magnetic strongly anisotropic dielectric cores. We develop an analytical
description of the mode propagation in these systems and show that the index
of refraction can be either positive or negative depending on the specific material
parameters. Propagating modes...
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...
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...
This thesis consists of five chapters: a general introduction, two manuscripts, a collection of published lesson plans, and a general conclusion. The works collected herein are united by the common theme of practical applications in plant breeding. The first manuscript reports a study performed on five malting barley lines grown...
Collaboration is crucial when advancing in scientific research. One person cannot
study all aspects of a system. That is why it is important for the scientific community to
communicate with each other and stay updated on research being conducted in other labs
around the world. In my research, I was...
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simple difference. A principal component of winterhardiness is low temperature
tolerance. However, low
Background: Functional annotations of large plant genome projects mostly provide information on gene function
and gene families based on the presence of protein domains and gene homology, but not necessarily in
association with gene expression or metabolic and regulatory networks. These additional annotations are necessary
to understand the physiology, development...
Symbiosis is the close and protracted interaction between organisms. The molecular interactions that occur during symbiosis are complex with multiple barriers that must be overcome. Many Gram-negative, host-associated bacteria use a type III secretion system to mediate associations with their eukaryotic hosts. This secretion system is a specialized apparatus for...
Bacteria are abundant in marine environments. They play important roles in nutrient cycling and form symbiotic interactions with eukaryotes. However, the vast majority of bacterial taxa are difficult to maintain in laboratory cultures, meaning that most microbiological research of the past century has focused on a small subset of bacteria....
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...
Barley (Hordeum vulgare L.) is one of the oldest known domesticated crops. Originally cultivated for human consumption, other end-uses have gained importance over the millennia. Barley is the fourth most important cereal crop in the world (FAO-STAT, 2011), and today it is mainly used as animal feed or malted for...
Strawberry is one of four crops included in the USDA-NIFA Specialty Crop Research Initiative-funded RosBREED project along with apple, peach, and cherry. Phenotyping strawberry for specific horticultural and commercial traits is important to identify associations with genotypic marker(s). This process is the first step in translating genomic knowledge into enhanced...
With the increasing international focus on transboundary cooperation as a part of the Sustainable Development Goal (SDG) Framework, there is global recognition of transboundary water cooperation as a tool for improved governance and management of transboundary surface and groundwaters. Yet, there is not an agreed upon definition of transboundary water...
Background: Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated...
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...
Load flow studies are one of the most essential engineering applications for grid operators because they provide a clear picture of the operating conditions of the power system. Traditionally, the load flow problem is assumed to be deterministic; that is, the system variables contain no randomness. Unfortunately, this assumption is...
Rocks are defined as aggregates or mixtures of minerals; rocks also include noncrystalline materials such as the natural glasses, and organic material such as coal. Rocks are found ready-made in nature. They are not homogeneous nor are they crystalline, although they may be made up of crystalline material. The composition...
One of the most serious problems confronting modern America
is the efficient and rational utilization of the recreation resource base,
not only in terms of present demands and needs, but future as well.
The resource manager, in the past, has had few guidelines from
which to determine the type and...
Fall-sown barley will be increasingly important in the era of climate change due to higher yield potential and efficient use of water resources. Resistance/tolerance to biotic and abiotic stresses will be critical. Low temperature is an abiotic stress of great importance. Resistance to barley stripe rust (incited by Puccinia striifomis...
Background: Little is known about the potential of Brachypodium distachyon as a model for low temperature stress
responses in Pooideae. The ice recrystallization inhibition protein (IRIP) genes, fructosyltransferase (FST) genes, and
many C-repeat binding factor (CBF) genes are Pooideae specific and important in low temperature responses. Here
we used comparative...
Using genetic approaches, particle image velocimetry and an inert tracer of cytoplasmic streaming, we have made a mechanistic connection between the motor proteins (myosins XI), cargo transported by these motors (distinct endomembrane compartment defined by membrane-anchored MyoB receptors) and the process of cytoplasmic streaming in plant cells. It is shown...
To characterize the mechanism through which myosin XI-K attaches to its principal endomembrane cargo, a yeast two-hybrid library of Arabidopsis thaliana cDNAs was screened using the myosin cargo binding domain as bait. This screen identified two previously uncharacterized transmembrane proteins (hereinafter myosin binding proteins or MyoB1/2) that share a myosin...
Spotted lanternfly (Lycorma delicatula) is an invasive insect that was first discovered in Pennsylvania in 2014, and has since spread across the Northeastern United States. States in the Northeast have created quarantine zones, regulations, outreach, reporting systems, and management efforts for the control of spotted lanternfly. Despite states’ efforts, spotted...
The genetic underpinnings associated with the earliest stages of plant and animal domestication have remained elusive. Because a genome-wide response to selection can take many generations, the earliest detectable changes associated with domestication may first manifest as heritable changes to global patterns of gene expression. Here, to test this hypothesis,...
Full Text:
. Fox, S., Filichkin, S. & Mockler, T. in Plant Systems Biology. (ed. Belostotsky, D. A.
553 chap. 5 79
We consider three problems on simplicial complexes: the Optimal Bounded Chain Problem, the Optimal Homologous Chain Problem, and 2-Dim-Bounded-Surface. The Optimal Bounded Chain Problem asks to find the minimum weight d-chain in a simplicial complex K bounded by a given (d−1)-chain, if such a d-chain exists. The Optimal Homologous Chain...