Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
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genomics and
pathway resources
MarcelaK. Tello-Ruiz1, Joshua Stein1, Sharon Wei1, Justin Preece2, Andrew
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
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., J. Preece, J. A. Kimbrel, G. L. Marchini, A. Sage, K. Youens-Clark, M.
B. Cruzan and P. Jaiswal
In the thrust to shift away from fossil fuels towards renewable options, Ecuador produces African palm-based biodiesel, which is currently imported by the Unites States. An analysis of this specific interaction was done via personal contact with the industry in Ecuador and extensive literature review of the topic. The results...
This dissertation investigates the problem of uncertainty in complex ecological models. The term "complex" is used to convey both the common and scientific meanings. Increasingly, ecological models have become complex because they are more complicated; ecological models are generally multi-variate and multi-leveled in structure. Many ecological models are complex because...
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
Equipment and procedures for the rapid measurement of the water vapor
permeability of polymer films and food coatings has been evaluated. The
method uses an electronic sensor to measure the concentration increase in
water vapor diffusing through a film into a chamber of known volume. Air of
known humidity is...
RNA silencing plays a critical role in plant defense against viral infection. Plants use virusderived
small interfering RNA to target and silence invading viruses. The antiviral silencing
pathway can be broken down into three conceptual stages: initiation, amplification, and systemic
movement. The molecular mechanisms of silencing initiation are not well...
The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated...
Propose a sampling plan to determine Hg contamination in the Nanay river basin.
The sampling plan is for a feasibility pilot, to investigate whether it is possible to safely collect samples for Hg analyses. Future studies will build on these initial results.
Multiplicative random cascades (MRCs) can parsimoniously generate highly intermittent patterns similar to those in rainfall. The elemental MRC model parameter is the cascade weight, which determines how rainfall at one scale is partitioned at the next smallest scale in the cascade. While it is known that the probability density of...
In CIAT, Centro Internacional de Agricultura Tropical, located
in Palmira, Colombia, a series of experiments were conducted to study
the biology and control of mudplantain (Heteranthera reniformis Ruiz
et Pavon), a member of Pontederiaceae family.
Mudplantain is a perennial aquatic plant which reproduces by both
seeds and stolons. It is...
Diverse scientific fields collect multiple time series data to investigate the dynamical behavior of complex systems: atmospheric and climate science, geophysics, neuroscience, epidemiology, ecology, and environmental science. Identifying patterns of mutual dependence among such data generates valuable knowledge that can be applied either for inferential or forecasting purposes. Vector autoregressive...
This paper, that follows from the ongoing Ecost project, departs from the reality of marine biodiversity degradation in the Caribbean. It first enquires how local fishing communities appreciate and measure the degradation of marine biodiversity. In this connection, it asks whether communities have social and cultural attachments to particular species....
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...
Production of Kþ mesons in charged-current νμ interactions on plastic scintillator (CH) is measured using MINERvA exposed to the low-energy NuMI beam at Fermilab. Timing information is used to isolate a sample of 885 charged-current events containing a stopping Kþ which decays at rest. The differential cross section in Kþ...
Vibrio cholerae a major health problem in developing countries because of its ability to cause the disease cholera in humans. As V. cholerae bacteria are common inhabitants of temperate marine and brackish water environments worldwide, they are subject to intense top-down pressure by amoebae, which can affect their survival and...
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. Solis-Ruiz
•John Snow postulated Cholera
to be a digestive disease (enters
through oral-fecal route
Vibrio cholerae a major health problem in developing countries because of its ability to cause the disease cholera in humans. As V. cholerae bacteria are common inhabitants of temperate marine and brackish water environments worldwide, they are subject to intense top-down pressure by amoebae, which can affect their survival and...
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By: Jose M. Solis-Ruiz
An Undergraduate Thesis Submitted to
Oregon State University
New methods, sensors, and devices based on redox indicators were developed to
monitor redox conditions in anoxic and anaerobic laboratory systems and the subsurface
environment. The primary application was monitoring redox conditions
during the dechlorination of tetrachioroethene (PCE) to ethene (ETH) in packed
columns and microcosm bottles containing an enriched...
Issues of injustice in society (e.g. racism, classism, sexism, ableism) are perpetuated in and through educational opportunities, including mathematics learning (Freire, 1970/2000). Those that are committed to disrupting the interlocking systems that create disparities and oppression in mathematics education are considered to be “pursuing justice.” Pursuit of justice can involve...
A framework for understanding the synthesis and catalysis of metabolites and other biochemicals by proteins is crucial for unraveling the physiology of cells. To create such a framework for Zea mays L. subsp. mays (maize), we developed MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary...
Gramene (http://www.gramene.org) is a curated
online resource for comparative functional
genomics in crops and model plant species, currently
hosting 27 fully and 10 partially sequenced
reference genomes in its build number 38. Its
strength derives from the application of a phylogenetic
framework for genome comparison and the
use of ontologies...
Gramene (http://www.gramene.org) is a curated
online resource for comparative functional
genomics in crops and model plant species, currently
hosting 27 fully and 10 partially sequenced
reference genomes in its build number 38. Its
strength derives from the application of a phylogenetic
framework for genome comparison and the
use of ontologies...
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Database
K-12
MG1655
BioCyc Keseler et al (2013)
(Escherichia coli)
SUPPLEMENTARY
Gramene (http://www.gramene.org) is a curated
online resource for comparative functional
genomics in crops and model plant species, currently
hosting 27 fully and 10 partially sequenced
reference genomes in its build number 38. Its
strength derives from the application of a phylogenetic
framework for genome comparison and the
use of ontologies...
Platelet-rich plasma (PRP) has been applied as a hemostatic agent since the 1970s, and a potent source of autologous growth factors since the 1990s. PRP is rich in growth factors such as platelet derived growth factor (PDGF), vascular endothelial growth factor (VEGF), transforming growth factor-β (TGF-β), fibroblast growth factor (FGF)...
The commercial Dungeness crab (Cancer magister) fishery is Oregon’s largest trap-based fishery. Each year, crab vessels discard millions of pounds of bait, including squid, razor clams, and sardines, into the near-coastal ocean. Although the fishery season typically runs from December 1st through August 14th, most landings occur within the first...
Population counts of aquatic insects can be a credible indicator of the overall health of a waterway. Stonefly (Plecoptera) larva are very sensitive to chemicals present within the waterway, however obtaining population counts of the larvae can be very labor intensive and thus costly. The BugID project has been working...
International development projects aimed at alleviating poverty often fall short when it comes to capacity for operation and maintenance. As a case in point, today it is estimated one-third of all African wells have fallen into disrepair due to lack of effective management, corresponding to as many as 250,000 broken...
With an increasing number of wireless applications at microwave frequencies, the frequency spectrum is becoming quite crowded. Due to this congestion, the current state of technology is leading towards upper microwave and millimeter wave spectra as they also offer other distinct advantages such as larger bandwidth and smaller component footprint....
Modern wind energy is the technology of choice with a short payback period for increasing renewable energy portfolios. Bonneville Power Administration (BPA), a United States power authority in the Pacific Northwest expects to increase their wind energy capacity from 2,000 megawatts to 6,000 megawatts within the next five years. Currently...
The nucleosome appears to be the basic structural unit of the
eukaryotic chromosome. The usual nucleosome preparation, isolated
from a micrococcal nuclease digest of nuclei, is heterogenous in DNA
length and protein composition with some particles containing spacer
DNA and associated protein. This heterogeneity complicated physical
and reconstitution studies. As...
Deoxyribonucleoside triphosphate (dNTP) concentrations measured in cells are not symmetric. dGTP almost always represents only 5-10% of the total dNTP pools in cells. In an in vitro replication system involving semiconservative replication from an SV 40 origin, the mutation frequency of an M13 phagemid replicated by human cell extracts in...
A theory is developed to provide an analytical solution to an
unsteady flow field which is partially occupied by a porous structure.
The flow is induced by a small amplitude incident wave
train. The porous structure may contain multi-layer anisotropic but
homogeneous media. Three typical porous structures are investigated:
a...
Influenza A and Respiratory Syncytial Virus (RSV) are both enveloped, negative strand
RNA viruses which infect the respiratory mucosa of animals and humans. Despite
decades of research and development of antivirals and vaccines, both of these viruses
continue to be a major health concern throughout the world. The focus of...
Breast cancer is the leading cancer in women with an estimated 13% of women in the United States developing a form of invasive breast cancer in her lifetime. The survival rate is estimated to be 85%, but the American Cancer Society estimates that early detection of breast cancer in the...
Quantification of contemporary sediment and carbon accumulation within Oregon tidal saline wetlands will: (1) fill a critical knowledge gap, and (2) naturally test without complicating variables whether sea level rise or sediment supply primarily control wetland growth. Here we measure vertical accretion rates and carbon burial rates in three Oregon...
High impact loading activities such as jumping, performed during childhood is advocated as one preventive method for increasing peak bone mass. Thus, we conducted a randomized intervention to examine the effect of high impact loading on bone mass in 34 pre-pubescent boys and girl over a seven month period. Participants...
The emerging field of regenerative medicine is mainly approached by two different aspects. First is the use of stem cell based models to generate a suite of differentiated cells for therapeutic applications and the alternative approach is to utilize the non-mammalian models that have the inherent capacity to regenerate their...
To examine the potential for exercise to build bone mass during growth, objectives of this dissertation included: 1) determine the effects of 7 months of jumping followed by 7 months of detraining on hip and spine bone mass in the prepubertal children; 2) determine variables that best predict bone mineral...
A low, but significant, fraction of the carbohydrate portion of herbaceous biomass may be composed of fructose/fructosyl-containing components (“fructose equivalents”); such carbohydrates include sucrose, fructo-oligosaccharides, and fructans. Standard methods used for the quantification of structural-carbohydrate-derived neutral monosaccharide-equivalents in biomass are not particularly well suited for the quantification of fructose equivalents...
Self-regulation in early childhood encompasses higher-order executive function processes and lower-order emotional responses that enable children to navigate the classroom environment. Although self-regulation and executive functions are overlapping constructs, self-regulation represents a broad assessment of children’s ability to call upon executive function processes in order to meet contextual demands. Prior...
Quantification and comparison of morphological changes over the last ~300 y in Oregon salt marshes provide valuable insights into the tectonic, hydroclimatic, and anthropogenic processes shaping this important intertidal zone. Understanding of the rates and drivers of salt marsh change contextualizes intertidal habitats within the sediment routing system (i.e., source...
Sustainable product design is becoming an important component of the development of consumer products. Currently there are limited design resources to aid in the creation of environmentally sustainable products. The purpose of this research is to theorize a new method for integrating sustainable design knowledge into the early design phase...
Snow Peak is a voluminous shield volcano located ~50 km west of the axis of
the modern Cascade arc. A previously published K-Ar age estimate indicates that the
Snow Peak lavas are ~3 Ma. Subsequently, the preliminary research framework for
studying the Snow Peak lavas focused on constraining the petrogenesis...
The intrusion-related Cerro Negro Norte Fe-oxide (Cu-Au) deposit is hosted in andesites and diorites of the early to middle Cretaceous Coastal Cordilleran arc of northern Chile. Tabular and irregularly shaped magnetite orebodies are localized on splays and fractures of the regional NINE striking Atacama Fault Zone. Production from this district...
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, Coastal Cordillera, northern Chile
AN ABSTRACT OF THE THESIS OF
Alexander K Raab for the degree of
Italian ryegrass (Lolium perenne L. spp. multiflorum (Lam.) Husnot) is one of the most troublesome weeds with respect to herbicide resistance selection. Some reasons for this are the numerous documented cases of multiple and cross herbicide resistance and some of the biological characteristics of this species, such as wind cross-pollination...
One of the most economically important genes in squash (Cucurbita spp.) is the B gene which conditions precocious depletion of chlorophyll in preanthesis fruit. The B genes are found naturally occurring in at least three of the five domesticated species of Cucurbita, including C. pepo, C. maxima and, most recently...
This report describes the partial characterization of the first cultivable calicivirus isolated from a European rabbit (Oryctolagus cuniculus), named rabbit calicivirus Oryctolagus-1 and abbreviated RaCv Ory-1. RaCv Ory-1 was isolated from juvenile feeder rabbits displaying symptoms of diarrhea. Absence of neutralization by type specific neutralizing antibodies for 40 caliciviruses and...
Research shows that women's lives are disproportionately impacted by the effects of climate change. While the topic of women is largely absent from climate discourse overall, the representations of women that occur reveal underlying structures of power rooted in imperialism and colonial dominance. This thesis presents an analysis of the...
Calcium alginate gels are widely used in the biotechnology, food, and pharmaceutical industries for cell immobilization, food additives, and controlling the release of therapeutic agents. Different gelation conditions can lead to different gel structures which affects the diffusion of solutes in gels, thus mathematical models were developed to describe diffusion...