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...
Important progress in understanding replication, interactions with host plants, and evolution of closteroviruses enabled engineering of several vectors for gene expression and virus-induced gene silencing. Due to the broad host range of closteroviruses, these vectors expanded vector applicability to include important woody plants such as citrus and grapevine. Furthermore, large...
Viruses were defined as one of the two principal types of organisms
in the biosphere, namely, as capsid-encoding organisms in
contrast to ribosome-encoding organisms, i.e., all cellular life
forms. Structurally similar, apparently homologous capsids are
present in a huge variety of icosahedral viruses that infect bacteria,
archaea, and eukaryotes. These...
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...
Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes
and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the
RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the...
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genomes
Krupovic, M., Dolja, V. V., & Koonin, E. V. (2015). Plant viruses of the
Amalgaviridae family
Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes
and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the
RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the...
Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses of the...
Deep sequencing analysis of an asymptomatic grapevine revealed a virome containing five RNA viruses and a viroid. Of these, Grapevine leafroll-associated virus 7 (GLRaV-7), an unassigned closterovirus, was by far the most prominently represented sequence in the analysis. Graft-inoculation of the infection to another grape variety confirmed the lack of...
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...
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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, Sergei A. Filichkin, Samuel E. Fox, Pankaj Jaiswal, Kira S. Makarova,
EugeneV. 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...
Expansive soils in Eugene, Oregon present a problem to
residents, consultants, contractors, and the city government. During
the years 1977 to 1979, the nature and extent of the problem was
identified, including an outline of the local occurrence of expansive
soils and possible engineering solutions to the most often encountered...
A steady-state computer simulation was developed for the
Chemico Urea Process which is owned and operated by Reichhold
Chemicals, Inc., St. Helens, Oregon. The DISCOSSA executive system
was used to process information input and output and to automatically
converge the complex recycle calculations in this process.
The models developed in...
N-ary relationships, which relate N entities where N is not necessarily two, are omnipresent in real life. In this thesis, we develop a visualization technique for N-ary relationships.
First, we propose a visual metaphor that utilizes vertices and polygons to represent entities and N-ary relationships. Based on this visual metaphor,...
A generalized modeling system was developed for digital computer
simulation of the pharmacodynamic response of selected chemicals
introduced into mammalian systems. The modeling system is based on
the compartmental approach used extensively in pharmacodynamic studies
in which the mammal is assumed to be subdivided into compartments
which interact by means...
Analysis, visualization, and design of vector fields on surfaces have a wide variety of major applications in both scientific visualization and computer graphics. On the one hand, analysis and visualization of vector fields provide critical insights to the flow data produced from simulation or experiments of various engineering processes. On...
3D symmetric tensor fields have a wide range of applications, such as in solid and fluid mechanics, medical imaging, meteorology, molecular dynamics, geophysics and computer graphics. There has been much research carried out in this field, yet our knowledge of the tensor field is still at its initial stage to...
A comparative study of three six-axis force sensors selected after an extensive literature survey is presented. A sensor to measure ground contact force at each foot of a walking machine is recommended.
Principles of force sensing are reviewed and characteristics of sensing elements are discussed. Results of simulation of three...
Merk's series solution to the momentum equation for steady
two-dimensional or axisymmetrical constant-property laminar
boundary layer flow was examined. Solutions were obtained to the
differential equations associated with the second term in the series.
Calculations using this series were made, and it was found to be unsatisfactory
because the second...
Fluid simulation is an interesting research problem with a wide range of applications including mechanical engineering, special effects in movies and games, and scientific simulation. Due to the complex nature of typical fluid flow equations, there are circumstances where a full volumetric fluid simulation may not be necessary to generate...
Asymmetric tensor fields are useful for understanding fluid flow and solid deformation. They present new challenges, however, for traditional tensor field visualization techniques such as hyperstreamline placement and glyph packing. This is because the physical behavior of tensors inside real domains where eigenvalues are real is fundamentally different from the...
Machine Vision has been extensively applied in industry.
This thesis project, which originated with a local food
processor, applies a vision system to inspection of packages
for cosmetric errors. The basic elements and theory of the
machine vision system are introduced, and some image
processing techniques, such as histogram analysis,...
Transportation infrastructure provides a vital service for the functionality of a
city. The efficient design of road networks poses an interesting topic in computer
science for digital content developers. For civil engineers, the visualization of
analysis results on infrastructure both efficiently and intuitively is crucial. The
following contributions are made...
Many applications in computer graphics and geometry processing rely on the ability to
locally orient 2D and 3D entities on a surface, or inside a volume, such as the sinusoidal
kernels in Gabor noise, the color and geometry textures in pattern synthesis, and the
finite elements in remeshing. In these...
Automatic painterly rendering systems have been proposed but they opted for selecting a single style to generate paintings from images, which lacks the ability of creatively using multiple styles to focus important objects and deemphasize unimportant part of the scenes. We provide a multi-style painting framework to
address this issue...
The first part of this work presents an executive system for
steady state process systems analysis. The executive is developed
to promote maximum flexibility, generality and a high degree of
man-machine interaction by allowing the user to write a Fortran
main calling program which permits special logic and control to...
Most flexible manufacturing systems (FMS) presently in use have generated only modest productivity increases in proportion to capital in vested in the process, or they have not been favorably reviewed when compared to the investment costs of other improved manufacturing systems. This thesis presents a simulator program which will assist...
The asymptotic convergence acceleration method used in steady
state process simulation is examined in detail, and a criterion is
developed to decide when it should be applied. The criterion is related
to the rate of convergence of each variable and does not require any
prejudgment of its tolerance level by...
The gradient of a velocity vector field is an asymmetric tensor field which can provide critical insight that is difficult to infer from traditional trajectory-based vector field visualization techniques. I describe the structures in the eigenvalue and eigenvector fields of the gradient tensor and how these structures can be used...
The importance of data visualization is becoming increasingly more substantial to the field of optimization and engineering design where a carefully designed visualization of the data on decision parameters (i.e Decision Space) and performance functions (i.e Objective Space) is critical to the success of the decision making process.
One of...
Branched covering spaces are a mathematical concept which originates from complex analysis and topology and has found applications in tensor field topology and geometry re-meshing. Given a manifold surface and an N-way rotational symmetry field, a branched covering space is a manifold surface that has an N-to-1 map to the...
An advanced laboratory interfacing capability was developed
for the Real-Time Digital Computer Laboratory in the Chemical
Engineering Department. A stationary interfacing unit located
beside the computer mainframe and two small remote units were
designed, developed and thoroughly tested. These interfacing
units permit experiments with a wide variety of analog and...
The purpose of this study was to investigate one individual difference,
i.e., rate of response, and the effect on student performance
when teachers recognize this difference. Using disadvantaged third
grade students as subjects, three null hypotheses were formulated as
follows:
1. Slow responding accurate students' (Group LH) scores will
show...
This study employed ethnographic methodology to investigate and record the post-camp, pre-assimilation period of Laotian refugees.The primary goal was to document the special problems and experiences of the Laotian population as they attempted to adjust to new roles and expectations within mainstream North American society.Oral histories and biographical statements focused...
Potential water scarcity and drought conditions are predicted in and around Eugene, Oregon due to decreased snowpack and subsequent decreased snowmelt in the Western Cascade Mountains. This phenomenon was triggered by a long-term trend of warmer winters scientifically linked to global climate change patterns (Dalton et al. 2013). Numerous stakeholders,...
Expert systems have been suggested as a solution
for difficult problems, including FMS scheduling. As
one of the aspects of artificial intelligence (AI), expert
systems have achieved considerable success in recent
years in medical science, chemistry, and engineering.
However, building an expert system is a difficult
task, the most crucial...
Flow separation is an important phenomenon in fluid dynamics because of the effect it has on lift and drag on immersed bodies. Areas of swirl within a separated flow region may have a distinct effect on the surface forces, modifying the lift and drag characteristics. A correlation between the passage...
Willamette Valley wetland and upland prairies are some of the most endangered ecosystems in the United States, and provide habitat for many federally listed species. These are dynamic systems, subject to ecological succession and invasion by aggressive non-native species, and require active management to maintain management goals. This is true...
Willamette Valley wetland and upland prairies are some of the most endangered ecosystems in the United States, and provide habitat for many federally listed species. Because these are dynamic systems, subject to ecological succession and invasion by aggressive non-native species, prairies require active management to maintain management goals. This is...
A method by which barrier heights in potential functions
hindering internal rotation in organic molecules can be obtained solely
from thermal data for the solid phase is studied. The observed
heat capacities are analyzed in terms of contributions from the lattice
vibrations, the intramolecular vibrations, the expansion of the lattice,...
Tensor mathematics provides a powerful language to visualize and analyze physical phenomena. In the last three decades, tensors have been used in various application areas. The visualization and analysis of tensors fields have seen much advance, both in 2D and 3D. However, the physical interpretations of the topological analysis are...
Seed size, abundance, viability, dormancy, and germination requirements strongly influence plant establishment and therefore are important considerations in restoration of native vegetation. These characteristics provide criteria for selection of suitable species, development of collection and pretreatment methods, and determination of seeding densities. The first set of objectives of this study...
A program has been written to investigate the
dynamics of robot manipulators during task execution.
The program simulates robot motion along a path specified
by the user. A smooth trajectory is generated by
interpolation in joint space. Forces and torques on
actuators are calculated at intermediate points, using a
recursive...
A method to design foot trajectory in Cartesian
coordinates for a six-leg walking machine is presented in
this thesis. The walking machine is based on the geometry of
the darkling beetle.
The walking procedure developed by Y.S. Baek is
introduced first to provide step length and leg swing time
for...
This thesis presents my research on the hardware and software for
control of a novel robot based on the Stewart Platform. The robot has
six actuators which must be adjusted to arrive at the desired position
of the platform. This position must be specified by six position
parameters; namely the...
This thesis presents a model of legged locomotion in
which position and velocity of body are directly controlled
by positions and velocities of feet. One central
relationship between foot acceleration, leg stroke and body
velocity is developed. Procedures for determining all
parameters of a step sequence including periods of constant...
This thesis presents a control system for a walking
machine leg. The leg is representative of one of the six
legs required for a proposed walking machine based on the
geometry of the darkling beetle.
Each of the three joints is controlled by a DC servo
motor mounted to the...
This thesis presents a discussion of motion of a six-legged walking
machine following removal of one leg constraint. To take a step, one leg
must be lifted and placed at some other position. As soon as the constraint
provided by the leg is removed, however the machine begins to fall....
This thesis investigates a simple dynamic model of the hind leg
of a beetle during initiation of a step. The primary assumption was
that the full load of the body was carried on the hind leg during
this time. That is, the only forces on the body were that of...
This thesis examines the influence on range-of-motion
of beetle body of changes in leg segment
parameters. From beetle's leg orientation, influence of
the following leg segment parameters are investigated:
coxa length, coxa twist and body-coxa joint.
Kinematic equations are derived for legs of the
beetle. Roots of quartic polynomials obtained...
There are many situations in which contact between two
bodies is at a single point so there can be no tensile
(force). This form of contact only provides a single degree
of restraint, and is defined as a unidirectional point
contact. The analysis of Reuleaux shows that four suitably
placed...
Willamette Valley wetland prairies are some of the most endangered ecosystems in the United States, and provide habitat for many federally listed species (Wilson et al. 1993, Noss et al. 1995, USFWS 2000, Schultz et al. 2003). A rigorous program of ecosystem restoration can protect and enhance wetland plants, animals,...
A total of 902 plasma samples from the Rambouillet, Targhee, Columbia, Lincoln, and Suffolk breeds of sheep were analyzed for transferrin type by disc electrophoresis. Six transferrin types, Tf[superscript A], Tf[superscript B], Tf[superscript C], Tf[superscript p], Tf[superscript E], and Tf[superscript P], were found in the Rambouillet, Targhee, and Columbia breeds...
Wetland prairies of the Willamette Valley, among the rarest of Oregon’s ecosystems, are threatened by invasion of woody species and non-native pest species. Because fire has been important in maintaining Willamette Valley prairies for at least 1000 years, prescribed burning is a top choice of managers for preventing encroachment of...
Given k terminal pairs (s₁,t₁),(s₂,t₂),..., (s[subscript k],t[subscript k]) in an edge-weighted graph G, the k Shortest Vertex-Disjoint Paths problem is to find a collection P₁, P₂,..., P[subscript k] of vertex-disjoint paths with minimum total length, where P[subscript i] is an s[subscript i]-to-t[subscript i] path. As a special case of the...
Traditional application of Voronoi diagrams for space partitioning creates Voronoi regions, with areas determined by the generators’ relative locations and weights. Especially in the area of information space (re)construction, however, there is a need for inverse solutions; i.e., finding weights that result in regions with predefined areas. In this thesis,...
An investigation of Mn uptake by five-day-old excised barley
roots revealed that a metabolically-mediated process was involved.
In short-term experiments, the rate of Mn absorption was comparable
to that of the macronutrient cations. Like other metabolically
absorbed cations, the Mn absorption rate was a direct function of
the ambient concentration...
Metropolitan areas today must dispose large volumes of
sewage sludge produced during the wastewater treatment process.
This research was conducted to study the effect of large applications
of municipal sewage sludge on (a) the distribution of N and trace
elements (Cd, Cr, Cu, Mn, Ni, Zn) in the soil profile,...
This thesis addresses numerical simulation of flow maldistribution in microchannels. Microchannels are often associated with two phase-flows which can generate many problems such as plugging the channel or perturbing the flow. In this study we have used CFD and fully resolved technique to simulate what would happen in the case...
More than half of the recognized genera of positive strand RNA viruses employ polyprotein processing as one of the strategies for their genome expression. Normally, this processing is mediated by virus-encoded proteinases that belong to the trypsin-like or papain-like family. In particular, papain-like, leader proteinases were found in diverse families...
Beet yellows virus (BYV) is a filamentous, positive-strand RNA virus that belongs to the family Closteroviridae. BYV particles encapsidate a 15.5 kb RNA and posses complex polar architecture. A long virion body is formed by the major capsid protein(CP), whereas the minor capsid protein (CPm) assembles a short tail that...
One goal of this environmental education curriculum is that students will gain an appreciation of Willamette Valley wetland prairies, a threatened ecosystem, and will gain an understanding of the importance of protecting these wetlands. A second goal is that students will see first-hand the processes involved in conducting scientific field...
To better understand the extreme local amplification of tsunami, the experimental investigation on counter-propagating solitary wave collisions over a horizontal bottom was conducted using the optical measurement techniques: Particle Image Velocimetry (PIV), and Laser Induced Fluoresce (LIF). Head-on collisions and oblique collisions of equal-amplitude as well as unequal-amplitude waves were...
The Salem and Eugene-Springfield Urban Areas are faced with the
task of managing the flood plain lands which lie near them. In
the past, flood plain usage was not regulated and many dollars worth
of damage has occurred to land and structures. This type of thinking
is now changing, and...
Published January 1946. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalog
This thesis presents a method for determining the
kinematic geometry of arthropod legs. A kinematic
description makes possible the analysis of arthropod leg
motion, as a prelude to investigating how various arthropod
species are able to negotiate diverse terrains. Such
knowledge will aid in design of legged vehicles.
The focus...
The gas absorption due to the entrainment effect of a plunging,
liquid, turbulent jet was studied.
The chemical system of carbon dioxide and water was chosen to expand the limited work already done
in this field.
The effects of jet diameter, jet Reynolds number, jet
Weber number, jet length and...
An all-glass gas chromatograph was developed for the analysis
of corrosive metal halides. Included in the apparatus is a new liquid
sampling system designed for fast repetitive sampling of corrosive
liquids in an inert atmosphere. A flame photometer detector was developed
to permit the detection of corrosive solutes in the...
The purpose of this study was to investigate the effects of
logging on the productivity, structure and biomass of a periphyton
community developed in mountain streams. The three streams used
in this investigation were located in the coast range of Lincoln
County, Oregon. They were selected for similarity of habitat,...
Annual ryegrass (Lolium multiflorum) is a major seed crop
in the Willamette Valley of Oregon. Persistent crop diseases have
necessitated annual field burning to protect future crops. This practice,
while very effective for disease eradication, produces large
quantities of air polluting smoke in the valley and a general wastage
of...
The Gran Chichimeca is a North American area extending from
the Tropic of Cancer to the south to the thirty-eighth parallel in
the north, thus embracing northern Mexico and the American Southwest.
The rise of the great mesoamerican civilizations to the south
of the Gran Chichimeca and the consequent pressure...
Latinos are less likely to be civically involved in their community than any other minority group, despite the fact that they are the biggest minority in the United States. A great concern exists over ways to effectively promote and improve this group’s participation in their community’s decision-making process [or civic...
An important problem in computer graphics is to determine where contour lines and ridges appear in a surface constructed from a triangle mesh. In this presentation we will investigate a new answer to this problem – the horizon measure. The horizon measure determines the likelihood of contour lines to appear...