Markov chains have long been used to sample from probability distributions and simulate dynamical systems. In both cases we would like to know how long it takes for the chain's distribution to converge to within varepsilon of the stationary distribution in total variation distance; the answer to this is, called...
The method of gas-phase electron diffraction is a very useful tool for determining
the geometry of a molecule in the gas-phase to a high degree of accuracy. In this thesis,
the structures of tropone and tropolone, which are similar molecules that are both based
on a 7-carbon ring, were investigated...
Blue-striped Brodiaea or Leach's Brodiaea (Triteleia hendersonii Greene var. leachiae [Peck] Hoover, or Brodiaea hendersonii Wats. var. leachiae ) Lily Family (Liliaceae) is found in the foothills of the Siskiyou Mountains of Curry, Coos and Josephine Counties of southwestern Oregon. It is occurs in a variety of habitats including meadow...
The data is a JSON format file containing the position, velocity, and fish identifier data for 300 golden shiners in a shallow (depth of 4.5 to 5 cm) rectangular water tank (2.1 by 1.2 meters). There are 5000 individual frames (samples of position and velocity) corresponding to video taken at...
In Islam, paying and receiving interest is prohibited based on the belief that money should not be a commodity that is “rented” out; instead, Islamic lending structures arrange loans on an equity basis. This work examines the historical origins of interest prohibition and explains how different Islamic financial products provide...
One of the distinctive features of mitochondria is that they have their own DNA. When compared to nuclear DNA, it is known that mitochondrial DNA (mtDNA) not only has a much higher rate of spontaneous mutation, but also arises from metabolically distinct precursor pools. Others from our laboratory have demonstrated...
Shallow landslides are destructive natural hazards that result in widespread losses, both of infrastructure and lives, throughout the world. To help mitigate the impact of landslide hazards, they are commonly characterized across a regional scale by (1) their location and likelihood using susceptibility maps, (2) their magnitude and frequency using...
For more than 35 years we have known that the accuracy of DNA replication is controlled in
large part by the relative concentrations of the four canonical deoxyribonucleoside 5'-triphosphates (dNTPs) at the replisome. Since this field was last reviewed, about eight years ago,
there has been increased understanding of the...
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...
We investigate several aspects of the numerical solution of the radiative transfer
equation in the context of coal combustion: the parallel efficiency of two commonly used
opacity models, the sensitivity of turbulent radiation interaction (TRI) effects
to the presence of coal particulate, and an improvement of the order of temporal...
Cancer was recognized as a genetic disease at least four decades ago, with the realization that the spontaneous mutation rate must increase early in tumorigenesis, to account for the many mutations in tumor cells as compared with their progenitor normal cells. The genetic basis for cancer was established also from...
Full Text:
(2001).
21. Fairman, J. W., et al. Structural basis for allosteric regulation of human
Vineyards in Oregon’s Willamette Valley are predominately planted to perennial grass cover in the alleyways of vineyards. This grass cover is grown to increase worker and equipment traction, as well as reduce erosion and manage vine vegetative vigor. However, with increasing frequencies of drought and warming temperatures, the use of...
The electrical conductivity of the pyromagmas from the Northeast
Crater of Mount Etna, Sicily was measured over the temperature
range 1032°C to 1071°C and over the frequency range 1 kHz to
400 kHz. Measurements were made using a four-terminal Wenner
array in conjunction with a Wavetek Model 110B portable signal...
This study was an ethnographic case study of a
Vietnamese unaccompanied minor in a post secondary setting.
There were two guiding questions for the study: (1) How
does the subject perceive language as it relates to
educational experience? (2) What kinds of observable
personality, cognitive, or affective factors have
contributed...
Ornithology is an exciting field with novel research emerging everyday. Researchers in bioacoustics often spend hours within the wilderness recording bird calls to analyze later in their lab. The burden of sifting through hours of audio recordings from the field continues to remain a time-consuming and manual task, despite the...
Background: The use of high-Z nanoparticles as radiation dose enhancers has been researched thoroughly over the past decade. High-Z nanoparticles introduced to a medium increase the probability of photoelectric absorption. This leads to an increase in the production of short range characteristic and Auger electrons and, thus, local radiation dose....
The intent of this work is to extend Implicit Monte Carlo Diffusion (IMD)[Gen.
2001] to account for frequency dependence and to incorporate the difference formulation[Szo. 2005] as a source manipulation variance reduction technique. This
work shows the derivation of the probabilities and the associated proofs which
govern the frequency dependent...
Nearest-neighbor resampling is a common procedure used by cartographers to
reproject raster data sets. This type of resampling is useful because it retains the data
from the original raster data set. However, during nearest-neighbor resampling some of
the original data will be lost as it is reprojected, while other data...
The purpose of this study was to determine the attitudes of
three Oregon State Penitentiary minority inmate groups -
Blacks, Hispanics, and Native Americans - towards the Activities
Programs as a rehabilitative tool. Two other purposes
were to (1) determine significant differences among group
attitudes, and (2) determine the degree...
Approximately one quarter of America's students
leave school prior to graduation. Teaching practices
need to be examined if schools are to effectively deal
with the student population. at highest risk of dropping
out. The purpose of this study was to investigate the
attending behaviors high school teachers directed to
students...
Baculoviruses comprise a diverse group of pathogens
infectious for members of the insect orders Lepidoptera, Hymenoptera
and Diptera. Of the three subgroups, two (subgroup A, nuclear
polyhedrosis virus (NPV) and subgroup B, granulosis virus (GV) are
occluded in a crystalline protein structure while the remaining
subgroup (subgroup C, non-occluded virus)...
This study examines the effects of corporate social responsibility (CSR) on merger and
acquisitions (M&A). Using data from Kinder, Lyndeberg, and Domini (KLD) Research
Analytics and Thomson’s Securities Data Corporation’s (SDC) Platinum Database, we
empirically test if CSR scores effect a firm’s propensity to pursue M&A activity.
Specifically, I examine...
Motivation: Many robots such as legged robots and prosthetic hands/arms are designed to interact with uncertain and time-varying environments to accomplish their tasks.
Observations on humans and animals during their daily tasks suggest that they adapt their leg compliance while traversing with different velocities on different grounds and adjust their...
The enzymes of dNTP synthesis in T4 infection associate to form a multienzyme complex, the T4 dNTP synthetase complex, facilitating the flow of metabolites en route to dNTPs, and their subsequent flow into DNA. Study of protein-protein interactions helps one to understand how the enzymes in the complex are organized...
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...
It is well known that the mitochondrial genome has a much higher spontaneous mutation rate than the nuclear genome. mtDNA mutations have been identified in association with many diseases and aging. mtDNA replication continues throughout the cell cycle, even in post-mitotic cells. Therefore, a constant supply of nucleotides is required...
With respect to a multienzyme complex of deoxyribonucleoside triphosphate (dNTP) synthesis somehow juxtaposed with DNA replication sites, our laboratory has demonstrated the existence of a multienzyme complex in T4-infected E. coli, named the T4 dNTP synthetase complex, but the idea of direct linkage of dNTP synthesis to DNA replication and...
Ribonucleotide reductase is a remarkable enzyme that catalyzes the rate-limiting
step in the synthesis of the 2'-deoxynucleoside triphosphates. The intent of this project
was to characterize the ribonucleotide reductase encoded by the orthopoxvirus,
vaccinia. The first objective was to study the structural and functional features of the
viral small subunit...
Structural health monitoring (SHM) systems perform automated non-destructive damage detection and characterization for a variety of large structures including civil structures such as bridges and aerospace structures such as aircrafts and space vehicles. The goals of SHM include preventing catastrophic structural failures, increasing reliability, reducing maintenance costs, and increasing the...
This dissertation describes an investigation of DNA precursor supply for mitochondrial and nuclear DNA synthesis in HeLa cells and Mouse L-cells. HeLa cells were used for the quantitation of cellular and mitochondrial deoxyribonucleoside triphosphate (dNTP) and ribonucleoside triphosphate (rNTP) pools and of changes in pools in response to treatment with...
Ribonucleoside diphosphate reductase (RR) from vaccinia virus was recently cloned and overexpressed rn Escherichia coli. The amino acid sequence identities of the small and large subunits between the mouse and the vaccinia virus reductase are approximately 80 and 72 percent, respectively. In addition, vaccinia virus RR displays similar complex allosteric...
Vaccinia virus-infected animal cells have been used to
study the interactions between the replication of
deoxyribonucleic acid (DNA) and the biosynthesis of its
nucleotide precursors. Some antimetabolites that inhibit
DNA replication have as their targets enzymes of nucleotide
biosynthesis. Furthermore, the disruption of nucleotide
metabolism can alter the fidelity of...
Ribonucleotide reductase is an important enzyme in the control of
DNA replication within the cell. Ribonucleotide reductase exerts its
control through enzymatic reduction of nucleoside diphosphates. The
bacteriophage T4 enzyme is an example of the class of iron-requiring
reductases which also includes E. coli and mammalian ribonucleotide
reductases. The two...
Electroencephalogram (EEG) signals have recently gained attention to classify associated hand movement. This is particularly useful for amputees with prostatic hands or people who are unable to move their hands voluntarily. Among the decoding algorithms used to classify hand movements are support vector machines and multilayer perceptron networks. In this...
The dihydrofolate reductase gene of bacteriophate T4
has been investigated at the structural level to elucide the
unusual regulation of expression of this gene and possible
evolutionary relationships between the ohage and drug resistance
factors-encoded dihydrofolate reductases (DHFR).
A 1.1-kilobase-pair restriction fragment of the T4
multiple mutant dec8 containing frd,...
Bacteriophage T4 gene 42 encodes dCMP hydroxymethylase, an
enzyme unique to the deoxyribonucleotide metabolism of T-even
bacteriophages. To study biochemical and biophysical properties of
the enzyme, as well as the interaction of dCMP hydroxymethylase with
other DNA precursor biosynthetic enzymes in vitro, availability of large
amounts of the enzyme is...
Vaccinia virus infected monkey kidney cells had been previously shown
to have an increased ribonucleoside diphosphate reductase (RR) activity. DNA
from mutant virus resistant to hydroxyurea were digested with restriction
endonucleases and were shown to have substoichiometric amounts of the Hind
III F fragment. Additional information from Southern blotting experiments...
The effects of oligoribonucleotides of identical or similar sequences to a
ribosomal protein binding site, specifically S8, on prokaryotic 30S ribosomal assembly
were investigated in Escherichia coli. The oligoribonucleotides were expected to bind to
the target protein S8 and block its incorporation into the 30S subunit, resulting in a nonfunctional...
The first committed step in DNA biosynthesis occurs by direct reduction of
ribonucleotides. This reduction is catalyzed by ribonucleotide reductase (RNR), an
enzyme which uses a unique radical mechanism to facilitate the transformation. All four
DNA precursors are synthesized by a single enzyme. Therefore, an intricate pattern of
regulation has...
Significance: Movement intent decoding algorithms can interpret human bioelectrical signals to control prosthetic limbs with many degrees of freedom (DOFs). This work involves decoding volitional movement intent from surface electromyogram (sEMG) signals to control prosthetic arms. To train these algorithms, patients flex their muscles to “follow” a movement prompt, and...
Movement intent decoders, which interpret volitional movement intent from human bioelectric signals, can be incorporated into modern neuroprostheses to offer people living with limb loss or paralysis the potential to regain their lost motor control. Machine learning methods have become the research standard for continuous decoders with high degrees of...
Investigators have been studying an aggregate
containing enzymes of deoxyribonucleoside triphosphate
biosynthesis in T4-phage infected bacteria. They suggest
that it behaves as an organized complex, efficiently
channeling DNA precursors to the replication apparatus.
Previous work has suggested that about 10 enzyme
activities remain associated through several fractionation
steps. This multi-enzyme...
In order to maintain genetic stability in eukaryotes, tight regulation of the relative sizes of deoxyribonucleoside triphosphate (dNTP) levels inside the cell is essential for optimal fidelity of DNA replication. Ribonucleotide reductase (RNR) is the enzyme responsible for proportional production of DNA precursors. Studies on regulation of this enzyme, the...
Loss of a limb can severely impact everyday way of life. Prosthetics provide a way to return functionality to the user and improve quality of life. However, most prosthetic systems currently available in the market lack sensory feedback making them comparatively more difficult to use resulting in prosthetic abandonment. Therefore,...
There are nearly two million limb amputees living in the United States of America. Loss of limbs results in profound changes in one's life. However, the underlying neural circuitry and much of the ability to sense and control movements of their missing limb is retained even after limb loss. This...
Although the Escherichia coli host has almost all of the enzymes necessary to
synthesize nucleotides needed for bacteriophage T4 DNA replication, phage genes
expressed early in infection encode enzymes for de novo DNA precursor biosynthesis
and salvage from degraded host DNA. Eight early enzymes and two host enzymes
comprise the...
Although the synthesis of DNA precursors is
closely coordinated with DNA replication, it is still
not clear whether deoxyribonucleoside triphosphates
(dNTPs) influence DNA replication independently of
their interactions with DNA polymerase catalytic sites.
In an effort to understand the extent to which rate and
fidelity of DNA replication are regulated...
A rapid nuclear isolation technique was adapted in
order to examine the question of DNA precursor
compartmentation in mammalian cells. By using this method
a reproducible proportion of the cellular nucleotides
remained associated with the isolated nuclei.
Examination, at several different cell densities, of
exponentially growing HeLa cells showed that...
A crucial factor in determining the accuracy of DNA replication is
maintenance of a balanced supply of deoxyribonucleoside triphosphates
(dNTPs) at replication forks. Perturbation of dNTP biosynthesis can
induce dNTP pool imbalance with deleterious genetic consequences,
including increased mutagenesis, recombination, chromosomal
abnormalities and cell death. Using the T4 bacteriophage system,...
Intracellular dNTP pool sizes are highly asymmetric, with dGTP usually comprising 5 to 10% of the sum of the dNTP pools. The work presented in this dissertation addresses the question of whether the underrepresentation of dGTP is related to its potential to be oxidized by reactive oxygen species. 8-oxo-guanine is...
Imbalanced deoxyribonucleoside triphosphate (dNTP) pools are mutagenic for DNA synthesis in both intact cells and cell-free replication systems. Almost certainly, such mutagenesis involves competition between correctly and incorrectly base-paired precursors at replication sites. However, there are certain differences between the intact cell and cell-free systems that do not always allow...
The ability to faithfully replicate DNA is dependent upon the maintenance
and regulation of its precursors, the deoxyribonucleoside triphosphates.
Enzymes encoded by the bacteriophage T4 have been widely used as models
of biochemical processes. A body of evidence supports the concept that the
bacteriophage T4 enzymes involved in deoxyribonucleotide biosynthesis...
The faithful replication of DNA depends on the appropriate balance of DNA precursors. From studies conducted in bacteriophage T4, models for deoxyribonucleotide biosynthesis producing pools appropriate for DNA replication have made it possible to understand more complex systems. A portion of that body of evidence supports the concept that deoxyribonucleotide...
Red fir (Abies magnifica) is a high elevation conifer generally growing between an altitude of 1,400 and 2,700 meters. In California, red fir grows in the Sierra Nevada, the Klamath Mountains, the eastern edges of the northern Californian Coast Ranges, and in the southern Cascades. Red fir commonly grows in...
Ribosomes are multicomponent macromolecular particles and
are essential for the survival of cells in all organisms. The ribosome's
universal function is to catalyze polypeptide synthesis through
translation of mRNA transcripts. Ribosomes from Escherichia coli,
eubacterial organisms, have a sedimentation coefficient of 70S and are
composed of 30S and 50S ribonucleoprotein...
Vaccinia virus encodes at least eight proteins that are modified post-translationally by the addition of a 16-carbon saturated fatty acid through thioester linkage to cysteine residues. This is referred to as palmitylation of proteins. The purpose of this work was to gain an understanding of palmitylation, focusing on what defined...
The accuracy of DNA synthesis depends on the accuracy of the polymerase as well as the quality and concentration(s) of the available 5'-deoxynucleoside-triphosphate DNA precursors (dNTPs). The relationships between dNTPs and error rates have been studied in vitro, but only limited insights exist into these correlations during in vivo replication....
Saccharomyces cerevisiae contains three NAD⁺/NADH kinases, one of which is localized in
mitochondria and phosphorylates NADH in preference to NAD⁺. Strand et al (Euk. Cell
2:809 (2003)) reported that a yeast mutation in POS5, which encodes the mitochondrial
NADH kinase, is a mutator, specific for mitochondrial genes. Because of the...
At the 2001 WTO Ministerial Conference in Doha, World Trade Ministers called for improved disciplines on fisheries subsidies, given the perceived impact of these subsidies in contributing to overfishing, overcapacity and other trade distortions. Subsequent deliberations have sought to determine which fisheries subsidies should be disciplined under the WTO framework....
As part of the Willamette Basin Geographic Initiative Program, the Environmental Protection Agency (EPA) funded The Nature Conservancy of Oregon to inventory, classify, and map native wetland and riparian plant communities and their threatened biota in the Willamette Valley. Between October 1994 and September 1996, we evaluated 172 wetland and...
As scaling of silicon (Si) based devices approaches fundamental limits, thin film metal-insulator-metal (MIM) tunnel diodes are attracting interest due to their potential for high speed operation. Because operation of these devices is based on tunneling, electrode / interfacial roughness is critical. Recently, it was shown that combining ultra-smooth bottom...
Mismatch repair is one of the mechanisms by which cells ensure genomic
stability. Deficiencies in mismatch repair (MMR) increase mutation rates and cancer
risks. In the well-characterized methyl-directed Escherichia co/i system, MMR is
initiated by MutS, Mut L, and MutH proteins. The single MutS protein and the
single MutL protein...
The effect of acetylcholine on vascular adrenergic
neuroeffector transmission was investigated. Caudal
arteries of rats were isolated and their responses to
electrical stimulation of the adrenergic nerves and/or
acetylcholine were monitored. Acetylcholine had no
effect on the basal perfusion pressure or the vascular
response to norepinephrine in arteries from non-stressed...
This classification lists the native plant associations known to occur in Oregon, and includes both successional and climax vegetation types that were an important part of the presettlement landscape of Oregon. It serves as an index to the diversity, distribution and relative rarity of the state's native plant associations, and...
Deoxyribonucleoside triphosphate pools in mammalian mitochondria are highly
asymmetric, and this asymmetry probably contributes toward the elevated
mutation rate for the mitochondrial genome as compared with the nuclear
genome. To understand this asymmetry, we must identify pathways for synthesis
and accumulation of dNTPs within mitochondria. We have identified
ribonucleotide reductase...
We examine the contribution of when-issued trading to price discovery and underpricing in the Indian IPO market. Besides the when-issued trading, there exists IPO grading, analyst recommendation, group affiliation, and the subscription rates in the bookbuilding process. We examine the impact of these activities and find three sequential factors that...
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...
Transmit beamforming is an important technique employed to improve efficiency and signal quality in wireless communication systems by steering signals towards their in- tended users. It often arises jointly with the antenna selection problem due to various reasons, such as limited number of radio frequency (RF) chains and energy/resource effi-...
DNA mismatch repair (MMR) is an evolutionarily conserved process used by cells to decrease mutation rates, thereby increasing genetic stability and reducing cancer risk. Germline mutations in the MMR gene MLH1 have been identified in Lynch Syndrome patients, and in many cases are suspected but not confirmed as causative for...
Fresh ripe, cantaloupes were processed into juice and
juice concentrate. Processing trials were conducted on
fresh and frozen fruits with and without rind. The effects
of maceration enzymes and fining agents on yield and quality
were investigated. Compositional measurement included
°Brix, pH, titratable acidity, formol values, ascorbic acid
content, total...
The attachment of myristic acid to the N-terminal glycine residue of many
eukaryotic and viral proteins is often essential for the acquisition of the protein's
biological activity. Vaccinia virus (VV), the prototype member of the Poxviridae,
expresses several myristylated proteins during the course of infection. Only one of
these proteins,...
Vitamin C is an essential component of the human diet. Uptake of vitamin C in the cell is regulated by the function of sodium-dependent vitamin C transporters (SVCTs). SVCT1 (encoded by the SLC23A1 gene) is expressed in the colon, liver and kidney, where it plays a vital role in determining...
The work in this thesis has provided conclusive genetic evidence
that "panhandle" intermediates form during adenovirus replication.
Adenovirus chromosomes lacking 51 by from their left -hand termini
are infectious and capable of regenerating the missing origin
sequence. Yet if an entire inverted terminal repeat is removed, the
adenovirus chromosome is...
Replication of plasmid molecules containing either a left-end or a
right-end adenovirus origin was investigated. When the plasmids were
linearized to expose their respective adenovirus termini, mixed, and
transfected with helper adenovirus DNA into the human 293 cell line, a
new molecule was detected. The new molecule was the size...
Vaccinia virus (VV) is a large DNA virus belonging to the Orthopoxvirus
family. The viral replicative life cycle takes place solely within the cytoplasm
of a mammalian host cell. The VV genome contains 196 open reading frames
which are expressed in a highly regulated and temporal fashion in order to...
A study of malolactic bacteria of the Leuconostoc
genus, especially L. oenos, and their bacteriophages was
conducted. A search for the presence of infectious
bacteriophages in grapes, musts, and juices employed in
malo-lactic fermentation (MLF) was conducted; no
evidence, either physical or biological, was found for
the existence of these...
Functional polymers and proteins at interfaces and surfaces are of fundamental importance for biomaterials, biocatalysis and microreactor applications. Candida antarctica lipase B immobilized on poly-DL-tryptophan tethers showed 30x higher
specific activity in aqueous and non-aqueous media than the same enzyme adsorbed or covalently bound directly to the surface. An excess...
Exposure to polycyclic aromatic hydrocarbons such as benzo[a]pyrene (B[a]P) has been determined to be a risk factor for various forms of human cancer. PAH DNA adducts have been shown to cause mutations, but carcinogenesis is also accompanied by alterations in gene expression. Inhibiting individual cytochrome P450s could clarify the interaction...
Our objectives were to determine 1) the concentration of prostaglandin
F2α (PGF2α) in whole and extended bovine semen, 2) if concentrations of
prostaglandins in extended bovine semen are correlated to fertility, and 3) if PGF2α
administered at the time of artificial insemination would improve conception rate.
Concentration of PGF2α tended...
The evaluated nuclear data widely used in computational tools suffer from inaccuracies and large relative uncertainties, particularly with respect to short-lived and low-yield fission products. The existing data are often based on nuclear models, and limited experimental measurements of these fission product yields have been performed. This work seeks to...
Described herein is the synthesis of an uncharged stereoregular oligonucleotide
analog consisting of cytosine bases linked at specific intervals to a polyamide backbone
derived from (L)-glutamic acid. Preparation of this analog entailed borane reduction of
(L)- pyroglutamic acid to give optically pure lactam alcohol 9. Tosylation and alkylation
with cytosine...