Oregon State University

About: Oregon State University is a education organization based out in Corvallis, Oregon, United States. It is known for research contribution in the topics: Population & Gene. The organization has 28192 authors who have published 64044 publications receiving 2634108 citations. The organization is also known as: Oregon Agricultural College & OSU.

Development and implementation of high-throughput SNP genotyping in barley

Abstract: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.

Computational recipes for electromagnetic inverse problems

Abstract: SUMMARY The Jacobian of the non-linear mapping from model parameters to observations is a key component in all gradient-based inversion methods, including variants on Gauss–Newton and non-linear conjugate gradients. Here, we develop a general mathematical framework for Jacobian computations arising in electromagnetic (EM) geophysical inverse problems. Our analysis, which is based on the discrete formulation of the forward problem, divides computations into components (data functionals, forward and adjoint solvers, model parameter mappings), and clarifies dependencies among these elements within realistic numerical inversion codes. To be concrete, we focus much of the specific discussion on 2-D and 3-D magnetotelluric (MT) inverse problems, but our analysis is applicable to a wide range of active and passive source EM methods. The general theory developed here provides the basis for development of a modular system of computer codes for inversion of EM geophysical data, which we summarize at the end of the paper.

Baculovirus Diversity and Molecular Biology

Abstract: With the identification and characterization of a number of structural and nonstructural protein genes, advances have been made in our understanding of baculovirus structure, regulation of gene expression, and replication. Since less than 30% of the AcMNPV genome has been sequenced and characterized, the continued identification and assignment of function to baculovirus genes is perhaps the most crucial of enterprises now facing baculovirologists and is critical to the development of our understanding of the baculovirus genome and its replication. The size and diversity of baculovirus genomes appears to be strongly influenced by mobile DNA from the insect host. Also, transposon-mediated mutations of baculoviruses provide examples of functional inactivation of viral genes (FP phenotype mutations) and transcriptional activation (TE-D insertion). Another role transposable elements may play is the introduction of insect promoters and enhancers to the baculovirus genome. Since early baculovirus genes are likely transcribed in a way similar to normal insect genes, transposons that insert strong constitutive promoters or cellular enhancers near early baculovirus genes may cause mutations that are subsequently selected for. If this does occur, baculovirus early gene promoters may exhibit a great deal of variability in sequence and may resemble host promoters. Given the overall similarity between the genomes of OpMNPV and AcMNPV and the apparent absence of a region, similar to the AcMNPV HindIII-K/EcoR1-S in OpMNPV, it is intriguing to speculate that this region which contains two ORFs and the hr5 enhancer, may have been inserted into the AcMNPV genome by transposition, possibly delivering several helpful genes (35k and 94k) and a powerful enhancer. The highly repeated enhancer may have been subsequently amplified by recombination. In such a model, the acquisition of general or species-specific enhancers might influence both virulence and host range. Acquisition of general enhancers could increase the level of early gene expression, thus accelerating the cellular infection cycle and making the virus more virulent. Similarly, the acquisition of species-specific enhancers might affect host range by accelerating the infection cycle, but only in a specific host or cell type. One might therefore postulate that diversity in baculoviruses may reflect not only different selection pressures but also the diversity of mobile DNA within host insect species. Although our understanding of baculovirus diversity and molecular biology is rapidly advancing, many of the fundamental characteristics that define the unique nature of baculoviruses remain poorly understood. One fundamental feature of baculoviruses is the production of the two virion phenotypes, PDV and BV.(ABSTRACT TRUNCATED AT 400 WORDS)

The state of the art in end-user software engineering

Abstract: Most programs today are written not by professional software developers, but by people with expertise in other domains working towards goals for which they need computational support. For example, a teacher might write a grading spreadsheet to save time grading, or an interaction designer might use an interface builder to test some user interface design ideas. Although these end-user programmers may not have the same goals as professional developers, they do face many of the same software engineering challenges, including understanding their requirements, as well as making decisions about design, reuse, integration, testing, and debugging. This article summarizes and classifies research on these activities, defining the area of End-User Software Engineering (EUSE) and related terminology. The article then discusses empirical research about end-user software engineering activities and the technologies designed to support them. The article also addresses several crosscutting issues in the design of EUSE tools, including the roles of risk, reward, and domain complexity, and self-efficacy in the design of EUSE tools and the potential of educating users about software engineering principles.