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 & Climate change. The organization has 28192 authors who have published 64044 publications receiving 2634108 citations. The organization is also known as: Oregon Agricultural College & OSU.

Genome-Wide Analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 Pathway in Arabidopsis Reveals Dependency on miRNA- and tasiRNA-Directed Targeting

Abstract: Posttranscriptional RNA silencing of many endogenous transcripts, viruses, and transgenes involves the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 (RDR6/DCL4)-dependent short interfering RNA (siRNA) biogenesis pathway. Arabidopsis thaliana contains several families of trans-acting siRNAs (tasiRNAs) that form in 21-nucleotide phased arrays through the RDR6/DCL4-dependent pathway and that negatively regulate target transcripts. Using deep sequencing technology and computational approaches, the phasing patterns of known tasiRNAs and tasiRNA-like loci from across the Arabidopsis genome were analyzed in wild-type plants and silencing-defective mutants. Several gene transcripts were found to be routed through the RDR6/DCL4-dependent pathway after initial targeting by one or multiple miRNAs or tasiRNAs, the most conspicuous example of which was an expanding clade of genes encoding pentatricopeptide repeat (PPR) proteins. Interestingly, phylogenetic analysis using Populus trichocarpa revealed evidence for small RNA-mediated regulatory mechanisms within a similarly expanded group of PPR genes. We suggest that posttranscriptional silencing mechanisms operate on an evolutionary scale to buffer the effects of rapidly expanding gene families.

Incorporating varying test costs and fault severities into test case prioritization

Abstract: Test case prioritization techniques schedule test cases for regression testing in an order that increases their ability to meet some performance goal. One performance goal, rate of fault detection, measures how quickly faults are detected within the testing process. In previous work (S. Elbaum et al., 2000; G. Rothermel et al., 1999), we provided a metric, APFD, for measuring rate of fault detection, and techniques for prioritizing test cases to improve APFD, and reported the results of experiments using those techniques. This metric and these techniques, however, applied only in cases in which test costs and fault severity are uniform. We present a new metric for assessing the rate of fault detection of prioritized test cases that incorporates varying test case and fault costs. We present the results of a case study illustrating the application of the metric. This study raises several practical questions that might arise in applying test case prioritization; we discuss how practitioners could go about answering these questions.

Fish oil supplementation and risk of ventricular tachycardia and ventricular fibrillation in patients with implantable defibrillators: a randomized controlled trial.

Abstract: ContextClinical studies of omega-3 polyunsaturated fatty acids (PUFAs) have shown a reduction in sudden cardiac death, suggesting that omega-3 PUFAs may have antiarrhythmic effects.ObjectiveTo determine whether omega-3 PUFAs have beneficial antiarrhythmic effects in patients with a history of sustained ventricular tachycardia (VT) or ventricular fibrillation (VF).Design and SettingRandomized, double-blind, placebo-controlled trial performed at 6 US medical centers with enrollment from February 1999 until January 2003.PatientsTwo hundred patients with an implantable cardioverter defibrillator (ICD) and a recent episode of sustained VT or VF.InterventionPatients were randomly assigned to receive fish oil, 1.8 g/d, 72% omega-3 PUFAs, or placebo and were followed up for a median of 718 days (range, 20-828 days).Main Outcome MeasuresTime to first episode of ICD treatment for VT/VF, changes in red blood cell concentrations of omega-3 PUFAs, frequency of recurrent VT/VF events, and predetermined subgroup analyses.ResultsPatients randomized to receive fish oil had an increase in the mean percentage of omega-3 PUFAs in red blood cell membranes from 4.7% to 8.3% (P<.001), with no change observed in patients receiving placebo. At 6, 12, and 24 months, 46% (SE, 5%), 51% (5%), and 65% (5%) of patients randomized to receive fish oil had ICD therapy for VT/VF compared with 36% (5%), 41% (5%), and 59% (5%) for patients randomized to receive placebo (P = .19). In the subset of 133 patients whose qualifying arrhythmia was VT, 61% (SE, 6%), 66% (6%), and 79% (6%) of patients in the fish oil group had VT/VF at 6, 12, and 24 months compared with 37% (6%), 43% (6%), and 65% (6%) of patients in the control group (P = .007). Recurrent VT/VF events were more common in patients randomized to receive fish oil (P<.001).ConclusionAmong patients with a recent episode of sustained ventricular arrhythmia and an ICD, fish oil supplementation does not reduce the risk of VT/VF and may be proarrhythmic in some patients.

Fluorochemical Mass Flows in a Municipal Wastewater Treatment Facility

Abstract: Fluorochemicals have widespread applications and are released into municipal wastewater treatment plants via domestic wastewater. A field study was conducted at a full-scale municipal wastewater treatment plant to determine the mass flows of selected fluorochemicals. Flow-proportional, 24 h samples of raw influent, primary effluent, trickling filter effluent, secondary effluent, and final effluent and grab samples of primary, thickened, activated, and anaerobically digested sludge were collected over 10 days and analyzed by liquid chromatography electrospray-ionization tandem mass spectrometry. Significant decreases in the mass flows of perfluorohexane sulfonate and perfluorodecanoate occurred during trickling filtration and primary clarification, while activated sludge treatment decreased the mass flow of perfluorohexanoate. Mass flows of the 6:2 fluorotelomer sulfonate and perfluorooctanoate were unchanged as a result of wastewater treatment, which indicates that conventional wastewater treatment is not...

FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar

Abstract: Annual plants grow vegetatively at early developmental stages and then transition to the reproductive stage, followed by senescence in the same year. In contrast, after successive years of vegetative growth at early ages, woody perennial shoot meristems begin repeated transitions between vegetative and reproductive growth at sexual maturity. However, it is unknown how these repeated transitions occur without a developmental conflict between vegetative and reproductive growth. We report that functionally diverged paralogs FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2), products of whole-genome duplication and homologs of Arabidopsis thaliana gene FLOWERING LOCUS T (FT), coordinate the repeated cycles of vegetative and reproductive growth in woody perennial poplar (Populus spp.). Our manipulative physiological and genetic experiments coupled with field studies, expression profiling, and network analysis reveal that reproductive onset is determined by FT1 in response to winter temperatures, whereas vegetative growth and inhibition of bud set are promoted by FT2 in response to warm temperatures and long days in the growing season. The basis for functional differentiation between FT1 and FT2 appears to be expression pattern shifts, changes in proteins, and divergence in gene regulatory networks. Thus, temporal separation of reproductive onset and vegetative growth into different seasons via FT1 and FT2 provides seasonality and demonstrates the evolution of a complex perennial adaptive trait after genome duplication.