Institution
Oregon State University
Education•Corvallis, Oregon, United States•
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.
Topics: Population, Climate change, Gene, Upwelling, Soil water
Papers published on a yearly basis
Papers
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TL;DR: The utility of genome skimming is demonstrated through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae) and the effect of divergence on reference-guided plastome assembly is addressed.
Abstract: Premise of the study: Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters Here we describe a genome skimming (shallow sequencing) approach for plant systematics Methods: Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae) Key results: Paired-end reads performed better than single-end reads Minimum sequencing depths for high quality rDNA and plastome assemblies were 40 × and 30 × , respectively Divergence from the reference signifi cantly affected plastome assembly, but relatively similar references are available for most seed plants Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths Nearly 160 000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC Conclusions: Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be effi ciently obtained for molecular phylogenetics studies
510 citations
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TL;DR: The deduced 466-amino acid polypeptide exhibits extensive structural and sequence homology with other receptors coupled to guanine nucleotide binding proteins, and predicts a structure of seven membrane-spanning regions distinguished by the disposition of a large cytoplasmic domain.
Abstract: A partial amino acid sequence obtained for porcine atrial muscarinic acetylcholine receptor was used to isolate complementary DNA clones containing the complete receptor coding region. The deduced 466-amino acid polypeptide exhibits extensive structural and sequence homology with other receptors coupled to guanine nucleotide binding (G) proteins (for example, the beta-adrenergic receptor and rhodopsins); this similarity predicts a structure of seven membrane-spanning regions distinguished by the disposition of a large cytoplasmic domain. Stable transfection of the Chinese hamster ovary cell line with the atrial receptor complementary DNA leads to the binding of muscarinic antagonists in these cells with affinities characteristic of the M2 receptor subtype. The atrial muscarinic receptor is encoded by a unique gene consisting of a single coding exon and multiple, alternatively spliced 5' noncoding regions. The atrial receptor is distinct from the cerebral muscarinic receptor gene product, sharing only 38% overall amino acid homology and possessing a completely nonhomologous large cytoplasmic domain, suggesting a role for the latter region in differential effector coupling.
509 citations
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TL;DR: The first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues, and novel analyses and visualisations include: ‘enrichment’ in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains.
Abstract: Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons—estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: ‘enrichment’ in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.
509 citations
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Utah State University1, University of Minnesota2, University of Oldenburg3, University of Zurich4, Iowa State University5, Oregon State University6, United States Geological Survey7, Wake Forest University8, University of Washington9, Colorado State University10, University of Queensland11, University of New Mexico12, Lanzhou University13, University of California, San Diego14, Dartmouth College15, Imperial College London16, University of Wisconsin-Madison17, University of Colorado Boulder18, United States Department of Agriculture19, Queensland University of Technology20, University of Maryland, College Park21, Yale University22, University of KwaZulu-Natal23, Agricultural Research Service24, University of St. Thomas (Minnesota)25, University of Nebraska–Lincoln26, University of Guelph27, University of Kentucky28, University of North Carolina at Chapel Hill29, University of Melbourne30, La Trobe University31, Commonwealth Scientific and Industrial Research Organisation32, Swiss Federal Institute for Forest, Snow and Landscape Research33, Open University34, Lancaster University35, Duke University36, University of California, Davis37
TL;DR: This article conducted a standardized sampling in 48 herbaceous-dominated plant communities on five continents and found no clear relationship between productivity and fine-scale (meters−2) richness within sites, within regions, or across the globe.
Abstract: For more than 30 years, the relationship between net primary productivity and species richness has generated intense debate in ecology about the processes regulating local diversity. The original view, which is still widely accepted, holds that the relationship is hump-shaped, with richness first rising and then declining with increasing productivity. Although recent meta-analyses questioned the generality of hump-shaped patterns, these syntheses have been criticized for failing to account for methodological differences among studies. We addressed such concerns by conducting standardized sampling in 48 herbaceous-dominated plant communities on five continents. We found no clear relationship between productivity and fine-scale (meters−2) richness within sites, within regions, or across the globe. Ecologists should focus on fresh, mechanistic approaches to understanding the multivariate links between productivity and richness.
509 citations
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TL;DR: The novel rise of water-column shelf anoxia in the northern California Current system highlights the potential for rapid and discontinuous ecosystem change in productive coastal systems that sustain a major portion of the world's fisheries.
Abstract: Eastern boundary current systems are among the world's most productive large marine ecosystems. Because upwelling currents transport nutrient-rich but oxygen-depleted water onto shallow seas, large expanses of productive continental shelves can be vulnerable to the risk of extreme low-oxygen events. Here, we report the novel rise of water-column shelf anoxia in the northern California Current system, a large marine ecosystem with no previous record of such extreme oxygen deficits. The expansion of anoxia highlights the potential for rapid and discontinuous ecosystem change in productive coastal systems that sustain a major portion of the world's fisheries.
509 citations
Authors
Showing all 28447 results
Name | H-index | Papers | Citations |
---|---|---|---|
Robert Stone | 160 | 1756 | 167901 |
Menachem Elimelech | 157 | 547 | 95285 |
Thomas J. Smith | 140 | 1775 | 113919 |
Harold A. Mooney | 135 | 450 | 100404 |
Jerry M. Melillo | 134 | 383 | 68894 |
John F. Thompson | 132 | 1420 | 95894 |
Thomas N. Williams | 132 | 1145 | 95109 |
Peter M. Vitousek | 127 | 352 | 96184 |
Steven W. Running | 126 | 355 | 76265 |
Vincenzo Di Marzo | 126 | 659 | 60240 |
J. D. Hansen | 122 | 975 | 76198 |
Peter Molnar | 118 | 446 | 53480 |
Michael R. Hoffmann | 109 | 500 | 63474 |
David Pollard | 108 | 438 | 39550 |
David J. Hill | 107 | 1364 | 57746 |