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E. Virginia Armbrust

Bio: E. Virginia Armbrust is an academic researcher from University of Washington. The author has contributed to research in topics: Thalassiosira pseudonana & Diatom. The author has an hindex of 54, co-authored 121 publications receiving 16305 citations. Previous affiliations of E. Virginia Armbrust include University of East Anglia & Washington University in St. Louis.


Papers
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Journal ArticleDOI
01 Oct 2004-Science
TL;DR: The 34 million-base-pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand base-pair mitochondrial genomes were reported in this article.
Abstract: Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

1,945 citations

Journal ArticleDOI
13 Nov 2008-Nature
TL;DR: Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms, and documents the presence of hundreds of genes from bacteria, likely to provide novel possibilities for metabolite management and for perception of environmental signals.
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

1,500 citations

Journal ArticleDOI
Patrick J. Keeling1, Patrick J. Keeling2, Fabien Burki2, Heather M. Wilcox3, Bassem Allam4, Eric E. Allen5, Linda A. Amaral-Zettler6, Linda A. Amaral-Zettler7, E. Virginia Armbrust8, John M. Archibald9, John M. Archibald1, Arvind K. Bharti10, Callum J. Bell10, Bank Beszteri11, Kay D. Bidle12, Connor Cameron10, Lisa Campbell13, David A. Caron14, Rose Ann Cattolico8, Jackie L. Collier4, Kathryn J. Coyne15, Simon K. Davy16, Phillipe Deschamps17, Sonya T. Dyhrman18, Bente Edvardsen19, Ruth D. Gates20, Christopher J. Gobler4, Spencer J. Greenwood21, Stephanie Guida10, Jennifer L. Jacobi10, Kjetill S. Jakobsen19, Erick R. James2, Bethany D. Jenkins22, Uwe John11, Matthew D. Johnson23, Andrew R. Juhl18, Anja Kamp24, Anja Kamp25, Laura A. Katz26, Ronald P. Kiene27, Alexander Kudryavtsev28, Alexander Kudryavtsev29, Brian S. Leander2, Senjie Lin30, Connie Lovejoy31, Denis H. Lynn2, Denis H. Lynn32, Adrian Marchetti33, George B. McManus30, Aurora M. Nedelcu34, Susanne Menden-Deuer22, Cristina Miceli35, Thomas Mock36, Marina Montresor37, Mary Ann Moran38, Shauna A. Murray39, Govind Nadathur40, Satoshi Nagai, Peter B. Ngam10, Brian Palenik5, Jan Pawlowski28, Giulio Petroni41, Gwenael Piganeau42, Matthew C. Posewitz43, Karin Rengefors44, Giovanna Romano37, Mary E. Rumpho30, Tatiana A. Rynearson22, Kelly B. Schilling10, Declan C. Schroeder, Alastair G. B. Simpson1, Alastair G. B. Simpson9, Claudio H. Slamovits9, Claudio H. Slamovits1, David Roy Smith45, G. Jason Smith46, Sarah R. Smith5, Heidi M. Sosik23, Peter Stief25, Edward C. Theriot47, Scott N. Twary48, Pooja E. Umale10, Daniel Vaulot49, Boris Wawrik50, Glen L. Wheeler51, William H. Wilson52, Yan Xu53, Adriana Zingone37, Alexandra Z. Worden3, Alexandra Z. Worden1 
Canadian Institute for Advanced Research1, University of British Columbia2, Monterey Bay Aquarium Research Institute3, Stony Brook University4, University of California, San Diego5, Brown University6, Marine Biological Laboratory7, University of Washington8, Dalhousie University9, National Center for Genome Resources10, Alfred Wegener Institute for Polar and Marine Research11, Rutgers University12, Texas A&M University13, University of Southern California14, University of Delaware15, Victoria University of Wellington16, University of Paris-Sud17, Columbia University18, University of Oslo19, University of Hawaii at Manoa20, University of Prince Edward Island21, University of Rhode Island22, Woods Hole Oceanographic Institution23, Jacobs University Bremen24, Max Planck Society25, Smith College26, University of South Alabama27, University of Geneva28, Saint Petersburg State University29, University of Connecticut30, Laval University31, University of Guelph32, University of North Carolina at Chapel Hill33, University of New Brunswick34, University of Camerino35, University of East Anglia36, Stazione Zoologica Anton Dohrn37, University of Georgia38, University of Technology, Sydney39, University of Puerto Rico40, University of Pisa41, Centre national de la recherche scientifique42, Colorado School of Mines43, Lund University44, University of Western Ontario45, California State University46, University of Texas at Austin47, Los Alamos National Laboratory48, Pierre-and-Marie-Curie University49, University of Oklahoma50, Plymouth Marine Laboratory51, Bigelow Laboratory For Ocean Sciences52, Princeton University53
TL;DR: In this paper, the authors describe a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans and their biology, evolution, and ecology.
Abstract: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.

852 citations

Journal ArticleDOI
TL;DR: Pplacer as discussed by the authors is a software package for phylogenetic placement and subsequent visualization, which can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, and is easy to run in parallel.
Abstract: Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets. This paper introduces pplacer, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. Pplacer features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence. Pplacer enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.

851 citations

Journal ArticleDOI
18 Apr 2008-Science
TL;DR: In this article, the authors present laboratory evidence that calcification and net primary production in the coccolithophore species Emiliania huxleyi are significantly increased by high CO2 partial pressures.
Abstract: Ocean acidification in response to rising atmospheric CO2 partial pressures is widely expected to reduce calcification by marine organisms. From the mid-Mesozoic, coccolithophores have been major calcium carbonate producers in the world's oceans, today accounting for about a third of the total marine CaCO3 production. Here, we present laboratory evidence that calcification and net primary production in the coccolithophore species Emiliania huxleyi are significantly increased by high CO2 partial pressures. Field evidence from the deep ocean is consistent with these laboratory conclusions, indicating that over the past 220 years there has been a 40% increase in average coccolith mass. Our findings show that coccolithophores are already responding and will probably continue to respond to rising atmospheric CO2 partial pressures, which has important implications for biogeochemical modeling of future oceans and climate.

812 citations


Cited by
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Journal ArticleDOI
TL;DR: This version of MAFFT has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update.
Abstract: We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

27,771 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
Abstract: Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

5,788 citations

01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

4,833 citations

Journal ArticleDOI
TL;DR: In this article, the authors proposed a new approach to global sustainability in which they define planetary boundaries within which they expect that humanity can operate safely. But the proposed concept of "planetary boundaries" lays the groundwork for shifting our approach to governance and management, away from the essentially sectoral analyses of limits to growth aimed at minimizing negative externalities, toward the estimation of the safe space for human development.
Abstract: Anthropogenic pressures on the Earth System have reached a scale where abrupt global environmental change can no longer be excluded. We propose a new approach to global sustainability in which we define planetary boundaries within which we expect that humanity can operate safely. Transgressing one or more planetary boundaries may be deleterious or even catastrophic due to the risk of crossing thresholds that will trigger non-linear, abrupt environmental change within continental- to planetary-scale systems. We have identified nine planetary boundaries and, drawing upon current scientific understanding, we propose quantifications for seven of them. These seven are climate change (CO2 concentration in the atmosphere <350 ppm and/or a maximum change of +1 W m-2 in radiative forcing); ocean acidification (mean surface seawater saturation state with respect to aragonite ≥ 80% of pre-industrial levels); stratospheric ozone (<5% reduction in O3 concentration from pre-industrial level of 290 Dobson Units); biogeochemical nitrogen (N) cycle (limit industrial and agricultural fixation of N2 to 35 Tg N yr-1) and phosphorus (P) cycle (annual P inflow to oceans not to exceed 10 times the natural background weathering of P); global freshwater use (<4000 km3 yr-1 of consumptive use of runoff resources); land system change (<15% of the ice-free land surface under cropland); and the rate at which biological diversity is lost (annual rate of <10 extinctions per million species). The two additional planetary boundaries for which we have not yet been able to determine a boundary level are chemical pollution and atmospheric aerosol loading. We estimate that humanity has already transgressed three planetary boundaries: for climate change, rate of biodiversity loss, and changes to the global nitrogen cycle. Planetary boundaries are interdependent, because transgressing one may both shift the position of other boundaries or cause them to be transgressed. The social impacts of transgressing boundaries will be a function of the social-ecological resilience of the affected societies. Our proposed boundaries are rough, first estimates only, surrounded by large uncertainties and knowledge gaps. Filling these gaps will require major advancements in Earth System and resilience science. The proposed concept of "planetary boundaries" lays the groundwork for shifting our approach to governance and management, away from the essentially sectoral analyses of limits to growth aimed at minimizing negative externalities, toward the estimation of the safe space for human development. Planetary boundaries define, as it were, the boundaries of the "planetary playing field" for humanity if we want to be sure of avoiding major human-induced environmental change on a global scale.

4,771 citations