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Showing papers by "Washington State University published in 2010"


Journal ArticleDOI
Riccardo Velasco, Andrey Zharkikh1, Jason P. Affourtit2, Amit Dhingra3, Alessandro Cestaro, Ananth Kalyanaraman3, Paolo Fontana, Satish Bhatnagar1, Michela Troggio, Dmitry Pruss1, Silvio Salvi4, Massimo Pindo, Paolo Baldi, Sara Castelletti, Marina Cavaiuolo, G. Coppola, Fabrizio Costa, V. Cova, Antonio Dal Ri, Vadim V. Goremykin, M. Komjanc, Sara Longhi, P. Magnago, Giulia Malacarne, Mickael Malnoy, Diego Micheletti, Marco Moretto, Michele Perazzolli, Azeddine Si-Ammour, Silvia Vezzulli, E. Zini, Glenn Eldredge1, Lisa M. Fitzgerald1, N. Gutin1, Jerry S. Lanchbury1, Teresita Macalma1, J.T. Mitchell1, Julia Reid1, Bryan Wardell1, Chinnappa D. Kodira2, Zhoutao Chen2, Brian Desany2, Faheem Niazi2, Melinda Palmer2, Tyson Koepke3, Derick Jiwan3, Scott Schaeffer3, Vandhana Krishnan3, Changjun Wu3, Vu T. Chu5, Stephen T. King5, Jessica Vick5, Quanzhou Tao, Amy Mraz, Aimee Stormo, Keith E. Stormo, Robert Bogden, Davide Ederle6, Alessandra Stella6, Alberto Vecchietti6, Martin M. Kater7, Simona Masiero7, Pauline Lasserre, Yves Lespinasse, Andrew C. Allan8, Vincent G. M. Bus8, David Chagné8, Ross N. Crowhurst8, Andrew P. Gleave8, Enrico Lavezzo9, Jeffrey A. Fawcett10, Jeffrey A. Fawcett11, Sebastian Proost11, Sebastian Proost10, Pierre Rouzé11, Pierre Rouzé10, Lieven Sterck10, Lieven Sterck11, Stefano Toppo9, Barbara Lazzari6, Roger P. Hellens8, Charles-Eric Durel, Alexander Gutin1, Roger E. Bumgarner5, Susan E. Gardiner8, Mark H. Skolnick1, Michael Egholm2, Yves Van de Peer11, Yves Van de Peer10, Francesco Salamini6, Roberto Viola 
TL;DR: It is shown that a relatively recent (>50 million years ago) genome-wide duplication has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae, which partly support the monophyly of the ancestral paleohexaploidy of eudicots.
Abstract: We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol.

1,718 citations


Journal ArticleDOI
John P. Vogel1, David F. Garvin2, Todd C. Mockler2, Jeremy Schmutz, Daniel S. Rokhsar3, Michael W. Bevan4, Kerrie Barry5, Susan Lucas5, Miranda Harmon-Smith5, Kathleen Lail5, Hope Tice5, Jane Grimwood, Neil McKenzie4, Naxin Huo6, Yong Q. Gu6, Gerard R. Lazo6, Olin D. Anderson6, Frank M. You7, Ming-Cheng Luo7, Jan Dvorak7, Jonathan M. Wright4, Melanie Febrer4, Dominika Idziak8, Robert Hasterok8, Erika Lindquist5, Mei Wang5, Samuel E. Fox2, Henry D. Priest2, Sergei A. Filichkin2, Scott A. Givan2, Douglas W. Bryant2, Jeff H. Chang2, Haiyan Wu9, Wei Wu10, An-Ping Hsia10, Patrick S. Schnable9, Anantharaman Kalyanaraman11, Brad Barbazuk12, Todd P. Michael, Samuel P. Hazen13, Jennifer N. Bragg6, Debbie Laudencia-Chingcuanco6, Yiqun Weng14, Georg Haberer, Manuel Spannagl, Klaus F. X. Mayer, Thomas Rattei15, Therese Mitros3, Sang-Jik Lee16, Jocelyn K. C. Rose16, Lukas A. Mueller16, Thomas L. York16, Thomas Wicker17, Jan P. Buchmann17, Jaakko Tanskanen18, Alan H. Schulman18, Heidrun Gundlach, Michael W. Bevan4, Antonio Costa de Oliveira19, Luciano da C. Maia19, William R. Belknap6, Ning Jiang, Jinsheng Lai9, Liucun Zhu20, Jianxin Ma20, Cheng Sun21, Ellen J. Pritham21, Jérôme Salse, Florent Murat, Michael Abrouk, Rémy Bruggmann, Joachim Messing, Noah Fahlgren2, Christopher M. Sullivan2, James C. Carrington2, Elisabeth J. Chapman, Greg D. May22, Jixian Zhai23, Matthias Ganssmann23, Sai Guna Ranjan Gurazada23, Marcelo A German23, Blake C. Meyers23, Pamela J. Green23, Ludmila Tyler3, Jiajie Wu7, James A. Thomson6, Shan Chen13, Henrik Vibe Scheller24, Jesper Harholt25, Peter Ulvskov25, Jeffrey A. Kimbrel2, Laura E. Bartley24, Peijian Cao24, Ki-Hong Jung26, Manoj Sharma24, Miguel E. Vega-Sánchez24, Pamela C. Ronald24, Chris Dardick6, Stefanie De Bodt27, Wim Verelst27, Dirk Inzé27, Maren Heese28, Arp Schnittger28, Xiaohan Yang29, Udaya C. Kalluri29, Gerald A. Tuskan29, Zhihua Hua14, Richard D. Vierstra14, Yu Cui9, Shuhong Ouyang9, Qixin Sun9, Zhiyong Liu9, Alper Yilmaz30, Erich Grotewold30, Richard Sibout31, Kian Hématy31, Grégory Mouille31, Herman Höfte31, Todd P. Michael, Jérôme Pelloux32, Devin O'Connor3, James C. Schnable3, Scott C. Rowe3, Frank G. Harmon3, Cynthia L. Cass33, John C. Sedbrook33, Mary E. Byrne4, Sean Walsh4, Janet Higgins4, Pinghua Li16, Thomas P. Brutnell16, Turgay Unver34, Hikmet Budak34, Harry Belcram, Mathieu Charles, Boulos Chalhoub, Ivan Baxter35 
11 Feb 2010-Nature
TL;DR: The high-quality genome sequence will help Brachypodium reach its potential as an important model system for developing new energy and food crops and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat.
Abstract: Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

1,603 citations


Journal ArticleDOI
M. Punturo, M. R. Abernathy1, Fausto Acernese2, Benjamin William Allen3, Nils Andersson4, K. G. Arun5, Fabrizio Barone2, B. Barr1, M. Barsuglia6, M. G. Beker7, N. Beveridge1, S. Birindelli8, Suvadeep Bose9, L. Bosi, S. Braccini, C. Bradaschia, Tomasz Bulik10, Enrico Calloni, G. Cella, E. Chassande Mottin6, Simon Chelkowski11, Andrea Chincarini, John A. Clark12, E. Coccia13, C. N. Colacino, J. Colas, A. Cumming1, L. Cunningham1, E. Cuoco, S. L. Danilishin14, Karsten Danzmann3, G. De Luca, R. De Salvo15, T. Dent12, R. De Rosa, L. Di Fiore, A. Di Virgilio, M. Doets7, V. Fafone13, Paolo Falferi16, R. Flaminio17, J. Franc17, F. Frasconi, Andreas Freise11, Paul Fulda11, Jonathan R. Gair18, G. Gemme, A. Gennai11, A. Giazotto, Kostas Glampedakis19, M. Granata6, Hartmut Grote3, G. M. Guidi20, G. D. Hammond1, Mark Hannam21, Jan Harms22, D. Heinert23, Martin Hendry1, Ik Siong Heng1, Eric Hennes7, Stefan Hild1, J. H. Hough, Sascha Husa24, S. H. Huttner1, Gareth Jones12, F. Y. Khalili14, Keiko Kokeyama11, Kostas D. Kokkotas19, Badri Krishnan24, M. Lorenzini, Harald Lück3, Ettore Majorana, Ilya Mandel25, Vuk Mandic22, I. W. Martin1, C. Michel17, Y. Minenkov13, N. Morgado17, Simona Mosca, B. Mours26, H. Müller–Ebhardt3, P. G. Murray1, Ronny Nawrodt1, John Nelson1, Richard O'Shaughnessy27, Christian D. Ott15, C. Palomba, A. Paoli, G. Parguez, A. Pasqualetti, R. Passaquieti28, D. Passuello, L. Pinard17, Rosa Poggiani28, P. Popolizio, Mirko Prato, P. Puppo, D. S. Rabeling7, P. Rapagnani29, Jocelyn Read24, Tania Regimbau8, H. Rehbein3, Stuart Reid1, Luciano Rezzolla24, F. Ricci29, F. Richard, A. Rocchi, Sheila Rowan1, Albrecht Rüdiger3, Benoit Sassolas17, Bangalore Suryanarayana Sathyaprakash12, Roman Schnabel3, C. Schwarz, Paul Seidel, Alicia M. Sintes24, Kentaro Somiya15, Fiona C. Speirits1, Kenneth A. Strain1, S. E. Strigin14, P. J. Sutton12, S. P. Tarabrin14, Andre Thüring3, J. F. J. van den Brand7, C. van Leewen7, M. van Veggel1, C. Van Den Broeck12, Alberto Vecchio11, John Veitch11, F. Vetrano20, A. Viceré20, Sergey P. Vyatchanin14, Benno Willke3, Graham Woan1, P. Wolfango30, Kazuhiro Yamamoto3 
TL;DR: The third-generation ground-based observatory Einstein Telescope (ET) project as discussed by the authors is currently in its design study phase, and it can be seen as the first step in this direction.
Abstract: Advanced gravitational wave interferometers, currently under realization, will soon permit the detection of gravitational waves from astronomical sources. To open the era of precision gravitational wave astronomy, a further substantial improvement in sensitivity is required. The future space-based Laser Interferometer Space Antenna and the third-generation ground-based observatory Einstein Telescope (ET) promise to achieve the required sensitivity improvements in frequency ranges. The vastly improved sensitivity of the third generation of gravitational wave observatories could permit detailed measurements of the sources' physical parameters and could complement, in a multi-messenger approach, the observation of signals emitted by cosmological sources obtained through other kinds of telescopes. This paper describes the progress of the ET project which is currently in its design study phase.

1,497 citations


Journal ArticleDOI
18 Nov 2010-Nature
TL;DR: The mechanism of jasmonate perception is unraveled, the ability of F-box proteins to evolve as multi-component signalling hubs is highlighted and inositol pentakisphosphate is identified, which interacts with both COI1 and JAZ adjacent to the ligand.
Abstract: Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of jasmonate perception remains unclear. Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved α-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of jasmonate perception and highlight the ability of F-box proteins to evolve as multi-component signalling hubs.

1,168 citations


Journal ArticleDOI
TL;DR: The results of this research are consistent with the widespread reactivity reported for base-activated persulfate when it is used for ISCO.
Abstract: Base is the most commonly used activator of persulfate for the treatment of contaminated groundwater by in situ chemical oxidation (ISCO). A mechanism for the base activation of persulfate is proposed involving the base-catalyzed hydrolysis of persulfate to hydroperoxide anion and sulfate followed by the reduction of another persulfate molecule by hydroperoxide. Reduction by hydroperoxide decomposes persulfate into sulfate radical and sulfate anion, and hydroperoxide is oxidized to superoxide. The base-catalyzed hydrolysis of persulfate was supported by kinetic analyses of persulfate decomposition at various base:persulfate molar ratios and an increased rate of persulfate decomposition in D2O vs H2O. Stoichiometric analyses confirmed that hydroperoxide reacts with persulfate in a 1:1 molar ratio. Addition of hydroperoxide to basic persulfate systems resulted in rapid decomposition of the hydroperoxide and persulfate and decomposition of the superoxide probe hexachloroethane. The presence of superoxide was...

1,111 citations


Journal ArticleDOI
TL;DR: In this paper, Nitrogen-doped graphene (N-graphene) is obtained by exposing graphene to nitrogen plasma, and it exhibits much higher electrocatalytic activity toward oxygen reduction and H2O2 reduction than graphene, and much higher durability and selectivity than the widely used expensive Pt for oxygen reduction.
Abstract: Nitrogen-doped graphene (N-graphene) is obtained by exposing graphene to nitrogen plasma. N-graphene exhibits much higher electrocatalytic activity toward oxygen reduction and H2O2 reduction than graphene, and much higher durability and selectivity than the widely-used expensive Pt for oxygen reduction. The excellent electrochemical performance of N-graphene is attributed to nitrogen functional groups and the specific properties of graphene. This indicates that N-graphene is promising for applications in electrochemical energy devices (fuel cells, metal–air batteries) and biosensors.

1,017 citations


Journal ArticleDOI
J. Abadie1, B. P. Abbott1, R. Abbott1, M. R. Abernathy2  +719 moreInstitutions (79)
TL;DR: In this paper, Kalogera et al. presented an up-to-date summary of the rates for all types of compact binary coalescence sources detectable by the initial and advanced versions of the ground-based gravitational-wave detectors LIGO and Virgo.
Abstract: We present an up-to-date, comprehensive summary of the rates for all types of compact binary coalescence sources detectable by the initial and advanced versions of the ground-based gravitational-wave detectors LIGO and Virgo. Astrophysical estimates for compact-binary coalescence rates depend on a number of assumptions and unknown model parameters and are still uncertain. The most confident among these estimates are the rate predictions for coalescing binary neutron stars which are based on extrapolations from observed binary pulsars in our galaxy. These yield a likely coalescence rate of 100 Myr−1 per Milky Way Equivalent Galaxy (MWEG), although the rate could plausibly range from 1 Myr−1 MWEG−1 to 1000 Myr−1 MWEG−1 (Kalogera et al 2004 Astrophys. J. 601 L179; Kalogera et al 2004 Astrophys. J. 614 L137 (erratum)). We convert coalescence rates into detection rates based on data from the LIGO S5 and Virgo VSR2 science runs and projected sensitivities for our advanced detectors. Using the detector sensitivities derived from these data, we find a likely detection rate of 0.02 per year for Initial LIGO–Virgo interferometers, with a plausible range between 2 × 10−4 and 0.2 per year. The likely binary neutron–star detection rate for the Advanced LIGO–Virgo network increases to 40 events per year, with a range between 0.4 and 400 per year.

1,011 citations


Journal ArticleDOI
30 Apr 2010-Science
TL;DR: A synthesis of grass evolutionary biology with grassland ecosystem science will further knowledge of the evolution of traits that promote dominance in grassland systems and will provide a new context in which to evaluate the relative importance of C4 photosynthesis in transforming ecosystems across large regions of Earth.
Abstract: The evolution of grasses using C4 photosynthesis and their sudden rise to ecological dominance 3 to 8 million years ago is among the most dramatic examples of biome assembly in the geological record. A growing body of work suggests that the patterns and drivers of C4 grassland expansion were considerably more complex than originally assumed. Previous research has benefited substantially from dialog between geologists and ecologists, but current research must now integrate fully with phylogenetics. A synthesis of grass evolutionary biology with grassland ecosystem science will further our knowledge of the evolution of traits that promote dominance in grassland systems and will provide a new context in which to evaluate the relative importance of C4 photosynthesis in transforming ecosystems across large regions of Earth.

878 citations


Journal ArticleDOI
TL;DR: The authors conducted a meta-analysis of studies that examined the cognitive correlates of bilingualism and found that bilingualism is reliably associated with several cognitive outcomes, including increased attentional control, working memory, metalinguistic awareness, and abstract and symbolic representation skills.
Abstract: A number of studies have documented the cognitive outcomes associated with bilingualism. To gain a clear understanding of the extent and diversity of these cognitive outcomes, the authors conducted a meta-analysis of studies that examined the cognitive correlates of bilingualism. Data from 63 studies (involving 6,022 participants) were extracted and analyzed following established protocols and procedures for conducting systematic reviews and guidelines for meta-analysis. Results indicate that bilingualism is reliably associated with several cognitive outcomes, including increased attentional control, working memory, metalinguistic awareness, and abstract and symbolic representation skills. Overall mean effect sizes varied from small to large, depending on the cognitive outcomes measured, and were moderated by methodological features of the studies.

845 citations


Journal ArticleDOI
TL;DR: This article focused on recognizing simple human activities, which can be exploited to great societal benefits, especially in real-life, human centric applications such as elder care and healthcare.
Abstract: In principle, activity recognition can be exploited to great societal benefits, especially in real-life, human centric applications such as elder care and healthcare. This article focused on recognizing simple human activities. Recognizing complex activities remains a challenging and active area of research and the nature of human activities poses different challenges. Human activity understanding encompasses activity recognition and activity pattern discovery. The first focuses on accurate detection of human activities based on a predefined activity model. An activity pattern discovery researcher builds a pervasive system first and then analyzes the sensor data to discover activity patterns.

679 citations


Journal ArticleDOI
TL;DR: This article found that younger adults, the well-educated, political liberals, Democrats, those raised and currently living in urban areas, and those employed outside of primary industries were consistently more supportive of environmental protection than were their respective counterparts.
Abstract: Using data obtained from National Opinion Research Center's General Social Surveys (1973–1990), this paper tests two hypotheses concerning possible changes in the sociopolitical correlates of environmental concern. The “broadening base” hypothesis predicts that environmental concern will diffuse throughout the populace, resulting in a broader base of support for environmental protection, while the “economic contingency” hypothesis predicts that the economically deprived will disproportionately withdraw support for environmental protection during poor economic conditions. Analysis of the data over the 18 years, however, failed to lend any clear support for either of the hypotheses. In marked contrast, results indicate that the social bases of environmental concern—at least as measured by the NORC environmental spending item—have remained remarkably stable over nearly two decades despite fluctuating economic, political, and environmental conditions. Younger adults, the well-educated, political liberals, Democrats, those raised and currently living in urban areas, and those employed outside of primary industries were found to be consistently more supportive of environmental protection than were their respective counterparts.

Journal ArticleDOI
TL;DR: An overview of the epigenetics and biology of how environmental factors can promote transgenerational phenotypes and disease is provided.
Abstract: The ability of environmental factors to promote a phenotype or disease state not only in the individual exposed but also in subsequent progeny for successive generations is termed transgenerational inheritance. The majority of environmental factors such as nutrition or toxicants such as endocrine disruptors do not promote genetic mutations or alterations in DNA sequence. However, these factors do have the capacity to alter the epigenome. Epimutations in the germline that become permanently programmed can allow transmission of epigenetic transgenerational phenotypes. This review provides an overview of the epigenetics and biology of how environmental factors can promote transgenerational phenotypes and disease.

Journal ArticleDOI
TL;DR: It is proposed that ecological opportunity could promote adaptive radiation by generating specific changes to the selective regimes acting on natural populations, both by relaxing effective stabilizing selection and by creating conditions that ultimately generate diversifying selection.
Abstract: Ecological opportunity – through entry into a new environment, the origin of a key innovation or extinction of antagonists – is widely thought to link ecological population dynamics to evolutionary diversification. The population-level processes arising from ecological opportunity are well documented under the concept of ecological release. However, there is little consensus as to how these processes promote phenotypic diversification, rapid speciation and adaptive radiation. We propose that ecological opportunity could promote adaptive radiation by generating specific changes to the selective regimes acting on natural populations, both by relaxing effective stabilizing selection and by creating conditions that ultimately generate diversifying selection. We assess theoretical and empirical evidence for these effects of ecological opportunity and review emerging phylogenetic approaches that attempt to detect the signature of ecological opportunity across geological time. Finally, we evaluate the evidence for the evolutionary effects of ecological opportunity in the diversification of Caribbean Anolis lizards. Some of the processes that could link ecological opportunity to adaptive radiation are well documented, but others remain unsupported. We suggest that more study is required to characterize the form of natural selection acting on natural populations and to better describe the relationship between ecological opportunity and speciation rates.

Journal ArticleDOI
TL;DR: Highlights gaps in knowledge and methodology are highlighted, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry are suggested.
Abstract: Landscape genetics has seen rapid growth in number of publications since the term was coined in 2003. An extensive literature search from 1998 to 2008 using keywords associated with landscape genetics yielded 655 articles encompassing a vast array of study organisms, study designs and methodology. These publications were screened to identify 174 studies that explicitly incorporated at least one landscape variable with genetic data. We systematically reviewed this set of papers to assess taxonomic and temporal trends in: (i) geographic regions studied; (ii) types of questions addressed; (iii) molecular markers used; (iv) statistical analyses used; and (v) types and nature of spatial data used. Overall, studies have occurred in geographic regions proximal to developed countries and more commonly in terrestrial vs. aquatic habitats. Questions most often focused on effects of barriers and/or landscape variables on gene flow. The most commonly used molecular markers were microsatellites and amplified fragment length polymorphism (AFLPs), with AFLPs used more frequently in plants than animals. Analysis methods were dominated by Mantel and assignment tests. We also assessed differences among journals to evaluate the uniformity of reporting and publication standards. Few studies presented an explicit study design or explicit descriptions of spatial extent. While some landscape variables such as topographic relief affected most species studied, effects were not universal, and some species appeared unaffected by the landscape. Effects of habitat fragmentation were mixed, with some species altering movement paths and others unaffected. Taken together, although some generalities emerged regarding effects of specific landscape variables, results varied, thereby reinforcing the need for species-specific work. We conclude by: highlighting gaps in knowledge and methodology, providing guidelines to authors and reviewers of landscape genetics studies, and suggesting promising future directions of inquiry.

Journal ArticleDOI
TL;DR: In this paper, the authors measured an increase in CO2 production from soils after biochar amendment which increased with increasing rates of biochar, confirming that biochar contributed to the CO2 flux.
Abstract: The low temperature pyrolysis of organic material produces biochar, a charcoal like substance. Biochar is being promoted as a soil amendment to enhance soil quality, it is also seen as a mechanism of long-term sequestration of carbon. Our experiments tested the hypothesis that biochar is inert in soil. However, we measured an increase in CO2 production from soils after biochar amendment which increased with increasing rates of biochar. The ∂13C signature of the CO2 evolved in the first several days of the incubation was the same as the ∂13C signature of the biochar, confirming that biochar contributed to the CO2 flux. This effect diminished by day 6 of the incubation suggesting that most of the biochar C is slowly decomposing. Thus, aside from this short-term mineralization increasing soil C with young biochar may indeed be a long-term C storage mechanism.

Journal ArticleDOI
01 Jul 2010-Nature
TL;DR: The argument that rejuvenation of ecosystem function requires restoration of species evenness, rather than just richness, is strengthened, as organic farming potentially offers a means of returning functional evenness to ecosystems.
Abstract: Declining species number (richness) harms ecosystems, and conservation efforts have largely focused on conserving or restoring particular rare species. However, greater disparity in species relative abundances (evenness) might also do ecological harm, which could only be reversed by altering the densities of many species at once. A new survey of organic and conventionally managed potato fields shows that species evenness is greater under organic management. Replicating these levels of evenness in a field trial shows that the evenness of natural enemies found in organic fields promotes pest control and increases crop biomass. In organic crops many beneficial species (that eat pest insects) are equally common, which in potatoes leads to fewer pests and larger plants. A survey of organic and conventional potato fields shows that species evenness is greater under organic management. Replicating these levels of evenness in a field trial shows that the evenness of natural enemies found in organic fields promotes pest control and increases crop biomass. This is independent of the identity of the dominant enemy species, so is a result of evenness itself. Human activity can degrade ecosystem function by reducing species number (richness)1,2,3,4 and by skewing the relative abundance of species (evenness)5,6,7. Conservation efforts often focus on restoring or maintaining species number8,9, reflecting the well-known impacts of richness on many ecological processes1,2,3,4. In contrast, the ecological effects of disrupted evenness have received far less attention7, and developing strategies for restoring evenness remains a conceptual challenge7. In farmlands, agricultural pest-management practices often lead to altered food web structure and communities dominated by a few common species, which together contribute to pest outbreaks6,7,10,11. Here we show that organic farming methods mitigate this ecological damage by promoting evenness among natural enemies. In field enclosures, very even communities of predator and pathogen biological control agents, typical of organic farms, exerted the strongest pest control and yielded the largest plants. In contrast, pest densities were high and plant biomass was low when enemy evenness was disrupted, as is typical under conventional management. Our results were independent of the numerically dominant predator or pathogen species, and so resulted from evenness itself. Moreover, evenness effects among natural enemy groups were independent and complementary. Our results strengthen the argument that rejuvenation of ecosystem function requires restoration of species evenness, rather than just richness. Organic farming potentially offers a means of returning functional evenness to ecosystems.


Journal ArticleDOI
TL;DR: The most recent version of the IS undergraduate model curriculum is IS 2002 (Gorgone et al., 2003) published in early 2003 as discussed by the authors, which is the most recent output from model curriculum work for Information Systems (IS) that began in the early 1970s.
Abstract: The IS 2010 report is the latest output from model curriculum work for Information Systems (IS) that began in the early 1970s. Prior to this current effort, the most recent version of the IS undergraduate model curriculum is IS 2002 (Gorgone et al., 2003), published in early 2003. IS 2002 was a relatively minor update of IS'97 (Davis et al., 1997). Both IS 2002 and IS '97 were joint efforts by ACM, AIS, and DPMA/AITP (Data Processing Management Association/ Association of Information Technology Professionals). IS'97 was preceded by DPMA'90 (Longenecker and Feinstein 1991) and ACM Curriculum Recommendations 1983 (ACM 1983) and 1973 (Couger 1973). IS 2002 has been widely accepted and it has also been the basis for accreditation of undergraduate programs of Information Systems. This report represents the combined effort of numerous individuals and reflects the interests of thousands of faculty and practitioners. It is grounded in the expected requirements of industry, represents the views of organizations employing the graduates, and is supported by other IS-related organizations.

Journal ArticleDOI
TL;DR: It is assumed that time synchronized measurements will be ubiquitously available at all high-voltage substations at very high rates and how this information can be utilized more effectively for real-time operation as well as for subsequent decision making is examined.
Abstract: In this paper we assume that time synchronized measurements will be ubiquitously available at all high-voltage substations at very high rates. We examine how this information can be utilized more effectively for real-time operation as well as for subsequent decision making. This new information available in real time is different, both in quality and in quantity, than the real-time measurements available today. The promise of new and improved applications to operate the power system more reliably and efficiently has been recognized but is still in conceptual stages. Also, the present system to handle this real-time data has been recognized to be inadequate but even conceptual designs of such infrastructure needed to store and communicate the data are in their infancy. In this paper, we first suggest the requirements for an information infrastructure to handle ubiquitous phasor measurements recognizing that the quantity and rate of data would make it impossible to store all the data centrally as done today. Then we discuss the new and improved applications, classified into two categories: one is the set of automatic wide-area controls and the other is the set of control center (EMS) functions with special attention to the state estimator. Finally, given that the availability of phasor measurements will grow over time, the path for smooth transition from present-day systems and applications to those discussed here is delineated.

Journal ArticleDOI
TL;DR: It is demonstrated that, through perception of Peps, PEPR1 and PEPR2 contribute to defense responses in Arabidopsis, and differential binding affinities of two receptors with a family of peptide ligands are demonstrated.
Abstract: Pep1 is a 23–amino acid peptide that enhances resistance to a root pathogen, Pythium irregulare. Pep1 and its homologs (Pep2 to Pep7) are endogenous amplifiers of innate immunity of Arabidopsis thaliana that induce the transcription of defense-related genes and bind to PEPR1, a plasma membrane leucine-rich repeat (LRR) receptor kinase. Here, we identify a plasma membrane LRR receptor kinase, designated PEPR2, that has 76% amino acid similarity to PEPR1, and we characterize its role in the perception of Pep peptides and defense responses. Both PEPR1 and PEPR2 were transcriptionally induced by wounding, treatment with methyl jasmonate, Pep peptides, and pathogen-associated molecular patterns. The effects of Pep1 application on defense-related gene induction and enhancement of resistance to Pseudomonas syringae pv tomato DC3000 were partially reduced in single mutants of PEPR1 and PEPR2 and abolished completely in double mutants. Photoaffinity labeling and binding assays using transgenic tobacco (Nicotiana tabacum) cells expressing PEPR1 and PEPR2 clearly demonstrated that PEPR1 is a receptor for Pep1-6 and that PEPR2 is a receptor for Pep1 and Pep2. Our analysis demonstrates differential binding affinities of two receptors with a family of peptide ligands and the corresponding physiological effects of the specific receptor–ligand interactions. Therefore, we demonstrate that, through perception of Peps, PEPR1 and PEPR2 contribute to defense responses in Arabidopsis.

Journal ArticleDOI
TL;DR: Dietary astaxanthin decreases a DNA damage biomarker and acute phase protein, and enhances immune response in young healthy females, and is effective in modulating immune response, oxidative status and inflammation in younghealthy adult female human subjects.
Abstract: Astaxanthin modulates immune response, inhibits cancer cell growth, reduces bacterial load and gastric inflammation, and protects against UVA-induced oxidative stress in in vitro and rodent models. Similar clinical studies in humans are unavailable. Our objective is to study the action of dietary astaxanthin in modulating immune response, oxidative status and inflammation in young healthy adult female human subjects. Participants (averaged 21.5 yr) received 0, 2, or 8 mg astaxanthin (n = 14/diet) daily for 8 wk in a randomized double-blind, placebo-controlled study. Immune response was assessed on wk 0, 4 and 8, and tuberculin test performed on wk 8. Plasma astaxanthin increased (P < 0.01) dose-dependently after 4 or 8 wk of supplementation. Astaxanthin decreased a DNA damage biomarker after 4 wk but did not affect lipid peroxidation. Plasma C-reactive protein concentration was lower (P < 0.05) on wk 8 in subjects given 2 mg astaxanthin. Dietary astaxanthin stimulated mitogen-induced lymphoproliferation, increased natural killer cell cytotoxic activity, and increased total T and B cell subpopulations, but did not influence populations of Thelper, Tcytotoxic or natural killer cells. A higher percentage of leukocytes expressed the LFA-1 marker in subjects given 2 mg astaxanthin on wk 8. Subjects fed 2 mg astaxanthin had a higher tuberculin response than unsupplemented subjects. There was no difference in TNF and IL-2 concentrations, but plasma IFN-γ and IL-6 increased on wk 8 in subjects given 8 mg astaxanthin. Therefore, dietary astaxanthin decreases a DNA damage biomarker and acute phase protein, and enhances immune response in young healthy females.

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TL;DR: This paper examined local residents' attitudes toward two different types of tourism development, mass tourism and alternative tourism, using data collected from residents of the Sunshine Coast, Australia, and found that host community support is affected directly and/or indirectly by the level of community concern, community attachment, ecocentric values, use of the tourism resource base, state of the local economy, and the perceived impacts.
Abstract: This study examines local residents’ attitudes toward two different types of tourism development, mass tourism and alternative tourism, using data collected from residents of Sunshine Coast, Australia. The study findings reveal that host community support is affected directly and/or indirectly by the level of community concern, community attachment, ecocentric values, use of the tourism resource base, state of the local economy, and the perceived impacts of tourism development. Findings suggested that even though some of the factors influence attitudes toward both mass and alternative tourism, attitudes toward each form of development is likely to be formed based on the perceptions of different factors.

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TL;DR: This article examined college students' use of online media for political purposes in the 2008 election and found significant positive relationships between attention to traditional Internet sources and political self-efficacy and situational political involvement.
Abstract: This study examined college students' use of online media for political purposes in the 2008 election. Social media attention, online expression, and traditional Internet attention were assessed in relation to political self-efficacy and situational political involvement. Data from a Web survey of college students showed significant positive relationships between attention to traditional Internet sources and political self-efficacy and situational political involvement. Attention to social media was not significantly related to political self-efficacy or involvement. Online expression was significantly related to situational political involvement but not political self-efficacy. Implications are discussed for political use of online media for young adults.

Journal ArticleDOI
TL;DR: Global NEWS as discussed by the authors is a global, spatially explicit, multi-element and multi-form model of nutrient exports by rivers, which is used to examine the impact of polices to reduce coastal eutrophication at regional to global scales.
Abstract: Global NEWS is a global, spatially explicit, multi-element and multi-form model of nutrient exports by rivers. Here we present NEWS 2, the new version of Global NEWS developed as part of a Millennium Ecosystem Assessment scenario implementation from hindcast (1970) to contemporary (2000) and future scenario trajectories (2030 & 2050). We provide a detailed model description and present an overview of enhancements to input datasets, emphasizing an integrated view of nutrient form sub-models and contrasts with previous NEWS models (NEWS 1). An important difference with NEWS 1 is our unified model framework (multi-element, multi-form) that facilitates detailed watershed comparisons regionally and by element or form. NEWS 2 performs approximately as well as NEWS 1 while incorporating previously uncharacterized factors. Although contemporary global river export estimates for dissolved inorganic nitrogen (DIN) and particulates show notable reductions, they are within the range of previous studies; global exports for other nutrient forms are comparable to NEWS 1. NEWS 2 can be used as an effective tool to examine the impact of polices to reduce coastal eutrophication at regional to global scales. Continued enhancements will focus on the incorporation of other forms and sub-basin spatial variability in drivers and retention processes.

Journal ArticleDOI
TL;DR: In this paper, the authors identify the key role played by the customer's perception of a firm's greed, i.e., an inferred negative motive about the firm's opportunistic intent, that dangerously energizes customer revenge.
Abstract: This article develops and tests a comprehensive model of customer revenge that contributes to the literature in three manners. First, we identify the key role played by the customer’s perception of a firm’s greed—that is, an inferred negative motive about a firm’s opportunistic intent—that dangerously energizes customer revenge. Perceived greed is found as the most influential cognition that leads to a customer desire for revenge, even after accounting for well studied cognitions (i.e., fairness and blame) in the service literature. Second, we make a critical distinction between direct and indirect acts of revenge because these sets of behaviors have different repercussions—in “face-to-face” vs. “behind a firm’s back”—that call for different interventions. Third, our extended model specifies the role of customer perceived power in predicting these types of behaviors. We find that power is instrumental—both as main and moderation effects—only in the case of direct acts of revenge (i.e., aggression and vindictive complaining). Power does not influence indirect revenge, however. Our model is tested with two field studies: (1) a study examining online public complaining, and (2) a multi-stage study performed after a service failure.

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TL;DR: In this paper, the advantages of both single-layer graphene and highly graphitic carbon were reported as a durable alternative support material for Pt nanoparticles for oxygen reduction in fuel cells.

Journal ArticleDOI
30 Sep 2010-PLOS ONE
TL;DR: It is confirmed that an environmental agent has the ability to induce epigenetic transgenerational changes in the sperm epigenome and identifies common genome features present in these regions.
Abstract: Previous observations have demonstrated that embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes transgenerational adult onset disease such as male infertility, kidney disease, prostate disease, immune abnormalities and tumor development. The current study investigates genome-wide promoter DNA methylation alterations in the sperm of F3 generation rats whose F0 generation mother was exposed to vinclozolin. A methylated DNA immunoprecipitation with methyl-cytosine antibody followed by a promoter tilling microarray (MeDIP-Chip) procedure was used to identify 52 different regions with statistically significant altered methylation in the sperm promoter epigenome. Mass spectrometry bisulfite analysis was used to map the CpG DNA methylation and 16 differential DNA methylation regions were confirmed, while the remainder could not be analyzed due to bisulfite technical limitations. Analysis of these validated regions identified a consensus DNA sequence (motif) that associated with 75% of the promoters. Interestingly, only 16.8% of a random set of 125 promoters contained this motif. One candidate promoter (Fam111a) was found to be due to a copy number variation (CNV) and not a methylation change, suggesting initial alterations in the germline epigenome may promote genetic abnormalities such as induced CNV in later generations. This study identifies differential DNA methylation sites in promoter regions three generations after the initial exposure and identifies common genome features present in these regions. In addition to primary epimutations, a potential indirect genetic abnormality was identified, and both are postulated to be involved in the epigenetic transgenerational inheritance observed. This study confirms that an environmental agent has the ability to induce epigenetic transgenerational changes in the sperm epigenome.

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TL;DR: In this paper, the core beliefs and values underlying these two approaches to agriculture were synthesized into a conventional agriculture paradigm and an alternative agriculture paradigm, and the writings of six major proponents of alternative agriculture were compared with those of six leading proponents of conventional agriculture to document the major components of the two agricultural paradigms.
Abstract: Analysts have described conflict between the economically dominant industrial sector of society and the environmental movement as representing competition between two opposing worldviews or social paradigms. There appears to be a similar schism developing in agriculture. The conventional paradigm of large-scale, highly industrialized agriculture is being challenged by an increasingly vocal alternative agriculture movement which advocates major shifts toward a more “ecologically sustainable agriculture.” Some have suggested that alternative agriculture represents a fundamentally new paradigm for agriculture. This paper seeks to clarify and synthesize the core beliefs and values underlying these two approaches to agriculture into a “conventional agriculture paradigm” and an “alternative agriculture paradigm.” The writings of six major proponents of alternative agriculture are compared with those of six leading proponents of conventional agriculture to document the major components of the two agricultural paradigms. The two sets of writings reveal dramatically divergent perspectives on a wide range of agricultural issues. The competing paradigms can be synthesized into six major dimensions: 1) centralization vs. decentralization, 2) dependence vs. independence, 3) competition vs. community, 4) domination of nature vs. harmony with nature, 5) specialization vs. diversity, and 6) exploitation vs. restraint. The emerging controversy over “low-input, sustainable agriculture” (LISA) illustrates the paradigmatic gulf between alternative and conventional agriculture, as well as the pitfalls facing alternative agriculturalists as they attempt to replace conventional agriculture as the dominant paradigm.

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TL;DR: In this paper, an in situ isotopic study of 68 Jack Hills zircons was conducted, in which the Hf and Pb isotope ratios were measured concurrently, allowing a better integration of isotope tracer information (176Hf/177Hf).

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TL;DR: In both studies, it was found that school harassment due to transgender identity was pervasive, and this harassment was negatively associated with feelings of safety, and when schools took action to reduce harassment, students reported greater connections to school personnel.
Abstract: Transgender youth experience negative school environments and may not benefit directly from interventions defined to support Lesbian, Gay and Bisexual (LGB) youth. This study utilized a multi-method approach to consider the issues that transgender students encounter in school environments. Using data from two studies, survey data (total n = 2260, 68 transgender youth) from study 1 and focus groups (n = 35) from study 2, we examine transgender youth’s experience of school harassment, school strategies implemented to reduce harassment, the protective role of supportive school personnel, and individual responses to harassment, including dropping out and changing schools. In both studies, we found that school harassment due to transgender identity was pervasive, and this harassment was negatively associated with feelings of safety. When schools took action to reduce harassment, students reported greater connections to school personnel. Those connections were associated with greater feelings of safety. The indirect effects of school strategies to reduce harassment on feelings of safety through connection to adults were also significant. Focus group data illuminate specific processes schools can engage in to benefit youth, and how the youth experience those interventions.