Showing papers by "Oregon State University published in 2011"
TL;DR: This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them, and summarizes cellulOSE nanoparticles in terms of particle morphology, crystal structure, and properties.
Abstract: This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).
4,920 citations
University of Zurich1, University of California, Berkeley2, Lawrence Berkeley National Laboratory3, Max Planck Society4, University of Oldenburg5, Leibniz University of Hanover6, University of Antwerp7, Oregon State University8, Technische Universität München9, Cornell University10, Newcastle University11, University of Florence12, Weizmann Institute of Science13
TL;DR: In this article, a new generation of experiments and soil carbon models were proposed to predict the SOM response to global warming, and they showed that molecular structure alone alone does not control SOM stability.
Abstract: Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily—and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.
4,219 citations
TL;DR: In this paper, the main ecological services across a variety of estuarine and coastal ecosystems (ECEs) including marshes, mangroves, nearshore coral reefs, seagrass beds, and sand beaches and dunes are reviewed.
Abstract: The global decline in estuarine and coastal ecosystems (ECEs) is affecting a number of critical benefits, or ecosystem services. We review the main ecological services across a variety of ECEs, including marshes, mangroves, nearshore coral reefs, seagrass beds, and sand beaches and dunes. Where possible, we indicate estimates of the key economic values arising from these services, and discuss how the natural variability of ECEs impacts their benefits, the synergistic relationships of ECEs across seascapes, and management implications. Although reliable valuation estimates are beginning to emerge for the key services of some ECEs, such as coral reefs, salt marshes, and mangroves, many of the important benefits of seagrass beds and sand dunes and beaches have not been assessed properly. Even for coral reefs, marshes, and mangroves, important ecological services have yet to be valued reliably, such as cross-ecosystem nutrient transfer (coral reefs), erosion control (marshes), and pollution control (mangroves). An important issue for valuing certain ECE services, such as coastal protection and habitat-fishery linkages, is that the ecological functions underlying these services vary spatially and temporally. Allowing for the connectivity between ECE habitats also may have important implications for assessing the ecological functions underlying key ecosystems services, such coastal protection, control of erosion, and habitat-fishery linkages. Finally, we conclude by suggesting an action plan for protecting and/or enhancing the immediate and longer-term values of ECE services. Because the connectivity of ECEs across land-sea gradients also influences the provision of certain ecosystem services, management of the entire seascape will be necessary to preserve such synergistic effects. Other key elements of an action plan include further ecological and economic collaborative research on valuing ECE services, improving institutional and legal frameworks for management, controlling and regulating destructive economic activities, and developing ecological restoration options.
3,750 citations
University of California, Santa Cruz1, Duke University2, University of California, Berkeley3, University of Montana4, University of Cape Town5, University of Wisconsin-Madison6, University of Washington7, University of Florida8, Scripps Institution of Oceanography9, University of Missouri–St. Louis10, Finnmark University College11, University of Turku12, Stony Brook University13, Oregon State University14, Wageningen University and Research Centre15, University of California, Davis16, University of British Columbia17, University of Oulu18, Swedish University of Agricultural Sciences19
TL;DR: This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles.
Abstract: Until recently, large apex consumers were ubiquitous across the globe and had been for millions of years. The loss of these animals may be humankind's most pervasive influence on nature. Although such losses are widely viewed as an ethical and aesthetic problem, recent research reveals extensive cascading effects of their disappearance in marine, terrestrial, and freshwater ecosystems worldwide. This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles. These findings emphasize the urgent need for interdisciplinary research to forecast the effects of trophic downgrading on process, function, and resilience in global ecosystems.
3,130 citations
TL;DR: This work determines the location and identity of every atom at a grain boundary and finds that different grains stitch together predominantly through pentagon–heptagon pairs, and reveals an unexpectedly small and intricate patchwork of grains connected by tilt boundaries.
Abstract: The properties of polycrystalline materials are often dominated by the size of their grains and by the atomic structure of their grain boundaries. These effects should be especially pronounced in two-dimensional materials, where even a line defect can divide and disrupt a crystal. These issues take on practical significance in graphene, which is a hexagonal, two-dimensional crystal of carbon atoms. Single-atom-thick graphene sheets can now be produced by chemical vapour deposition on scales of up to metres, making their polycrystallinity almost unavoidable. Theoretically, graphene grain boundaries are predicted to have distinct electronic, magnetic, chemical and mechanical properties that strongly depend on their atomic arrangement. Yet because of the five-order-of-magnitude size difference between grains and the atoms at grain boundaries, few experiments have fully explored the graphene grain structure. Here we use a combination of old and new transmission electron microscopy techniques to bridge these length scales. Using atomic-resolution imaging, we determine the location and identity of every atom at a grain boundary and find that different grains stitch together predominantly through pentagon-heptagon pairs. Rather than individually imaging the several billion atoms in each grain, we use diffraction-filtered imaging to rapidly map the location, orientation and shape of several hundred grains and boundaries, where only a handful have been previously reported. The resulting images reveal an unexpectedly small and intricate patchwork of grains connected by tilt boundaries. By correlating grain imaging with scanning probe and transport measurements, we show that these grain boundaries severely weaken the mechanical strength of graphene membranes but do not as drastically alter their electrical properties. These techniques open a new window for studies on the structure, properties and control of grains and grain boundaries in graphene and other two-dimensional materials.
1,824 citations
TL;DR: In this paper, an automated procedure for identifying and tracking mesoscale features based on their SSH signatures yields 35,891 eddies with average lifetime of 32 weeks and an average propagation distance of 550 km.
1,744 citations
TL;DR: In this paper, four promising alternative binders available as alternatives to Portland cement are discussed, namely calcium aluminate cement, calcium sulfoaluminate cements, alkali-activated binders, and supersulfated cements.
1,237 citations
Indiana University1, University of Notre Dame2, Utah State University3, University of New Hampshire4, University of California, Santa Barbara5, University of Tokyo6, United States Department of Energy7, Ludwig Maximilian University of Munich8, National Institutes of Health9, J. Craig Venter Institute10, University of Illinois at Urbana–Champaign11, Hebrew University of Jerusalem12, University of North Texas13, Harvard University14, University of Geneva15, Research Institute of Molecular Pathology16, Oregon State University17, Utrecht University18, University of California, Davis19, University of Iowa20, Hoffmann-La Roche21, University of Strasbourg22, University of Washington23, University of Texas at Arlington24, University of California, Santa Cruz25, Life Technologies26, New York University27, University of Guelph28, Imperial College London29, University of California, Berkeley30
TL;DR: The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions, and the coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random.
Abstract: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.
1,204 citations
TL;DR: In this article, the authors evaluated the classification accuracy of five sets of independently developed ActiGraph cut points using energy expenditure, measured by indirect calorimetry, as a criterion reference standard.
Abstract: TROST, S. G., P. D. LOPRINZI, R. MOORE, and K. A. PFEIFFER. Comparison of Accelerometer Cut Points for Predicting Activity Intensity in Youth. Med. Sci. Sports Exerc., Vol. 43, No. 7, pp. 1360–1368, 2011. The absence of comparative validity studies has prevented researchers from reaching consensus regarding the application of intensity-related accelerometer cut points for children and adolescents. Purpose: This study aimed to evaluate the classification accuracy of five sets of independently developed ActiGraph cut points using energy expenditure, measured by indirect calorimetry, as a criterion reference standard. Methods: A total of 206 participants between the ages of 5 and 15 yr completed 12 standardized activity trials. Trials consisted of sedentary activities (lying down, writing, computer game), lifestyle activities (sweeping, laundry, throw and catch, aerobics, basketball), and ambulatory activities
1,149 citations
University of North Texas1, East Malling Research Station2, Plant & Food Research3, Oregon State University4, University of Maryland, College Park5, Indiana University6, Virginia Tech7, Georgia Institute of Technology8, University of New Hampshire9, United States Department of Agriculture10, Hoffmann-La Roche11, University of Auckland12, Rutgers University13, University of the Western Cape14, University of Florida15, University of Chile16, Andrés Bello National University17, Weizmann Institute of Science18, University of Pittsburgh19, University of Georgia20, Technische Universität München21, University of Illinois at Urbana–Champaign22, Institut national de la recherche agronomique23
TL;DR: New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted, and macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes.
Abstract: The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.
1,085 citations
TL;DR: It is shown that top predators exploit their environment in predictable ways, providing the foundation for spatial management of large marine ecosystems, and critical habitats across multinational boundaries are identified.
Abstract: Pelagic marine predators face unprecedented challenges and uncertain futures. Overexploitation and climate variability impact the abundance and distribution of top predators in ocean ecosystems. Improved understanding of ecological patterns, evolutionary constraints and ecosystem function is critical for preventing extinctions, loss of biodiversity and disruption of ecosystem services. Recent advances in electronic tagging techniques have provided the capacity to observe the movements and long-distance migrations of animals in relation to ocean processes across a range of ecological scales. Tagging of Pacific Predators, a field programme of the Census of Marine Life, deployed 4,306 tags on 23 species in the North Pacific Ocean, resulting in a tracking data set of unprecedented scale and species diversity that covers 265,386 tracking days from 2000 to 2009. Here we report migration pathways, link ocean features to multispecies hotspots and illustrate niche partitioning within and among congener guilds. Our results indicate that the California Current large marine ecosystem and the North Pacific transition zone attract and retain a diverse assemblage of marine vertebrates. Within the California Current large marine ecosystem, several predator guilds seasonally undertake north-south migrations that may be driven by oceanic processes, species-specific thermal tolerances and shifts in prey distributions. We identify critical habitats across multinational boundaries and show that top predators exploit their environment in predictable ways, providing the foundation for spatial management of large marine ecosystems.
Max Planck Society1, Laval University2, Harvard University3, McMaster University4, Lund University5, Karlsruhe Institute of Technology6, Dresden University of Technology7, Institut national de la recherche agronomique8, University of Toledo9, University College Cork10, Oregon State University11, ETH Zurich12, United States Forest Service13, Free University of Bozen-Bolzano14, Wageningen University and Research Centre15, National Research Council16, Clark University17
TL;DR: In this paper, the authors upscaled FLUXNET observations of carbon dioxide, water, and energy fluxes to the global scale using the machine learning technique, model tree ensembles (MTE), to predict site-level gross primary productivity (GPP), terrestrial ecosystem respiration (TER), net ecosystem exchange (NEE), latent energy (LE), and sensible heat (H) based on remote sensing indices, climate and meteorological data, and information on land use.
Abstract: We upscaled FLUXNET observations of carbon dioxide, water, and energy fluxes to the global scale using the machine learning technique, model tree ensembles (MTE). We trained MTE to predict site-level gross primary productivity (GPP), terrestrial ecosystem respiration (TER), net ecosystem exchange (NEE), latent energy (LE), and sensible heat (H) based on remote sensing indices, climate and meteorological data, and information on land use. We applied the trained MTEs to generate global flux fields at a 0.5 degrees x 0.5 degrees spatial resolution and a monthly temporal resolution from 1982 to 2008. Cross-validation analyses revealed good performance of MTE in predicting among-site flux variability with modeling efficiencies (MEf) between 0.64 and 0.84, except for NEE (MEf = 0.32). Performance was also good for predicting seasonal patterns (MEf between 0.84 and 0.89, except for NEE (0.64)). By comparison, predictions of monthly anomalies were not as strong (MEf between 0.29 and 0.52). Improved accounting of disturbance and lagged environmental effects, along with improved characterization of errors in the training data set, would contribute most to further reducing uncertainties. Our global estimates of LE (158 +/- 7 J x 10(18) yr(-1)), H (164 +/- 15 J x 10(18) yr(-1)), and GPP (119 +/- 6 Pg C yr(-1)) were similar to independent estimates. Our global TER estimate (96 +/- 6 Pg C yr(-1)) was likely underestimated by 5-10%. Hot spot regions of interannual variability in carbon fluxes occurred in semiarid to semihumid regions and were controlled by moisture supply. Overall, GPP was more important to interannual variability in NEE than TER. Our empirically derived fluxes may be used for calibration and evaluation of land surface process models and for exploratory and diagnostic assessments of the biosphere.
TL;DR: The 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47, based on 8.3× dideoxy sequence coverage, is reported, indicating pervasive selection for a smaller genome in this outcrossing species.
Abstract: We present the 207 Mb genome sequence of the outcrosser Arabidopsis lyrata, which diverged from the self-fertilizing species A. thaliana about 10 million years ago. It is generally assumed that the much smaller A. thaliana genome, which is only 125 Mb, constitutes the derived state for the family. Apparent genome reduction in this genus can be partially attributed to the loss of DNA from large-scale rearrangements, but the main cause lies in the hundreds of thousands of small deletions found throughout the genome. These occurred primarily in non-coding DNA and transposons, but protein-coding multi-gene families are smaller in A. thaliana as well. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome.
TL;DR: Early-successional forest ecosystems that develop after stand-replacement or partial disturbances are diverse in species, processes, and structure as mentioned in this paper, including surviving organisms and organically derived structures, such as woody debris.
Abstract: Early-successional forest ecosystems that develop after stand-replacing or partial disturbances are diverse in species, processes, and structure. Post-disturbance ecosystems are also often rich in biological legacies, including surviving organisms and organically derived structures, such as woody debris. These legacies and post-disturbance plant communities provide resources that attract and sustain high species diversity, including numerous early-successional obligates, such as certain woodpeckers and arthropods. Early succession is the only period when tree canopies do not dominate the forest site, and so this stage can be characterized by high productivity of plant species (including herbs and shrubs), complex food webs, large nutrient fluxes, and high structural and spatial complexity. Different disturbances contrast markedly in terms of biological legacies, and this will influence the resultant physical and biological conditions, thus affecting successional pathways. Management activities, such as post-disturbance logging and dense tree planting, can reduce the richness within and the duration of early-successional ecosystems. Where maintenance of biodiversity is an objective, the importance and value of these natural early-successional ecosystems are underappreciated.
TL;DR: Mechanism-based effects of vitamin C and E supplementation on biomarkers and on clinical outcomes from randomized, placebo-controlled trials are emphasized in this review.
TL;DR: Spotted wing drosophila, Drosophila suzukii Matsumura, a native of eastern and southeastern Asia, is a pest of small and stone fruits and a potential economic threat to a host of soft- and thin-skinned fruit crops.
Abstract: Spotted wing drosophila, Drosophila suzukii Matsumura, a native of eastern and southeastern Asia, is a pest of small and stone fruits. First detected in California in 2008, the insect is now found across the Pacific Coast states. Its penchant for attacking healthy, ripening fruit (as opposed to overripe and rotting fruit favored by other so-called “vinegar flies”) makes it a potential economic threat to a host of soft- and thin-skinned fruit crops including cherry, raspberry, blackberry, blueberry, strawberry, peach, plums, pluots, nectarines, juice grape, table grape, and wine grape. Coordinated research projects to determine host preference, seasonal phenology, biology, and management options are taking place among entomologists in Washington, Oregon, and California. A description of the pest and initial findings on its biology, life history, known and expected geographic range, management and monitoring techniques, and economic considerations are presented and discussed.
TL;DR: In this paper, the authors use theory-building through case studies to answer the question: how do organizations balance short-term profitability and long-term environmental sustainability when making supply chain decisions under conditions of uncertainty?
Swedish University of Agricultural Sciences1, University of Exeter2, Commonwealth Scientific and Industrial Research Organisation3, University of Bath4, George Washington University5, Ghent University6, Centre for DNA Fingerprinting and Diagnostics7, University of Copenhagen8, Kansas State University9, University of Montpellier10, Max Planck Society11, University of Warsaw12, University of Georgia13, National Autonomous University of Mexico14, Australian National University15, University of Valencia16, Wageningen University and Research Centre17, Agriculture and Agri-Food Canada18, University of Saskatchewan19, Stockholm University20, Eötvös Loránd University21, University of Tokyo22, National Institute of Advanced Industrial Science and Technology23, Plant & Food Research24, Oregon State University25, Agricultural Research Service26, Leiden University27, University of Manitoba28
TL;DR: Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involved in immunity and that gene expression in epidermal tissues seems to be most difficult to silence.
TL;DR: In this article, the authors studied the role of biogeochemical feedbacks such as desorption (release) of phosphorus bound to clay as salinity increases, lack of planktonic N fixation in most coastal ecosystems, and flux of relatively P-rich, N-poor waters from coastal oceans into estuaries.
Abstract: Nutrient fluxes to coastal areas have risen in recent decades, leading to widespread hypoxia and other ecological damage, particularly from nitrogen (N). Several factors make N more limiting in estuaries and coastal waters than in lakes: desorption (release) of phosphorus (P) bound to clay as salinity increases, lack of planktonic N fixation in most coastal ecosystems, and flux of relatively P-rich, N-poor waters from coastal oceans into estuaries. During eutrophication, biogeochemical feedbacks further increase the supply of N and P, but decrease availability of silica - conditions that can favor the formation and persistence of harmful algal blooms. Given sufficient N inputs, estuaries and coastal marine ecosystems can be driven to P limitation. This switch contributes to greater far-field N pollution; that is, the N moves further and contributes to eutrophication at greater distances. The physical oceanography (extent of stratification, residence time, and so forth) of coastal systems determines their sensitivity to hypoxia, and recent changes in physics have made some ecosystems more sensitive to hypoxia. Coastal hypoxia contributes to ocean acidification, which harms calcifying organisms such as mollusks and some crustaceans. (Less)
TL;DR: Genome-wide analyses from several plant species have revealed that variation in miRNA foldback expression, structure, processing efficiency, and miRNA size have resulted in the unique functionality of MIRNA loci and resulting miRNAs.
Abstract: MicroRNAs (miRNAs) are small regulatory RNAs found in diverse eukaryotic lineages. In plants, a minority of annotated MIRNA gene families are conserved between plant families, while the majority are family- or species-specific, suggesting that most known MIRNA genes arose relatively recently in evolutionary time. Given the high proportion of young MIRNA genes in plant species, new MIRNA families are likely spawned and then lost frequently. Unlike highly conserved, ancient miRNAs, young miRNAs are often weakly expressed, processed imprecisely, lack targets, and display patterns of neutral variation, suggesting that young MIRNA loci tend to evolve neutrally. Genome-wide analyses from several plant species have revealed that variation in miRNA foldback expression, structure, processing efficiency, and miRNA size have resulted in the unique functionality of MIRNA loci and resulting miRNAs. Additionally, some miRNAs have evolved specific properties and functions that regulate other transcriptional or posttranscriptional silencing pathways. The evolution of miRNA processing and functional diversity underscores the dynamic nature of miRNA-based regulation in complex regulatory networks.
TL;DR: In this article, a critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them, focusing on neat and high fraction cellulose composites.
Abstract: This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).
TL;DR: This article summarizes and classifies research on end-user software engineering activities, defining the area of End-User Software Engineering (EUSE) and related terminology, and addresses several crosscutting issues in the design of EUSE tools.
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.
University of Notre Dame1, Michigan State University2, University of New Hampshire3, University of Wyoming4, Oak Ridge National Laboratory5, University of Tennessee6, Marine Biological Laboratory7, Oregon State University8, University of Maryland, College Park9, University of New Mexico10, Kansas State University11, United States Department of Agriculture12, Montana State University13, Virginia Tech14, Central Washington University15, Ball State University16, Wright State University17, University of Georgia18, Indiana University19, University of Canterbury20, Arizona State University21, United States Geological Survey22, Washington State University Vancouver23
TL;DR: It is found that stream denitrification produces N2O at rates that increase with stream water nitrate (NO3−) concentrations, but that <1% of denitrified N is converted to N1O, and it is suggested that increased stream NO3− loading stimulatesDenitrification and concomitant N2o production, but does not increase the N2 O yield.
Abstract: Nitrous oxide (N2O) is a potent greenhouse gas that contributes to climate change and stratospheric ozone destruction. Anthropogenic nitrogen (N) loading to river networks is a potentially important source of N2O via microbial denitrification that converts N to N2O and dinitrogen (N2). The fraction of denitrified N that escapes as N2O rather than N2 (i.e., the N2O yield) is an important determinant of how much N2O is produced by river networks, but little is known about the N2O yield in flowing waters. Here, we present the results of whole-stream 15N-tracer additions conducted in 72 headwater streams draining multiple land-use types across the United States. We found that stream denitrification produces N2O at rates that increase with stream water nitrate (NO3−) concentrations, but that <1% of denitrified N is converted to N2O. Unlike some previous studies, we found no relationship between the N2O yield and stream water NO3−. We suggest that increased stream NO3− loading stimulates denitrification and concomitant N2O production, but does not increase the N2O yield. In our study, most streams were sources of N2O to the atmosphere and the highest emission rates were observed in streams draining urban basins. Using a global river network model, we estimate that microbial N transformations (e.g., denitrification and nitrification) convert at least 0.68 Tg·y−1 of anthropogenic N inputs to N2O in river networks, equivalent to 10% of the global anthropogenic N2O emission rate. This estimate of stream and river N2O emissions is three times greater than estimated by the Intergovernmental Panel on Climate Change.
TL;DR: A review of the social science literature related to the concept of amenity migration, focusing on the ways in which it has been conceptualized, theorized, and documented by different communities of scholars is presented in this paper.
Abstract: Rural communities throughout the postindustrial world are in the midst of a significant transition, sometimes referred to as rural restructuring, as traditional land uses, economic activities, and social arrangements transition to those associated with “post-productivist” or “multifunctional” landscapes. Amenity migration, the movement of people based on the draw of natural and/or cultural amenities, can be thought of as both driver and implication of this transition, resulting in significant changes in the ownership, use, and governance of rural lands, as well as in the composition and socioeconomic dynamics of rural communities. In concert with other social, economic and political processes, amenity migration is contributing to the fundamental transformation of rural communities throughout the world. This paper presents a review of the social science literature related to the concept of amenity migration, focusing on the ways in which it has been conceptualized, theorized, and documented by different communities of scholars. We then profile and summarize diverse perspectives on drivers and socioeconomic impacts, highlighting emerging challenges and opportunities related to this type of migration occurring at multiple scales and in multiple sites. The paper also identifies and discusses particular areas where further research is needed.
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, University of KwaZulu-Natal22, Yale University23, 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.
University of California, Davis1, Virginia Tech2, University of North Carolina at Chapel Hill3, University of Birmingham4, University of Manchester5, Kyoto University6, Saitama University7, Rutgers University8, University of Copenhagen9, Aberystwyth University10, Durham University11, James Hutton Institute12, Ghent University13, Oregon State University14, Wageningen University and Research Centre15, Karolinska Institutet16, Swedish University of Agricultural Sciences17
TL;DR: A classification based on morphological criteria is suggested of PCD associated with the hypersensitive response to biotrophic pathogens, which can express features of both necrosis and vacuolar cell death, PCD in starchy cereal endosperm and during self-incompatibility.
Abstract: Programmed cell death (PCD) is an integral part of plant development and of responses to abiotic stress or pathogens. Although the morphology of plant PCD is, in some cases, well characterised and molecular mechanisms controlling plant PCD are beginning to emerge, there is still confusion about the classification of PCD in plants. Here we suggest a classification based on morphological criteria. According to this classification, the use of the term 'apoptosis' is not justified in plants, but at least two classes of PCD can be distinguished: vacuolar cell death and necrosis. During vacuolar cell death, the cell contents are removed by a combination of autophagy-like process and release of hydrolases from collapsed lytic vacuoles. Necrosis is characterised by early rupture of the plasma membrane, shrinkage of the protoplast and absence of vacuolar cell death features. Vacuolar cell death is common during tissue and organ formation and elimination, whereas necrosis is typically found under abiotic stress. Some examples of plant PCD cannot be ascribed to either major class and are therefore classified as separate modalities. These are PCD associated with the hypersensitive response to biotrophic pathogens, which can express features of both necrosis and vacuolar cell death, PCD in starchy cereal endosperm and during self-incompatibility. The present classification is not static, but will be subject to further revision, especially when specific biochemical pathways are better defined.
Yale University1, University of California, Irvine2, United States Department of Agriculture3, Environment Canada4, University of British Columbia5, Ohio State University6, University of Florida7, Smithsonian Institution8, University of California, Berkeley9, Oak Ridge National Laboratory10, Duke University11, Northern Arizona University12, Oregon State University13, Laval University14, National Oceanic and Atmospheric Administration15, University of Colorado Boulder16, Harvard University17, University of California, Davis18, Karlsruhe Institute of Technology19
TL;DR: It is shown that surface air temperature is lower in open land than in nearby forested land, and latitudinal dependence is consistent with theoretical expectation of changes in energy loss from convection and radiation across latitudes in both the daytime and night-time phase of the diurnal cycle, the latter of which remains uncertain in climate models.
Abstract: Deforestation in mid- to high latitudes is hypothesized to have the potential to cool the Earth's surface by altering biophysical processes. In climate models of continental-scale land clearing, the cooling is triggered by increases in surface albedo and is reinforced by a land albedo-sea ice feedback. This feedback is crucial in the model predictions; without it other biophysical processes may overwhelm the albedo effect to generate warming instead. Ongoing land-use activities, such as land management for climate mitigation, are occurring at local scales (hectares) presumably too small to generate the feedback, and it is not known whether the intrinsic biophysical mechanism on its own can change the surface temperature in a consistent manner. Nor has the effect of deforestation on climate been demonstrated over large areas from direct observations. Here we show that surface air temperature is lower in open land than in nearby forested land. The effect is 0.85 ± 0.44 K (mean ± one standard deviation) northwards of 45° N and 0.21 ± 0.53 K southwards. Below 35° N there is weak evidence that deforestation leads to warming. Results are based on comparisons of temperature at forested eddy covariance towers in the USA and Canada and, as a proxy for small areas of cleared land, nearby surface weather stations. Night-time temperature changes unrelated to changes in surface albedo are an important contributor to the overall cooling effect. The observed latitudinal dependence is consistent with theoretical expectation of changes in energy loss from convection and radiation across latitudes in both the daytime and night-time phase of the diurnal cycle, the latter of which remains uncertain in climate models.
University of Massachusetts Medical School1, Massachusetts Institute of Technology2, Hebrew University of Jerusalem3, Harvard University4, National Institute of Genetics5, National Institutes of Health6, University of Edinburgh7, State University of New York System8, Oregon State University9, Cold Spring Harbor Laboratory10, University of Cambridge11, University of Nottingham12, Södertörn University13, Karolinska Institutet14, University of Warwick15, Stowers Institute for Medical Research16, Howard Hughes Medical Institute17, University of Kansas18
TL;DR: Differences in gene content and regulation explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source and provide tools for investigation across the Schizosaccharomyces clade.
Abstract: The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus--occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.
TL;DR: The genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans is reported and its repertoire of protein effectors is characterized, revealing an unusual bipartite structure that underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
Abstract: Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
University of Leeds1, National Institute of Amazonian Research2, Forestry Commission3, Wageningen University and Research Centre4, James Cook University5, University of St Andrews6, Indiana University7, Paul Sabatier University8, Forest Research Institute9, University of São Paulo10, University of Edinburgh11, University of Waterloo12, University of New Hampshire13, Hokkaido University14, Universiti Brunei Darussalam15, Forest Research Institute Malaysia16, United States Forest Service17, Oregon State University18, University of Twente19, Universidade do Estado de Mato Grosso20, University of York21, Commonwealth Scientific and Industrial Research Organisation22, National University of Colombia23, University of Cambridge24, University of Yaoundé I25
TL;DR: In this article, the authors developed a new global tropical forest database consisting of 39 955 concurrent H and D measurements encompassing 283 sites in 22 tropical countries, and used this database to determine if H:D relationships differ by geographic region and forest type (wet to dry forests, including zones of tension where forest and savanna overlap).
Abstract: . Tropical tree height-diameter (H:D) relationships may vary by forest type and region making large-scale estimates of above-ground biomass subject to bias if they ignore these differences in stem allometry. We have therefore developed a new global tropical forest database consisting of 39 955 concurrent H and D measurements encompassing 283 sites in 22 tropical countries. Utilising this database, our objectives were: 1. to determine if H:D relationships differ by geographic region and forest type (wet to dry forests, including zones of tension where forest and savanna overlap). 2. to ascertain if the H:D relationship is modulated by climate and/or forest structural characteristics (e.g. stand-level basal area, A). 3. to develop H:D allometric equations and evaluate biases to reduce error in future local-to-global estimates of tropical forest biomass. Annual precipitation coefficient of variation (PV), dry season length (SD), and mean annual air temperature (TA) emerged as key drivers of variation in H:D relationships at the pantropical and region scales. Vegetation structure also played a role with trees in forests of a high A being, on average, taller at any given D. After the effects of environment and forest structure are taken into account, two main regional groups can be identified. Forests in Asia, Africa and the Guyana Shield all have, on average, similar H:D relationships, but with trees in the forests of much of the Amazon Basin and tropical Australia typically being shorter at any given D than their counterparts elsewhere. The region-environment-structure model with the lowest Akaike's information criterion and lowest deviation estimated stand-level H across all plots to within amedian −2.7 to 0.9% of the true value. Some of the plot-to-plot variability in H:D relationships not accounted for by this model could be attributed to variations in soil physical conditions. Other things being equal, trees tend to be more slender in the absence of soil physical constraints, especially at smaller D. Pantropical and continental-level models provided less robust estimates of H, especially when the roles of climate and stand structure in modulating H:D allometry were not simultaneously taken into account.