Showing papers by "University of Guelph published in 2011"
Max Planck Society1, National University of Cordoba2, Centre national de la recherche scientifique3, Macquarie University4, University of Paris-Sud5, University of Minnesota6, University of Western Sydney7, VU University Amsterdam8, University of Arizona9, University of California, Berkeley10, University of Guelph11, Australian National University12, University of Innsbruck13, University of Leeds14, University of Groningen15, Universidade Federal do Rio Grande do Sul16, University of Cape Town17, University of Wollongong18, New Jersey Institute of Technology19, Centro Agronómico Tropical de Investigación y Enseñanza20, Lawrence Berkeley National Laboratory21, University of Alaska Fairbanks22, University of Cambridge23, Kansas State University24, Helmholtz Centre for Environmental Research - UFZ25, Arizona State University26, University of Giessen27, Autonomous University of Barcelona28, University of Maryland, College Park29, Universidad del Tolima30, University of São Paulo31, University of La Réunion32, University of York33, University of Sydney34, Harvard University35, Goethe University Frankfurt36, University of Sheffield37, University of Ulm38, State University of Campinas39, Kenyon College40, Royal Botanic Gardens41, University of Florida42, University of Oldenburg43, University of Nebraska–Lincoln44, Tohoku University45, Northern Arizona University46, University of Wisconsin–Eau Claire47, Naturalis48, James Cook University49, Institut national de la recherche agronomique50, Newcastle University51, University of New South Wales52, Leipzig University53, Columbia University54, Estonian University of Life Sciences55, Polish Academy of Sciences56, Moscow State University57, Kyushu University58, Wageningen University and Research Centre59, Spanish National Research Council60, University of Regensburg61, University of Rennes62, Université du Québec à Trois-Rivières63, Potsdam Institute for Climate Impact Research64, Technical University of Denmark65, University of California, Los Angeles66, Hokkaido University67, Université de Sherbrooke68, Syracuse University69, Empresa Brasileira de Pesquisa Agropecuária70, University of Aberdeen71, Michigan State University72, Oak Ridge National Laboratory73, University of Leicester74, Utah State University75, Smithsonian Institution76, University of Missouri77
TL;DR: TRY as discussed by the authors is a global database of plant traits, including morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs, which can be used for a wide range of research from evolutionary biology, community and functional ecology to biogeography.
Abstract: Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.
2,017 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, Research Institute of Molecular Pathology15, University of Geneva16, Oregon State University17, Utrecht University18, University of California, Davis19, Hoffmann-La Roche20, University of Iowa21, 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
Spanish National Research Council1, University of Western Ontario2, Ghent University3, University of Utah4, SupAgro5, University of Lisbon6, Instituto Gulbenkian de Ciência7, University of Arizona8, Johns Hopkins University School of Medicine9, University of Bordeaux10, Valparaiso University11, Autonomous University of Madrid12, Georgia Institute of Technology13, University of Texas at Arlington14, Centre national de la recherche scientifique15, Graduate University for Advanced Studies16, Katholieke Universiteit Leuven17, Max Planck Society18, University of Guelph19, Boyce Thompson Institute for Plant Research20, Agriculture and Agri-Food Canada21, Joint Genome Institute22, University of Nice Sophia Antipolis23
TL;DR: The Tetranychus urticae genome is the smallest known arthropod genome as discussed by the authors, which represents the first complete chelicerate genome for a pest and has been annotated with genes associated with feeding on different hosts.
Abstract: The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.
894 citations
TL;DR: In this article, the authors describe a new approach to the performance management process that includes employee engagement and the key drivers of employee engagement at each stage, and suggest a new perspective for thinking about how to foster and manage employee engagement to achieve high levels of job performance.
759 citations
TL;DR: Carry-over effects are likely to be far more widespread than currently indicated, and they could feasibly be responsible for a large amount of the observed variation in performance among individuals, and warrant a wealth of new research designed specifically to decompose components of variation in fitness attributes related to processes across and within seasons.
Abstract: 1. Carry-over effects occur when processes in one season influence the success of an individual in the following season. This phenomenon has the potential to explain a large amount of variation in individual fitness, but so far has only been described in a limited number of species. This is largely due to difficulties associated with tracking individuals between periods of the annual cycle, but also because of a lack of research specifically designed to examine hypotheses related to carry-over effects. 2. We review the known mechanisms that drive carry-over effects, most notably macronutrient supply, and highlight the types of life histories and ecological situations where we would expect them to most often occur. We also identify a number of other potential mechanisms that require investigation, including micronutrients such as antioxidants. 3. We propose a series of experiments designed to estimate the relative contributions of extrinsic and intrinsic quality effects in the pre-breeding season, which in turn will allow an accurate estimation of the magnitude of carry-over effects. To date this has proven immensely difficult, and we hope that the experimental frameworks described here will stimulate new avenues of research vital to advancing our understanding of how carry-over effects can shape animal life histories. 4. We also explore the potential of state-dependent modelling as a tool for investigating carry-over effects, most notably for its ability to calculate optimal rates of acquisition of a multitude of resources over the course of the annual cycle, and also because it allows us to vary the strength of density-dependent relationships which can alter the magnitude of carry-over effects in either a synergistic or agonistic fashion. 5. In conclusion carry-over effects are likely to be far more widespread than currently indicated, and they are likely to be driven by a multitude of factors including both macro- and micronutrients. For this reason they could feasibly be responsible for a large amount of the observed variation in performance among individuals, and consequently warrant a wealth of new research designed specifically to decompose components of variation in fitness attributes related to processes across and within seasons.
743 citations
Journal Article•
TL;DR: Inadequate training or inattention to detail during this aspect of a study may result in unintentional adverse effects on experimental animals and confounded results.
Abstract: Administration of substances to laboratory animals requires careful consideration and planning to optimize delivery of the agent to the animal while minimizing potential adverse experiences from the procedure. For all species, many different routes are available for administration of substances. The research team and IACUC members should be aware of reasons for selecting specific routes and of training and competency necessary for personnel to use these routes effectively. Once a route is selected, issues such as volume of administration, site of delivery, pH of the substance, and other factors must be considered to refine the technique. Inadequate training or inattention to detail during this aspect of a study may result in unintentional adverse effects on experimental animals and confounded results.
701 citations
Jacobs University Bremen1, Max Planck Society2, University of Colorado Boulder3, Howard Hughes Medical Institute4, Michigan State University5, Marine Biological Laboratory6, University of Chicago7, Plymouth Marine Laboratory8, Argonne National Laboratory9, National Institutes of Health10, Yonsei University11, University of Manchester12, University of Oxford13, Harvard University14, New York University15, University of Pennsylvania16, Los Alamos National Laboratory17, United States Department of Energy18, University of Maryland, Baltimore19, Ghent University20, Lawrence Berkeley National Laboratory21, University of Southern California22, National Ecological Observatory Network23, Baylor College of Medicine24, University of New Mexico25, Washington University in St. Louis26, University of Queensland27, San Diego State University28, Cornell University29, Technische Universität München30, J. Craig Venter Institute31, University of Waterloo32, Oak Ridge National Laboratory33, Vrije Universiteit Brussel34, University of Guelph35, Stanford University36, United States Department of Veterans Affairs37
TL;DR: To establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, the minimum information about any (x) sequence is presented (MIxS).
Abstract: Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
600 citations
TL;DR: The results indicate the potential of an environmental barcoding approach for biomonitoring programs and show the ability of 454 pyrosequencing of mini-barcodes to accurately identify all species with more than 1% abundance in the pooled mixture.
Abstract: Timely and accurate biodiversity analysis poses an ongoing challenge for the success of biomonitoring programs. Morphology-based identification of bioindicator taxa is time consuming, and rarely supports species-level resolution especially for immature life stages. Much work has been done in the past decade to develop alternative approaches for biodiversity analysis using DNA sequence-based approaches such as molecular phylogenetics and DNA barcoding. On-going assembly of DNA barcode reference libraries will provide the basis for a DNA-based identification system. The use of recently introduced next-generation sequencing (NGS) approaches in biodiversity science has the potential to further extend the application of DNA information for routine biomonitoring applications to an unprecedented scale. Here we demonstrate the feasibility of using 454 massively parallel pyrosequencing for species-level analysis of freshwater benthic macroinvertebrate taxa commonly used for biomonitoring. We designed our experiments in order to directly compare morphology-based, Sanger sequencing DNA barcoding, and next-generation environmental barcoding approaches. Our results show the ability of 454 pyrosequencing of mini-barcodes to accurately identify all species with more than 1% abundance in the pooled mixture. Although the approach failed to identify 6 rare species in the mixture, the presence of sequences from 9 species that were not represented by individuals in the mixture provides evidence that DNA based analysis may yet provide a valuable approach in finding rare species in bulk environmental samples. We further demonstrate the application of the environmental barcoding approach by comparing benthic macroinvertebrates from an urban region to those obtained from a conservation area. Although considerable effort will be required to robustly optimize NGS tools to identify species from bulk environmental samples, our results indicate the potential of an environmental barcoding approach for biomonitoring programs.
515 citations
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.
509 citations
TL;DR: The data suggest that E. coli can persist, for varying periods of time, in such terrestrial and aquatic habitats as soil, manure and water and its acid tolerance may be expected to confer a fitness asset in the more acidic environments.
Abstract: In this review, our current understanding of the species Escherichia coli and its persistence in the open environment is examined. E. coli consists of six different subgroups, which are separable by genomic analyses. Strains within each subgroup occupy various ecological niches, and can be broadly characterized by either commensalistic or different pathogenic behaviour. In relevant cases, genomic islands can be pinpointed that underpin the behaviour. Thus, genomic islands of, on the one hand, broad environmental significance, and, on the other hand, virulence, are highlighted in the context of E. coli survival in its niches. A focus is further placed on experimental studies on the survival of the different types of E. coli in soil, manure and water. Overall, the data suggest that E. coli can persist, for varying periods of time, in such terrestrial and aquatic habitats. In particular, the considerable persistence of the pathogenic E. coli O157:H7 is of importance, as its acid tolerance may be expected to confer a fitness asset in the more acidic environments. In this context, the extent to which E. coli interacts with its human/animal host and the organism's survivability in natural environments are compared. In addition, the effect of the diversity and community structure of the indigenous microbiota on the fate of invading E. coli populations in the open environment is discussed. Such a relationship is of importance to our knowledge of both public and environmental health.
501 citations
TL;DR: There are several potential genetic and molecular approaches for the improvement of crop NUE discussed in this review, and increased knowledge of how plants respond to different N levels as well as to other environmental conditions is required.
Abstract: Development of genetic varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Generally, NUE can be divided into two parts. First, assimilation efficiency involves nitrogen (N) uptake and assimilation and second utilization efficiency involves N remobilization. Understanding the mechanisms regulating these processes is crucial for the improvement of NUE in crop plants. One important approach is to develop an understanding of the plant response to different N regimes, especially to N limitation, using various methods including transcription profiling, analysing mutants defective in their normal response to N limitation, and studying plants that show better growth under N-limiting conditions. One can then attempt to improve NUE in crop plants using the knowledge gained from these studies. There are several potential genetic and molecular approaches for the improvement of crop NUE discussed in this review. Increased knowledge of how plants respond to different N levels as well as to other environmental conditions is required to achieve this.
TL;DR: X-ray crystal structure shows that drugs interact with Pgp within the transmembrane regions by fitting into a large flexible binding pocket, which can accommodate several substrate molecules simultaneously, and it is still not clear whether transport is driven by ATP hydrolysis or ATP binding.
Abstract: Pgp (P-glycoprotein) (ABCB1) is an ATP-powered efflux pump which can transport hundreds of structurally unrelated hydrophobic amphipathic compounds, including therapeutic drugs, peptides and lipid-like compounds This 170 kDa polypeptide plays a crucial physiological role in protecting tissues from toxic xenobiotics and endogenous metabolites, and also affects the uptake and distribution of many clinically important drugs It forms a major component of the blood-brain barrier and restricts the uptake of drugs from the intestine The protein is also expressed in many human cancers, where it probably contributes to resistance to chemotherapy treatment Many chemical modulators have been identified that block the action of Pgp, and may have clinical applications in improving drug delivery and treating cancer Pgp substrates are generally lipid-soluble, and partition into the membrane before the transporter expels them into the aqueous phase, much like a 'hydrophobic vacuum cleaner' The transporter may also act as a 'flippase', moving its substrates from the inner to the outer membrane leaflet An X-ray crystal structure shows that drugs interact with Pgp within the transmembrane regions by fitting into a large flexible binding pocket, which can accommodate several substrate molecules simultaneously The nucleotide-binding domains of Pgp appear to hydrolyse ATP in an alternating manner; however, it is still not clear whether transport is driven by ATP hydrolysis or ATP binding Details of the steps involved in the drug-transport process, and how it is coupled to ATP hydrolysis, remain the object of intensive study
TL;DR: Concept component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny, but there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology.
Abstract: Endophytes are non-pathogenic microbes living inside plants. We asked whether endophytic species were conserved in the agriculturally important plant genus Zea as it became domesticated from its wild ancestors (teosinte) to modern maize (corn) and moved from Mexico to Canada. Kernels from populations of four different teosintes and 10 different maize varieties were screened for endophytic bacteria by culturing, cloning and DNA fingerprinting using terminal restriction fragment length polymorphism (TRFLP) of 16S rDNA. Principle component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny. However, there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology. The majority of seed endophytes in the wild ancestor persist today in domesticated maize, though ancient selection against the hard fruitcase surrounding seeds may have altered the abundance of endophytes. Four TRFLP signals including two predicted to represent Clostridium and Paenibacillus species were conserved across all Zea genotypes, while culturing showed that Enterobacter, Methylobacteria, Pantoea and Pseudomonas species were widespread, with γ-proteobacteria being the prevalent class. Twenty-six different genera were cultured, and these were evaluated for their ability to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. Of these traits, phosphate solubilization and production of acetoin/butanediol were the most commonly observed. An isolate from the giant Mexican landrace Mixteco, with 100% identity to Burkholderia phytofirmans, significantly promoted shoot potato biomass. GFP tagging and maize stem injection confirmed that several seed endophytes could spread systemically through the plant. One seed isolate, Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration.
TL;DR: In this article, the vulnerability of the North American high-latitude soil organic carbon (SOC) pool to climate change has been discussed, where the authors divide the current northern highlatitude organic carbon pools into near-surface soils where SOC is affected by seasonal freeze-thaw processes and changes in moisture status, and deeper permafrost and peatland strata down to several tens of meters depth where organic carbon is usually not affected by short-term changes.
Abstract: [1] This synthesis addresses the vulnerability of the North American high‐latitude soil organic carbon (SOC) pool to climate change Disturbances caused by climate warming in arctic, subarctic, and boreal environments can result in significant redistribution of C among major reservoirs with potential global impacts We divide the current northern high‐latitude SOC pools into (1) near‐surface soils where SOC is affected by seasonal freeze‐thaw processes and changes in moisture status, and (2) deeper permafrost and peatland strata down to several tens of meters depth where SOC is usually not affected by short‐term changes We address key factors (permafrost, vegetation, hydrology, paleoenvironmental history) and processes (C input, storage, decomposition, and output) responsible for the formation of the large high‐latitude SOC pool in North America and highlight how climate‐related disturbances could alter this pool’s character and size Press disturbances of relatively slow but persistent nature such as top‐down thawing of permafrost, and changes in hydrology, microbiological communities, pedological processes, and vegetation types, as well as pulse disturbances of relatively rapid and local nature such as wildfires and thermokarst, could substantially impact SOC stocks Ongoing climate warming in the North American high‐latitude region could result in crossing environmental thresholds, thereby accelerating press disturbances and increasingly triggering pulse disturbances and eventually affecting the C source/sink net character of northern high‐latitude soils Finally, we assess postdisturbance feedbacks, models, and predictions for the northern high‐latitude SOC pool, and discuss data and research gaps to be addressed by future research
TL;DR: In this article, an analysis of the depth of burning in forests and peatlands in Alaska indicates that ground-layer combustion has accelerated regional carbon losses, indicating that climate change has increased the area affected by forest fires in boreal North America.
Abstract: Climate change has increased the area affected by forest fires in boreal North America. An analysis of the depth of burning in forests and peatlands in Alaska indicates that ground-layer combustion has accelerated regional carbon losses.
TL;DR: Although considerable evidence supports the notion that GCs increase lipolysis through glucocorticoid-induced increases of lipase expression, they clearly have antilipolytic effects within these same tissues and cell line models.
Abstract: Glucocorticoids (GCs) have long been accepted as being catabolic in nature, liberating energy substrates during times of stress to supply the increased metabolic demand of the body. The effects of GCs on adipose tissue metabolism are conflicting, however, because patients with elevated GCs present with central adiposity. We performed an extensive literature review of the effects of GCs on adipose tissue metabolism. The contradictory effects of GCs on lipid metabolism occur through a number of different mechanisms, some of which are well defined and others remain to be elucidated. Firstly, through increases in caloric and dietary fat intake, along with increased hydrolysis of circulating triglycerides (chylomicrons, very low-density lipoproteins) by lipoprotein lipase activity, GCs increase the amount of fatty acids in circulation, which are then available for ectopic fat distribution (liver, muscle, and central adipocytes). Glucocorticoids also increase de novo lipid production in hepatocytes through increased expression of fatty acid synthase. There is some controversy as to whether these same mechanisms occur in adipocytes, thereby contributing to adipose hypertrophy. Glucocorticoids promote preadipocyte conversion to mature adipocytes, causing hyperplasia of the adipose tissue. Glucocorticoids also have acute antilipolytic effect on adipocytes, whereas their genomic actions facilitate increased lipolysis after about 48 hours of exposure. The acute and long-term effects of GCs on adipose tissue lipolysis remain unclear. Although considerable evidence supports the notion that GCs increase lipolysis through glucocorticoid-induced increases of lipase expression, they clearly have antilipolytic effects within these same tissues and cell line models.
TL;DR: This review summarizes the recent application of both thermal and non-thermal processing technologies on bioactive content of exotic fruits and their products and discusses the impact of processing conditions on the stability of bioactive compounds in exotic fruits.
TL;DR: This study indicates that colonization of the intestinal mucosa by highly invasive strains of F. nucleatum may be a useful biomarker for gastrointestinal disease.
Abstract: Background: Fusobacterium nucleatum is a heterogeneous oral pathogen that is also a common resident of the human gut mucosa. Given that some strains of F. nucleatum are known to be invasive and proinflammatory in the oral mucosa, we compared strains isolated from patients with inflammatory bowel disease (IBD) with strains isolated from healthy controls to determine 1) whether this species was more commonly associated with IBD patients; and 2) whether gut-derived F. nucleatum strains from IBD patients showed an increased capacity for invasion. Methods: Biopsy material was obtained from 56 adult patients undergoing colonoscopy for colon cancer screening purposes or assessment of irritable bowel syndrome status (34 patients), or to assess for presence of gastrointestinal disease (i.e., IBD or indeterminate colitis, 22 patients). We enumerated Fusobacterium spp. strains isolated from human gut biopsy material in a blinded fashion, and then compared the virulence potential of a subset of F. nucleatum strains using an invasion assay in a Caco-2 model system. Results: Fusobacterium spp. were isolated from 63.6% of patients with gastrointestinal disease compared to 26.5% of healthy controls (P ¼ 0.01). In total, 69% of all Fusobacterium spp. recovered from patients were identified as F. nucleatum. F. nucleatum strains originating from inflamed biopsy tissue from IBD patients were significantly more invasive in a Caco-2 cell invasion assay than strains that were isolated from healthy tissue from either IBD patients or control patients (P < 0.05 to 0.001). Conclusions: This study indicates that colonization of the intestinal mucosa by highly invasive strains of F. nucleatum may be a useful biomarker for gastrointestinal disease. (Inflamm Bowel Dis 2011;17:1971–1978)
TL;DR: In this article, the impact of drying-rewetting events and thawing of frozen soils on larger scale ecosystem fluxes is increasingly recognized, and a growing number of studies show that these events affect fluxes of soil gases such as carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), ammonia (NH3) and nitric oxide (NO).
Abstract: . The rewetting of dry soils and the thawing of frozen soils are short-term, transitional phenomena in terms of hydrology and the thermodynamics of soil systems. The impact of these short-term phenomena on larger scale ecosystem fluxes is increasingly recognized, and a growing number of studies show that these events affect fluxes of soil gases such as carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), ammonia (NH3) and nitric oxide (NO). Global climate models predict that future climatic change is likely to alter the frequency and intensity of drying-rewetting events and thawing of frozen soils. These future scenarios highlight the importance of understanding how rewetting and thawing will influence dynamics of these soil gases. This study summarizes findings using a new database containing 338 studies conducted from 1956 to 2011, and highlights open research questions. The database revealed conflicting results following rewetting and thawing in various terrestrial ecosystems and among soil gases, ranging from large increases in fluxes to non-significant changes. Studies reporting lower gas fluxes before rewetting tended to find higher post-rewetting fluxes for CO2, N2O and NO; in addition, increases in N2O flux following thawing were greater in warmer climate regions. We discuss possible mechanisms and controls that regulate flux responses, and recommend that a high temporal resolution of flux measurements is critical to capture rapid changes in gas fluxes after these soil perturbations. Finally, we propose that future studies should investigate the interactions between biological (i.e., microbial community and gas production) and physical (i.e., porosity, diffusivity, dissolution) changes in soil gas fluxes, apply techniques to capture rapid changes (i.e., automated measurements), and explore synergistic experimental and modelling approaches.
TL;DR: In this paper, the authors highlight some of the most promising and important nanotechnology applications in agriculture; and recommend several strategies for advancing the best scientific and technological knowledge presently being examined, with implications for human and environmental health, and technical, financial and capacity-related challenges as they relate to developing countries.
Abstract: Nanoscale science and nanotechnology have been demonstrated to have great potential in providing novel and improved solutions to many grand challenges facing agriculture and society today and in the future. This review highlights some of the most promising and important nanotechnology applications in agriculture; and recommends several strategies for advancing the best scientific and technological knowledge presently being examined. In addition, implications for human and environmental health, and technical, financial and capacity-related challenges as they relate to developing countries are identified. Finally, some suggested mechanisms for partnerships and collaborations are also identified and suggested.
TL;DR: A review of the different structural principles involved in the assembly of the casein micellar particles present in mammalian milks is given in this article, where the evidence for particular models is given, and it is concluded that a model based on calcium phosphate nanoclusters is the most appropriate in view of electron microscopic and scattering experiments.
Abstract: A review is made of the different structural principles involved in the assembly of the casein micellar particles present in mammalian milks. The properties of the constituent casein proteins are described, and how these can lead to different structural models. The evidence for particular models is given, and it is concluded that a model based on calcium phosphate nanoclusters is the most appropriate in view of electron microscopic and scattering experiments. A modification of the nanocluster model is presented, which allows many of the known structural properties of the micelles to be incorporated.
Michigan State University1, National Institutes of Health2, Amgen3, University of Guelph4, Charles River Laboratories5, University of Florida6, University of Pennsylvania7, University of Georgia8, Bristol-Myers Squibb9, Purdue University10, Armed Forces Institute of Pathology11, Utrecht University12, University of Wyoming13, Royal Veterinary College14, Ohio State University15, Charles Sturt University16
TL;DR: According to the novel grading system, high-grade MCTs were significantly associated with shorter time to metastasis or new tumor development, and with shorter survival time.
Abstract: Currently, prognostic and therapeutic determinations for canine cutaneous mast cell tumors (MCTs) are primarily based on histologic grade. However, the use of different grading systems by veterinary pathologists and institutional modifications make the prognostic value of histologic grading highly questionable. To evaluate the consistency of microscopic grading among veterinary pathologists and the prognostic significance of the Patnaik grading system, 95 cutaneous MCTs from 95 dogs were graded in a blinded study by 28 veterinary pathologists from 16 institutions. Concordance among veterinary pathologists was 75% for the diagnosis of grade 3 MCTs and less than 64% for the diagnosis of grade 1 and 2 MCTs. To improve concordance among pathologists and to provide better prognostic significance, a 2-tier histologic grading system was devised. The diagnosis of high-grade MCTs is based on the presence of any one of the following criteria: at least 7 mitotic figures in 10 high-power fields (hpf); at least 3 multinucleated (3 or more nuclei) cells in 10 hpf; at least 3 bizarre nuclei in 10 hpf; karyomegaly (ie, nuclear diameters of at least 10% of neoplastic cells vary by at least two-fold). Fields with the highest mitotic activity or with the highest degree of anisokaryosis were selected to assess the different parameters. According to the novel grading system, high-grade MCTs were significantly associated with shorter time to metastasis or new tumor development, and with shorter survival time. The median survival time was less than 4 months for high-grade MCTs but more than 2 years for low-grade MCTs.
TL;DR: This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene.
Abstract: More than 230,000 known species representing 31 metazoan phyla populate the world’s oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may outpace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a ∼648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.
TL;DR: Elevated serum NEFA concentrations within 1 wk before calving were associated with increased risk of RP, metritis, and DA after calving, and Serum NEFA and calcium concentrations in the 2 wk around calving in combination wereassociated with the risk of DA.
University of Illinois at Urbana–Champaign1, University of Guelph2, Boehringer Ingelheim3, University of Pennsylvania4, Colorado State University5, Idexx Laboratories6, Michigan State University7, Purdue University8, University of California, Davis9, University of Milan10, Swedish University of Agricultural Sciences11
TL;DR: A study was carried out to test the accuracy and consistency of veterinary pathologists, not specialists in hematopathology, in applying the World Health Organization (WHO) system of classification of canine lymphomas.
Abstract: A study was carried out to test the accuracy and consistency of veterinary pathologists, not specialists in hematopathology, in applying the World Health Organization (WHO) system of classification of canine lymphomas. This study represents an initiative of the ACVP Oncology Committee, and the classification has been endorsed by the World Small Animal Veterinary Association (WASVA). Tissue biopsies from cases of canine lymphoma were received from veterinary oncologists, and a study by pathologists given only signalment was carried out on 300 cases. Twenty pathologists reviewed these 300 cases with each required to choose a diagnosis from a list of 43 B and T cell lymphomas. Three of the 20 were hematopathologists who determined the consensus diagnosis for each case. The 17 who formed the test group were experienced but not specialists in hematopathology, and most were diplomates of the American or European Colleges of Veterinary Pathology. The overall accuracy of the 17 pathologists on the 300 cases was 83%. When the analysis was limited to the 6 most common diagnoses, containing 80% of all cases, accuracy rose to 87%. In a test of reproducibility enabled by reintroducing 5% of cases entered under a different identity, the overall agreement between the first and second diagnosis ranged from 40 to 87%. The statistical review included 43,000 data points for each of the 20 pathologists.
TL;DR: A uniform statistical framework is proposed to separate migration from other movement behaviours, quantify migration parameters without the need for arbitrary cut-off criteria and test predictability across individuals, time and space and suggests it can help increase the understanding of the drivers of migration.
Abstract: Summary 1. Animal migration has long intrigued scientists and wildlife managers alike, yet migratory species face increasing challenges because of habitat fragmentation, climate change and over-exploitation. Central to the understanding migratory species is the objective discrimination between migratory and nonmigratory individuals in a given population, quantifying the timing, duration and distance of migration and the ability to predict migratory movements. 2. Here, we propose a uniform statistical framework to (i) separate migration from other movement behaviours, (ii) quantify migration parameters without the need for arbitrary cut-off criteria and (iii) test predictability across individuals, time and space. 3. We first validated our novel approach by simulating data based on established theoretical movement patterns. We then formulated the expected shapes of squared displacement patterns as nonlinear models for a suite of movement behaviours to test the ability of our method to distinguish between migratory movement and other movement types. 4. We then tested our approached empirically using 108 wild Global Positioning System (GPS)collared moose Alces alces in Scandinavia as a study system because they exhibit a wide range of movement behaviours, including resident, migrating and dispersing individuals, within the same population. Applying our approach showed that 87% and 67% of our Swedish and Norwegian subpopulations, respectively, can be classified as migratory. 5. Using nonlinear mixed effects models for all migratory individuals we showed that the distance, timing and duration of migration differed between the sexes and between years, with additional individual differences accounting for a large part of the variation in the distance of migration but not in the timing or duration. Overall, the model explained most of the variation (92%) and also had high predictive power for the same individuals over time (69%) as well as between study populations (74%). 6. The high predictive ability of the approach suggests that it can help increase our understanding of the drivers of migration and could provide key quantitative information for understanding and managing a broad range of migratory species.
TL;DR: The results demonstrate that NLA and miR827 have pivotal roles in regulating Pi homeostasis in plants in a nitrate-dependent fashion.
Abstract: Plants need abundant nitrogen and phosphorus for higher yield. Improving plant genetics for higher nitrogen and phosphorus use efficiency would save potentially billions of dollars annually on fertilizers and reduce global environmental pollution. This will require knowledge of molecular regulators for maintaining homeostasis of these nutrients in plants. Previously, we reported that the NITROGEN LIMITATION ADAPTATION (NLA) gene is involved in adaptive responses to low-nitrogen conditions in Arabidopsis, where nla mutant plants display abrupt early senescence. To understand the molecular mechanisms underlying NLA function, two suppressors of the nla mutation were isolated that recover the nla mutant phenotype to wild type. Map-based cloning identified these suppressors as the phosphate (Pi) transport-related genes PHF1 and PHT1.1. In addition, NLA expression is shown to be regulated by the low-Pi induced microRNA miR827. Pi analysis revealed that the early senescence in nla mutant plants was due to Pi toxicity. These plants accumulated over five times the normal Pi content in shoots specifically under low nitrate and high Pi but not under high nitrate conditions. Also the Pi overaccumulator pho2 mutant shows Pi toxicity in a nitrate-dependent manner similar to the nla mutant. Further, the nitrate and Pi levels are shown to have an antagonistic crosstalk as displayed by their differential effects on flowering time. The results demonstrate that NLA and miR827 have pivotal roles in regulating Pi homeostasis in plants in a nitrate-dependent fashion.
Goddard Space Flight Center1, University of Maryland, Baltimore County2, Science Applications International Corporation3, Hokkaido University4, European Centre for Medium-Range Weather Forecasts5, University of Guelph6, Florida State University7, Catalan Institution for Research and Advanced Studies8, National Oceanic and Atmospheric Administration9, University of Gothenburg10, Environment Canada11, Princeton University12, Michigan State University13, ETH Zurich14, Royal Netherlands Meteorological Institute15
TL;DR: The second phase of the Global Land-Atmosphere Coupling Experiment (GLACE-2) is a multi-institutional numerical modeling experiment focused on quantifying, for boreal summer, the subseasonal forecast skill for precipitation and air temperature that can be derived from the realistic initialization of land surface states, notably soil moisture as mentioned in this paper.
Abstract: The second phase of the Global Land–Atmosphere Coupling Experiment (GLACE-2) is a multi-institutional numerical modeling experiment focused on quantifying, for boreal summer, the subseasonal (out to two months) forecast skill for precipitation and air temperature that can be derived from the realistic initialization of land surface states, notably soil moisture. An overview of the experiment and model behavior at the global scale is described here, along with a determination and characterization of multimodel “consensus” skill. The models show modest but significant skill in predicting air temperatures, especially where the rain gauge network is dense. Given that precipitation is the chief driver of soil moisture, and thereby assuming that rain gauge density is a reasonable proxy for the adequacy of the observational network contributing to soil moisture initialization, this result indeed highlights the potential contribution of enhanced observations to prediction. Land-derived precipitation forec...
TL;DR: The aim of this study was to determine the presence of 33 pharmaceutically active compounds in specific points of the main rivers of the Madrid Region as well as tap water samples from the metropolitan area of Madrid, and to report the highest concentration of the cytostatic ifosfamide, detected for the first time in Spain in surface water.
TL;DR: Two methods to monitor the convergence and estimate the uncertainty of sensitivity analysis techniques are proposed based on the central limit theorem and the bootstrap technique to assess five differentensitivity analysis techniques applied to an environmental model.
Abstract: Sensitivity analysis plays an important role in model development, calibration, uncertainty analysis, scenario analysis, and, hence, decision making. With the availability of different sensitivity analysis techniques, selecting an appropriate technique, monitoring the convergence and estimating the uncertainty of the sensitivity indices are very crucial for environmental modelling, especially for distributed models due to their high non-linearity, non-monotonicity, highly correlated parameters, and intensive computational requirements. It would be useful to identify whether some techniques outperform others with respect to computational requirements, reliability, and other criteria. This paper proposes two methods to monitor the convergence and estimate the uncertainty of sensitivity analysis techniques. One is based on the central limit theorem and the other on the bootstrap technique. These two methods are implemented to assess five different sensitivity analysis techniques applied to an environmental model. These techniques are: the Sobol' method, the Morris method, Linear Regression (LR), Regionalized Sensitivity Analysis (RSA), and non-parametric smoothing. The results show that: (i) the Sobol' method is very robust in quantifying sensitivities and ranking parameters despite a large number of model evaluations; (ii) the Morris method is efficient to rank out unimportant parameters at a medium cost; (iii) the non-parametric smoothing is reliable and robust in quantifying the main effects and low-order interactions while requiring a small number of model evaluations; finally (iv) the other two techniques, that is, LR and RSA, should be used with care.