Showing papers by "Colorado State University published in 2016"
TL;DR: In this paper, a theoretical basis for maximum TC intensity appears now to be well established, but a climate theory of TC formation remains elusive Climate models mostly continue to predict future decreases in global TC numbers, projected increases in the intensities of the strongest storms and increased rainfall rates Sea level rise will likely contribute toward increased storm surge risk.
Abstract: Recent research has strengthened the understanding of the links between climate and tropical cyclones (TCs) on various timescales Geological records of past climates have shown century-long variations in TC numbers While no significant trends have been identified in the Atlantic since the late 19th century, significant observed trends in TC numbers and intensities have occurred in this basin over the past few decades, and trends in other basins are increasingly being identified However, understanding of the causes of these trends is incomplete, and confidence in these trends continues to be hampered by a lack of consistent observations in some basins A theoretical basis for maximum TC intensity appears now to be well established, but a climate theory of TC formation remains elusive Climate models mostly continue to predict future decreases in global TC numbers, projected increases in the intensities of the strongest storms and increased rainfall rates Sea level rise will likely contribute toward increased storm surge risk Against the background of global climate change and sea level rise, it is important to carry out quantitative assessments on the potential risk of TC-induced storm surge and flooding to densely populated cities and river deltas Several climate models are now able to generate a good distribution of both TC numbers and intensities in the current climate Inconsistent TC projection results emerge from modeling studies due to different downscaling methodologies and warming scenarios, inconsistencies in projected changes of large-scale conditions, and differences in model physics and tracking algorithms WIREs Clim Change 2016, 7:65–89 doi: 101002/wcc371
For further resources related to this article, please visit the WIREs website
1,496 citations
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TL;DR: ‘state of the art’ soil greenhouse gas research is highlighted, mitigation practices and potentials are summarized, gaps in data and understanding are identified and ways to close such gaps are suggested through new research, technology and collaboration.
Abstract: Soils are integral to the function of all terrestrial ecosystems and to food and fibre production. An overlooked aspect of soils is their potential to mitigate greenhouse gas emissions. Although proven practices exist, the implementation of soil-based greenhouse gas mitigation activities are at an early stage and accurately quantifying emissions and reductions remains a substantial challenge. Emerging research and information technology developments provide the potential for a broader inclusion of soils in greenhouse gas policies. Here we highlight 'state of the art' soil greenhouse gas research, summarize mitigation practices and potentials, identify gaps in data and understanding and suggest ways to close such gaps through new research, technology and collaboration.
1,221 citations
TL;DR: This work provides the first direct evidence that soil microbes produce chemically diverse, stable SOM, and shows that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived Som accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.
Abstract: Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production. Soil microbes process plant remnants and are hypothesized to synthesize soil organic matter (SOM). Here, Kallenbach and colleagues directly measure chemically diverse and stable SOM derived from microbial communities in the absence of plant compounds.
853 citations
Pacific Northwest National Laboratory1, Yale University2, National Center for Atmospheric Research3, Marine Biological Laboratory4, Colorado State University5, Wageningen University and Research Centre6, University of California, Irvine7, Kansas State University8, University of Oregon9, Michigan Technological University10, University of Sydney11, University of Minnesota12, Duke University13, University of Tennessee14, University of Copenhagen15, Spanish National Research Council16, University of New Hampshire17, Northeast Normal University18, University of California, Berkeley19, University of Oklahoma20, Hungarian Academy of Sciences21, Swedish University of Agricultural Sciences22, University of Manchester23, Tsinghua University24, National University of Singapore25, Chinese Academy of Sciences26, University of Hohenheim27, University of Georgia28, Hampshire College29, Boston University30, University of Alaska Anchorage31
TL;DR: In this article, the authors present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia, and provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections.
Abstract: The majority of the Earth's terrestrial carbon is stored in the soil. If anthropogenic warming stimulates the loss of this carbon to the atmosphere, it could drive further planetary warming. Despite evidence that warming enhances carbon fluxes to and from the soil, the net global balance between these responses remains uncertain. Here we present a comprehensive analysis of warming-induced changes in soil carbon stocks by assembling data from 49 field experiments located across North America, Europe and Asia. We find that the effects of warming are contingent on the size of the initial soil carbon stock, with considerable losses occurring in high-latitude areas. By extrapolating this empirical relationship to the global scale, we provide estimates of soil carbon sensitivity to warming that may help to constrain Earth system model projections. Our empirical relationship suggests that global soil carbon stocks in the upper soil horizons will fall by 30 ± 30 petagrams of carbon to 203 ± 161 petagrams of carbon under one degree of warming, depending on the rate at which the effects of warming are realized. Under the conservative assumption that the response of soil carbon to warming occurs within a year, a business-as-usual climate scenario would drive the loss of 55 ± 50 petagrams of carbon from the upper soil horizons by 2050. This value is around 12-17 per cent of the expected anthropogenic emissions over this period. Despite the considerable uncertainty in our estimates, the direction of the global soil carbon response is consistent across all scenarios. This provides strong empirical support for the idea that rising temperatures will stimulate the net loss of soil carbon to the atmosphere, driving a positive land carbon-climate feedback that could accelerate climate change.
787 citations
TL;DR: In this article, the authors provide a comprehensible theoretical overview that aims to define and pinpoint the differences and connections between these three facets of meaning, and point toward a new future for research on meaning in life.
Abstract: Despite growing interest in meaning in life, many have voiced their concern over the conceptual refinement of the construct itself. Researchers seem to have two main ways to understand what meaning in life means: coherence and purpose, with a third way, significance, gaining increasing attention. Coherence means a sense of comprehensibility and one’s life making sense. Purpose means a sense of core goals, aims, and direction in life. Significance is about a sense of life’s inherent value and having a life worth living. Although some researchers have already noted this trichotomy, the present article provides the first comprehensible theoretical overview that aims to define and pinpoint the differences and connections between these three facets of meaning. By arguing that the time is ripe to move from indiscriminate understanding of meaning into looking at these three facets separately, the article points toward a new future for research on meaning in life.
636 citations
TL;DR: The promises and challenges of these genome scan methods are reviewed, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations.
Abstract: Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, ...
627 citations
University of Aberdeen1, University of Bristol2, University of Brasília3, Murdoch University4, Nanjing Agricultural University5, University of Minnesota6, University of Reading7, KIIT University8, Agro ParisTech9, Colorado State University10, Wageningen University and Research Centre11, Environment Canada12, AgResearch13, Nagoya University14, Aix-Marseille University15, University of Illinois at Urbana–Champaign16, University of Exeter17, Karlsruhe Institute of Technology18
TL;DR: The state-of-the-art understanding of these global change pressures on soils is reported, knowledge gaps and research challenges are identified and actions and policies to minimize adverse environmental impacts arising from theseglobal change drivers are highlighted.
Abstract: Soils are subject to varying degrees of direct or indirect human disturbance, constituting a major global change driver. Factoring out natural from direct and indirect human influence is not always straightforward, but some human activities have clear impacts. These include land-use change, land management and land degradation (erosion, compaction, sealing and salinization). The intensity of land use also exerts a great impact on soils, and soils are also subject to indirect impacts arising from human activity, such as acid deposition (sulphur and nitrogen) and heavy metal pollution. In this critical review, we report the state-of-the-art understanding of these global change pressures on soils, identify knowledge gaps and research challenges and highlight actions and policies to minimize adverse environmental impacts arising from these global change drivers. Soils are central to considerations of what constitutes sustainable intensification. Therefore, ensuring that vulnerable and high environmental value soils are considered when protecting important habitats and ecosystems, will help to reduce the pressure on land from global change drivers. To ensure that soils are protected as part of wider environmental efforts, a global soil resilience programme should be considered, to monitor, recover or sustain soil fertility and function, and to enhance the ecosystem services provided by soils. Soils cannot, and should not, be considered in isolation of the ecosystems that they underpin and vice versa. The role of soils in supporting ecosystems and natural capital needs greater recognition. The lasting legacy of the International Year of Soils in 2015 should be to put soils at the centre of policy supporting environmental protection and sustainable development.
575 citations
TL;DR: It is recommended that future research efforts focus stronger on the causal understanding of why tree species classification approaches work under certain conditions or – maybe even more important - why they do not work in other cases as this might require more complex field acquisitions than those typically used in the reviewed studies.
575 citations
Commonwealth Scientific and Industrial Research Organisation1, International Institute for Applied Systems Analysis2, CGIAR3, Colorado State University4, University of Aberdeen5, Chalmers University of Technology6, Pennsylvania State University7, Wageningen University and Research Centre8, Karlsruhe Institute of Technology9, International Livestock Research Institute10, University of Oxford11, Netherlands Environmental Assessment Agency12
TL;DR: In this article, the authors estimated that between 1995 and 2005, the livestock sector was responsible for greenhouse gas emissions of 5.6-7.5GtCO(2)e yr(-1).
Abstract: The livestock sector supports about 1.3 billion producers and retailers, and contributes 40-50% of agricultural GDP. We estimated that between 1995 and 2005, the livestock sector was responsible for greenhouse gas emissions of 5.6-7.5GtCO(2)e yr(-1). Livestock accounts for up to half of the technical mitigation potential of the agriculture, forestry and land-use sectors, through management options that sustainably intensify livestock production, promote carbon sequestration in rangelands and reduce emissions from manures, and through reductions in the demand for livestock products. The economic potential of these management alternatives is less than 10% of what is technically possible because of adoption constraints, costs and numerous trade-offs. The mitigation potential of reductions in livestock product consumption is large, but their economic potential is unknown at present. More research and investment are needed to increase the affordability and adoption of mitigation practices, to moderate consumption of livestock products where appropriate, and to avoid negative impacts on livelihoods, economic activities and the environment.
570 citations
TL;DR: A systematic and standardised review of the scientific literature published from 1990 to 2013 on the effects of anthropogenic noise on wildlife, including both terrestrial and aquatic studies shows that terrestrial wildlife responses begin at noise levels of approximately 40’dBA, and 20% of papers documented impacts below 50 dBA.
Abstract: Global increases in environmental noise levels – arising from expansion of human populations, transportation networks, and resource extraction – have catalysed a recent surge of research into the effects of noise on wildlife. Synthesising a coherent understanding of the biological consequences of noise from this literature is challenging. Taxonomic groups vary in auditory capabilities. A wide range of noise sources and exposure levels occur, and many kinds of biological responses have been observed, ranging from individual behaviours to changes in ecological communities. Also, noise is one of several environmental effects generated by human activities, so researchers must contend with potentially confounding explanations for biological responses. Nonetheless, it is clear that noise presents diverse threats to species and ecosystems and salient patterns are emerging to help inform future natural resource-management decisions. We conducted a systematic and standardised review of the scientific literature published from 1990 to 2013 on the effects of anthropogenic noise on wildlife, including both terrestrial and aquatic studies. Research to date has concentrated predominantly on European and North American species that rely on vocal communication, with approximately two-thirds of the data set focussing on songbirds and marine mammals. The majority of studies documented effects from noise, including altered vocal behaviour to mitigate masking, reduced abundance in noisy habitats, changes in vigilance and foraging behaviour, and impacts on individual fitness and the structure of ecological communities. This literature survey shows that terrestrial wildlife responses begin at noise levels of approximately 40 dBA, and 20% of papers documented impacts below 50 dBA. Our analysis highlights the utility of existing scientific information concerning the effects of anthropogenic noise on wildlife for predicting potential outcomes of noise exposure and implementing meaningful mitigation measures. Future research directions that would support more comprehensive predictions regarding the magnitude and severity of noise impacts include: broadening taxonomic and geographical scope, exploring interacting stressors, conducting larger-scale studies, testing mitigation approaches, standardising reporting of acoustic metrics, and assessing the biological response to noise-source removal or mitigation. The broad volume of existing information concerning the effects of anthropogenic noise on wildlife offers a valuable resource to assist scientists, industry, and natural-resource managers in predicting potential outcomes of noise exposure.
531 citations
United States Geological Survey1, Wake Forest University2, University of Minnesota3, Utah State University4, Martin Luther University of Halle-Wittenberg5, Utrecht University6, University of Oldenburg7, University of Tartu8, University of Washington9, Trinity College, Dublin10, Imperial College London11, University of Wisconsin-Madison12, University of Colorado Boulder13, United States Department of Agriculture14, Queensland University of Technology15, University of Maryland, College Park16, University of Oxford17, University of Nebraska–Lincoln18, University of Guelph19, La Trobe University20, Commonwealth Scientific and Industrial Research Organisation21, Colorado State University22
TL;DR: It is found that an integrative model has substantially higher explanatory power than traditional bivariate analyses and several surprising findings that conflict with classical models are revealed.
Abstract: How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.
TL;DR: It is found that while extinction risk is highly situation dependent, genetic swamping is much more frequent than demographic swamping, and it is concluded that halting the introduction of hybridization‐prone exotics and restoring mature and diverse habitats that are resistant to hybrid establishment should be management priorities.
Abstract: Hybridization may drive rare taxa to extinction through genetic swamping, where the rare form is replaced by hybrids, or by demographic swamping, where population growth rates are reduced due to the wasteful production of maladaptive hybrids. Conversely, hybridization may rescue the viability of small, inbred populations. Understanding the factors that contribute to destructive versus constructive outcomes of hybridization is key to managing conservation concerns. Here, we survey the literature for studies of hybridization and extinction to identify the ecological, evolutionary, and genetic factors that critically affect extinction risk through hybridization. We find that while extinction risk is highly situation dependent, genetic swamping is much more frequent than demographic swamping. In addition, human involvement is associated with increased risk and high reproductive isolation with reduced risk. Although climate change is predicted to increase the risk of hybridization-induced extinction, we find little empirical support for this prediction. Similarly, theoretical and experimental studies imply that genetic rescue through hybridization may be equally or more probable than demographic swamping, but our literature survey failed to support this claim. We conclude that halting the introduction of hybridization-prone exotics and restoring mature and diverse habitats that are resistant to hybrid establishment should be management priorities.
California Institute of Technology1, University of Washington2, University of Leeds3, University of Manchester4, Colorado State University5, National Academies6, National Oceanic and Atmospheric Administration7, Pacific Northwest National Laboratory8, University of California, Irvine9, Goddard Space Flight Center10, University of California, San Diego11, Foundation for Research & Technology – Hellas12, University of Michigan13, Hebrew University of Jerusalem14
TL;DR: This work suggests strategies for improving estimates of aerosol−cloud relationships in climate models, for new remote sensing and in situ measurements, and for quantifying and reducing model uncertainty.
Abstract: The effect of an increase in atmospheric aerosol concentrations on the distribution and radiative properties of Earth’s clouds is the most uncertain component of the overall global radiative forcing from preindustrial time. General circulation models (GCMs) are the tool for predicting future climate, but the treatment of aerosols, clouds, and aerosol−cloud radiative effects carries large uncertainties that directly affect GCM predictions, such as climate sensitivity. Predictions are hampered by the large range of scales of interaction between various components that need to be captured. Observation systems (remote sensing, in situ) are increasingly being used to constrain predictions, but significant challenges exist, to some extent because of the large range of scales and the fact that the various measuring systems tend to address different scales. Fine-scale models represent clouds, aerosols, and aerosol−cloud interactions with high fidelity but do not include interactions with the larger scale and are therefore limited from a climatic point of view. We suggest strategies for improving estimates of aerosol−cloud relationships in climate models, for new remote sensing and in situ measurements, and for quantifying and reducing model uncertainty.
TL;DR: Evidence of reliability; convergent, discriminant, and content validity assessments; and test-retest reliabilities at 1- and 3-month time lags for single-item measures using a multistage and multisource validation strategy are examined.
Abstract: The validity of organizational research relies on strong research methods, which include effective measurement of psychological constructs. The general consensus is that multiple item measures have better psychometric properties than single-item measures. However, due to practical constraints (e.g., survey length, respondent burden) there are situations in which certain single items may be useful for capturing information about constructs that might otherwise go unmeasured. We evaluated 37 items, including 18 newly developed items as well as 19 single items selected from existing multiple-item scales based on psychometric characteristics, to assess 18 constructs frequently measured in organizational and occupational health psychology research. We examined evidence of reliability; convergent, discriminant, and content validity assessments; and test-retest reliabilities at 1- and 3-month time lags for single-item measures using a multistage and multisource validation strategy across 3 studies, including data from N = 17 occupational health subject matter experts and N = 1,634 survey respondents across 2 samples. Items selected from existing scales generally demonstrated better internal consistency reliability and convergent validity, whereas these particular new items generally had higher levels of content validity. We offer recommendations regarding when use of single items may be more or less appropriate, as well as 11 items that seem acceptable, 14 items with mixed results that might be used with caution due to mixed results, and 12 items we do not recommend using as single-item measures. Although multiple-item measures are preferable from a psychometric standpoint, in some circumstances single-item measures can provide useful information.
University of Florida1, University of Minnesota2, University of Oklahoma3, United States Department of Agriculture4, Donald Danforth Plant Science Center5, Stony Brook University6, Eckerd College7, Purdue University8, Cold Spring Harbor Laboratory9, University of Rhode Island10, University of California, Berkeley11, Colorado State University12, University of California, Riverside13, University of California, Davis14, Boyce Thompson Institute for Plant Research15, Stanford University16, Iowa State University17, University of Missouri18, University of Tennessee19
TL;DR: The state of plant transformation is reviewed and innovations needed to enable genome editing in crops are pointed to, including a potential game-changer in crop genetics when plant transformation systems are optimized.
Abstract: Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than thirty years of technological advances. Genome editing provides new opportunities to enhance crop productivity, but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Herein we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimize time in culture. Currently, specialized facilities exist for crop transformation. Single cell and robotic techniques should be developed for high throughput genomic screens. Utilization of plant genes involved in developmental reprogramming, wound response, and/or homologous recombination could boost recovery of transformed plants. Engineering universal Agrobacterium strains and recruitment of other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.
TL;DR: A new spatiotemporal data fusion method that uses simple principles and needs only one fine-resolution image as input has the potential to increase the availability of high-resolution time-series data that can support studies of rapid land surface dynamics.
TL;DR: This analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms and uncovers APA of ∼11,000 expressed genes and more than 2,100 novel genes.
Abstract: Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ∼11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism.
Purdue University1, University of Nevada, Reno2, Monsanto3, Old Dominion University4, North Carolina State University5, University College London6, Spanish National Research Council7, Oklahoma State University–Stillwater8, National Institutes of Health9, Wellcome Trust10, University of Cambridge11, J. Craig Venter Institute12, Leidos13, Broad Institute14, University of Notre Dame15, University of Nevada, Las Vegas16, University of Barcelona17, Carlos III Health Institute18, University of Massachusetts Medical School19, University of Connecticut20, University of Lausanne21, University of Oxford22, West Virginia University23, Virginia Tech24, Indiana University25, University of Maryland, Baltimore26, Kansas State University27, Texas A&M University28, University of Minnesota29, University of Manchester30, National University of Singapore31, University of California, San Francisco32, Iowa State University33, Colorado State University34, Pennsylvania State University35, Max Planck Society36, University of California, Riverside37, ANSES38, University of Santiago de Compostela39, Pompeu Fabra University40, California State Polytechnic University, Pomona41, University of Queensland42, University of the Sunshine Coast43, University of Geneva44, Swiss Institute of Bioinformatics45, University of Copenhagen46, University of Tennessee Health Science Center47, University of Vigo48, Wellcome Trust Sanger Institute49, University of Illinois at Urbana–Champaign50, Quinnipiac University51, International Livestock Research Institute52
TL;DR: Insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival are reported.
Abstract: Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
United States Department of Agriculture1, Washington University in St. Louis2, Hungarian Academy of Sciences3, National Institutes of Health4, Georgia State University5, United States Army Medical Research Institute of Infectious Diseases6, Commonwealth Scientific and Industrial Research Organisation7, Columbia University8, University of Texas Medical Branch9, Colorado State University10, Yeshiva University11, Huazhong Agricultural University12, University of Queensland13, University of Marburg14, University of Illinois at Urbana–Champaign15, University of Warwick16, Empresa Brasileira de Pesquisa Agropecuária17, World Health Organization18, Erasmus University Rotterdam19, New York University20, University of Kentucky21, Public Health England22, Kagoshima University23, Murdoch University24, University of São Paulo25, Public Health Agency of Canada26, Okayama University27, United States Geological Survey28, Northwestern University29, Centers for Disease Control and Prevention30, University of Cambridge31, Boston University32, Novosibirsk State University33, University of Medicine and Health Sciences34, University of Veterinary Medicine Vienna35, Texas Biomedical Research Institute36, Texas A&M University37, University of St Andrews38, Queen's University Belfast39, University of Freiburg40, Chinese Center for Disease Control and Prevention41, Defence Science and Technology Laboratory42, Hokkaido University43, Kyoto University44, Pasteur Institute45, Wageningen University and Research Centre46, University of Lyon47, National University of Singapore48, Kansas State University49, University of Hong Kong50
TL;DR: The updated taxonomy of the order Mononegavirales is presented as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Abstract: In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Food and Drug Administration1, University of Birmingham2, Colorado State University3, Cornell University4, University of Barcelona5, University of Alberta6, University of Turku7, Leiden University8, Edith Cowan University9, Markey Cancer Center10, Research Triangle Park11, University of Luxembourg12, King Abdulaziz University13, University of California, Davis14, Duke University15
TL;DR: The narrow range of chemical analyses in current use by the medical community today will be replaced in the future by analyses that reveal a far more comprehensive metabolic signature, expected to describe global biochemical aberrations that reflect patterns of variance in states of wellness, more accurately describe specific diseases and their progression, and greatly aid in differential diagnosis.
Abstract: Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or “-omics” level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person’s metabolic state provides a close representation of that individual’s overall health status. This metabolic state reflects what has been encoded by the genome, and modified by diet, environmental factors, and the gut microbiome. The metabolic profile provides a quantifiable readout of biochemical state from normal physiology to diverse pathophysiologies in a manner that is often not obvious from gene expression analyses. Today, clinicians capture only a very small part of the information contained in the metabolome, as they routinely measure only a narrow set of blood chemistry analytes to assess health and disease states. Examples include measuring glucose to monitor diabetes, measuring cholesterol and high density lipoprotein/low density lipoprotein ratio to assess cardiovascular health, BUN and creatinine for renal disorders, and measuring a panel of metabolites to diagnose potential inborn errors of metabolism in neonates. We anticipate that the narrow range of chemical analyses in current use by the medical community today will be replaced in the future by analyses that reveal a far more comprehensive metabolic signature. This signature is expected to describe global biochemical aberrations that reflect patterns of variance in states of wellness, more accurately describe specific diseases and their progression, and greatly aid in differential diagnosis. Such future metabolic signatures will: (1) provide predictive, prognostic, diagnostic, and surrogate markers of diverse disease states; (2) inform on underlying molecular mechanisms of diseases; (3) allow for sub-classification of diseases, and stratification of patients based on metabolic pathways impacted; (4) reveal biomarkers for drug response phenotypes, providing an effective means to predict variation in a subject’s response to treatment (pharmacometabolomics); (5) define a metabotype for each specific genotype, offering a functional read-out for genetic variants: (6) provide a means to monitor response and recurrence of diseases, such as cancers: (7) describe the molecular landscape in human performance applications and extreme environments. Importantly, sophisticated metabolomic analytical platforms and informatics tools have recently been developed that make it possible to measure thousands of metabolites in blood, other body fluids, and tissues. Such tools also enable more robust analysis of response to treatment. New insights have been gained about mechanisms of diseases, including neuropsychiatric disorders, cardiovascular disease, cancers, diabetes and a range of pathologies. A series of ground breaking studies supported by National Institute of Health (NIH) through the Pharmacometabolomics Research Network and its partnership with the Pharmacogenomics Research Network illustrate how a patient’s metabotype at baseline, prior to treatment, during treatment, and post-treatment, can inform about treatment outcomes and variations in responsiveness to drugs (e.g., statins, antidepressants, antihypertensives and antiplatelet therapies). These studies along with several others also exemplify how metabolomics data can complement and inform genetic data in defining ethnic, sex, and gender basis for variation in responses to treatment, which illustrates how pharmacometabolomics and pharmacogenomics are complementary and powerful tools for precision medicine. Our metabolomics community believes that inclusion of metabolomics data in precision medicine initiatives is timely and will provide an extremely valuable layer of data that compliments and informs other data obtained by these important initiatives. Our Metabolomics Society, through its “Precision Medicine and Pharmacometabolomics Task Group”, with input from our metabolomics community at large, has developed this White Paper where we discuss the value and approaches for including metabolomics data in large precision medicine initiatives. This White Paper offers recommendations for the selection of state of-the-art metabolomics platforms and approaches that offer the widest biochemical coverage, considers critical sample collection and preservation, as well as standardization of measurements, among other important topics. We anticipate that our metabolomics community will have representation in large precision medicine initiatives to provide input with regard to sample acquisition/preservation, selection of optimal omics technologies, and key issues regarding data collection, interpretation, and dissemination. We strongly recommend the collection and biobanking of samples for precision medicine initiatives that will take into consideration needs for large-scale metabolic phenotyping studies.
Laboratory of Molecular Biology1, Wellcome Trust Sanger Institute2, Papworth Hospital3, European Bioinformatics Institute4, Colorado State University5, University of North Carolina at Chapel Hill6, University of Queensland7, QIMR Berghofer Medical Research Institute8, Boston Children's Hospital9, Queen's University Belfast10, Queensland University of Technology11, National Health Service12, Cardiff University13, Newcastle upon Tyne Hospitals NHS Foundation Trust14, University of Oxford15, Nottingham University Hospitals NHS Trust16, University Hospital of South Manchester NHS Foundation Trust17, Aberdeen Royal Infirmary18, Leeds Teaching Hospitals NHS Trust19, Royal Liverpool and Broadgreen University Hospital NHS Trust20, University Hospital Southampton NHS Foundation Trust21, Aarhus University Hospital22, University of Gothenburg23, University of Copenhagen24, Statens Serum Institut25, NHS Greater Glasgow and Clyde26, Barts Health NHS Trust27, University Hospitals of Leicester NHS Trust28, Heart of England NHS Foundation Trust29, University of Cambridge30, Western General Hospital31, Radboud University Nijmegen32
TL;DR: Using whole-genome analysis of a global collection of clinical isolates, it is shown that the majority of M. abscessus infections are acquired through transmission, potentially via fomites and aerosols, of recently emerged dominant circulating clones that have spread globally.
Abstract: Lung infections with Mycobacterium abscessus, a species of multidrug-resistant nontuberculous mycobacteria, are emerging as an important global threat to individuals with cystic fibrosis (CF), in whom M. abscessus accelerates inflammatory lung damage, leading to increased morbidity and mortality. Previously, M. abscessus was thought to be independently acquired by susceptible individuals from the environment. However, using whole-genome analysis of a global collection of clinical isolates, we show that the majority of M. abscessus infections are acquired through transmission, potentially via fomites and aerosols, of recently emerged dominant circulating clones that have spread globally. We demonstrate that these clones are associated with worse clinical outcomes, show increased virulence in cell-based and mouse infection models, and thus represent an urgent international infection challenge.
TL;DR: This work reports a method for the formation of C–C bonds by directed cleavage of traditionally non-reactive C–H bonds and their subsequent coupling with readily available alkenes through a relayed photoredox-catalysed oxidation of a nitrogen–hydrogen bond.
Abstract: Carbon-carbon (C-C) bond formation is paramount in the synthesis of biologically relevant molecules, modern synthetic materials and commodity chemicals such as fuels and lubricants. Traditionally, the presence of a functional group is required at the site of C-C bond formation. Strategies that allow C-C bond formation at inert carbon-hydrogen (C-H) bonds enable access to molecules that would otherwise be inaccessible and the development of more efficient syntheses of complex molecules. Here we report a method for the formation of C-C bonds by directed cleavage of traditionally non-reactive C-H bonds and their subsequent coupling with readily available alkenes. Our methodology allows for amide-directed selective C-C bond formation at unactivated sp3 C-H bonds in molecules that contain many such bonds that are seemingly indistinguishable. Selectivity arises through a relayed photoredox-catalysed oxidation of a nitrogen-hydrogen bond. We anticipate that our findings will serve as a starting point for functionalization at inert C-H bonds through a strategy involving hydrogen-atom transfer.
TL;DR: It is reported that the ROP of γ-BL can, with a suitable catalyst, proceed smoothly to high conversions under ambient pressure to produce PγBL materials with a number-average molecular weight up to 30 kg mol(-1) and with controlled linear and/or cyclic topologies.
Abstract: Ring-opening polymerization (ROP) is a powerful synthetic methodology for the chemical synthesis of technologically important biodegradable aliphatic polyesters from cyclic esters or lactones. However, the bioderived five-membered γ-butyrolactone (γ-BL) is commonly referred as ‘non-polymerizable’ because of its low strain energy. The chemical synthesis of poly(γ-butyrolactone) (PγBL) through the ROP process has been realized only under ultrahigh pressure (20,000 atm, 160 °C) and only produces oligomers. Here we report that the ROP of γ-BL can, with a suitable catalyst, proceed smoothly to high conversions (90%) under ambient pressure to produce PγBL materials with a number-average molecular weight up to 30 kg mol–1 and with controlled linear and/or cyclic topologies. Remarkably, both linear and cyclic PγBLs can be recycled back into the monomer in quantitative yield by simply heating the bulk materials at 220 °C (linear polymer) or 300 °C (cyclic polymer) for one hour, which thereby demonstrates the complete recyclability of PγBL. Bio-derived γ-butyrolactone (γ-BL) is commonly referred to as ‘non-polymerizable’ due to its low strain energy. Now it has been shown that ring-opening polymerization of γ-BL can in fact proceed to high conversions under ambient pressure with a suitable catalyst, producing high-molecular-weight polymers with controlled topologies and complete recyclability.
TL;DR: A new decision framework, eco-engineering decision scaling (EEDS), is introduced that explicitly and quantitatively explores trade-offs in stake - holder-defined engineering and ecological performance metrics across a range of possible management actions under unknown future hydrological and climate states.
Abstract: Managing freshwater resources sustainably under future climatic and hydrological uncertainty poses novel challenges. Rehabilitation of ageing infrastructure and construction of new dams are widely viewed as solutions to diminish climate risk, but attaining the broad goal of freshwater sustainability will require expansion of the prevailing water resources management paradigm beyond narrow economic criteria to include socially valued ecosystem functions and services. We introduce a new decision framework, eco-engineering decision scaling (EEDS), that explicitly and quantitatively explores trade-offs in stake - holder-defined engineering and ecological performance metrics across a range of possible management actions under unknown future hydrological and climate states. We illustrate its potential application through a hypothetical case study of the Iowa River, USA. EEDS holds promise as a powerful framework for operationalizing freshwater sustainability under future hydrologi- cal uncertainty by fostering collaboration across historically conflicting perspectives of water resource engineering and river conservation ecology to design and operate water infrastructure for social and environmental benefits. evaluation a significant challenge 7,8 . These costs can be substantial, as evidenced by human displacement 5,9 , local species extinctions 10
TL;DR: In this article, the authors identify a particular type of person, one who is both highly knowledgeable about politics and lacking in trust, who is most susceptible to ideologically motivated conspiracy endorsement and demonstrate that the moderators of belief in conspiracy theories are strikingly different for conservatives and liberals.
Abstract: Given the potential political and social significance of conspiracy beliefs, a substantial and growing body of work examines the individual-level correlates of belief in conspiracy theories and general conspiratorial predispositions. However, although we know much about the psychological antecedents of conspiracy endorsement, we know less about the individual-level political causes of these prevalent and consequential beliefs. Our work draws from the extant literature to posit that endorsement of conspiracy theories is a motivated process that serves both ideological and psychological needs. In doing so, we develop a theory that identifies a particular type of person-one who is both highly knowledgeable about politics and lacking in trust-who is most susceptible to ideologically motivated conspiracy endorsement. Further, we demonstrate that the moderators of belief in conspiracy theories are strikingly different for conservatives and liberals. [ABSTRACT FROM AUTHOR]
TL;DR: A review of the role of plant inputs and the nature and dynamics of soil organic matter (SOM), often known as humus, can be found in this article, where the authors discuss the challenges in nutrient cycling, biogeochemistry, soil ecosystem functioning, pollution control, feeding the expanding global population and global change.
Abstract: This review covers historical perspectives, the role of plant inputs, and the nature and dynamics of soil organic matter (SOM), often known as humus. Information on turnover of organic matter components, the role of microbial products, and modeling of SOM, and tracer research should help us to anticipate what future research may answer today's challenges. Our globe's most important natural resource is best studied relative to its chemistry, dynamics, matrix interactions, and microbial transformations. Humus has similar, worldwide characteristics, but varies with abiotic controls, soil type, vegetation inputs and composition, and the soil biota. It contains carbohydrates, proteins, lipids, phenol-aromatics, protein-derived and cyclic nitrogenous compounds, and some still unknown compounds. Protection of transformed plant residues and microbial products occurs through spatial inaccessibility-resource availability, aggregation of mineral and organic constituents, and interactions with sesquioxides, cations, silts, and clays. Tracers that became available in the mid-20th century made the study of SOM dynamics possible. Carbon dating identified resistant, often mineral-associated, materials to be thousands of years old, especially at depth in the profile. The 13C associated with C3 C4 plant switches characterized slow turnover pools with ages ranging from dozens to hundreds of years. Added tracers, in conjunction with compound-specific product analysis and incubation, identified active pools with fast turnover rates. Physical fractionations of the intra- and inter-aggregate materials, and those associated with silt and clay, showed that all pools contain both old and young materials. Charcoal is old but not inert. The C:N ratio changes from 25 to 70:1 for plant residues to 6 to 9:1 for soil biota and microbial products associated with soil minerals. Active, slow and passive (resistant) pool concepts have been well used in biogeochemical models. The concepts discussed herein have implications for today's challenges in nutrient cycling, biogeochemistry, soil ecosystem functioning, pollution control, feeding the expanding global population and global change.
TL;DR: In this article, the authors found that RDI is largely implemented through three approaches: (1) growth stage-based deficit irrigation, (2) partial root-zone irrigation, and (3) subsurface dripper irrigation.
Abstract: Agriculture consumes more than two thirds of the total freshwater of the planet. This issue causes substantial conflict in freshwater allocation between agriculture and other economic sectors. Regulated deficit irrigation (RDI) is key technology because it helps to improve water use efficiency. Nonetheless, there is a lack of understanding of the mechanisms with which plants respond to RDI. In particular, little is known about how RDI might increase crop production while reducing the amount of irrigation water in real-world agriculture. In this review, we found that RDI is largely implemented through three approaches: (1) growth stage-based deficit irrigation, (2) partial root-zone irrigation, and (3) subsurface dripper irrigation. Among these, partial root-zone irrigation is the most popular and effective because many field crops and some woody crops can save irrigation water up to 20 to 30 % without or with a minimal impact on crop yield. Improved water use efficiency with RDI is mainly due to the following: (1) enhanced guard cell signal transduction network that decreases transpiration water loss, (2) optimized stomatal control that improves the photosynthesis to transpiration ratio, and (3) decreased evaporative surface areas with partial root-zone irrigation that reduces soil evaporation. The mechanisms involved in the plant response to RDI-induced water stress include the morphological traits, e.g., increased root to shoot ratio and improved nutrient uptake and recovery; physiological traits, e.g., stomatal closure, decreased leaf respiration, and maintained photosynthesis; and biochemical traits, e.g., increased signaling molecules and enhanced antioxidation enzymatic activity.
TL;DR: A simplified perspective based on extensive experimental and theoretical analysis provides a platform from which to understand structure-property relationships in functional perovskite halides.
Abstract: Vacancy-ordered double perovskites of the general formula A2BX6 are a family of perovskite derivatives composed of a face-centered lattice of nearly isolated [BX6] units with A-site cations occupying the cuboctahedral voids Despite the presence of isolated octahedral units, the close-packed iodide lattice provides significant electronic dispersion, such that Cs2SnI6 has recently been explored for applications in photovoltaic devices To elucidate the structure–property relationships of these materials, we have synthesized solid-solution Cs2Sn1–xTexI6 However, even though tellurium substitution increases electronic dispersion via closer I–I contact distances, the substitution experimentally yields insulating behavior from a significant decrease in carrier concentration and mobility Density functional calculations of native defects in Cs2SnI6 reveal that iodine vacancies exhibit a low enthalpy of formation, and that the defect energy level is a shallow donor to the conduction band rendering the material
Colorado State University1, University of California, San Diego2, Carnegie Mellon University3, University of British Columbia4, Hankuk University of Foreign Studies5, University of Wyoming6, Clarkson University7, Brookhaven National Laboratory8, Environment Canada9, University of Toronto10, University of Michigan11, University of Puerto Rico12, University of Iowa13, University of Wisconsin-Madison14
TL;DR: It is shown that INPs are emitted using real wave breaking in a laboratory flume to produce sea spray aerosol (SSA) emissions, and the number concentrations of INPs from laboratory-generated SSA, when normalized to typical total aerosol number concentrations in the marine boundary layer, agree well with measurements from diverse regions over the oceans.
Abstract: Ice nucleating particles (INPs) are vital for ice initiation in, and precipitation from, mixed-phase clouds. A source of INPs from oceans within sea spray aerosol (SSA) emissions has been suggested in previous studies but remained unconfirmed. Here, we show that INPs are emitted using real wave breaking in a laboratory flume to produce SSA. The number concentrations of INPs from laboratory-generated SSA, when normalized to typical total aerosol number concentrations in the marine boundary layer, agree well with measurements from diverse regions over the oceans. Data in the present study are also in accord with previously published INP measurements made over remote ocean regions. INP number concentrations active within liquid water droplets increase exponentially in number with a decrease in temperature below 0 °C, averaging an order of magnitude increase per 5 °C interval. The plausibility of a strong increase in SSA INP emissions in association with phytoplankton blooms is also shown in laboratory simulations. Nevertheless, INP number concentrations, or active site densities approximated using "dry" geometric SSA surface areas, are a few orders of magnitude lower than corresponding concentrations or site densities in the surface boundary layer over continental regions. These findings have important implications for cloud radiative forcing and precipitation within low-level and midlevel marine clouds unaffected by continental INP sources, such as may occur over the Southern Ocean.
Tsinghua University1, University of Oklahoma2, Stanford University3, Lund University4, University of California, Irvine5, Max Planck Society6, Universidade Nova de Lisboa7, Commonwealth Scientific and Industrial Research Organisation8, Centre national de la recherche scientifique9, University of Maryland Center for Environmental Science10, Boston University11, University of California, Berkeley12, Lawrence Berkeley National Laboratory13, Canadian Forest Service14, United States Geological Survey15, Met Office16, University of Alaska Fairbanks17, Colorado State University18, Université du Québec à Montréal19, Purdue University20, Microsoft21, Auburn University22, Pacific Northwest National Laboratory23, Northern Arizona University24, Joint Global Change Research Institute25, Oak Ridge National Laboratory26, National Center for Atmospheric Research27, East China Normal University28, Iowa State University29, University of Texas at El Paso30, Beijing Normal University31
TL;DR: In this article, the authors suggest that model structures should reflect real-world processes, parameters should be calibrated to match model outputs with observations, and external forcing variables should accurately prescribe the environmental conditions that soils experience.
Abstract: Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool- and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. We recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure, constrain parameters, and prescribe forcing fields.