67 research outputs found

    Genomic features of bacterial adaptation to plants

    Get PDF
    Author(s): Levy, A; Salas Gonzalez, I; Mittelviefhaus, M; Clingenpeel, S; Herrera Paredes, S; Miao, J; Wang, K; Devescovi, G; Stillman, K; Monteiro, F; Rangel Alvarez, B; Lundberg, DS; Lu, TY; Lebeis, S; Jin, Z; McDonald, M; Klein, AP; Feltcher, ME; Rio, TG; Grant, SR; Doty, SL; Ley, RE; Zhao, B; Venturi, V; Pelletier, DA; Vorholt, JA; Tringe, SG; Woyke, T; Dangl, JL | Abstract: © 2017 The Author(s). Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering

    Linking behaviour and climate change in intertidal ectotherms: insights from littorinid snails

    Get PDF
    A key element missing from many predictive models of the impacts of climate change on intertidal ectotherms is the role of individual behaviour. In this synthesis, using littorinid snails as a case study, we show how thermoregulatory behaviours may buffer changes in environmental temperatures. These behaviours include either a flight response, to escape the most extreme conditions and utilize warmer or cooler environments; or a fight response, where individuals modify their own environments to minimize thermal extremes. A conceptual model, generated from studies of littorinid snails, shows that various flight and fight thermoregulatory behaviours may allow an individual to widen its thermal safety margin (TSM) under warming or cooling environmental conditions and hence increase species’ resilience to climate change. Thermoregulatory behaviours may also buffer sublethal fitness impacts associated with thermal stresses. Through this synthesis, we emphasise that future studies need to consider not only animals' physiological limits but also their capacities to buffer the impact of climate change through behavioural responses. Current generalizations, made largely on physiological limits of species, often neglect the buffering effects of behaviour and may, therefore, provide an over-estimation of vulnerability, and consequently poor prediction of the potential impacts of climate change on intertidal ectotherms

    Whole Genomes of Chandipura Virus Isolates and Comparative Analysis with Other Rhabdoviruses

    Get PDF
    The Chandipura virus (CHPV) belonging to the Vesiculovirus genus and Rhabdoviridae family, has recently been associated with a number of encephalitis epidemics, with high mortality in children, in different parts of India. No full length genome sequences of CHPV isolates were available in GenBank and little is known about the molecular markers for pathogenesis. In the present study, we provide the complete genomic sequences of four isolates from epidemics during 2003–2007. These sequences along with the deduced sequence of the prototype isolate of 1965 were analysed using phylogeny, motif search, homology modeling and epitope prediction methods. Comparison with other rhaboviruses was also done for functional extrapolations. All CHPV isolates clustered with the Isfahan virus and maintained several functional motifs of other rhabdoviruses. A notable difference with the prototype vesiculovirus, Vesicular Stomatitis Virus was in the L-domain flanking sequences of the M protein that are known to be crucial for interaction with host proteins. With respect to the prototype isolate, significant additional mutations were acquired in the 2003–2007 isolates. Several mutations in G mapped onto probable antigenic sites. A mutation in N mapped onto regions crucial for N-N interaction and a putative T-cell epitope. A mutation in the Casein kinase II phosphorylation site in P may attribute to increased rates of phosphorylation. Gene junction comparison revealed changes in the M-G junction of all the epidemic isolates that may have implications on read-through and gene transcription levels. The study can form the basis for further experimental verification and provide additional insights into the virulence determinants of the CHPV

    Returning to Work from Injury: Longitudinal Evidence on Employment and Earnings

    No full text
    New Zealand has a unique accident insurance system that pays the direct costs of all injuries and compensates workers up to 80% of their earnings for any time that they are unable to work. To estimate the effect of injuries on labor market outcomes, the authors use Statistics New Zealand’s Linked Employer-Employee Database (LEED) covering the period April 1999 to March 2004 using a “difference-in-differences” matching approach. They use two alternative matching criteria to construct control groups of non-injured workers whose pre-injury characteristics are similar to those of injured workers: the first uses only characteristics of the workers whereas the second exploits the nature of the LEED and matches workers in the same firm. Findings indicate that injuries resulting in more than three months of earnings compensation have negative effects on future labor market outcomes that do not decline with time post-injury. The results are broadly similar using both matching criteria, providing more validity to the authors’ findings

    Returning to Work from Injury: Longitudinal Evidence on Employment and Earnings

    No full text
    New Zealand has a comprehensive accident insurance system, administered by the Accident Compensation Corporation (ACC), which both pays the direct medical and rehabilitative costs of all accidental injuries and compensates all workers 80 percent of their earnings for any time postinjury that they are unable to work. This paper uses data from Statistics New Zealand’s experimental Linked Employer-Employee Database (LEED) to examine the effect of suffering an injury on individual labour market outcomes. The experimental LEED database contains monthly information on ACC, benefit and earnings receipt for all New Zealanders over the three-year period from April 1999 to March 2002. Using receipt of ACC earnings compensation as a proxy for being injured, we examine the effect of injuries on employment and benefit rates, earnings and benefit income. Individuals who are injured and receive earnings compensation are unlikely to be a random sample of the working population. For example, workers in particular industries and occupations are likely to be more exposed to hazardous situations. Thus, we estimate the effect of injury by comparing the observed changes in labour market outcomes for our injured population with a matched ‘control’ group of non-injured individuals who have similar observed characteristics as the injured population. We allow the magnitude of these effects to differ for individuals with different lengths of time receiving ACC compensation as a proxy for the severity of injury. We find that injuries which result in more than three months of earnings compensation have negative effects on future labour market outcomes. For example, individuals who receive four months’ compensation have 2-4 percent lower employment rates, 2 percent higher benefit receipt rates, and 6-8 percent lower monthly income six months after compensation ends than comparable non-injured workers. For individuals who receive seven to nine months of compensation, these negative effects are larger, with employment rates 8-10 percent lower, benefit rates 7 percent higher, and monthly income 13-17 percent lower. Furthermore, these negative effects remain at a similar magnitude 12 months after compensation ends

    Predicting the effect of local and global environmental change on shorebirds: a case study on the Exe estuary, U.K.

    Get PDF
    We used an individual-based model to assess site quality and to predict the effect of local (i.e. disturbance from a cycle path) and global (i.e. climate change) environmental change on the survival of six species of overwintering shorebirds on the Exe estuary, U.K. We also compare site quality on the Exe estuary with three other estuary Special Protection Areas (SPAs) and compare our predictions for the effects of climate change with predictions made for another southern U.K. estuary, Poole Harbour. Prey biomass densities in the Exe estuary were high for all six shorebirds, being as high as or higher than those found on other estuary SPAs. Simulations of increased levels of disturbance from a proposed cycle path along the side of the estuary predicted that disturbance of upper mudflat areas was unlikely to affect shorebird survival but that increased disturbance of nearby fields would reduce curlew survival. Shorebirds on the Exe estuary were far less seriously affected than those in Poole Harbour by reductions in mean daily temperatures, loss of terrestrial habitats and simulated sea-level rise. We conclude that the Exe estuary is a high quality estuary and that the shorebird populations modelled were less susceptible to climate change than those in Poole Harbour
    corecore