Agropolis International

Background: Chronic diseases are currently the main cause of morbidity and mortality and represent a major challenge to healthcare systems. The objective of this study is to know Spanish public opinion about chronic disease and how it affects their daily lives. Methods: Through a telephone or online survey of 24 questions, data was gathered on the characteristics of the respondents and their knowledge and experiences of chronic diseases. Results: Of the 2522 survey respondents, 325 had a chronic disease and were carers, 1088 had a chronic disease and were not carers, 140 did not have a chronic disease but were carers, and 969 did not have chronic disease and were not carers. The degree of knowledge on these diseases was good or very good for 69.4%, 56.0%, 62.2%, and 46.7%, respectively, for each group. All the groups agreed that chronic diseases mainly affect mood, quality of life and having to make sacrifices. Conclusions: Knowledge about chronic diseases is relatively good, although it can be improved among the Spanish population, especially among patients who report having a chronic disease and play the role of carers. However, it is important to continue maintaining the level of information and training concerning these diseases.

Understanding the functional consequences of genetic variation, and how it affects complex human disease and quantitative traits, remains a critical challenge for biomedicine. We present an analysis of RNA sequencing data from 1641 samples across 43 tissues from 175 individuals, generated as part of the pilot phase of the Genotype-Tissue Expression (GTEx) project. We describe the landscape of gene expression across tissues, catalog thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants, describe complex network relationships, and identify signals from genome-wide association studies explained by eQTLs. These findings provide a systematic understanding of the cellular and biological consequences of human genetic variation and of the heterogeneity of such effects among a diverse set of human tissues.

GENECLASS2 is a software that computes various genetic assignment criteria to assign or exclude reference populations as the origin of diploid or haploid individuals, as well as of groups of individuals, on the basis of multilocus genotype data. In addition to traditional assignment aims, the program allows the specific task of first-generation migrant detection. It includes several Monte Carlo resampling algorithms that compute for each individual its probability of belonging to each reference population or to be a resident (i.e., not a first-generation migrant) in the population where it was sampled. A user-friendly interface facilitates the treatment of large datasets.

It is often claimed that we do not understand the forces driving the global diversity gradient. However, an extensive literature suggests that contemporary climate constrains terrestrial taxonomic richness over broad geographic extents. Here, we review the empirical literature to examine the nature and form of the relationship between climate and richness. Our goals were to document the support for the climatically based energy hypothesis, and within the constraints imposed by correlative analyses, to evaluate two versions of the hypothesis: the productivity and ambient energy hypotheses. Focusing on studies extending over 800 km, we found that measures of energy, water, or water–energy balance explain spatial variation in richness better than other climatic and non-climatic variables in 82 of 85 cases. Even when considered individually and in isolation, water/energy variables explain on average over 60% of the variation in the richness of a wide range of plant and animal groups. Further, water variables usually represent the strongest predictors in the tropics, subtropics, and warm temperate zones, whereas energy variables (for animals) or water–energy variables (for plants) dominate in high latitudes. We conclude that the interaction between water and energy, either directly or indirectly (via plant productivity), provides a strong explanation for globally extensive plant and animal diversity gradients, but for animals there also is a latitudinal shift in the relative importance of ambient energy vs. water moving from the poles to the equator. Although contemporary climate is not the only factor influencing species richness and may not explain the diversity pattern for all taxonomic groups, it is clear that understanding water–energy dynamics is critical to future biodiversity research. Analyses that do not include water–energy variables are missing a key component for explaining broad-scale patterns of diversity.

Many plant bacteriologists, if not all, feel that their particular microbe should appear in any list of the most important bacterial plant pathogens. However, to our knowledge, no such list exists. The aim of this review was to survey all bacterial pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate the bacterial pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 458 votes from the international community, and allowed the construction of a Top 10 bacterial plant pathogen list. The list includes, in rank order: (1) Pseudomonas syringae pathovars; (2) Ralstonia solanacearum; (3) Agrobacterium tumefaciens; (4) Xanthomonas oryzae pv. oryzae; (5) Xanthomonas campestris pathovars; (6) Xanthomonas axonopodis pathovars; (7) Erwinia amylovora; (8) Xylella fastidiosa; (9) Dickeya (dadantii and solani); (10) Pectobacterium carotovorum (and Pectobacterium atrosepticum). Bacteria garnering honourable mentions for just missing out on the Top 10 include Clavibacter michiganensis (michiganensis and sepedonicus), Pseudomonas savastanoi and Candidatus Liberibacter asiaticus. This review article presents a short section on each bacterium in the Top 10 list and its importance, with the intention of initiating discussion and debate amongst the plant bacteriology community, as well as laying down a benchmark. It will be interesting to see, in future years, how perceptions change and which bacterial pathogens enter and leave the Top 10.

1 Once neglected, the role of facilitative interactions in plant communities has received considerable attention in the last two decades, and is now widely recognized. It is timely to consider the progress made by research in this field. 2 We review the development of plant facilitation research, focusing on the history of the field, the relationship between plant–plant interactions and environmental severity gradients, and attempts to integrate facilitation into mainstream ecological theory. We then consider future directions for facilitation research. 3 With respect to our fundamental understanding of plant facilitation, clarification of the relationship between interactions and environmental gradients is central for further progress, and necessitates the design and implementation of experiments that move beyond the clear limitations of previous studies. 4 There is substantial scope for exploring indirect facilitative effects in plant communities, including their impacts on diversity and evolution, and future studies should connect the degree of non-transitivity in plant competitive networks to community diversity and facilitative promotion of species coexistence, and explore how the role of indirect facilitation varies with environmental severity. 5 Certain ecological modelling approaches (e.g. individual-based modelling), although thus far largely neglected, provide highly useful tools for exploring these fundamental processes. 6 Evolutionary responses might result from facilitative interactions, and consideration of facilitation might lead to re-assessment of the evolution of plant growth forms. 7 Improved understanding of facilitation processes has direct relevance for the development of tools for ecosystem restoration, and for improving our understanding of the response of plant species and communities to environmental change drivers. 8 Attempts to apply our developing ecological knowledge would benefit from explicit recognition of the potential role of facilitative plant–plant interactions in the design and interpretation of studies from the fields of restoration and global change ecology. 9 Synthesis: Plant facilitation research provides new insights into classic ecological theory and pressing environmental issues. Awareness and understanding of facilitation should be part of the basic ecological knowledge of all plant ecologists.

Abstract Broad‐scale variation in taxonomic richness is strongly correlated with climate. Many mechanisms have been hypothesized to explain these patterns; however, testable predictions that would distinguish among them have rarely been derived. Here, we examine several prominent hypotheses for climate–richness relationships, deriving and testing predictions based on their hypothesized mechanisms. The ‘energy–richness hypothesis’ (also called the ‘more individuals hypothesis’) postulates that more productive areas have more individuals and therefore more species. More productive areas do often have more species, but extant data are not consistent with the expected causal relationship from energy to numbers of individuals to numbers of species. We reject the energy–richness hypothesis in its standard form and consider some proposed modifications. The ‘physiological tolerance hypothesis’ postulates that richness varies according to the tolerances of individual species for different sets of climatic conditions. This hypothesis predicts that more combinations of physiological parameters can survive under warm and wet than cold or dry conditions. Data are qualitatively consistent with this prediction, but are inconsistent with the prediction that species should fill climatically suitable areas. Finally, the ‘speciation rate hypothesis’ postulates that speciation rates should vary with climate, due either to faster evolutionary rates or stronger biotic interactions increasing the opportunity for evolutionary diversification in some regions. The biotic interactions mechanism also has the potential to amplify shallower, underlying gradients in richness. Tests of speciation rate hypotheses are few (to date), and their results are mixed.

The sequencing and analysis of the banana genome is reported; these results inform plant phylogenetic relationships and genome evolution, and provide a resource for future genetic improvement of this important crop species. Bananas (Musa spp.) are a staple food and a major source of income in many tropical and subtropical countries. This paper reports the sequencing and analysis of the banana genome. This is the first non-grass monocotyledon to have its genome sequenced, providing an important bridge for comparative genome analysis in plants. Global banana production is under threat from increasingly well-adapted pests and diseases, so the availability of the genome sequence is an important resource for future crop development and improvement. Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3,4. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence.

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.

Abstract Terrestrial ecosystems sequester 2.1 Pg of atmospheric carbon annually. A large amount of the terrestrial sink is realized by forests. However, considerable uncertainties remain regarding the fate of this carbon over both short and long timescales. Relevant data to address these uncertainties are being collected at many sites around the world, but syntheses of these data are still sparse. To facilitate future synthesis activities, we have assembled a comprehensive global database for forest ecosystems, which includes carbon budget variables (fluxes and stocks), ecosystem traits (e.g. leaf area index, age), as well as ancillary site information such as management regime, climate, and soil characteristics. This publicly available database can be used to quantify global, regional or biome‐specific carbon budgets; to re‐examine established relationships; to test emerging hypotheses about ecosystem functioning [e.g. a constant net ecosystem production (NEP) to gross primary production (GPP) ratio]; and as benchmarks for model evaluations. In this paper, we present the first analysis of this database. We discuss the climatic influences on GPP, net primary production (NPP) and NEP and present the CO 2 balances for boreal, temperate, and tropical forest biomes based on micrometeorological, ecophysiological, and biometric flux and inventory estimates. Globally, GPP of forests benefited from higher temperatures and precipitation whereas NPP saturated above either a threshold of 1500 mm precipitation or a mean annual temperature of 10 °C. The global pattern in NEP was insensitive to climate and is hypothesized to be mainly determined by nonclimatic conditions such as successional stage, management, site history, and site disturbance. In all biomes, closing the CO 2 balance required the introduction of substantial biome‐specific closure terms. Nonclosure was taken as an indication that respiratory processes, advection, and non‐CO 2 carbon fluxes are not presently being adequately accounted for.

Both Aedes aegytpi and Ae. albopictus are major vectors of 5 important arboviruses (namely chikungunya virus, dengue virus, Rift Valley fever virus, yellow fever virus, and Zika virus), making these mosquitoes an important factor in the worldwide burden of infectious disease. Vector control using insecticides coupled with larval source reduction is critical to control the transmission of these viruses to humans but is threatened by the emergence of insecticide resistance. Here, we review the available evidence for the geographical distribution of insecticide resistance in these 2 major vectors worldwide and map the data collated for the 4 main classes of neurotoxic insecticide (carbamates, organochlorines, organophosphates, and pyrethroids). Emerging resistance to all 4 of these insecticide classes has been detected in the Americas, Africa, and Asia. Target-site mutations and increased insecticide detoxification have both been linked to resistance in Ae. aegypti and Ae. albopictus but more work is required to further elucidate metabolic mechanisms and develop robust diagnostic assays. Geographical distributions are provided for the mechanisms that have been shown to be important to date. Estimating insecticide resistance in unsampled locations is hampered by a lack of standardisation in the diagnostic tools used and by a lack of data in a number of regions for both resistance phenotypes and genotypes. The need for increased sampling using standard methods is critical to tackle the issue of emerging insecticide resistance threatening human health. Specifically, diagnostic doses and well-characterised susceptible strains are needed for the full range of insecticides used to control Ae. aegypti and Ae. albopictus to standardise measurement of the resistant phenotype, and calibrated diagnostic assays are needed for the major mechanisms of resistance.

The genome of Ectocarpus, a model organism for brown algae, has been sequenced. Brown algae are complex photosynthetic organisms that have adapted to life in rocky coastal environments. Genome analysis sheds light on this adaptation and reveals an extended set of light-harvesting and pigment biosynthesis genes and novel metabolic processes such as halide metabolism. Comparative genomic analyses highlight the likely importance of a family of receptor kinases and related molecules in the evolution of multicellularity in plants, animals and brown algae. The genome of Ectocarpus siliculosis, a model for the study of brown algae, has been sequenced. These seaweeds are complex photosynthetic organisms that have adapted to rocky coastal environments. Genome analysis sheds light on this adaptation, revealing an extended set of light-harvesting and pigment biosynthesis genes, and new metabolic processes such as halide metabolism. Comparative analyses are also significant with respect to the evolution of multicellularity in plants, animals and brown algae. Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related1. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae2,3,4,5, closely related to the kelps6,7 (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic2 approaches to explore these and other4,5 aspects of brown algal biology further.

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications.

Human immunodeficiency virus type 1 (HIV-1), the cause of human acquired immunodeficiency syndrome (AIDS), is a zoonotic infection of staggering proportions and social impact. Yet uncertainty persists regarding its natural reservoir. The virus most closely related to HIV-1 is a simian immunodeficiency virus (SIV) thus far identified only in captive members of the chimpanzee subspecies Pan troglodytes troglodytes. Here we report the detection of SIVcpz antibodies and nucleic acids in fecal samples from wild-living P. t. troglodytes apes in southern Cameroon, where prevalence rates in some communities reached 29 to 35%. By sequence analysis of endemic SIVcpz strains, we could trace the origins of pandemic (group M) and nonpandemic (group N) HIV-1 to distinct, geographically isolated chimpanzee communities. These findings establish P. t. troglodytes as a natural reservoir of HIV-1.

Insects have presented human society with some of its greatest development challenges by spreading diseases, consuming crops and damaging infrastructure. Despite the massive human and financial toll of invasive insects, cost estimates of their impacts remain sporadic, spatially incomplete and of questionable quality. Here we compile a comprehensive database of economic costs of invasive insects. Taking all reported goods and service estimates, invasive insects cost a minimum of US$70.0 billion per year globally, while associated health costs exceed US$6.9 billion per year. Total costs rise as the number of estimate increases, although many of the worst costs have already been estimated (especially those related to human health). A lack of dedicated studies, especially for reproducible goods and service estimates, implies gross underestimation of global costs. Global warming as a consequence of climate change, rising human population densities and intensifying international trade will allow these costly insects to spread into new areas, but substantial savings could be achieved by increasing surveillance, containment and public awareness.

The erosion of biological diversity pertains to the category of problems that are brought to the fore in ddebated universesT.There are scientific controversies about their definition, import and possible solutions and they involve opposing economicinterests and political strategies. A dconventionT–commonly shared values, set of definitions, rules and norms–implying acompromise among various actors and groups is needed to define and enforce policies. The Convention on biological diversitycan be seen as an attempt to define such a middle ground. The rights and policy orientations it promotes are however challengedby overlapping norms and rules enacted in other arenas, such as the WTO. The purpose of this paper is to take up aconventionalist stance on the complex international regime that governs biodiversity management and conservation policies.

Almost half of the total organic carbon (C) in terrestrial ecosystems is stored in forest soils. By altering rates of input or release of C from soils, forest management activities can influence soil C stocks in forests. In this review, we synthesize current evidence regarding the influences of 13 common forest management practices on forest soil C stocks. Afforestation of former croplands generally increases soil C stocks, whereas on former grasslands and peatlands, soil C stocks are unchanged or even reduced following afforestation. The conversion of primary forests to secondary forests generally reduces soil C stocks, particularly if the land is converted to an agricultural land-use prior to reforestation. Harvesting, particularly clear-cut harvesting, generally results in a reduction in soil C stocks, particularly in the forest floor and upper mineral soil. Removal of residues by harvesting whole-trees and stumps negatively affects soil C stocks. Soil disturbance from site preparation decreases soil C stocks, particularly in the organic top soil, however improved growth of tree seedlings may outweigh soil C losses over a rotation. Nitrogen (N) addition has an overall positive effect on soil C stocks across a wide range of forest ecosystems. Likewise, higher stocks and faster accumulation of soil C occur under tree species with N-fixing associates. Stocks and accumulation rates of soil C also differ under different tree species, with coniferous species accumulating more C in the forest floor and broadleaved species tending to store more C in the mineral soil. There is some evidence that increased tree species diversity could positively affect soil C stocks in temperate and subtropical forests, but tree species identity, particularly N-fixing species, seems to have a stronger impact on soil C stocks than tree species diversity. Management of stand density and thinning have small effects on forest soil C stocks. In forests with high populations of ungulate herbivores, reduction in herbivory levels can increase soil C stocks. Removal of plant biomass for fodder and fuel is related to a reduction in the soil C stocks. Fire management practices such as prescribed burning reduce soil C stocks, but less so than wildfires which are more intense. For each practice, we identify existing gaps in knowledge and suggest research to address the gaps.

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

Background Oxidation-reduction and acid-base reactions are essential for the maintenance of all living organisms. However, redox potential (Eh) has received little attention in agronomy, unlike pH, which is regarded as a master variable. Agronomists are probably depriving themselves of a key factor in crop and soil science which could be a useful integrative tool. Scope This paper reviews the existing literature on Eh in various disciplines connected to agronomy, whether associated or not with pH, and then integrates this knowledge within a composite framework. Conclusions This transdisciplinary review offers evidence that Eh and pH are respectively and jointly major drivers of soil/plant/microorganism systems. Information on the roles of Eh and pH in plant and microorganism physiology and in soil genesis converges to form an operational framework for further studies of soil/plant/microorganism functioning. This framework is based on the hypothesis that plants physiologically function within a specific internal Eh-pH range and that, along with microorganisms, they alter Eh and pH in the rhizosphere to ensure homeostasis at the cell level. This new perspective could help in bridging several disciplines related to agronomy, and across micro and macro-scales. It should help to improve cropping systems design and management, in conventional, organic, and conservation agriculture.

BACKGROUND: Observational studies showed that the profile of infective endocarditis (IE) significantly changed over the past decades. However, most studies involved referral centers. We conducted a population-based study to control for this referral bias. The objective was to update the description of characteristics of IE in France and to compare the profile of community-acquired versus healthcare-associated IE. METHODS: A prospective population-based observational study conducted in all medical facilities from 7 French regions (32% of French individuals aged ≥18 years) identified 497 adults with Duke-Li-definite IE who were first admitted to the hospital in 2008. Main measures included age-standardized and sex-standardized incidence of IE and multivariate Cox regression analysis for risk factors of in-hospital death. RESULTS: The age-standardized and sex-standardized annual incidence of IE was 33.8 (95% confidence interval [CI], 30.8-36.9) cases per million inhabitants. The incidence was highest in men aged 75-79 years. A majority of patients had no previously known heart disease. Staphylococci were the most common causal agents, accounting for 36.2% of cases (Staphylococcus aureus, 26.6%; coagulase-negative staphylococci, 9.7%). Healthcare-associated IE represented 26.7% of all cases and exhibited a clinical pattern significantly different from that of community-acquired IE. S. aureus as the causal agent of IE was the most important factor associated with in-hospital death in community-acquired IE (hazard ratio [HR], 2.82 [95% CI, 1.72-4.61]) and the single factor in healthcare-associated IE (HR, 2.54 [95% CI, 1.33-4.85]). CONCLUSIONS: S. aureus became both the leading cause and the most important prognostic factor of IE, and healthcare-associated IE appeared as a major subgroup of the disease.