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First detection and molecular identification of the zoonotic Anaplasma capra in deer in France
No full textCervids are known to be reservoirs of zoonotic bacteria transmitted by ticks. This study aimed to identify the Anaplasma species carried by captive red deer and swamp deer in a wild fauna reserve in France. Blood from 59 red deer and 7 swamp deer was collected and analyzed over a period of two years. A semi-nested PCR targeting the 23S rRNA was performed to detect and characterize Anaplasma spp. and determine the presence of zoonotic species. Anaplasma phagocytophilum was identified in 14/59 red deer (23.7%) but it was not identified in any of the swamp deer (7 animals). Three sequences could not be assigned to any particular species based on the 23S rRNA sequences. Complementary nested PCR targeting 16S rRNA, gltA and groEL genes and sequencing analysis then identified these sequences as a recently reported zoonotic species, Anaplasma capra; this species was found in 2 red deer (Cervus elaphus) and 1 swamp deer (Rucervus duvaucelii). This is the first report of the tick-borne zoonotic bacterium A. capra in France, a species otherwise described only in China, Japan, Malaysia and South Korea in goats, sheep, deer, cattle and Japanese serows (Capricornis crispus). While this bacterium may have been introduced into the reserve by infected imported animals, its local epidemiological cycle via tick transmission seems possible as locally born deer were found infected. Diagnostic methods, especially molecular ones, should take into account the potential infection of animals and humans with this species
Alfa: annotation landscape for aligned reads
No full textBackground: The last 10 years have seen the rise of countless functional genomics studies based on Next-Geriemtion Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the experiment, the two first steps of data analysis consist of a quality control of the raw reads followed by a mapping of those reads to a reference genome/transcriptome. Subsequent steps then depend on the type of study that is being made. While some tools have been proposed for investigating data quality after the mapping step, there is no commonly adopted framework that would be easy to use and broadly applicable to any NGS data type. Results: We present ALFA, a simple but universal tool that can be used after the mapping step on any kind of NGS experiment data for any organism with available genomic annotations. In a single command line, ALFA can compute and display distribution of reads by categories (exon, intron, UTR, etc.) and biotypes (protein coding, miRNA, etc.) for a given aligned dataset with nucleotide precision. We present applications of ALFA to Ribo-Seq and RNA-Seq on Homo sapiens, CLIP-Seq on Mus musculus, RNA-Seq on Saccharomyces cerevisiae, Bisulfite sequencing on Arabidopsis thaliana and ChIP-Seq on Caenorhabditis elegans. Conclusions: We show that ALFA provides a powerful and broadly applicable approach for post mapping quality control and to produce a global overview using common or dedicated annotations. It is made available to the community as an easy to install command line tool and from the Galaxy Tool Shed
Coupling economic and GHG emission accounting models to evaluate the sustainability of biogas policies
No full textThe aim of this study is to evaluate and quantify the impacts of different biogas and related policies on the agricultural sector as well as their performance in terms of climate change mitigation and associated costs. To do so we coupled the partial equilibrium approach simulating the market clearing process with the perspective of Life Cycle Assessment of GHG applying it to the well-documented Lombardy case. Results show that the recent Italian biogas policy – prompting manure utilization and reducing the average subsidy per kWh – effectively increased the environmental sustainability of the system, which only now seems able to counteract global warming. Synergies are observed when the recent Common Agricultural Policy greening reform is simultaneously considered by the model
ArchiTechDoseViti - Optimisation agro-environnementale de la pulvérisation sur vigne en fonction de l’architecture de la végétation et du matériel d’application utilisé.
No full textLa mise en œuvre des concepts d’agriculture de précision et d’optimisation culturale en protection
phytosanitaire de la vigne se heurte aujourd’hui à une difficulté : les quantités de produit reçues par
unité de surface de végétal à protéger sont mal connues. Les doses sont homologuées à l’hectare
cadastral et le ratio entre quantités émises et reçues dépend du matériel de pulvérisation et du stade de
croissance du végétal cible. L’objectif du projet ArchiTechDoseViti était de connaître les relations
végétal-matériel-dépôts de pulvérisation. Des méthodes d’échantillonnage des dépôts ont été
développées sur le banc de vigne artificielle EvaSprayViti et au champ, et une instrumentation de
caractérisation du végétal par capteur LiDAR 2D a été proposée. Les modèles empiriques développés
sont une étape vers la modélisation prédictive des dépôts et une pulvérisation de précision. En tenant
compte du développement de la plante cible dans le choix de la dose utilisée, les quantités d’intrants
épandues au niveau de la filière pourraient être réduites de 20 à 30%.The implementation of precision farming and cropping systems optimization concepts for plant
protection in vine are currently facing a difficulty: the quantities of product received per unit area of plant
to be protected are poorly known. Doses are registered per hectare of ground and the ratio between the
quantities sprayed and received on the plant depends on sprayer performance and on crop growth
stage. The objective of ArchiTechDoseViti project was to understand the plant-equipment-spray
relationships. Methods for sampling of deposits and for plant characterization have been developed on
the EvaSprayViti artificial vine bench and in the field. A sensing system based on a 2D LiDAR has been
proposed. The empirical models developed are a step towards predictive modelling of deposits and
precision spraying. By taking into account the growth of the plant to protect for choosing the dose rate,
quantities of inputs for the vine crop in France may probably be reduced by 20 or 30%
The neuropeptide 26RFa in the human gut and pancreas: potential involvement in glucose homeostasis
No full textOBJECTIVE: Recent studies performed in mice revealed that the neuropeptide 26RFa regulates glucose homeostasis by acting as an incretin, and by increasing insulin sensitivity. However, in human, an association between 26RFa and the regulation of glucose homeostasis is poorly documented. In this study, we have thus investigated in detail the distribution of 26RFa and its receptor, GPR103, in the gut and the pancreas, and determined the response of this peptidergic system to an oral glucose challenge in obese patients. DESIGN AND METHODS: Distribution of 26RFa and GPR103 was examined by immunohistochemistry using gut and pancreas tissue sections. Circulating 26RFa was determined using a specific radioimmunoassay in plasma samples collected during an oral glucose tolerance test. RESULTS: 26RFa and GPR103 are present all along the gut but are more abundant in the stomach and duodenum. In the stomach, the peptide and its receptor are highly expressed in the gastric glands, whereas in the duodenum, ileum and colon they are present in the enterocytes and the goblet cells. In the pancreatic islets, the 26RFa/GPR103 system is mostly present in the beta cells. During an oral glucose tolerance test, plasma 26RFa profile is different between obese patients and healthy volunteers, and we found strong positive correlations between 26RFa blood levels and the BMI, and with various parameters of insulin secretion and insulin resistance. CONCLUSION: the present data suggest an involvement of the 26RFa/GPR103 peptidergic system in the control of human glucose homeostasis
Reviews and syntheses: influences of landscape structure and land uses on local to regional climate and air quality
No full textThe atmosphere and the land surface interact in multiple ways, for instance through the radiative-energy balance, the water cycle or the emission and deposition of natural and anthropogenic compounds. By modifying the land surface, land use and land cover changes (LULCCs) and land management changes (LMCs) alter the physical, chemical, and biological processes of the biosphere and therefore all land–atmosphere interactions, from local to global scales. Through socio-economic drivers and regulatory policies adopted at different levels (local, regional, national, or supranational), human activities strongly interfere in the land–atmosphere interactions, and those activities lead to a patchwork of natural, semi-natural, agricultural, urban, and semi-urban areas. In this context, urban and peri-urban areas, which have a high population density, are of particular attention since land transformation can lead to important environmental impacts and affect the health and life of millions of people. The objectives of this review are to synthesize the existing experimental and modelling works that investigate physical, chemical, and/or biogeochemical interactions between land surfaces and the atmosphere, therefore potentially impacting local/regional climate and air quality, mainly in urban or peri-urban landscapes at regional and local scales. The conclusions we draw from our synthesis are the following. (1) The adequate temporal and spatial description of land use and land management practices (e.g. areas concerned, type of crops, whether or not they are irrigated, quantity of fertilizers used and actual seasonality of application) necessary for including the effects of LMC in global and even more in regional climate models is inexistent (or very poor). Not taking into account these characteristics may bias the regional projections used for impact studies. (2) Land–atmosphere interactions are often specific to the case study analysed; therefore, one can hardly propose general solutions or recommendations. (3) Adaptation strategies, proposed after climatic impacts on the targeted resource have been derived, are often biased as they do not account for feedbacks on local/regional climate. (4) There is space for considering atmospheric chemistry, through land–atmosphere interactions, as a factor for land management, helping to maintain air quality and supporting ecosystem functioning. (5) There is a lack of an integrated tool, which includes the many different processes of importance in an operational model, to test different land use or land management scenarios at the scale of a territory
Early exit from business, performance and neighbours’ influence: a study of farmers in France
No full textThe Ethics of Eliminating Harmful Species: The Case of the Tsetse Fly
No full textWildlife species harmful to humans are often targets of control and elimination programs. A contemporary example is the tsetse fly, a vector of sleeping sickness and African animal trypanosomosis. Tsetse flies have recently been targeted by a pan-African eradication campaign. If it is successful, the campaign could push the entire tsetse family to extinction. With the emergence of effective and efficient elimination technologies, ethical assessment of proposed elimination campaigns is urgently needed. We examine the ethics of tsetse fly elimination by considering arguments predicated on both the instrumental and the intrinsic values of the species at local and global scales. We conclude that, although global eradication of tsetse flies is not ethically justified, localized elimination campaigns targeting isolated populations are ethically defensible. We urge assessments of this kind be conducted regularly and in context, so that all relevant factors underlying decisions on species elimination are routinely laid bare for evaluation
Histogenesis of Merkel Cell Carcinoma: A Comprehensive Review
No full textMerkel cell carcinoma (MCC) is a primary neuroendocrine carcinoma of the skin. This neoplasia features aggressive behavior, resulting in a 5-year overall survival rate of 40%. In 2008, Feng et al. identified Merkel cell polyomavirus (MCPyV) integration into the host genome as the main event leading to MCC oncogenesis. However, despite identification of this crucial viral oncogenic trigger, the nature of the cell in which MCC oncogenesis occurs is actually unknown. In fact, several hypotheses have been proposed. Despite the large similarity in phenotype features between MCC tumor cells and physiological Merkel cells (MCs), a specialized subpopulation of the epidermis acting as mechanoreceptor of the skin, several points argue against the hypothesis that MCC derives directly from MCs. Alternatively, MCPyV integration could occur in another cell type and induce acquisition of an MC-like phenotype. Accordingly, an epithelial as well as a fibroblastic or B-cell origin of MCC has been proposed mainly based on phenotype similarities shared by MCC and these potential ancestries. The aim of this present review is to provide a comprehensive review of the current knowledge of the histogenesis of MCC
Evolution and comparative genomics of the most common Trichoderma species
No full textBackgroundThe growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood.ResultsWe selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function.Conclusions p id=Par3 Our study presents a time scaled pattern of genome evolution in12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist