eKhSACIR інституційному репозитарії Харківської державної академії культури
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Heat production in ruminants: from experimental data to feed unit systems through meta-analysis
No full textInternational audienc
The influence of tillage on N<sub>2</sub>O fluxes from an intensively managed grazed grassland in Scotland
No full textInternational audienceIntensively managed grass production in highrainfall temperate climate zones is a globally important source of N2O. Many of these grasslands are occasionally tilled to rejuvenate the sward, and this can lead to increased N2O emissions. This was investigated by comparing N2O fluxes from two adjacent intensively managed grazed grasslands in Scotland, one of which was tilled. A combination of eddy covariance, high-resolution dynamic chamber and static chamber methods was used. N2O emissions from the tilled field increased significantly for several days immediately after ploughing and remained elevated for approximately 2 months after the tillage event contributing to an estimated increase in N2O fluxes of 0.85 0.11 kgN2O-N ha 1. However, any influence on N2O emissions after this period appears to be minimal. The cumulative N2O emissions associated with the tillage event and a fertiliser application of 70 kg N ammonia nitrate from one field were not significantly different from the adjacent untilled field, in which two fertiliser applications of 70 kg N ammonia nitrate occurred during the same period. Total cumulative fluxes calculated for the tilled and untilled fields over the entire 175-day measurement period were 2.14 0.18 and 1.65 1.02 kgN2O-N ha 1, respectivel
Cover crops prevent the deleterious effect of nitrogen fertilisation on bacterial diversity by maintaining the carbon content of ploughed soil
No full textInternational audienceSynthetic nitrogen (N) fertilisers are widely used for enhancing agrosystem productivity and are thus thought to increase organic inputs from crop residues. However, many crop rotations have a low amount of organic residue returned to the soil since the whole aboveground crop biomass is harvested and exported. To compensate for such organic outputs and to improve soil quality, the introduction of winter cover crops in rotations has been suggested. A 4-year controlled field experiment was conducted to quantify the respective and combined effects of chemical N fertilisation and winter cover crops on plant productivity, organic carbon (C) and N inputs from crop residues and cover crops, changes in soil C and N concentrations, C:N ratio, soil mineral N, pH, soil moisture and soil bacterial biodiversity. A ploughing tillage system with low organic input was assessed, for which the main crops were spring wheat, green pea, forage maize, along with cover crops of different legume and non-legume species. N fertilisation did not have an impact on the aboveground biomass except following forage maize. Cover crops increased the total amount of C and N inputs, irrespective of N fertilisation which had no significant effect The soil N concentration decreased in all treatments, particularly when N fertilisers were applied under bare-fallow conditions. The latter treatment also caused decreased soil C concentrations (slightly increased in the other treatments) and decreased bacterial biodiversity (no change in the other treatments). Bacteria from the Proteobacteria and Bacterioidetes phyla were highly correlated with soil from fertilised bare fallow conditions. While Verrucomicrobia was characteristic of non-fertilised bare fallow soils, Acidobacteria and Cyanobacteria were associated with the high C and N concentrations present in soils following cover crop treatments. Taken together, these results demonstrate that in ploughing systems, under low organic restitution regimes, intensive N fertilisation decreases the diversity of the bacterial soil community and reduces soil C and N concentrations, but only in bare fallow conditions. There is a protective effect of winter cover crops against the deleterious effect of chemical N fertilisation on soil biodiversity and nutrient cycling, since they can maintain soil C and N concentrations. The use of winter cover crops containing legumes is thus a practice that is able to meet the criteria of a sustainable agriculture
A part toolbox to tune genetic expression in Bacillus subtilis
No full textInternational audienceLibraries of well-characterised components regulating gene expression levels are essential to many synthetic biology applications. While widely available for the Gram-negative model bacterium Escherichia coli, such libraries are lacking for the Gram-positive model Bacillus subtilis, a key organism for basic research and biotechnological applications. Here, we engineered a genetic toolbox comprising libraries of promoters, Ribosome Binding Sites (RBS), and protein degradation tags to precisely tune gene expression in B. subtilis We first designed a modular Expression Operating Unit (EOU) facilitating parts assembly and modifications and providing a standard genetic context for gene circuits implementation. We then selected native, constitutive promoters of B. subtilis and efficient RBS sequences from which we engineered three promoters and three RBS sequence libraries exhibiting ∼14 000-fold dynamic range in gene expression levels. We also designed a collection of SsrA proteolysis tags of variable strength. Finally, by using fluorescence fluctuation methods coupled with two-photon microscopy, we quantified the absolute concentration of GFP in a subset of strains from the library. Our complete promoters and RBS sequences library comprising over 135 constructs enables tuning of GFP concentration over five orders of magnitude, from 0.05 to 700 μM. This toolbox of regulatory components will support many research and engineering applications in B. subtilis
Role of Vitamin D in the hygiene hypothesis: the interplay between vitamin D, vitamin D receptors, gut microbiota, and immune response
No full textThe hygiene hypothesis postulates that higher levels of cleanliness and improper exposure to microorganisms early in childhood could disturb the intestinal microbiome resulting in abnormal immune responses. Recently, more attention has been put on how a lack of sun exposure and consequently vitamin D deficiency could lead to less immune tolerance and aberrant immune responses. Moreover, vitamin D receptor (VDR) function has been positioned to be a critical aspect of immune response and gut homeostasis. Therefore, this review focuses on the role that the interaction between vitamin D, VDR function, and gut microbiome might have on autoimmune diseases in the context of the hygiene hypothesis. Literature shows that there is a high correlation between vitamin D deficiency, VDR dysfunction, gut microbiota composition, and autoimmune diseases. The biologically active form of vitamin D, 1,25(OH)(2)D-3, serves as the primary ligand for VDRs, which have been shown to play a fundamental role in reducing autoimmune disease symptoms. Although the biological functions of VDR, the effects of its genetic variants, and the effects of epigenetic profiles in its promoter region are largely unknown in humans, studies in murine models are increasingly demonstrating that VDRs play a crucial role in attenuating autoimmune disease symptoms by regulating autophagy and the production of antimicrobial peptides, such cathelicidin and beta-defensin, which are responsible for modifying the intestinal microbiota to a healthier composition. Remarkably, evidence shows that hormonal compounds and byproducts of the microbiota such as secondary bile acids might also activate VDR. Therefore, understanding the interaction between VDR and gut microbiota is of the utmost importance toward understanding the rise in autoimmune diseases in Western countries. We have gained insights on how the VDR functions affects inflammation, autophagy, and microbiota composition that could lead to the development of pathogenesis of autoimmune diseases, while confirming the role vitamin D and VDRs have in the context of hygiene hypothesis
Peanut-allergic patients in the MIRABEL survey: characteristics, allergists' dietary advice and lessons from real life
No full textInternational audienceBackgroundThe MIRABEL survey is an observational study on peanut allergy in France, Belgium and Luxemburg. The objectives are to provide data on a large population, to analyse the consumer behaviour, to study the presence of peanut traces in pre-packed foods with/without precautionary allergen labelling (PAL), and to combine these data to quantify allergic risk and produce a cost/benefit analysis. This paper reports a real-life observatory of 785 patients (<16y: 86%): medical characteristics, eliciting doses (ED) in real life and in oral food challenges (OFC), factors associated with severe reactions, allergist dietary advice and patients' anxiety regarding their allergy. MethodsAge and symptoms at diagnosis, route of exposure, comorbidities, allergy tests, ED (OFC/real life; mg peanut protein), dietary advice about PAL, and anxiety score were recorded. ResultsMedian age was 3years; 85% were declared allergic. Severe/potentially severe reactions were reported in 30% of the allergic patients: serious systemic reaction (15%), laryngeal angioedema (8%), shock (4%) and acute asthma (3%); 66% had atopic dermatitis, 58% asthma. Median ara h 2 sIgE level was 11.5kUA/L. Of the 278 OFCs, 225 were positive (median ED: 67.3 mg). Real-life ED was <100mg in 44.3%. Severe reactions were significantly more frequent in teenagers and adults (P=0.004), asthmatic patients (P=0.033), and patients who reacted to inhalation (P<0.001). No significant association was found for OFC ED or ara h 2 sIgE. Factors associated with strict avoidance advice including PAL were OFC ED <100mg (P<0.001), but not severe reaction history (P=0.051) or asthma (P=0.34). Anxiety was significantly associated with strict avoidance (P<0.001). Conclusion and clinical relevanceSevere/potentially severe reactions, allergic comorbidities, and low EDs in real life are frequent in peanut-allergic patients. Asthma, teenage/adulthood and reaction to inhalation are associated with severe symptoms. PAL and criteria guiding dietary advice need to be improved
Effect of the type of contamination and land use on soil enzymatic activities. Results of the French "Bioindicator program"
No full textSince many decades, enzymatic activities are used to assess the effects of land use changes, agricultural practices and soil contamination on soil functioning. A lot of studies point out contradictory results depending notably on the methodology used, as well as soil characteristics… To overcome the lack of consensus concerning indicators available to assess soil quality and functioning, the national research programme “Bioindicator” (overseen by ADEME) was set up in France to develop and assay biological indicators (2006–2012). We aimed at standardizing and emphasizing the number of biochemical measurements, and developed miniaturized colorimetric methods to obtain a great enzymatic dataset. Thirteen activities (from three laboratories) were measured within this programme, in 47 modalities of 13 experimental sites differing in terms of land use (Corine land cover), contamination type – Polycyclic Aromatic Hydrocarbures or metals – and pollution levels (Vibrisse 8th decile). This dataset allows an analysis of the effect of atmospheric or added contamination gradients on the enzymatic activities. Our objectives are to point out the sensitivity of enzymes for each type of pollution and land use, to offer the most appropriate panel for a sensible analysis. Data were analysed for the all datasets, each site and each land use. Our main conclusions are as follows: enzymes are more sensitive to metallic contamination than to organic ones; enzymes are good indicators of metal bioavailability; Alkaline phosphatase and Arylamidase are the most relevant enzymes to assess the effect of soil contaminatio
Mining data from the national DEPHY farm network : potential for reconciling low pesticide use and high economic profitability
No full textEA GESTADInternational audienceIntroduction Reducing pesticide use in agriculture is a major challenge to improve sustainability that requires a holistic approach. Agronomists have addressed the question using field experiments at the cropping system level for decades. Another emerging approach relies on large commercial farm networks producing data for contrasted management strategies in various production situations (Lechenet et al., 2014). Here we used data from the French DEPHY farm network to address two major questions: (i) what management strategies are associated to low pesticide use in arable farming, in different farming contexts? (ii) Is the objective of reducing pesticide use antagonistic with maintaining economic profitability at the cropping system level ? Materials and Methods The DEPHY network is based on 1000 arable farms throughout the French territory, with much contrasted levels of pesticide use. The treatment Frequency Index (TFI = number of treatments weighted by the relative dose to registered dose and by the proportion of sprayed area) computed at the cropping system level varies in the range [0-15] (mean=3.3) in conventional farms. First we used regression tree methods to partition TFI according to variables describing the farming context (soil type, climatic feature, local markets…), to identify types of situations favoring high vs. low TFI. Then, in each type of production situation, we used similar methods to identify management strategies (combinations of technical options) associated with high vs. low TFIs. Finally, we performed a LASSO regression to estimate for each farm of the network the marginal effect of TFI on yield and profitability (net margin). Results and Discussion We identified six groups of production situations, with increasing average level of pesticide use from PS1 to PS6. The main aspects of the farming context associated with low pesticide requirement were (i) the combination of arable crops with livestock breeding, (ii) the absence of local market opportunities for industrial crop outlets, and (iii) climatic conditions characterized by high solar radiation and low precipitations. Our results reveal that the range of TFI was large within each production situation. Across the whole dataset, we identified 54 profiles of management strategies with contrasted TFI (see the distribution of TFI for the 21 strategies identified in PS2, fig. 1). The main technical options associated with low TFI were related to crop rotation (high proportion of grasslands and rustic crops, diversity of sowing periods), spraying at low doses, low level of fertilization and tillage strategies based on ploughing. However, strategies with low TFI differed from one farming context to one another. As an example, in cereal-based regions, both diversification of crops with legumes and spring crops, and diversification of cultivars, were majors options associated with low TFI, whereas in maize-based areas, diversification was not such a major issue. Low TFI were there mostly associated with mechanical weeding and low doses applications, combined with ploughing. Our statistical analysis of the relationship between TFI and profitability failed to detect any antagonism between high profitability and low TFI in 82% of farms of the network. The main exception concerned farms producing industrial crops with both high added value and high pesticide requirements, mainly in northern France (sugar beet, potatoes), and in south-western France (seed maize). Conclusions The analysis of data from this large farm network proved to be very powerful to produce knowledge on cropping systems. We identified management strategies with low pesticide use, but we also showed that combinations of IPM-based measures should be adapted as the function of the farming context. Finally we were able to quantify the potential decrease of pesticide use, and its distribution at the national scale, that would not affect the profitability for farmers. Acknowledgements This study was funded by the PSPE program. The DEPHY network is supported by ONEMA. We thank all the farmers and the advisors involved in the network for providing the data
What evolutions for wege earner's work in farms after hiring? A case study in dairy farms in Auvergne, France
No full textEnlargement of farms in association with the decrease in the family workforce are inducing the development of permanent wage earners. In dairy farms, permanent wage earners have been recruited to carry out milking in particular. Studies show that human resource management practices can help farmers to retain wage earners in farms, but the authors do not take into account changes in wage earners' work over time. Our hypothesis is that dynamic aspects in work content are crucial for wage earners, because they give them some perspective and good reasons to stay. In this paper, we analyze the evolution of permanent wage earners' work in dairy farms according to a human resource management approach. Individual interviews were carried out with farmers and permanent wage earners who work in specialized or diversified dairy farms. Five pathways of evolution of wage earners' work were identified as well five variables and categories were identified to describe the pathways of evolution according to the assignment of tasks and versatility/specialization
CN-wheat: a mechanistic structural-functional model for carbon and nitrogen metabolism in wheat
No full textIn a context of global change, it is necessary to identify new practices and plant characteristics determining crop production and that can be potential targets for plant breeding. This could be achieved by numerical simulation, using mechanistic and integrative models that provide a holistic view of plant functioning. However, a central difficulty lies in building a coherent view of the involved processes and how to integrate them at plant and crop level. The model proposed here, called CN-Wheat, represents a significant progress to address these issues by using a fully mechanistic approach for integration of Carbon (C) and Nitrogen (N) metabolisms within wheat plants after anthesis. CN-Wheat is defined at culm scale; the crop is represented as a population of individual culms that compete for light and soil N. Culm structure is composed of a root compartment, a set of photosynthetic organs and the grains. Each module includes structural, storage and mobile materials. Fluxes of C-N among modules take place through a common pool and/or through the transpiration flow. The modelled physiological activities are the acquisition of C and N, the synthesis and degradation of primary metabolites (sucrose, fructans, starch, amino acids, proteins and nitrates), C respiration, C-N exudation and tissue death. A central role is given to metabolite concentrations as drivers of (i) physiological activities and (ii) transfers between organs. Thus, the integration within the plant results from that all processes act in parallel on interconnected metabolite pools, which is represented as a set of differential equations, solved numerically. Model behavior was evaluated against a field experimentation with three levels of N fertilization applied at anthesis. For each N treatment, CN-Wheat accurately predicted the post-anthesis kinetics of (i) C-N distribution among organs, (ii) green areas of laminae and (iii) dry mass and N content of grains. In our simulations, when soil N was non-limiting, N in grains was ultimately determined by the availability of C for root activity. Dry matter accumulation in grains was mostly affected by photosynthetic organ lifespan which was regulated by protein turn-over and C-regulated root activity. Whereas the use of response functions to metabolite concentration is accepted for each of the processes described in the model, here we show that it can be used for an integrative modelling of the whole plant. Besides, CN-Wheat provides insights into the interplay of C-N metabolism which is expected to improve our knowledge on the regulation of plant functioning. This approach also enables to identify potential targets for plant breeding in order to improve crop production and N efficiency as well as crop adaptation to climate changes and low N agronomical practices