Pratiques agricoles et propriétés agro-écologiques des prairies dans un processus d’intensification écologique : le cas de l’élevage bovin dans le Vercors

National audienceL'élevage bovin pour la production laitière est la composante agricole majeure sur le territoire des Quatre Montagnes dans le massif du Vercors. Sur ce territoire, un enjeu fort soulevé par une grande partie des agriculteurs concerne la question de l'autonomie fourragère. Cet aspect de la production est d'autant plus central qu'il est fortement dépendant des caractéristiques des prairies qui permettent d'assurer la production de fourrage en dépit d'aléas de plus en plus contraignants (sécheresses, dégâts de campagnols…). Comprendre comment maintenir un niveau de production suffisant en s'appuyant sur les propriétés écosystémiques des prairies relève du contexte de l'intensification écologique en abordant les relations entre l'organisation des systèmes d'élevage (usages à l'échelle des parcelles, diversité des types de parcelles au sein des exploitations, distribution au sein du paysage) et les valeurs d'usage et services écosystémiques fournis par les prairies. Au sein du projet multi-sites ANR-SYSTERRA MOUVE (Les interactions Elevage et Territoire dans la mise en mouvement de l’intensification écologique), le territoire des Quatre Montagnes constitue l'un des terrains d'approfondissement pour analyser comment l'évolution des pratiques dans le sens de l'intensification écologique peut permettre d'augmenter le niveau des services écologiques et d'améliorer les capacités d'adaptation des élevages. En nous appuyant sur une typologie préétablie des prairies, basée le type d'usage (fauche, pâturage) et la composition simplifiée de la végétation nous avons mesuré un large panel de propriétés écosystémiques sur un échantillon de 50 parcelles représentant la diversité des types d'usage sur le territoire. Les propriétés mesurée couvrent notamment la structure spécifique (diversité, hétérogénéité) et fonctionnelle des communautés (traits foliaires, structuraux, phénologiques), les caractéristiques agronomiques (teneur en N, C, P…) et écologique (biomasse et diversité microbienne) du sol et du fourrage (production, qualité), autant de proxys pour les grands types de services reconnus : (i) services intrants, (ii) services de production fourragère et (iii) services en lien avec la valeur écologique des prairies. Les premiers résultats révèlent le rôle prépondérant de deux facteurs liés aux usages pour les propriétés agro-écologiques des prairies : la date de première fauche ou pâturage et le caractère temporaire ou permanent des prairies (date du dernier retournement). Les prairies temporaires offrent un bon niveau de services intrant (fertilité, matière organique) et de production et qualité fourragère mais une faible valeur écologique (faible diversité). Cette distinction sur la base des propriétés agro-écologiques est d'autant plus intéressante que les entretiens auprès des éleveurs ont souligné l'importance de la place des prairies temporaires comme une des clés pour l'autonomie fourragère. Ces prairies productives étant également les plus sensibles aux aléas et offrant une moindre souplesse d'utilisation. A terme, notre objectif est d'identifier les compromis, synergies et antagonismes entre les différents types de services rendus (agronomiques, écologiques) en fonction de différents scénarios d'intensification écologique à l'échelle du territoire

The impact of quantitative optimization of hybridization conditions on gene expression analysis.

BACKGROUND: With the growing availability of entire genome sequences, an increasing number of scientists can exploit oligonucleotide microarrays for genome-scale expression studies. While probe-design is a major research area, relatively little work has been reported on the optimization of microarray protocols. RESULTS: As shown in this study, suboptimal conditions can have considerable impact on biologically relevant observations. For example, deviation from the optimal temperature by one degree Celsius lead to a loss of up to 44% of differentially expressed genes identified. While genes from thousands of Gene Ontology categories were affected, transcription factors and other low-copy-number regulators were disproportionately lost. Calibrated protocols are thus required in order to take full advantage of the large dynamic range of microarrays.For an objective optimization of protocols we introduce an approach that maximizes the amount of information obtained per experiment. A comparison of two typical samples is sufficient for this calibration. We can ensure, however, that optimization results are independent of the samples and the specific measures used for calibration. Both simulations and spike-in experiments confirmed an unbiased determination of generally optimal experimental conditions. CONCLUSIONS: Well calibrated hybridization conditions are thus easily achieved and necessary for the efficient detection of differential expression. They are essential for the sensitive pro filing of low-copy-number molecules. This is particularly critical for studies of transcription factor expression, or the inference and study of regulatory networks.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species.

Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasised desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole-genome sequences of 3 bdelloid species: Rotaria macrura and R. magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccation tolerant. In combination with the published assembly of A. vaga, which is also desiccation tolerant, we apply a comparative genomics approach to evaluate the potential effects of desiccation tolerance and asexuality on genome evolution in bdelloids. We find that ancestral tetraploidy is conserved among all 4 bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is unexpectedly low. This finding is contrary to current models regarding the role of desiccation in shaping bdelloid genomes. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. Consequently, several features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call into question the proposed role of desiccation in mediating horizontal genetic transfer

Farmer perceptions and responses to soil degradation in Swaziland

Soil degradation is globally concerning due to its adverse effects on the environment and agricultural production. Much of Swaziland is at risk from degradation. This paper assesses farmer perceptions and responses to soil degradation in 2002 and 2014, focusing on two land uses that underpin rural livelihoods: arable land and rangeland areas. It uses repeat household surveys and semi-structured interviews, in two case study chiefdoms in the country’s middleveld (KaBhudla and Engcayini) in the first longitudinal study of its kind. We find that observations of land degradation are perceived mainly through changes in land productivity, with chemical degradation occurring predominantly on arable land and physical degradation and erosion mainly in rangeland areas. Changes in rainfall are particularly important in determining responses. While perceptions of the causes and impacts of degradation largely concur with the scientific literature, responses were constrained by poor land availability, shorter and more unpredictable cropping seasons because of changing rains and low awareness, access to or knowledge of agricultural inputs. We suggest that sustainable arable land management can be enhanced through improved access to alternative sources of water, use of management practices that retain soil and moisture and greater access to agricultural inputs and capacity building to ensure their appropriate use. We suggest collaborative management for settlement planning that integrates soil conservation and livestock management strategies such as controlled stocking levels and rotational grazing could improve land quality in rangeland areas. Together, these approaches can help land users to better manage change

Insights into olfactory ensheathing cell development from a laser-microdissection and transcriptome-profiling approach.

Olfactory ensheathing cells (OECs) are neural crest-derived glia that ensheath bundles of olfactory axons from their peripheral origins in the olfactory epithelium to their central targets in the olfactory bulb. We took an unbiased laser microdissection and differential RNA-seq approach, validated by in situ hybridization, to identify candidate molecular mechanisms underlying mouse OEC development and differences with the neural crest-derived Schwann cells developing on other peripheral nerves. We identified 25 novel markers for developing OECs in the olfactory mucosa and/or the olfactory nerve layer surrounding the olfactory bulb, of which 15 were OEC-specific (that is, not expressed by Schwann cells). One pan-OEC-specific gene, Ptprz1, encodes a receptor-like tyrosine phosphatase that blocks oligodendrocyte differentiation. Mutant analysis suggests Ptprz1 may also act as a brake on OEC differentiation, and that its loss disrupts olfactory axon targeting. Overall, our results provide new insights into OEC development and the diversification of neural crest-derived glia.Cambridge Commonwealth Trust Cambridge Philosophical Societ

Molecular Characterization and Patient Outcome of Melanoma Nodal Metastases and an Unknown Primary Site

Background Melanoma of unknown primary site (MUP) is not a completely understood entity with nodal metastases as the most common first clinical manifestation. The aim of this multicentric study was to assess frequency and type of oncogenic BRAF/NRAS/KIT mutations in MUP with clinically detected nodal metastases in relation to clinicopathologic features and outcome. Materials and Methods We analyzed series of 103 MUP patients (period: 1992-2010) after therapeutic lymphadenectomy (LND): 40 axillary, 47 groin, 16 cervical, none treated with BRAF inhibitors. We performed molecular characterization of BRAF/NRAS/KIT mutational status in nodal metastases using direct sequencing of respective coding sequences. Median follow-up time was 53 months. Results BRAF mutations were detected in 55 cases (53 %) (51 V600E, 93 %; 4 others, 7 %), and mutually exclusive NRAS mutations were found in 14 cases (14 %) (7 p.Q61R, 4 p.Q61K, 2 p.Q61H, 1 p.Q13R). We have not detected any mutations in KIT. The 5-year overall survival (OS) was 34 %; median was 24 months. We have not found significant correlation between mutational status (BRAF/NRAS) and OS; however, for BRAF or NRAS mutated melanomas we observed significantly shorter disease-free survival (DFS) when compared with wild-type melanoma patients (p = .04; 5-year DFS, 18 vs 19 vs 31 %, respectively). The most important factor influencing OS was number of metastatic lymph nodes >1 (p = .03). Conclusions Our large study on molecular characterization of MUP with nodal metastases showed that MUPs had molecular features similar to sporadic non-chronic-sun-damaged melanomas. BRAF/NRAS mutational status had negative impact on DFS in this group of patients. These observations might have potential implication for molecular-targeted therapy in MUPs

Reliable, resilient and sustainable urban drainage systems: an analysis of robustness under deep uncertainty (article)

This is the author accepted manuscript. The final version is available from the American Chemical Society via the DOI in this record.The dataset associated with this article is available in ORE at: https://doi.org/10.24378/exe.563Reliability, resilience and sustainability are key goals of any urban drainage system. However, only a few studies have recently focused on measuring, operationalizing and comparing such concepts in a world of deep uncertainty. In this study, these key concepts are defined and quantified for a number of gray, green and hybrid strategies, aimed at improving the capacity issues of an existing integrated urban wastewater system. These interventions are investigated by means of a regret-based approach, which evaluates the robustness (that is the ability to perform well under deep uncertainty conditions) of each strategy in terms of the three qualities through integration of multiple objectives (i.e. sewer flooding, river water quality, combined sewer overflows, river flooding, greenhouse gas emissions, cost and acceptability) across four different future scenarios. The results indicate that strategies found to be robust in terms of sustainability were typically also robust for resilience and reliability across future scenarios. However, strategies found to be robust in terms of their resilience and, in particular, for reliability did not guarantee robustness for sustainability. Conventional gray infrastructure strategies were found to lack robustness in terms of sustainability due to their unbalanced economic, environmental and social performance. Such limitations were overcome, however, by implementing hybrid solutions that combine green retrofits and gray rehabilitation solutions.This study was funded by the UK Engineering and Physical Sciences Research Council through STREAM (EP/G037094/1) with Northumbrian Water Limited, BRIM (EP/N010329/1) and the final author’s fellowship Safe & SuRe (EP/K006924/1)