Elasticity of Ingestive Behaviour and Intake in Sheep Associated with Food Diversity on Plurispecific Swards

Animals on heterogeneous swards generally opt for a varied diet. This may stimulate their intake, unless searching constraints limit intake rate (Champion et al., 1998). However the management of plurispecific swards presents a risk of overgrazing the preferred species and undergrazing the less-preferred species. This study aimed to test the effect of type of diversity and type of management on the elasticity of ingestive behaviour and intake in sheep

Effets du dérangement par la chasse sur les oiseaux d'eau : revue de littérature

La chasse aux oiseaux d'eau, activité humaine largement pratiquée sur les zones humides du continent eurasiatique, présente deux composantes pouvant affecter la dynamique des populations de ces espèces migratrices : le prélèvement (qui concerne la mortalité) et le dérangement. Ce dernier aspect fait l'objet d'études de plus en plus nombreuses et détaillées, ici synthétisées, incluant des protocoles expérimentaux et des approches conceptuelles. Le dérangement par la chasse est considéré comme important pour une espèce lorsque les modifications qu'il induit ont un effet sur la « fitness » des individus de cette espèce (diminution de la survie et/ou du succès reproducteur). Les études montrent que le dérangement modifie presque toujours la distribution géographique des oiseaux en favorisant leur regroupement (5 à 50 fois plus) sur des espaces non chassés, induisant une sous-exploitation des ressources trophiques présentes sur les espaces chassés. Le dérangement peut aussi provoquer un accroissement du taux de renouvellement (« turnover ») des individus sur leur étape migratoire. Ces transferts d'oiseaux, bien quantifiés localement, ont un impact encore inconnu sur la taille des populations concernées, la large distribution de ces populations sur plusieurs continents rendant cette évaluation difficile. Le dérangement provoque une modification comportementale soit en favorisant des activités plus coûteuses que celles pratiquées sans dérangement, soit en diminuant le temps passé à des activités qui permettent d'acquérir de l'énergie. Les estimations ou simulations de ces pertes peuvent atteindre 25 % de la dépense énergétique journalière. Les oiseaux dérangés développent des capacités d'adaptation physiologique face aux contraintes associées au dérangement, par exemple une augmentation de la prise alimentaire, une augmentation du rendement de l'assimilation énergétique ou une augmentation de la sécrétion de corticostérone qui stimule l'activité de recherche de nourriture. L'évaluation directe du bilan énergétique de ces adaptations n'a pas encore été réalisée et l'on peut admettre qu'elles permettent à l'oiseau de maintenir un apport énergétique analogue à celui obtenu sans dérangement; mais le coût à terme de cette acquisition est élevé. Ainsi, une étude récente sur la Grande Oie des neiges Anser caerules-cens atlantica au Canada révèle que lorsque les individus sont dérangés par la chasse sur leur étape migratoire de printemps, ils sont contraints d'exploiter des sites moins riches que s'il n'y avait pas de chasse; ils sont alors dans de moins bonnes conditions corporelles (lipidiques et protéiniques) lors du départ vers leurs lieux de reproduction et ils ont finalement un moindre succès de reproduction que les individus n'ayant pas subi le dérangement par la chasse. Certes, des lacunes et des incertitudes persistent, par exemple au niveau spécifique (peu d'études sur les limicoles), mais tous les auteurs qui les ont mises en évidence s'accordent aussi pour reconnaître que, pour contrebalancer les effets du dérangement par la chasse, des mesures de protection doivent être prises.Waterbird hunting is a widespread human activity over wetlands of the Eurasian continent. It has two components that can influence the population dynamics of migratory species : mortality and disturbance. Disturbance is the focus of an increasing number of detailed studies, using both experimental and theoretical approaches. They are synthesized herein. Disturbance is considered important when induced changes influence the fitness of the individuals of a species (decrease in survival or breeding success). Studies show that disturbance almost always change the geographical distribution of birds, conducting to an under-exploitation of food resources available in hunting areas. Disturbance can also favour an increase in the turnover rate of individuals on their migratory stopover. These changes in bird distribution, although precisely quantified at a local scale, have an unknown impact on the population size of the concerned species. The wide distribution of several of these species ranging over several continents makes the precise evaluation of this impact difficult. Disturbance changes behaviour either by increasing time spent in activities more costly than those done without disturbance or by decreasing time spent gaining energy. Estimation or simulation of these lost can reach 25% of the daily energy expenses. Facing disturbance, birds can develop several physiological adaptations, for instance an increased food intake, an increased efficiency of energy assimilation or an augmentation of corticosterone secretion stimulating food searching. The direct evaluation of the energy balance of these adaptations has not been made yet and it can be acknowledged that they allow birds to maintain energy gains similar to those obtained without disturbance. However, the long-term cost of this compensation is high. A recent study of the Greater Snow Goose Anser caerulescens atlantica on their spring stopover in Canada indicates that hunting disturbance makes geese use lower quality habitats, decreases their body condition (fat and protein) when they depart to the breeding sites and decreases their breeding success relative to individuals that have not experienced hunting. Uncertainties remain, for instance at the species level (few studies on waders), but all authors that emphasized them also agree to acknowledge that protection measures must be taken to counter-balance the effects of hunting disturbance. They recommend the increase of protected areas (hunt-free areas), the elaboration of a network of reserves and the establishment of non hunted zones around existing reserves to reduce to the minimum the negative effects of disturbance on birds that use these reserves. The implementation of these management actions must favour the widening of the distribution of these populations and facilitate the local and regional increase of their numbers. These protection measures are positive responses to the recommendations of the European Union birds and habitats directives

Evaluation of a novel antibody to define histone 3.3 G34R mutant brain tumours

Missense somatic mutations affecting histone H3.1 and H3.3 proteins are now accepted as the hallmark of paediatric diffuse intrinsic pontine gliomas (DIPG), non-brain stem paediatric high grade gliomas (pHGG) as well as a subset of adult glioblastoma multiforme (GBM). Different mutations give rise to one of three amino acid substitutions at two critical positions within the histone tails, K27M, G34R/V. Several studies have highlighted gene expression and epigenetic changes associated with histone H3 mutations; however their precise roles in tumourigenesis remain incompletely understood. Determining how such amino acid substitutions in a protein affect its properties can be challenging because of difficulties in detecting and tracking mutant proteins within cells and tissues. Here we describe a strategy for the generation of antibodies to discriminate G34R and G34V mutant histone H3 proteins from their wild-type counterparts. Antibodies were validated by western blotting and immunocytochemistry, using recombinant H3.3 proteins and paediatric GBM cell lines. The H3-G34R antibody demonstrated a high degree of selectivity towards its target sequence. Accordingly, immunostaining on a cohort of 22 formalin-fixed paraffin embedded tumours with a previously known H3.3 G34R mutation status, detected successfully the corresponding mutant protein in 11/11 G34R cases. Since there was a high concordance between genotype and immunohistochemical analysis of G34R mutant tumour samples, we analysed a series of tissue microarrays (TMAs) to assess the specificity of the antibody in a range of paediatric brain tumours, and noted immunoreactivity in 2/634 cases. Importantly, we describe the generation and validation of highly specific antibodies for G34 mutations. Overall our work adds to an extremely valuable portfolio of antibodies, not only for histopathologic detection of tumour-associated mutant histone sequences, but also facilitating the study of spatial/anatomical aspects of tumour formation and the identification of downstream targets and pathways in malignant glioma progression

Beyond inverse Ising model: structure of the analytical solution for a class of inverse problems

I consider the problem of deriving couplings of a statistical model from measured correlations, a task which generalizes the well-known inverse Ising problem. After reminding that such problem can be mapped on the one of expressing the entropy of a system as a function of its corresponding observables, I show the conditions under which this can be done without resorting to iterative algorithms. I find that inverse problems are local (the inverse Fisher information is sparse) whenever the corresponding models have a factorized form, and the entropy can be split in a sum of small cluster contributions. I illustrate these ideas through two examples (the Ising model on a tree and the one-dimensional periodic chain with arbitrary order interaction) and support the results with numerical simulations. The extension of these methods to more general scenarios is finally discussed.Comment: 15 pages, 6 figure

Thermal diffusivity measurements of metastable austenite during continuous cooling

The thermal diffusivity of the metastable undercooled austenite is relevant for the quantitative analysis of the carbon and low-alloy steel quench. The standard laser-flash method requires prior thermal equilibrium between the sample and the furnace, which may not be possible to achieve without allowing the metastable phase to transform. Nevertheless, depending upon the steel's hardenability, the thermal transient due to a laser pulse may be much shorter than a cooling transient sufficiently steep to prevent the transformation of the austenite. In one such case, flash measurements were performed during continuous sample cooling and the thermal diffusivity of the metastable austenite was determined by using an extension of the standard analytical model. The adopted analytical model and data reduction procedure are described and the limitations and uncertainties of this method are discussed, also with the aid of a non-linear numerical simulation. The measured thermal diffusivity of the under cooled low-alloy austenite decreases linearly from 5.4•10−6 m2 s−1 at 1133 K to 4.3•10−6 m2 s−1 at 755 K; this trend is in broad agreement with one previous set of measurements upon a low-alloy undercooled austenite and with a large number of previous standard measurements upon stable (high-alloy) austenitic stainless steels

Reverse Engineering Gene Networks with ANN: Variability in Network Inference Algorithms

Motivation :Reconstructing the topology of a gene regulatory network is one of the key tasks in systems biology. Despite of the wide variety of proposed methods, very little work has been dedicated to the assessment of their stability properties. Here we present a methodical comparison of the performance of a novel method (RegnANN) for gene network inference based on multilayer perceptrons with three reference algorithms (ARACNE, CLR, KELLER), focussing our analysis on the prediction variability induced by both the network intrinsic structure and the available data. Results: The extensive evaluation on both synthetic data and a selection of gene modules of "Escherichia coli" indicates that all the algorithms suffer of instability and variability issues with regards to the reconstruction of the topology of the network. This instability makes objectively very hard the task of establishing which method performs best. Nevertheless, RegnANN shows MCC scores that compare very favorably with all the other inference methods tested. Availability: The software for the RegnANN inference algorithm is distributed under GPL3 and it is available at the corresponding author home page (http://mpba.fbk.eu/grimaldi/regnann-supmat

The LPL/ADAM29 expression ratio is a novel prognosis indicator in chronic lymphocytic leukemia

Although the zeta-associated protein of 70 kDa (ZAP-70) is overexpressed in patients with chronic lymphocytic leukemia (CLL) displaying unmutated IGVH genes and poor prognosis, a previous microarray study from our group identified overexpression of LPL and ADAM29 genes among unmutated and mutated CLL, respectively. To assess the prognostic value of these genes, we quantified their expression by real-time quantitative polymerase chain reaction (PCR) in a cohort of 127 patients with CLL and correlated this with clinical outcome, IGVH mutational status, and ZAP-70 protein expression. IGVH mutational status, ZAP-70, and the LPL and ADAM29 mRNA ratios (L/A ratio) were predictive of event-free survival for the whole cohort and for patients with stage A disease. in patients in stage B and C, the L/A ratio was an independent prognostic factor, whereas ZAP-70 did not predict survival. Simultaneous usage of the L/A ratio and ZAP-70 expression allowed an almost perfect (99%) assessment of the IGVH status in the 80% of patients with concordant results (L/A(+), ZAP-70(+) or L/A(-), ZAP-70(-)). LPL and ADAM29 gene expression could also be determined by a simple competitive multiplex reverse transcription PCR assay. Overall, quantification of LPL and ADAM29 gene expression is a strong prognostic indicator in CLL, providing better prognostic assessment than ZAP-70 in advanced stages of the disease.Hop La Pitie Salpetriere, Serv Hematol Biol, F-75013 Paris, FranceInst Pasteur, Unite Immunohematol & Immunopathol, F-75724 Paris, FranceUniversidade Federal de São Paulo, Disciplina Hematol & Hemoterapia, São Paulo, BrazilInst Pasteur, Dept Ecosyst & Epidemiol Malad Infect, Paris, FranceHop La Pitie Salpetriere, Serv Immunol, Paris, FranceInst Pasteur, Ctr Rech Vaccinale & Biomed, Paris, FranceUniversidade Federal de São Paulo, Disciplina Hematol & Hemoterapia, São Paulo, BrazilWeb of Scienc

Inference algorithms for gene networks: a statistical mechanics analysis

The inference of gene regulatory networks from high throughput gene expression data is one of the major challenges in systems biology. This paper aims at analysing and comparing two different algorithmic approaches. The first approach uses pairwise correlations between regulated and regulating genes; the second one uses message-passing techniques for inferring activating and inhibiting regulatory interactions. The performance of these two algorithms can be analysed theoretically on well-defined test sets, using tools from the statistical physics of disordered systems like the replica method. We find that the second algorithm outperforms the first one since it takes into account collective effects of multiple regulators

Specific detection of methionine 27 mutation in histone 3 variants (H3K27M) in fixed tissue from high-grade astrocytomas

Studies in pediatric high-grade astrocytomas (HGA) by our group and others have uncovered recurrent somatic mutations affecting highly conserved residues in histone 3 (H3) variants. One of these mutations leads to analogous p.Lys27Met (K27M) mutations in both H3.3 and H3.1 variants, is associated with rapid fatal outcome, and occurs specifically in HGA of the midline in children and young adults. This includes diffuse intrinsic pontine gliomas (80 %) and thalamic or spinal HGA (>90 %), which are surgically challenging locations with often limited tumor material available and critical need for specific histopathological markers. Here, we analyzed formalin-fixed paraffin-embedded tissues from 143 pediatric HGA and 297 other primary brain tumors or normal brain. Immunohistochemical staining for H3K27M was compared to tumor genotype, and also compared to H3 tri-methylated lysine 27 (H3K27me3) staining, previously shown to be drastically decreased in samples carrying this mutation. There was a 100 % concordance between genotype and immunohistochemical analysis of H3K27M in tumor samples. Mutant H3K27M was expressed in the majority of tumor cells, indicating limited intra-tumor heterogeneity for this specific mutation within the limits of our dataset. Both H3.1 and H3.3K27M mutants were recognized by this antibody while non-neoplastic elements, such as endothelial and vascular smooth muscle cells or lymphocytes, did not stain. H3K27me3 immunoreactivity was largely mutually exclusive with H3K27M positivity. These results demonstrate that mutant H3K27M can be specifically identified with high specificity and sensitivity using an H3K27M antibody and immunohistochemistry. Use of this antibody in the clinical setting will prove very useful for diagnosis, especially in the context of small biopsies in challenging midline tumors and will help orient care in the context of the extremely poor prognosis associated with this mutation. Electronic supplementary material The online version of this article (doi:10.1007/s00401-014-1337-4) contains supplementary material, which is available to authorized users