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

First astronomical unit scale image of the GW Ori triple. Direct detection of a new stellar companion

Young and close multiple systems are unique laboratories to probe the initial dynamical interactions between forming stellar systems and their dust and gas environment. Their study is a key building block to understanding the high frequency of main-sequence multiple systems. However, the number of detected spectroscopic young multiple systems that allow dynamical studies is limited. GW Orionis is one such system. It is one of the brightest young T Tauri stars and is surrounded by a massive disk. Our goal is to probe the GW Orionis multiplicity at angular scales at which we can spatially resolve the orbit. We used the IOTA/IONIC3 interferometer to probe the environment of GW Orionis with an astronomical unit resolution in 2003, 2004, and 2005. By measuring squared visibilities and closure phases with a good UV coverage we carry out the first image reconstruction of GW Ori from infrared long-baseline interferometry. We obtain the first infrared image of a T Tauri multiple system with astronomical unit resolution. We show that GW Orionis is a triple system, resolve for the first time the previously known inner pair (separation $\rho\sim$1.4 AU) and reveal a new more distant component (GW Ori C) with a projected separation of $\sim$8 AU with direct evidence of motion. Furthermore, the nearly equal (2:1) H-band flux ratio of the inner components suggests that either GW Ori B is undergoing a preferential accretion event that increases its disk luminosity or that the estimate of the masses has to be revisited in favour of a more equal mass-ratio system that is seen at lower inclination. Accretion disk models of GW Ori will need to be completely reconsidered because of this outer companion C and the unexpected brightness of companion B.Comment: 5 pages, 9 figures, accepted Astronomy and Astrophysics Letters. 201

Environmental assessment of the behavior of a BOF steel slag used in road construction : the PRECODD-ECLAIR research program

International audienceSteel production generate great amounts of by-products as steel slags. The use of Basic Oxygen Furnace slags (BOF slags) has been restrained due to insufficient volume stability, and due to the lack of environmental regulations. The purpose of the PRECODD-ECLAIR research program is to develop a behavior model based on a multi-scale physico-chemical, mechanical, hydrodynamic and ecotoxicological characterizations of a BOF slag used in a public works scenario. This paper aims at presenting the overall ECLAIR research program, the equipped experimental platform constructed using a BOF steel slag, and the first results of the slag characterization

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

Influence of the microstructure on fatigue and fracture toughness properties of large heat-treated mold steels

The standard ISO 1.2738 medium-carbon low-alloy steel has long been used to fabricate plastic molds for injection molding of large automotive components, such as bumpers and dashboards. These molds are usually machined from large pre-hardened steel blooms. Due to the bloom size, the heat treatment yields mixed microstructures, continuously varying from surface to core. Negative events (such as microcracks due to improper weld bed deposition or incomplete extraction of already formed plastic objects) or too large thermal/mechanical stresses can conceivably cause mold failure during service due to the low fracture toughness and fatigue resistance typically encountered in large slack quenched and tempered ISO 1.2738 steel blooms. Alternative steel grades, including both non-standard microalloyed steels, designed for the same production process, and precipitation hardening steels, have recently been proposed by steelworks. However, the fracture toughness and the fatigue properties of these steels, and hence their response during the service, are not well known. Results of an experimental campaign to assess the fracture toughness and fatigue properties, as well as the basic mechanical properties, of a microalloyed and a precipitation hardening plastic mold steel blooms are presented and commented, also in respect to the results previously obtained by two commercial ISO 1.2738 ones. Experimental results show that these steels generally exhibit low fracture toughness values; in the traditional quenched and tempered bloom steels the brittleness may be caused both by the presence of mixed microstructures and by grain boundaries segregation, while in the precipitation hardened one the brittleness probably stems from the precipitation phenomena. This study suggests that microalloyed and precipitation hardening steels may be used to produce large plastic mold, yet the fracture toughness still remains the most critical propert

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

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