Updating the mechanisms of common fragile site instability: how to reconcile the different views?

Common fragile sites (CFSs) are large chromosomal regions long identified by conventional cytogenetics as sequences prone to breakage in cells subjected to replication stress. The interest in CFSs came from their key role in the formation of DNA damage, resulting in chromosomal rearrangements. The instability of CFSs was notably correlated with the appearance of genome instability in precancerous lesions and during tumor progression. Identification of the molecular mechanisms responsible for their instability therefore represents a major challenge. A number of data show that breaks result from mitotic entry before replication completion but the mechanisms responsible for such delayed replication of CFSs and relaxed checkpoint surveillance are still debated. In addition, clues to the molecular events leading to breakage just start to emerge. We present here the results of recent reports addressing these questions

Numerical comparison between the Boltzmann and ES-BGK models for rarefied gases

Projet M3NRarefied gas flows obey to the Boltzmann equation, but numerical simulations of this equation are not always possible, so that simpler models have been introduced. The ES-BGK equation is one of these models. It gives the correct transport coefficients for the Navier Stokes approximation, so that Boltzmann or ES-BGK simulations are expected to give the same results for dense gases, but in the case of a rarefied flow, complete numerical comparisons are needed. In this paper we present numerical comparisons between the two models in transitional regimes (where the ES-BGK model is expected to be useful) for reentry flows around a compression ramp and a plate. We also emphasize that the ES-BGK model gives flow predictions closer to the Boltzmann result than the simpler BGK model

The Gaussian-BGK Model of Boltzmann Equation with Small Prandtl Number

Projet M3NIn this paper we prove the entropy inequality for the Gaussian-BGK model of Boltzmann equation. This model, also called ellipsoidal statistical model, was introduced in order to fit realistic values of the transport coefficients (Prandtl number, second viscosity) in the Navier-Stokes approxima- tion, which cannot be achieved by the usual relaxation towards isotropic Maxwellians introduced in standard BGK models. Moreover, we introduce new entropic kinetic models for polyatomic gases which suppress the internal energy variable in the phase space by using two distribution functions (one for particles mass and one for their internal energy). This reduces the cost of their numerical solution while keeping a kinetic description well adapted to desequilibrium regions

Coupling Boltzmann and Navier-Stokes

Projet MENUSINThe objective of the present work is the computation of hypersonic flows around reentry vehicles at high altitude. This work was supported by the European project Hermès (ESA funding under contract ALG91/10, ATP DPH n$^\circ$ 6464/91, phase Hermès R/Q) and was performed under the technical supervision of Dassault Aviation. The proposed method couples Boltzmann equations, used next to the body, and Navier-Stokes equations used in the far field. This coupling is imposed without domain overlapping by imposing adequate interface boundary conditions on incoming half-fluxes. These boundary conditions are based on a kinetic interpretation of the Navier-Stokes equations. The numerical implementation of this technique uses a time marching algorithm, a SUPG Navier-Stokes solver developed by Dassault Aviation and solves the Boltzmann equations by a Monte Carlo technique. Different numerical results are finally presented, mainly using a nonadaptative partitioning technique

Combining SystemC, IP-XACT and UML/MARTE in model-based SoC design

International audienceModern SoC design may rely on models, or on highlevel description languages. Although very close, the benefits obtained from either sides can be substantially different (and mismatch may occur). The IP-Xact formalism, now a standard (IEEE 1685), was introduced to help assemble component IP from distinct sources into an integrated design. Components could be expressed in high-level HDLs such as SystemC, so should be the full design after translation. Experience shows that in fact this is hardly the case, specially in publicly available methods and tools. The present contribution goes one step into linking SystemC designs to their IP-Xact structural representation by translation. It then exports the resulting IP-Xact model into the UML/MARTE profile modeling framework, to allow to annotating existing models with additional information (again in a publicly available fashion, as opposed to vendor extensions). Even if our approach is still far from being complete, it bridges a number of gaps induce by the combined uses of SystemC and IP-Xact

Identification et caractérisation de nouveaux facteurs d'assemblage du protéasome 26S chez la levure Saccharomyces cerevisiae

DNA checkpoints are activated upon detection of DNA damage or replication blocks and coordinate several processes of the DNA damage response. In Saccharomyces cerevisiae, Rad53 protein kinase plays a key role in DNA checkpoints. A genetic approach has been developed in our laboratory to identify positive regulators and new substrates of Rad53, using a dominant-lethal form of RAD53, RAD53-DL, which triggers physiological events normally induced by DNA damage. We reasoned that RAD53-DL toxicity should be reduced in the absence of Rad53 activators or substrates. Therefore, we carried out a genome-wide screen for genes whose deletion could suppress RAD53-DL toxicity. 110 suppressor genes have been isolated and classified into functional groups. We further analyzed one of these groups, which is made of 8 genes that lead to hyperresistance to genotoxic stress when they are inactivated. Three genes encode components of the 26S proteasome, the central enzyme of ubiquitin-dependant proteolysis that plays crucial roles in most essential cellular processes. Proteasome is a highly sophisticated macromolecular stucture that comprises the catalytic core particle (20S) and the regulatory particle (19S), itself composed of two subcomplexes, the base and the lid. Its assembly proceeds in a multistep and orderly fashion. At the time of our screen, only one proteasome chaperone was well-described in yeast, Ump1, which participates in the final stages of 20S proteasome maturation. By combining genetical and biochemical analyses, we have assigned a molecular function to the five other members of the ?proteasome? functional group, which were previously unchararacterized. YLR021W, YPL144W, YLR199C and YKL206C genes, which we have named POC1-4 (Proteasome Chaperone), encode 4 proteins that form two pairs of chaperones of the 20S proteasome (Poc1-Poc2 and Poc3-Poc4) acting upstream of Ump1. HSM3 encodes the first chaperone protein of the regulatory particle. Hm3 associates with the base subcomplex of the 19S and is specifically required for its assembly. Hsm3 also modulates the association between the nascent 19S and the 20S proteasome. We have identified functional mammalian homologs of yeast Poc1-4 (PAC1-4) and Hsm3 (S5b) and provided evidence for a remarkable conservation of a chaperone-assisted proteasome assembly throughout evolution.Les checkpoints de l'ADN coordonnent les réponses cellulaires aux dommages de l'ADN et au blocage de la réplication des cellules eucaryotes. Chez Saccharomyces cerevisiae, la protéine kinase Rad53 occupe une place centrale au sein des checkpoints de l'ADN. Afin d'identifier de nouveaux partenaires de Rad53, une approche génétique a été développée, utilisant l'allèle dominant létal RAD53-DL qui déclenche constitutivement des réponses cellulaires normalement induites par des lésions de l'ADN. Notre hypothèse est que l'absence des activateurs ou des substrats de Rad53 pourrait rétablir la croissance. Nous avons donc recherché, à l'échelle du génome de S. cerevisiae, les gènes qui suppriment la toxicité de RAD53-DL lorsqu'ils sont inactivés. 110 gènes ont été isolés et classés en groupes fonctionnels. Un groupe a particulièrement retenu notre attention. Il est composé de huit gènes dont l'inactivation confère à la cellule une hyper-résistance à plusieurs stress génotoxiques. Trois de ces gènes codent des composants du protéasome 26S, l'enzyme central du système de dégradation ubiquitine-dépendante des protéines qui joue un rôle crucial dans la plupart des processus cellulaires. Le protéasome est une structure macromoléculaire très sophistiquée composée d'une partie catalytique, la particule 20S, associée au complexe régulateur 19S, lui même formé de 2 sous-complexes, la base et le couvercle. Son assemblage comprend de nombreuses étapes ordonnées. Au moment du crible, un seul chaperon du protéasome était connu chez la levure, la protéine Ump1, impliquée dans les étapes finales de maturation du protéasome 20S. Par des analyses génétiques et biochimiques, nous avons caractérisé les cinq autres membres du groupe fonctionnel « protéasome », dont la fonction était jusqu'alors inconnue. Les gènes YLR021W, YPL144W, YLR199C et YKL206C, que nous avons baptisés POC1-4 (Proteasome Chaperone), codent 4 protéines formant deux paires de chaperons du protéasome 20S (Poc1-Poc2 et Poc3-Poc4) agissant en amont de Ump1. HSM3 code la première protéine chaperonne de la particule régulatrice du protéasome. Hsm3 s'associe avec la base du 19S et assiste son assemblage. Son rôle est également de réguler l'association du 19S en formation avec le protéasome 20S. Nous avons identifié les homologues mammifères de Poc1-4 (PAC1-4) et Hsm3 (S5b), mettant ainsi en lumière une conservation remarquable des facteurs d'assemblage du protéasome au cours de l'évolutio

Identification et caractérisation de nouveaux facteurs d'assemblage du protéasome 26S chez la levure Saccharomyces cerevisiae

Chez S. cerevisiae, Rad53 occupe une place centrale au sein des checkpoints de l ADN qui coordonnent les réponses cellulaires aux dommages de l ADN et au blocage de la réplication. Afin d identifier de nouveaux activateurs ou substrats de Rad53, nous avons recherché, à l échelle du génome, les gènes qui suppriment la toxicité d un allèle dominant létal de RAD53 lorsqu ils sont inactivés. 110 gènes ont été isolés et classés en groupes fonctionnels. Un groupe composé de huit gènes dont l inactivation confère à la cellule une hyper-résistance à plusieurs stress génotoxiques a retenu notre attention. Trois de ces gènes codent des composants du protéasome 26S, l enzyme central du système de dégradation ubiquitine-dépendante des protéines. Le 26S est composé d une partie catalytique 20S associée au complexe régulateur 19S, lui même formé de 2 sous-complexes, la base et le couvercle. Avant le crible, un seul chaperon du protéasome était connu chez la levure, la protéine Ump1, impliquée dans la maturation du 20S. Par des analyses génétiques et biochimiques, nous avons caractérisé les cinq autres membres du groupe fonctionnel protéasome . Les gènes POC1-4 (Proteasome Chaperone) codent 4 protéines formant deux paires de chaperons du protéasome 20S (Poc1-Poc2 et Poc3-Poc4) agissant en amont de Ump1. HSM3 code la première protéine chaperon de la particule régulatrice du protéasome. Hsm3 assiste l assemblage de la base du 19S et régule l association du 19S en formation avec le protéasome 20S. Nous avons identifié les homologues mammifères de Poc1-4 (PAC1-4) et Hsm3 (S5b), révélant ainsi une remarquable conservation des facteurs d assemblage du protéasome au cours de l évolution.In S. cerevisiae, Rad53 plays a key role in DNA checkpoints which coordinate several processes of the DNA damage response. In order to identify new activators and substrates of Rad53, we carried out a genome-wide screen for genes whose deletion could suppress the toxicity of a dominant-lethal form of RAD53. 110 suppressor genes have been isolated and classified into functional groups. We further analyzed one of these groups, which is made of 8 genes that lead to hyperresistance to genotoxic stress when they are inactivated. Three genes encode components of the 26S proteasome, the central enzyme of ubiquitin-dependant proteolysis. Proteasome comprises the catalytic core particle (20S) and the regulatory particle (19S), itself composed of two subcomplexes, the base and the lid. At the time of our screen, only one proteasome chaperone was known in yeast, Ump1, which participates in 20S proteasome maturation. By combining genetical and biochemical analyses, we have assigned a molecular function to the five other members of the proteasome functional group. POC1-4 (Proteasome Chaperone) encode 4 proteins that form two pairs of chaperones of the 20S proteasome (Poc1-Poc2 and Poc3-Poc4) acting upstream of Ump1. HSM3 encodes the first chaperon protein of the regulatory particle. Hm3 associates with the base subcomplex of the 19S and is specifically required for its assembly. Hsm3 also modulates the association between the nascent 19S and the 20S proteasome. We have identified functional mammalian homologs of yeast Poc1-4 (PAC1-4) and Hsm3 (S5b) and provided evidence for a remarkable conservation of a chaperone-assisted proteasome assembly throughout evolution.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Transferrin saturation is independently associated with the severity of obstructive sleep apnea syndrome and hypoxia among obese subjects

International audienceIntroduction & aims - Obstructive sleep apnea syndrome (OSAS) is a frequent complication of obesity. Intermittent chronic hypoxia which frequently results from OSAS could modulate the systemic control of iron metabolism and alter serum iron parameters, especially among obese patients.Aims - to evaluate whether serum parameters of iron bioavailability and storage (primary), as well as age, waist circumference, arterial hypertension and tobacco use (secondary) are associated with OSAS severity and/or hypoxia. Methods - design: a single-center retrospective study with prospective data collection; inclusion criteria: consecutive patients referred for initial assessment for obesity underwent nocturnal respiratory polygraphy and iron status serum assessment within a 3-month period. The adjusted analyzes were performed using ANOVA and reported as adjusted means and 95% confidence interval (95% CI).Results - 13 men and 56 women were included. OSAS prevalence: 72% (n = 50). Ferritin (mean ± SD, 260 ± 276 vs. 111 ± 89 μg/l, p = 0.01) and transferrin saturation (31 ± 10 vs. 24 ± 9%, p = 0.002) were significantly higher in case of moderate/severe OSAS than in absent/mild OSAS, independently from gender and tobacco use. Serum iron (19.4 μg/l [CI95%, 16.5-22.3] vs. 16.2 μg/l ([14.1-18.2], p = 0.056) and transferrin saturation (31.5% [26.3-36.7]) vs. 25.3% [21.6-29.1], p = 0.043) were higher when time under oxygen saturation 15%. Age (mean ± SD, 51 ± 11 vs. 41 ± 12 yr, p = 0.001), waist circumference (136 ± 18 vs. 123 ± 12 cm, p = 0.003), arterial hypertension (59% (n = 13/22) vs. 23% (n = 11/47), p = 0.004) and tobacco use (64% (n = 14/22) vs. 32% (n = 15/47), p = 0.01) were significantly greater in moderate/severe OSAS than in absent/mild OSAS.Conclusions - Transferrin saturation was associated with OSAS severity and time under hypoxia. This suggests a relationship between OSAS-induced hypoxia and iron metabolism among obese patients

Common Fragile Site Profiling in Epithelial and Erythroid Cells Reveals that Most Recurrent Cancer Deletions Lie in Fragile Sites Hosting Large Genes

Cancer genomes exhibit numerous deletions, some of which inactivate tumor suppressor genes and/or correspond to unstable genomic regions, notably common fragile sites (CFSs). However, 70%–80% of recurrent deletions cataloged in tumors remain unexplained. Recent findings that CFS setting is cell-type dependent prompted us to reevaluate the contribution of CFS to cancer deletions. By combining extensive CFS molecular mapping and a comprehensive analysis of CFS features, we show that the pool of CFSs for all human cell types consists of chromosome regions with genes over 300 kb long, and different subsets of these loci are committed to fragility in different cell types. Interestingly, we find that transcription of large genes does not dictate CFS fragility. We further demonstrate that, like CFSs, cancer deletions are significantly enriched in genes over 300 kb long. We now provide evidence that over 50% of recurrent cancer deletions originate from CFSs associated with large genes

DNA molecular combing-based replication fork directionality profiling

International audienceThe replication strategy of metazoan genomes is still unclear, mainly because definitive maps of replication origins are missing. High-throughput methods are based on population average and thus may exclusively identify efficient initiation sites, whereas inefficient origins go undetected. Single-molecule analyses of specific loci can detect both common and rare initiation events along the targeted regions. However, these usually concentrate on positioning individual events, which only gives an overview of the replication dynamics. Here, we computed the replication fork directionality (RFD) profiles of two large genes in different transcriptional states in chicken DT40 cells, namely untranscribed and transcribed DMD and CCSER1 expressed at WT levels or overexpressed, by aggregating hundreds of oriented replication tracks detected on individual DNA fibres stretched by molecular combing. These profiles reconstituted RFD domains composed of zones of initiation flanking a zone of termination originally observed in mammalian genomes and were highly consistent with independent population-averaging profiles generated by Okazaki fragment sequencing. Importantly, we demonstrate that inefficient origins do not appear as detectable RFD shifts, explaining why dispersed initiation has remained invisible to population-based assays. Our method can both generate quantitative profiles and identify discrete events, thereby constituting a comprehensive approach to study metazoan genome replication