Asymptotic results on the length of coalescent trees

We give the asymptotic distribution of the length of partial coalescent trees for Beta and related coalescents. This allows us to give the asymptotic distribution of the number of (neutral) mutations in the partial tree. This is a first step to study the asymptotic distribution of a natural estimator of DNA mutation rate for species with large families

DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii

In prokaryotes the genome is organized in a dynamic structure called the nucleoid, which is embedded in the cytoplasm. We show here that in the archaeon Haloferax volcanii, compaction and reorganization of the nucleoid is induced by stresses that damage the genome or interfere with its replication. The fraction of cells exhibiting nucleoid compaction was proportional to the dose of the DNA damaging agent, and results obtained in cells defective for nucleotide excision repair suggest that breakage of DNA strands triggers reorganization of the nucleoid. We observed that compaction depends on the Mre11-Rad50 complex, suggesting a link to DNA double-strand break repair. However, compaction was observed in a radA mutant, indicating that the role of Mre11-Rad50 in nucleoid reorganisation is independent of homologous recombination. We therefore propose that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate their targets, and facilitating the search for intact DNA sequences during homologous recombination

Fan-C, a Frama-C plug-in for data flow verification

International audienceDO-178B compliant avionics development processes must both define the data and control flows of embedded software at design level, and verify flows are faithfully implemented in the source code. This verification is traditionally performed during dedicated code reviews, but such intellectual activities are costly and error-prone, especially for large and complex software. In this paper, we present the Fan-C plug-in, developed by Airbus on top of the abstract-interpretation-based value and dataflow analyses of the Frama-C platform, in order to automate this verification activity for C avionics software. We therefore describe the Airbus context, the Frama-C platform, its value analysis and related plug-ins, the Fan-C plug-in, and discuss analysis results and ongoing industrial deployment and qualification activities

Circuit-Switched Gossiping in the 3-Dimensional Torus Networks

In this paper we describe, in the case of short messages, an efficient gossiping algorithm for 3-dimensional torus networks (wrap-around or toroidal meshes) that uses synchronous circuit-switched routing. The algorithm is based on a recursive decomposition of a torus. The algorithm requires an optimal number of rounds and a quasi-optimal number of intermediate switch settings to gossip in an $7^i \times 7^i \times 7^i$ torus

Spreading Static Analysis with Frama-C in Industrial Contexts

International audienceThis article deals with the usage of Frama-C to detect runtime-errors. As static analysis for runtime-error detection is not a novelty, we will present significant new usages in industrial contexts, which represent a change in the ways this kind of tool is employed. The main goal is to have a scalable methodology for using static analysis through the development process and by a development team. This goal is achieved by performing analysis on partial pieces of code, by using the ACSL language for interface definitions, by choosing a bottom-up strategy to process the code, and by enabling a well-balanced definition of actors and skills. The methodology, designed during the research project U3CAT, has been applied in industrial contexts with good results as for the quality of verifications and for the performance in the industrial process

Boosting the analysis of protein interfaces with Multiple Interface String Alignments: illustration on the spikes of coronaviruses

International audienceWe introduce multiple interface string alignment (MISA), a visualization tool to display coherently various sequence and structure based statistics at protein–protein interfaces (SSE elements, buried surface area, ΔASA, B factor values, etc). The amino acids supporting these annotations are obtained from Voronoi interface models. The benefit of MISA is to collate annotated sequences of (homologous) chains found in different biological contexts, that is, bound with different partners or unbound. The aggregated views MISA/SSE, MISA/BSA, MISA/ΔASA, and so forth, make it trivial to identify commonalities and differences between chains, to infer key interface residues, and to understand where conformational changes occur upon binding. As such, they should prove of key relevance for knowledge-based annotations of protein databases such as the Protein Data Bank. Illustrations are provided on the receptor binding domain of coronaviruses, in complex with their cognate partner or (neutralizing) antibodies. MISA computed with a minimal number of structures complement and enrich findings previously reported. The corresponding package is available from the Structural Bioinformatics Library (http://sbl.inria.frand https://sbl.inria.fr/doc/Multiple_interface_string_alignment-user-manual.html)

Design of fault-tolerant on-board network

An $(n,k,r)$-network is a triple $N=(G,in,out)$ where $G=(V,E)$ is a graph and $in,out$ are integral functions defined on $V$ called input and output functions, such that for any v \inV, $in(v)+out(v)+ deg(v)\leq2r$ with $deg(v)$ the degree of $v$ in the graph $G$. The total number of inputs is in(V)=\sum_v\inVin(v)=n, and the total number of outputs is out(V)=\sum_v\inVout(v)=n+k. An $(n,k,r)$-network is valid, if for any faulty output function $out'$ (that is such that out'(v) \leqout(v) for any v \inV, and $out'(V) = n$), there are $n$ edge-disjoint paths in $G$ such that each vertex v\inV is the initial vertex of $in(v)$ paths and the terminal vertex of $out'(v)$ paths. We investigate the design problem of determining the minimum number of vertices in a valid $(n,k,r)$-network and of constructing minimum $(n,k,r)$-networks, or at least valid $(n,k,r)$-networks with a number of vertices close to the optimal value. We first show \frac3n+k2r-2+ \frac3r^2k \leq\calN(n,k,r)\leq\left\lceil\frack+22r-2\right\rceil\fracn2. We prove a better upper bound when r\geqk/2: \calN(n,k,r) \leq\fracr-2+k/2r^2-2r+k/2 n + O(1). Finally, we give the exact value of \calN(n,k,r) when $k\leq6$ and exhibit the corresponding networks

topIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB

International audienceType IB DNA topoisomerases can eliminate torsional stresses produced during replication and transcription. These enzymes are found in all eukaryotes and a short version is present in some bacteria and viruses. Among prokaryotes, the long eukaryotic version is only observed in archaea of the phylum Thau-marchaeota. However, the activities and the roles of these topoisomerases have remained an open question. Here, we demonstrate that all available thaumar-chaeal genomes contain a topoisomerase IB gene that defines a monophyletic group closely related to the eukaryotic enzymes. We show that the topIB gene is expressed in the model thaumarchaeon Ni-trososphaera viennensis and we purified the recom-binant enzyme from the uncultivated thaumarchaeon Candidatus Caldiarchaeum subterraneum. This enzyme is active in vitro at high temperature, making it the first thermophilic topoisomerase IB characterized so far. We have compared this archaeal type IB enzyme to its human mitochondrial and nuclear counterparts. The archaeal enzyme relaxes both negatively and positively supercoiled DNA like the eukaryotic enzymes. However, its pattern of DNA cleavage specificity is different and it is resistant to camptothecins (CPTs) and non-CPT Top1 inhibitors, LMP744 and lamellarin D. This newly described ther-mostable topoisomerases IB should be a promising new model for evolutionary, mechanistic and structural studies