Computing the likelihood of sequence segmentation under Markov modelling

I tackle the problem of partitioning a sequence into homogeneous segments, where homogeneity is defined by a set of Markov models. The problem is to study the likelihood that a sequence is divided into a given number of segments. Here, the moments of this likelihood are computed through an efficient algorithm. Unlike methods involving Hidden Markov Models, this algorithm does not require probability transitions between the models. Among many possible usages of the likelihood, I present a maximum \textit{a posteriori} probability criterion to predict the number of homogeneous segments into which a sequence can be divided, and an application of this method to find CpG islands

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

<p>Abstract</p> <p>Background</p> <p>Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria.</p> <p>Results</p> <p>To get a whole genome view of <it>Aquifex </it>relationships, all trees containing sequences from <it>Aquifex </it>in the HOGENOM database were surveyed. This study revealed that <it>Aquifex </it>is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the <it>Aquifex </it>lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found.</p> <p>Conclusion</p> <p>Methods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage has undergone many horizontal gene transfers. However, if a tree of vertical descent can be reconstructed for Bacteria, our results suggest Aquificales should be placed close to Thermotogales.</p

Iongel Soft Solid Electrolytes Based on [DEME][TFSI] Ionic Liquid for Low Polarization Lithium-O-2 Batteries

Lithium-air/O-2 batteries are a promising battery technology for automotive applications due to their high energy density. However, many challenges need to be solved, particularly the high reactivity of the electrolyte with oxygen superoxide radicals and its low cyclability. In this work, we present a simple and fast way to prepare polymer-based iongel soft solid electrolytes. Thermally and mechanically stable iongels are prepared by fast UV-photopolymerisation exhibiting a high ionic conductivity (similar to 1.2 x 10(-3) S cm(-1) at 25 degrees C). When used as solid electrolytes in lithium symmetrical cells, they can withstand a critical current density of 0.5 mA cm(-2). Performance in Li-O-2 cells showed capacities as large as 3.3 mAh cm(-2), and cycling capability of 25 cycles, exceeding results on liquid-counterpart cells.European Commission's funded Marie Skłodowska-Curie. Grant Number: 76582

Single-ion polymer/LLZO hybrid electrolytes with high lithium conductivity

Hybrid solid electrolytes which combine the properties of inorganic and polymeric ion conductors are being investigated for lithium batteries which use lithium metal anodes. The number of inorganic/polymer compositions and their synergy in ion-conducting properties are limited by the hybrid fabrication method and the limited compatibility between both types of materials. Here we report a hybrid solid electrolyte formed by a poly(ethylene glycol) type single-ion polymer network and ceramic garnet-type nanoparticles of Li7−3XAlXLa3Zr2O12 (LLZO) with very high lithium conductivity. The combination of a lithium-single ion polymer matrix with LLZO inorganic particles results in flexible free-standing films by using a fast UV-photopolymerization process with facile control of its composition. This methodology showed excellent dispersion of the LLZO nanoparticles within the gel polymer network with up to 50 wt% ceramic content, as shown in the enviromental ESEM images. These hybrid electrolytes have high ionic conductivity values (1.4 × 10−4 S cm−1 at 25 °C) and high lithium transference number as compared to previous hybrid electrolytes. The effect of LLZO nanoparticle content on the lithium transport was investigated in detail using solid-state nuclear magnetic resonance spectroscopy (NMR). Finally, determination of the critical current density (CCD) before lithium dendrites are initiated has been carried out on both pristine and hybrid electrolytes, so as to assess their potential as solid electrolytes for lithium metal batteries.This work was supported by the European Commission’s funded Marie Sklodowska-Curie project POLYTE-EID (Project No. 765828). L.P. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie grant agreement No 797295

Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation

International audienceModels of evolution by genome rearrangements are prone to two types of flaws: One is to ignore the diversity of susceptibility tobreakage across genomic regions, and the other is to suppose that susceptibility values are given. Without necessarily supposing theirprecise localization,we call “solid” the regions that are improbably broken by rearrangements and “fragile” the regions outside solidones.We propose a model of evolution by inversions where breakage probabilities vary across fragile regions and over time. It containsas a particular case the uniform breakage model on the nucleotidic sequence,where breakage probabilities are proportional to fragileregion lengths. This is very different from the frequently used pseudo uniform model where all fragile regions have the same probabilityto break. Estimations of rearrangement distances based on the pseudo uniform model completely fail on simulations with thetruly uniform model. On pairs of amniote genomes, we show that identifying coding genes with solid regions yields incoherentdistance estimations, especially with the pseudo uniform model, and to a lesser extent with the truly uniform model. This incoherenceis solved when we coestimate the number of fragile regions with the rearrangement distance. The estimated number of fragileregions is surprisingly small, suggesting that a minority of regions are recurrently used by rearrangements. Estimations for several pairsof genomes at different divergence times are in agreement with a slowly evolvable colocalization of active genomic regions in the cell

Single-ion lithium conducting polymers with high ionic conductivity based on borate pendant groups

This communication reports a family of single-ion lithium conducting polymer electrolytes based on highly delocalized borate groups is reported. The effect of the nature of the substituents on the boron atom on the ionic conductivity of the resultant methacrylic polymers was analyzed. To the best of our knowledge the lithium borate polymers endowed with flexible and electron-withdrawing substituents presents the highest ionic conductivity reported for a lithium single-ion conducting homopolymer (1.65×10−4 S cm−1 at 60 °C). This together with its high lithium transference number tLi+= =0.93 and electrochemical stability window of 4.2 V vs Li0/Li+ show promise for application in lithium batteries. To illustrate this, a lithium borate monomer was integrated into a single-ion gel polymer electrolyte which showed good performance on lithium symmetrical cells (<0.85 V at ±0.2 mA cm−2 for 175 h).This work was supported by a Grant for Basque Government through grant IT1309-19, and European Commission’s funded Marie Skłodowska-Curie project POLYTE-EID (project no. 765828) and Spanish MCIN/ AEI/ PID2020-119026GB-I00. G.G-G. is grateful to "Secretaría de Educación, Ciencia, Tecnología e Innovación" from Ciudad de México for the postdoctoral fellowship through grant (SECTEI/133/2019)

Embedded subspace-based modal analysis and uncertainty quantification on wireless sensor platform PEGASE

International audienceOperational modal analysis is an important step in many methods for vibration-based structural health monitoring. These methods provide the modal parameters (frequencies, damping ratios and mode shapes) of the structure and can be used for monitoring over time. For a continuous monitoring the excitation of a structure is usually ambient, thus unknown and assumed to be noise. Hence, all estimates from the vibration measurements are realizations of random variables with inherent uncertainty due to unknown excitation, measurement noise and finite data length. Estimating the standard deviation of the modal parameters on the same dataset offers significant information on the accuracy and reliability of the modal parameter estimates. However, computational and memory usage of such algorithms are heavy even on standard PC systems in Matlab, where reasonable computational power is provided. In this paper, we examine an implementation of the covariance-driven stochastic subspace identification on the wireless sensor platform PEGASE, where computational power and memory are limited. Special care is taken for computational efficiency and low memory usage for an on-board implementation, where all numerical operations are optimized. The approach is validated from an engineering point of view in all its steps, using simulations and field data from a highway road sign structure

Phased and synchronous sampling between multiple smart network sensors for modal assessment of large structures

International audienc

Less effective selection leads to larger genomes

International audienceThe evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven independent habitat shifts from surface water to resource-poor groundwater. We show that these habitat shifts are associated with higher transcriptome-wide dN/dS. After ruling out the role of positive selection and pseudogenization, we show that these transcriptome-wide dN/dS increases are the consequence of a reduction in selection efficacy imposed by the smaller effective population size of subterranean species. This reduction is paralleled by an important increase in genome size (25% increase on average), an increase also confirmed in subterranean decapods and mollusks. We also control for an adaptive impact of genome size on life history traits but find no correlation between body size, or growth rate, and genome size. We show instead that the independent increases in genome size measured in subterranean isopods are the direct consequence of increasing invasion rates by repeated elements, which are less efficiently purged out by purifying selection. Contrary to selection efficacy, polymorphism is not correlated to genome size. We propose that recent demographic fluctuations and the difficulty to observe polymorphism variations in polymorphism-poor species can obfuscate the link between effective population size and genome size when polymorphism data is used alone

Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species