Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies.

Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools.

Bradyrhizobium BclA Is a Peptide Transporter Required for Bacterial Differentiation in Symbiosis with Aeschynomene Legumes.

Nodules of legume plants are highly integrated symbiotic systems shaped by millions of years of evolution. They harbor nitrogen-fixing rhizobium bacteria called bacteroids. Several legume species produce peptides called nodule-specific cysteine-rich (NCR) peptides in the symbiotic nodule cells which house the bacteroids.

Theoretical study of radiative electron attachment to CN, C2H, and C4H radicals.

A first-principle theoretical approach to study the process of radiative electron attachment is developed and applied to the negative molecular ions CN(-), C4H(-), and C2H(-). Among these anions, the first two have already been observed in the interstellar space. Cross sections and rate coefficients for formation of these ions by direct radiative electron attachment to the corresponding neutral radicals are calculated.

Long-range interactions between polar bialkali ground-state molecules in arbitrary vibrational levels.

We have calculated the isotropic C6 coefficients characterizing the long-range van der Waals interaction between two identical heteronuclear alkali-metal diatomic molecules in the same arbitrary vibrational level of their ground electronic state X(1)Σ(+). We consider the ten species made up of (7)Li, (23)Na, (39)K, (87)Rb, and (133)Cs. Following our previous work [Lepers et al.

Factorized molecular wave functions: Analysis of the nuclear factor.

The exact factorization of molecular wave functions leads to nuclear factors which should be nodeless functions. We reconsider the case of vibrational perturbations in a diatomic species, a situation usually treated by combining Born-Oppenheimer products. It was shown [R.

Molecular Analysis of the embCAB Locus and embR Gene Involved in Ethambutol Resistance in Clinical Isolates of Mycobacterium tuberculosis in France.

Modification of codon 306 in embB is regarded as the main mechanism leading to ethambutol (ETB) resistance in clinical isolates of Mycobacterium tuberculosis. However, numerous mutations elsewhere in the embCAB locus and in embR, a putative transcriptional activator of this locus, have been reported to be involved in ETB resistance. Here, we investigated the diversity of nucleotide variations observed in embCAB and embR in M.

Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites.

G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or function in vivo are unknown. In S.

Pathogenic bacteria and timing of laying.

Pathogenic bacteria constitute a serious threat to viability of many organisms. Because growth of most bacteria is favored by humid and warm environmental conditions, earlier reproducers in seasonal environments should suffer less from the negative consequences of pathogenic bacteria. These relationships, and the effects on reproductive success, should be particularly prominent in predators because they are frequently exposed to pathogenic microorganisms from sick prey.

Atomistic near-field nanoplasmonics: reaching atomic-scale resolution in nanooptics.

Electromagnetic field localization in nanoantennas is one of the leitmotivs that drives the development of plasmonics. The near-fields in these plasmonic nanoantennas are commonly addressed theoretically within classical frameworks that neglect atomic-scale features. This approach is often appropriate since the irregularities produced at the atomic scale are typically hidden in far-field optical spectroscopies.

Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome.

Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome.

Radiolysis as a solution for accelerated ageing studies of electrolytes in Lithium-ion batteries.

Diethyl carbonate and dimethyl carbonate are prototype examples of eco-friendly solvents used in lithium-ion batteries. Nevertheless, their degradation products affect both the battery performance and its safety. Therefore, it is of paramount importance to understand the reaction mechanisms involved in the ageing processes.

Atomic Hong-Ou-Mandel experiment.

Two-particle interference is a fundamental feature of quantum mechanics, and is even less intuitive than wave-particle duality for a single particle. In this duality, classical concepts--wave or particle--are still referred to, and interference happens in ordinary space-time. On the other hand, two-particle interference takes place in a mathematical space that has no classical counterpart.

Electron-induced growth mechanism of conducting polymers: a coupled experimental and computational investigation.

Pulse radiolysis was used to study the mechanism of HO(•)-induced polymerization of poly(3,4-ethylenedioxythiophene), PEDOT, in aqueous solution. A step-by-step mechanism has been found which involves a recurrent oxidation process by HO(•) hydroxyl radicals produced by water radiolysis. Furthermore, the cation radical, EDOT(•)(+), has been proposed as the promoter of the first step of polymerization.

Complete series of chiral paramagnetic molecular conductors based on tetramethyl-bis(ethylenedithio)-tetrathiafulvalene (TM-BEDT-TTF) and Chloranilate-bridged heterobimetallic honeycomb layers.

Electrocrystallization of enantiopure (S,S,S,S)- and (R,R,R,R)-tetramethyl-bis(ethylenedithio)-tetrathiafulvalene (TM-BEDT-TTF) donors, as well as the racemic mixture, in the presence of potassium cations and the tris(chloranilato)ferrate(III) [Fe(Cl2An)3](3-) paramagnetic anion afforded a complete series of chiral magnetic molecular conductors formulated as β-[(S,S,S,S)-TM-BEDT-TTF]3PPh4[K(I)Fe(III)(Cl2An)3]·3H2O (1), β-[(R,R,R,R)-TM-BEDT-TTF]3PPh4[K(I)Fe(III)(Cl2An)3]·3H2O (2), and β-[(rac)-TM-BEDT-TTF]3PPh4[K(I)Fe(III)(Cl2An)3]·3H2O (3). Compounds 1-3 are isostructural and crystallize in triclinic space groups (P1 for 1 and 2, P-1 for 3) showing a segregated organic-inorganic crystal structure, where anionic honeycomb layers obtained by self-assembling of the Λ and Δ enantiomers of the paramagnetic complex with potassium cations alternate with organic layers where the chiral donors are arranged in the β packing motif. Compounds 1-3 show a molecular packing strongly influenced by the topology of the inorganic layers and behave as molecular semiconductors with room-temperature conductivity values of ca.

Effect of dopaminergic D1 receptors on plasticity is dependent of serotoninergic 5-HT1A receptors in L5-pyramidal neurons of the prefrontal cortex.

Major depression and schizophrenia are associated with dysfunctions of serotoninergic and dopaminergic systems mainly in the prefrontal cortex (PFC). Both serotonin and dopamine are known to modulate synaptic plasticity. 5-HT1A receptors (5-HT1ARs) and dopaminergic type D1 receptors are highly represented on dendritic spines of layer 5 pyramidal neurons (L5PyNs) in PFC.

Colonization of plant substrates at hydrothermal vents and cold seeps in the northeast Atlantic and Mediterranean and occurrence of symbiont-related bacteria.

Reducing conditions with elevated sulfide and methane concentrations in ecosystems such as hydrothermal vents, cold seeps or organic falls, are suitable for chemosynthetic primary production. Understanding processes driving bacterial diversity, colonization and dispersal is of prime importance for deep-sea microbial ecology. This study provides a detailed characterization of bacterial assemblages colonizing plant-derived substrates using a standardized approach over a geographic area spanning the North-East Atlantic and Mediterranean.

Identification of the optic recess region as a morphogenetic entity in the zebrafish forebrain.

Regionalization is a critical, highly conserved step in the development of the vertebrate brain. Discrepancies exist in how regionalization of the anterior vertebrate forebrain is conceived since the "preoptic area" is proposed to be a part of the telencephalon in tetrapods but not in teleost fish. To gain insight into this complex morphogenesis, formation of the anterior forebrain was analyzed in 3D over time in zebrafish embryos, combining visualization of proliferation and differentiation markers, with that of developmental genes.

Surfactant-induced rigidity of interfaces: a unified approach to free and dip-coated films.

The behavior of thin liquid films is known to be strongly affected by the presence of surfactants at the interfaces. The detailed mechanism by which the latter enhance film stability is still a matter of debate, in particular concerning the influence of surface elastic effects on the hydrodynamic boundary condition at the liquid/air interfaces. In the present work, "twin" hydrodynamic models neglecting surfactant transport to the interfaces are proposed to describe the coating of films onto a solid plate (Landau-Levich-Derjaguin configuration) as well as soap film pulling (Frankel configuration).

A balance between membrane elasticity and polymerization energy sets the shape of spherical clathrin coats.

In endocytosis, scaffolding is one of the mechanisms to create membrane curvature by moulding the membrane into the spherical shape of the clathrin cage. However, the impact of membrane elastic parameters on the assembly and shape of clathrin lattices has never been experimentally evaluated. Here, we show that membrane tension opposes clathrin polymerization.

Channel characteristics of VDAC-3 from Arabidopsis thaliana.

Four different isoforms of the Voltage-Dependent Anion Channel (VDAC) have been identified in Arabidopsis plant cells. The electrophysiological characteristics of several VDAC channels from animal as well as plant cells are well documented, but those of this model plant are unknown. One isoform, AtVDAC-3 was obtained either directly by cell-free synthesis or produced in Escherichia coli, as inclusion bodies, and re-natured.

Comet 67P/Churyumov-Gerasimenko sheds dust coat accumulated over the past four years.

Comets are composed of dust and frozen gases. The ices are mixed with the refractory material either as an icy conglomerate, or as an aggregate of pre-solar grains (grains that existed prior to the formation of the Solar System), mantled by an ice layer. The presence of water-ice grains in periodic comets is now well established.

Molecular epidemiology of tuberculosis in Sicily, Italy: what has changed after a decade?

Background: We aimed to investigate the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) isolates in the province of Palermo, Sicily, Italy, by characterizing 183 isolates identified in the years 2004-2012. A comparison with 104 MTBC strains identified in the same geographic area in the years 1994-2000 was also carried out.

Methods: One hundred eighty-three MTBC isolates identified in Palermo, Italy, in the years 2004-2012 were analyzed by spoligotyping and the 24 mycobacterial interspersed repetitive unit (MIRU)-variable-number tandem-repeat (VNTR) method typing.

Characterization of the secretomes of two vibrios pathogenic to mollusks.

Vibrio tapetis causes the brown ring disease in the Japanese clam Ruditapes philippinarum while Vibrio aestuarianus is associated with massive oyster mortalities. As extracellular proteins are often associated with the virulence of pathogenic bacteria, we undertook a proteomic approach to characterize the secretomes of both vibrios. The extracellular proteins (ECPs) of both species were fractionated by SEC-FPLC and in vitro assays were performed to measure the effects of each fraction on hemocyte cellular parameters (phagocytosis and adhesion).