Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.Fil: Antelo, Verónica. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Giménez, Matías. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Azziz, Gastón. Universidad de la Republica. Facultad de Agricultura; UruguayFil: Valdespino Castillo, Patricia. Lawrence Berkeley National Laboratory; Estados UnidosFil: Falcón, Luisa I.. Universidad Nacional Autónoma de México; MéxicoFil: Ruberto, Lucas Adolfo Mauro. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: MacCormack, Walter P.. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: Mazel, Didier. Institut Pasteur de Paris.; FranciaFil: Batista, Silvia. Instituto de Investigaciones Biológicas "Clemente Estable"; Urugua

Ordering and Demixing Transitions in Multicomponent Widom-Rowlinson Models

We use Monte Carlo techniques and analytical methods to study the phase diagram of multicomponent Widom-Rowlinson models on a square lattice: there are M species all with the same fugacity z and a nearest neighbor hard core exclusion between unlike particles. Simulations show that for M between two and six there is a direct transition from the gas phase at z < z_d (M) to a demixed phase consisting mostly of one species at z > z_d (M) while for M \geq 7 there is an intermediate ``crystal phase'' for z lying between z_c(M) and z_d(M). In this phase, which is driven by entropy, particles, independent of species, preferentially occupy one of the sublattices, i.e. spatial symmetry but not particle symmetry is broken. The transition at z_d(M) appears to be first order for M \geq 5 putting it in the Potts model universality class. For large M the transition between the crystalline and demixed phase at z_d(M) can be proven to be first order with z_d(M) \sim M-2 + 1/M + ..., while z_c(M) is argued to behave as \mu_{cr}/M, with \mu_{cr} the value of the fugacity at which the one component hard square lattice gas has a transition, and to be always of the Ising type. Explicit calculations for the Bethe lattice with the coordination number q=4 give results similar to those for the square lattice except that the transition at z_d(M) becomes first order at M>2. This happens for all q, consistent with the model being in the Potts universality class.Comment: 26 pages, 15 postscript figure

Pseudo-Random Streams for Distributed and Parallel Stochastic Simulations on GP-GPU

International audienceRandom number generation is a key element of stochastic simulations. It has been widely studied for sequential applications purposes, enabling us to reliably use pseudo-random numbers in this case. Unfortunately, we cannot be so enthusiastic when dealing with parallel stochastic simulations. Many applications still neglect random stream parallelization, leading to potentially biased results. In particular parallel execution platforms, such as Graphics Processing Units (GPUs), add their constraints to those of Pseudo-Random Number Generators (PRNGs) used in parallel. This results in a situation where potential biases can be combined with performance drops when parallelization of random streams has not been carried out rigorously. Here, we propose criteria guiding the design of good GPU-enabled PRNGs. We enhance our comments with a study of the techniques aiming to parallelize random streams correctly, in the context of GPU-enabled stochastic simulations

A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae

International audienceBacteria with multiple chromosomes represent up to 10% of all bacterial species. Unlike eukaryotes, these bacteria use chromosome-specific initiators for their replication. In all cases investigated, the machineries for secondary chromosome replication initiation are of plasmid origin. One of the important differences between plasmids and chromosomes is that the latter replicate during a defined period of the cell cycle, ensuring a single round of replication per cell. Vibrio cholerae carries two circular chromosomes, Chr1 and Chr2, which are replicated in a well-orchestrated manner with the cell cycle and coordinated in such a way that replication termination occurs at the same time. However, the mechanism coordinating this synchrony remains speculative. We investigated this mechanism and revealed that initiation of Chr2 replication is triggered by the replication of a 150-bp locus positioned on Chr1, called crtS. This crtS replication-mediated Chr2 replication initiation mechanism explains how the two chromosomes communicate to coordinate their replication. Our study reveals a new checkpoint control mechanism in bacteria, and highlights possible functional interactions mediated by contacts between two chromosomes, an unprecedented observation in bacteria

PP/PP-HI/silica nanocomposites for HVDC cable insulation: Are silica clusters beneficial for space charge accumulation?

New potential High Voltage Direct Current (HVDC) cable insulation materials based on nanocomposites are developed in this study. The nanocomposites are produced by blending of polypropylene (PP), propylene-ethylene copolymer (PP–HI) and a modified fumed silica (A-silica) in a concentration of 1 and 2 wt %. The A-silica is successfully modified with (3-aminopropyl)triethoxysilane (APTES) via a solvent-free method, as proven by infrared spectroscopy, thermogravimetry and transmission electron microscope mapping. A-silica in the polymer matrix acts as a nucleating agent resulting in an increase of the crystallization temperature of the polymers and a smaller crystal size. Moreover, the silica addition modified the crystals morphology of the unfilled PP/PP-HI blend. The composite containing A-silica with 2 wt% contains bigger-size silica clusters than the composite filled with 1 wt%. The composite with the higher A-silica concentration shows lower space charge accumulation and a lower charge current value. Besides, much deeper traps and lower trap density are observed in the composite with 2 wt% A-silica addition compared to the one with a lower concentration. Surprisingly, the presence of silica clusters with dimensions of more than 200 nm exhibit a positive effect on reducing the space charge accumulation. However, the real cause of this improvement might be due to change of the electron distribution stemming from the amine-amine hydrogen bond formation, or the change of the chain mobility due to the presence of occluded polymer macromolecules constrained inside the high structure silica clusters. Both phenomena may lead to a higher energetic barrier of charge de-trapping, thus increasing the depth of the charge traps

Rigorous Proof of a Liquid-Vapor Phase Transition in a Continuum Particle System

We consider particles in ${\Bbb R}^d, d \geq 2$, interacting via attractive pair and repulsive four-body potentials of the Kac type. Perturbing about mean field theory, valid when the interaction range becomes infinite, we prove rigorously the existence of a liquid-gas phase transition when the interaction range is finite but long compared to the interparticle spacing.Comment: 11 pages, in ReVTeX, e-mail addresses: [email protected], [email protected], [email protected]

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae

In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC neighboring regions are in higher dose due to multifork replication. Relocation of s10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its expression, and bacterial growth rate. However, a mechanism linking S10 dosage to cell physiology has still not been determined.We hypothesized that S10 dosage perturbations impact protein synthesis capacity. Strikingly, we observed that in Vibrio cholerae, protein production capacity was independent of S10 position. Deep sequencing revealed that S10 relocation altered chromosomal replication dynamics and genome-wide transcription. Such changes increased as a function of oriC-S10 distance. Since RP constitutes a large proportion of cell mass, lower S10 dosage could lead to changes in macromolecular crowding, impacting cell physiology. Accordingly, cytoplasm fluidity was higher in mutants where S10 is most distant from oriC. In hyperosmotic conditions, when crowding differences are minimized, the growth rate and replication dynamics were highly alleviated in these strains.The genomic location of RP genes ensures its optimal dosage. However, besides of its essential function in translation, their genomic position sustains an optimal macromolecular crowding essential for maximizing growth. Hence, this could be another mechanism coordinating DNA replication to bacterial growth.Fil: Soler Bistue, Alfonso J. C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Aguilar Pierlé, Sebastián. Institut Pasteur; FranciaFil: Garcia Garcerá, Marc. Institut Pasteur; FranciaFil: Val, Marie Eve. Institut Pasteur; FranciaFil: Sismeiro, Odile. Institut Pasteur; FranciaFil: Varet, Hugo. Institut Pasteur; FranciaFil: Sieira, Rodrigo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Krin, Evelyne. Institut Pasteur; FranciaFil: Skovgaard, Ole. Roskilde Universitet; DinamarcaFil: Comerci, Diego José. Universidad Nacional de San Martin. Instituto de Investigaciones Biotecnologicas. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Pque. Centenario. Instituto de Investigaciones Biotecnologicas.; ArgentinaFil: Rocha, Eduardo P. C.. Institut Pasteur; FranciaFil: Mazel, Didier. Institut Pasteur; Franci

Using an electrochemical assay to determine the biofilm elasticity change as a response to toxicant exposure

Elasticity is a trait of biofilm physiognomy which relates to cell clustering and can be measured by means of an electrochemical assay based on rotating disc electrode (RDE). This study aimed at testing the hypothesis according to which exposure of phototrophic biofilm to toxicant could reduce its elasticity. We compared biofilms developed for 21 days, in four sets of 6 replicated experimental units, in absence and presence of isoproturon at two concentrations of the inoculating suspension of biofilm, 103 and 104 diatom cell mL-1. Biofilm thickness and elasticity were measured based on RDE assay, bacterial and diatom density were measured by microscope-based numerations.Very thin biofilms (< 10 µm) were obtained as compared with a previous study. This might be linked with the way we selected the initial biofilm providing the suspension and the way we developed its growth. The biofilm elasticity mean values in the presence of isoproturon was quasi twice lower (60 ± 10 and 60 ± 41 µm rpm0.5) than the treatment without isoproturon (138 ± 93 and 115 ± 104 µm rpm0.5), for initial biofilm concentration of 103 and 104 respectively, but there was no significant difference between the mean values of each treatment. Nevertheless, the present preliminary study demonstrated the feasibility of an experiment dedicated to assessing biofilm elasticity changes as a response to toxicant exposure

Inverse Correlation between Promoter Strength and Excision Activity in Class 1 Integrons

Class 1 integrons are widespread genetic elements that allow bacteria to capture and express gene cassettes that are usually promoterless. These integrons play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria. They typically consist of a gene (intI) encoding an integrase (that catalyzes the gene cassette movement by site-specific recombination), a recombination site (attI1), and a promoter (Pc) responsible for the expression of inserted gene cassettes. The Pc promoter can occasionally be combined with a second promoter designated P2, and several Pc variants with different strengths have been described, although their relative distribution is not known. The Pc promoter in class 1 integrons is located within the intI1 coding sequence. The Pc polymorphism affects the amino acid sequence of IntI1 and the effect of this feature on the integrase recombination activity has not previously been investigated. We therefore conducted an extensive in silico study of class 1 integron sequences in order to assess the distribution of Pc variants. We also measured these promoters' strength by means of transcriptional reporter gene fusion experiments and estimated the excision and integration activities of the different IntI1 variants. We found that there are currently 13 Pc variants, leading to 10 IntI1 variants, that have a highly uneven distribution. There are five main Pc-P2 combinations, corresponding to five promoter strengths, and three main integrases displaying similar integration activity but very different excision efficiency. Promoter strength correlates with integrase excision activity: the weaker the promoter, the stronger the integrase. The tight relationship between the aptitude of class 1 integrons to recombine cassettes and express gene cassettes may be a key to understanding the short-term evolution of integrons. Dissemination of integron-driven drug resistance is therefore more complex than previously thought