Statistical Mechanics of Horizontal Gene Transfer in Evolutionary Ecology

The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living cells communicate genetically through transferred genes, as well as the ways in which they can reorganize their genomes in response to environmental pressure. We discuss how genome evolution can be thought of as related to the physical phenomenon of annealing, and describe the sense in which genomes can be said to exhibit an analogue of information entropy. As a direct application of these ideas, we analyze the variation with ocean depth of transposons in marine microbial genomes, predicting trends that are consistent with recent observations using metagenomic surveys.Comment: Accepted by Journal of Statistical Physic

Velocity-space sensitivity of the time-of-flight neutron spectrometer at JET

The velocity-space sensitivities of fast-ion diagnostics are often described by so-called weight functions. Recently, we formulated weight functions showing the velocity-space sensitivity of the often dominant beam-target part of neutron energy spectra. These weight functions for neutron emission spectrometry (NES) are independent of the particular NES diagnostic. Here we apply these NES weight functions to the time-of-flight spectrometer TOFOR at JET. By taking the instrumental response function of TOFOR into account, we calculate time-of-flight NES weight functions that enable us to directly determine the velocity-space sensitivity of a given part of a measured time-of-flight spectrum from TOFOR

Relationship of edge localized mode burst times with divertor flux loop signal phase in JET

A phase relationship is identified between sequential edge localized modes (ELMs) occurrence times in a set of H-mode tokamak plasmas to the voltage measured in full flux azimuthal loops in the divertor region. We focus on plasmas in the Joint European Torus where a steady H-mode is sustained over several seconds, during which ELMs are observed in the Be II emission at the divertor. The ELMs analysed arise from intrinsic ELMing, in that there is no deliberate intent to control the ELMing process by external means. We use ELM timings derived from the Be II signal to perform direct time domain analysis of the full flux loop VLD2 and VLD3 signals, which provide a high cadence global measurement proportional to the voltage induced by changes in poloidal magnetic flux. Specifically, we examine how the time interval between pairs of successive ELMs is linked to the time-evolving phase of the full flux loop signals. Each ELM produces a clear early pulse in the full flux loop signals, whose peak time is used to condition our analysis. The arrival time of the following ELM, relative to this pulse, is found to fall into one of two categories: (i) prompt ELMs, which are directly paced by the initial response seen in the flux loop signals; and (ii) all other ELMs, which occur after the initial response of the full flux loop signals has decayed in amplitude. The times at which ELMs in category (ii) occur, relative to the first ELM of the pair, are clustered at times when the instantaneous phase of the full flux loop signal is close to its value at the time of the first ELM

Observational study of vaccination in cancer patients: How can vaccine coverage be improved?

International audienceBackground: Chemotherapy increases the risk of infections, often severe, and some of them are vaccine-preventable infections. We aimed to assess vaccination coverage and associated factors in oncology and hematology patients.Methods: Consecutive adult patients followed in a French university hospital for hematological malignancy or solid cancer voluntarily completed an anonymous questionnaire in September and October 2016. It included questions on underlying disease, chemotherapy, flu, and pneumococcal vaccination uptakes, and attitudes toward vaccination. Factors associated with vaccination uptake were assessed by multivariate logistic regression.Results: The response rate was 41.9% (N=671) among 1,600 questionnaires distributed; 232 patients had underlying hematological malignancy and 439 had solid cancer. Half of the patients were aged over 65 years. Chemotherapy was ongoing or discontinued for less than one year in 74.7% of patients. In patients aged 65 years had coverage of 47%. Pneumococcal vaccine uptake was 7.3%. However, 64.7% of patients were favorable to vaccination. Vaccine uptake was associated with age >65 years (OR 4.5 [2.9-7.0]), information about vaccination delivered by the family physician (OR 12.9 [5.5-30.1]), follow-up in hematology unit (OR 2.0 [1.3-3.1]), and positive opinion about vaccination (OR 2.0 [1.3-3.1]).Conclusion: Despite specific recommendations regarding immunocompromised patients, anti-pneumococcal and flu vaccinations were rarely conducted, even in elderly patients. Targeted information campaigns to family physicians, oncologists, and patients should be implemented to improve vaccine coverage in patients with underlying malignancies

Bacterial spot and early blight biocontrol by epiphytic bacteria in tomato plants

The objective of this work was to evaluate in vitro and in vivo biocontrol of bacterial spot (Xanthomonas vesicatoria) and early blight (Alternaria solani) by the epiphytic bacteria Paenibacillus macerans and Bacillus pumilus. Tomato plants were previously sprayed with epiphytic bacteria, benzalkonium chloride and PBS buffer and, after four days, they were inoculated with A. solani and X. vesicatoria. To determine the phytopathogenic bacteria population, leaflet samples were collected from each treatment every 24 hours, for seven days, and plated on semi-selective medium. The effect of epiphytic bacteria over phytopathogens was performed by the antibiosis test and antagonistic activity measured by inhibition zone diameter. The epiphytic and benzalkonium chloride drastically reduced the severity of early blight and bacterial spot in comparison to the control (PBS). In detached leaflets, the epiphytic bacteria reduced in 70% the number of phytopathogenic bacteria cells in the phylloplane. The antibiosis test showed that the epiphytic bacteria efficiently inhibit the phytopathogens growth. In all the bioassays, the epiphytic bacteria protect tomato plants against the phytopathogen

La microbiologie moléculaire au service du diagnostic environnemental.

L'étude a pour objectif de décrire les différentes techniques relevant de la microbiologie moléculaire en termes d'état d'avancement, de limites techniques et de sensibilité pour étudier l'abondance, la diversité, l'activité et les potentialités fonctionnelles des communautés microbiennes indigènes de diverses matrices environnementales (eau, sol, air, substrats déchets). On trouve dans l'étude neuf fiches de présentation des méthodes, puis vingt-neuf fiches d'application sur les milieux/substrats eau, sol, air et déchets. Des indicateurs de microbiologie moléculaire permettant un diagnostic environnemental ont été recherchés. Une trentaine d'entreprise qui les propose en routine sont données dans le rapport. Ces indicateurs microbiens sont opérationnels pour des prestations de diagnostic de la qualité de différentes matrices environnementales par différents types d'opérateurs (agriculteurs, industriels, gestionnaires de déchets, aménageurs du territoire

Recommandations d'un collectif franco-suisse d'experts pour une meilleure évaluation de la qualité écotoxicologique des sédiments par l'étude des communautés benthiques

National audienceLes sédiments ont un rôle écologique essentiel pour de nombreuses espèces aquatiques. Toutefois, leur capacité à capter les polluants persistants peut participer à long terme à la contamination des milieux aquatiques. Aussi, afin de mieux prendre en compte les impacts écotoxicologiques de la contamination des sédiments et appréhender le risque écologique qui en découle, il est important de disposer de méthodes d'évaluation robustes. Cet article présente la contribution d'un groupe franco-suisse réunissant chercheurs, gestionnaires et représentants de bureaux d'études qui ont travaillé ensemble afin de dresser un état des lieux et formuler des recommandations pour mieux caractériser la contamination des sédiments, les niveaux d'exposition des communautés benthiques et les effets possibles sur ces espèces