Apport de l'altimétrie à l'étude des tourbillons à méso et subméso-échelle : application régionale au Golfe de Gascogne

Le Golfe de Gascogne, en Atlantique Nord Est, est le lieu d'une dynamique complexe dans laquelle le courant de pente influe le développement de structures (sub)méso-échelles, contribuant aux échanges des eaux et traceurs océaniques entre le plateau continental et le large. Grâce aux séries temporelles et sa précision, l'altimétrie est idéale pour observer de tels processus. Ici, il est nécessaire de bénéficier des récents travaux sur l'altimétrie côtière pour étudier cette dynamique. Une méthode d'analyse en ondelette a été développée pour déterminer l'observabilité de ces processus: ceux-ci sont sous-évalués sur les cartes de niveau de la mer actuelles. Une méthode de cartographie, adaptée aux échelles régionales de variabilité a été mise en place sur une période de couverture spatiale optimale (4 satellites, 2002-2005). Les cartes régionales ont ensuite été sujettes à une intercomparaison à des observations indépendantes (in-situ ou satellite). La cartographie fine échelle améliore les estimations d'énergie cinétique tourbillonnaire par rapport aux données standard ainsi que la variabilité du courant de pente. Les filaments, déduits des exposants de Lyapunov dérivés de nos cartes, sont cohérents avec les images satellites. Le suivi d'un épisode de détachement de tourbillon fine-échelle (< 50 km) du courant de pente est rendu possible par l'utilisation combinée des cartes altimétriques régionales, des images satellites et des données in-situ. L'analyse de la variabilité spatiale et temporelle de ces dynamiques est ensuite faite. Cette thèse ouvre des perspectives en termes d'observations, avec des pistes d'amélioration de la cartographie et des budgets d'erreurs. Cette méthodologie peut être étendue à d'autres zones d'études, et données altimétriques. Ces cartes régionales fournissent une observation importante pour l'interprétation de la physique océanique du Golfe de Gascogne ainsi que pour la validation des modèles régionaux.The Bay of Biscay, in the North East Atlantic, is the scene of a particularly complex ocean dynamics in which the slope current plays a role in the development of (sub)mesoscale structures offshore, contributing to water exchanges between the continental shelf and the open ocean. Thanks to long time series and its precision, altimetry is an ideal tool to their observation. Due to the regional dynamics, it is necessary to benefit from recent advances in coastal altimetry. First, wavelet analysis was developed to determine the observability of the (sub)mesoscale: these processes are currently under evaluated in maps of sea level. A regional fine scale mapping methodology was then put in place over a period of optimal spatial coverage (4 satellites, 2002-2005). Regional maps were then the subject of intense intercomparison using independent observations (in-situ & satellite). Fine-scale mapping improve regional estimates of eddy kinetic energy levels compared to standard data as well as the of the slope current variability. Filaments based on the Lyapunov exponents, derived from our regional maps, are more consistent with satellite images. A sequence of fine-scale eddy detachment from the slope current is made possible by the combined use of regional sea level maps, satellite images and in-situ data. The spatial and temporal variability of the meso and submeso-scale dynamics can then be studied and phase lags are observed between the continental slope and offshore variability. Finally, this thesis opens up the perspective of observations, including the provision of areas for the development of regional mapping methodologies and the improvement observational error budgets. These methodological developments can be extended to other regions and altimetry datasets. Regional maps provide an important observation for the interpretation of the Bay of Biscay ocean dynamics and for the validation of regional models

Both TLR2 and TRIF Contribute to Interferon-β Production during Listeria Infection

Synthesis of interferon-β (IFN-β) is an innate response to cytoplasmic infection with bacterial pathogens. Our recent studies showed that Listeria monocytogenes limits immune detection and IFN-β synthesis via deacetylation of its peptidoglycan, which renders the bacterium resistant to lysozyme degradation. Here, we examined signaling requirements for the massive IFN-β production resulting from the infection of murine macrophages with a mutant strain of L. monocytogenes, ΔpgdA, which is unable to modify its peptidoglycan. We report the identification of unconventional signaling pathways to the IFN-β gene, requiring TLR2 and bacterial internalization. Induction of IFN-β was independent of the Mal/TIRAP adaptor protein but required TRIF and the transcription factors IRF3 and IRF7. These pathways were stimulated to a lesser degree by wild-type L. monocytogenes. They operated in both resident and inflammatory macrophages derived from the peritoneal cavity, but not in bone marrow-derived macrophages. The novelty of our findings thus lies in the first description of TLR2 and TRIF as two critical components leading to the induction of the IFN-β gene and in uncovering that individual macrophage populations adopt different strategies to link pathogen recognition signals to IFN-β gene expression

Mycobacterium tuberculosis ClpP Proteases Are Co-transcribed but Exhibit Different Substrate Specificities

PMCID: PMC3613350This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Listeria monocytogenes Traffics from Maternal Organs to the Placenta and Back

Infection with Listeria monocytogenes is a significant health problem during pregnancy. This study evaluates the role of trafficking between maternal organs and placenta in a pregnant guinea pig model of listeriosis. After intravenous inoculation of guinea pigs, the initial ratio of bacteria in maternal organs to placenta was 10(3)–10(4):1. Rapid increase of bacteria in the placenta changed the ratio to 1:1 after 24 h. Utilizing two wild-type strains, differentially marked by their susceptibility to erythromycin, we found that only a single bacterium was necessary to cause placental infection, and that L. monocytogenes trafficked from maternal organs to the placenta in small numbers. Surprisingly, bacteria trafficked in large numbers from the placenta to maternal organs. Bacterial growth, clearance, and transport between organs were simulated with a mathematical model showing that the rate of bacterial clearance relative to the rate of bacterial replication in the placenta was sufficient to explain the difference in the course of listeriosis in pregnant versus nonpregnant animals. These results provide the basis for a new model where the placenta is relatively protected from infection. Once colonized, the placenta becomes a nidus of infection resulting in massive reseeding of maternal organs, where L. monocytogenes cannot be cleared until trafficking is interrupted by expulsion of the infected placental tissues

Sea Surface Salinity and Temperature Budgets in the North Atlantic Subtropical Gyre during SPURS Experiment: August 2012-August 2013

Variability at large to meso-scale in sea surface salinity (SSS) and sea surface temperature (SST) is investigated in the subtropical North Atlantic Ocean during the Subtropical Atlantic Surface Salinity Experiment Strasse/SPURS in August 2012 - August 2013. The products of the Soil Moisture and Ocean Salinity (SMOS) mission corrected from large scale systematic errors are tested and used to retrieve meso-scale salinity features, while OSTIA products, resolving meso-scale temperature features are used for SST. The comparison of corrected SMOS SSS data with drifter's in situ measurements from SPURS experiment shows a reasonable agreement, especially during winter time with RMS differences on the order of 0.15 pss (for 10 days, 75 km resolution SMOS product). The analysis of SSS (SST) variability reveals that the meso-scale eddies contribute to a substantial freshening (cooling) in the central high salinity region of the subtropical gyre, albeit smaller than Ekman and atmospheric freshwater (heat) seasonal flux, which are the leading terms in SSS (SST) budget. An error is estimated along with SSS and SST budgets; as well as sensitivity to the different products in use and residuals are discussed. The residuals in the SSS budget are large and can arise from errors in the advection fields and freshwater flux, from neglected small scale or unresolved local processes (salt fingering, vertical mixing and small scale subduction, etc.). However, their magnitude is similar to what is often parameterized as eddy horizontal diffusion to close large scale budgets

An unstructured 5′-coding region of the prfA mRNA is required for efficient translation

Expression of virulence factors in the human bacterial pathogen Listeria monocytogenes is almost exclusively regulated by the transcriptional activator PrfA. The translation of prfA is controlled by a thermosensor located in the 5′-untranslated RNA (UTR), and is high at 37°C and low at temperatures <30°C. In order to develop a thermoregulated translational expression system, the 5′-UTR and different lengths of the prfA-coding sequences were placed in front of lacZ. When expressed in Escherichia coli, the β-galactosidase expression was directly correlated to the length of the prfA-coding mRNA lying in front of lacZ. A similar effect was detected with gfp as a reporter gene in both L. monocytogenes and E. coli, emphasizing the requirement of the prfA-coding RNA for maximal expression. In vitro transcription/translation and mutational analysis suggests a role for the first 20 codons of the native prfA-mRNA for maximal expression. By toe-print and RNA-probing analysis, a flexible hairpin-loop located immediately downstream of the start-codon was shown to be important for ribosomal binding. The present work determines the importance of an unstructured part of the 5′-coding region of the prfA-mRNA for efficient translation

EmbA is an essential arabinosyltransferase in Mycobacterium tuberculosis

The Emb proteins (EmbA, EmbB, EmbC) are mycobacterial arabinosyltransferases involved in the biogenesis of the mycobacterial cell wall. EmbA and EmbB are predicted to work in unison as a heterodimer. EmbA and EmbB are involved in the formation of the crucial terminal hexaarabinoside motif [Araβ(1→2)Araα(1→5)] [Araβ(1→2)Araα(1→3)]Araα(1→5)Araα1→(Ara6) in the cell wall polysaccharide arabinogalactan. Studies conducted in Mycobacterium smegmatis revealed that mutants with disruptions in embA or embB are viable, although the growth rate was affected. In contrast, we demonstrate here that embA is an essential gene in Mycobacterium tuberculosis, since a deletion of the chromosomal gene could only be achieved when a second functional copy was provided on an integrated vector. Complementation of an embA mutant of M. smegmatis by M. tuberculosis embA confirmed that it encodes a functional arabinosyltransferase. We identified a promoter for M. tuberculosis embA located immediately upstream of the gene, indicating that it is expressed independently from the upstream gene, embC. Promoter activity from PembA(Mtb) was sevenfold lower when assayed in M. smegmatis compared to M. tuberculosis, indicating that the latter is not a good host for genetic analysis of M. tuberculosis embA expression. PembA(Mtb) activity remained constant throughout growth phases and after stress treatment, although it was reduced during hypoxia-induced non-replicating persistence. Ethambutol exposure had no effect on PembA(Mtb) activity. These data demonstrate that M. tuberculosis embA encodes a functional arabinosyltransferase which is constitutively expressed and plays a critical role in M. tuberculosis

inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons

BACKGROUND: Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics. Furthermore, such comparisons provide important clues for vaccines and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of similar genes identified and genome-wide reports and lists on specific functions. All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in Java with Biojava subroutines. RESULTS: InGeno provides a user-friendly interactive visualization platform for sequence comparisons (comprehensive reciprocal protein – protein comparisons) between complete genome sequences and all associated annotations and features. The comparison data can be acquired from several different sequence analysis programs in flexible formats. Automatic dot-plot analysis includes output reduction, filtering, ortholog testing and linear regression, followed by smart clustering (local collinear blocks; LCBs) to reveal similar genome regions. Further, the system provides genome alignment and visualization editor, collinear relationships and strain-specific islands. Specific annotations and functions are parsed, recognized, clustered, logically concatenated and visualized and summarized in reports. CONCLUSION: As shown in this study, inGeno can be applied to study and compare in particular prokaryotic genomes against each other (gram positive and negative as well as close and more distantly related species) and has been proven to be sensitive and accurate. This modular software is user-friendly and easily accommodates new routines to meet specific user-defined requirements

Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets

To identify noncoding RNAs (ncRNAs) in the pathogenic bacterium Listeria monocytogenes, we analyzed the intergenic regions (IGRs) of strain EGD-e by in silico-based approaches. Among the twelve ncRNAs found, nine are novel and specific to the Listeria genus, and two of these ncRNAs are expressed in a growth-dependent manner. Three of the ncRNAs are transcribed in opposite direction to overlapping open reading frames (ORFs), suggesting that they act as antisense on the corresponding mRNAs. The other ncRNA genes appear as single transcription units. One of them displays five repeats of 29 nucleotides. Five of these new ncRNAs are absent from the non-pathogenic species L. innocua, raising the possibility that they might be involved in virulence. To predict mRNA targets of the ncRNAs, we developed a computational method based on thermodynamic pairing energies and known ncRNA–mRNA hybrids. Three ncRNAs, including one of the putative antisense ncRNAs, were predicted to have more than one mRNA targets. Several of them were shown to bind efficiently to the ncRNAs suggesting that our in silico approach could be used as a general tool to search for mRNA targets of ncRNAs

The Use of Flagella and Motility for Plant Colonization and Fitness by Different Strains of the Foodborne Pathogen Listeria monocytogenes

The role of flagella and motility in the attachment of the foodborne pathogen Listeria monocytogenes to various surfaces is mixed with some systems requiring flagella for an interaction and others needing only motility for cells to get to the surface. In nature this bacterium is a saprophyte and contaminated produce is an avenue for infection. Previous studies have documented the ability of this organism to attach to and colonize plant tissue. Motility mutants were generated in three wild type strains of L. monocytogenes by deleting either flaA, the gene encoding flagellin, or motAB, genes encoding part of the flagellar motor, and tested for both the ability to colonize sprouts and for the fitness of that colonization. The motAB mutants were not affected in the colonization of alfalfa, radish, and broccoli sprouts; however, some of the flaA mutants showed reduced colonization ability. The best colonizing wild type strain was reduced in colonization on all three sprout types as a result of a flaA deletion. A mutant in another background was only affected on alfalfa. The third, a poor alfalfa colonizer was not affected in colonization ability by any of the deletions. Fitness of colonization was measured in experiments of competition between mixtures of mutant and parent strains on sprouts. Here the flaA and motAB mutants of the three strain backgrounds were impaired in fitness of colonization of alfalfa and radish sprouts, and one strain background showed reduced fitness of both mutant types on broccoli sprouts. Together these data indicate a role for flagella for some strains to physically colonize some plants, while the fitness of that colonization is positively affected by motility in almost all cases