Transient Rayleigh-Benard-Marangoni Convection due to Evaporation : a Linear Non-normal Stability Analysis

The convective instability in a plane liquid layer with time-dependent temperature profile is investigated by means of a general method suitable for linear stability analysis of an unsteady basic flow. The method is based on a non-normal approach, and predicts the onset of instability, critical wave number and time. The method is applied to transient Rayleigh-Benard-Marangoni convection due to cooling by evaporation. Numerical results as well as theoretical scalings for the critical parameters as function of the Biot number are presented for the limiting cases of purely buoyancy-driven and purely surface-tension-driven convection. Critical parameters from calculations are in good agreement with those from experiments on drying polymer solutions, where the surface cooling is induced by solvent evaporation.Comment: 31 pages, 8 figure

Importance Of Toll-Like Receptors For B Lymphocyte Survival In Primary Sjögren’s Syndrome

The Sjögren's syndrome is a systemic autoimmune disease characterized by lymphocytic infiltration of the glands responsible for mouth and eyes dryness. A minority of infiltrating B cells is organized as germinal centers while the majority is aggregated into clusters of transitional and marginal zone B cells. The Toll-like receptor 9 (TLR9) recognizes microbial DNA but also, sometimes, the self DNA. It appears to be a key determinant of the survival and differentiation of B lymphocytes. After laser micro-dissection of B cells from salivary glands, analyses by quantitative RT-PCR showed that transitional B cells express high level of TLR9 mRNA unlike B cells from germinal centers. B lymphocytes from healthy donors were sorted by flow cytometry and stimulated in vitro with their TLR9. It induces survival, activation and proliferation associated with phenotypic changes. Transitional B cells exhibited characteristics of the marginal zone, whereas mature B cells expressed follicular germinal center specificities. Finally, IgM and IgG were secreted by both population, but with elevated production of autoantibodies by the transitional B cells. Increased expression of TLR9 by transitional B cells suggests that they may be highly sensitive to differentiate into autoantibody secreting cells through maturation into the marginal zone into the salivary glands. TLR9 might be a target for forthcoming biotherapies. Le syndrome de Gougerot-Sjögren est une maladie autoimmune systémique caractérisée par une infiltration lymphocytaire des glandes responsable d'une sécheresse buccale et oculaire. Une minorité des lymphocytes B infiltrants est organisée en centres germinatifs tandis que la majorité est regroupée en agrégats de lymphocytes B transitionnels et de la zone marginale. Le Toll-like receptor 9 (TLR9) reconnaît l'ADN microbien mais aussi, parfois, l'ADN du soi. Il apparaît donc comme un élément déterminant de la survie et la différenciation des lymphocytes B. Après micro-dissection laser des lymphocytes B des glandes salivaires, une analyse par RT-PCR quantitative a montré que les lymphocytes B transitionnels expriment fortement l'ARNm de TLR9 contrairement à ceux des centres germinatifs. Des lymphocytes B de donneurs sains ont été triés par cytométrie en flux puis stimulés in vitro par leur TLR9. Il s’ensuit une survie, une activation et une prolifération associées à des modifications phénotypiques. Les lymphocytes B transitionnels présentent des caractéristiques de la zone marginale, tandis que les lymphocytes B matures expriment des spécificités folliculaires des centres germinatifs. Enfin, des IgM et des IgG sont sécrétées par les deux types de population, mais avec une production d'auto-anticorps plus élevée issue de la différenciation des lymphocytes B transitionnels. L’expression accrue de TLR9 par les lymphocytes B transitionnels suggère qu'ils pourraient être particulièrement sensibles à une différenciation en cellules sécrétrices d'auto-anticorps par une maturation vers la zone marginale au sein des glandes salivaires. Le TLR9 pourrait bien devenir la cible des futures biothérapies.The Sjögren's syndrome is a systemic autoimmune disease characterized by lymphocytic infiltration of the glands responsible for mouth and eyes dryness. A minority of infiltrating B cells is organized as germinal centers while the majority is aggregated into clusters of transitional and marginal zone B cells. The Toll-like receptor 9 (TLR9) recognizes microbial DNA but also, sometimes, the self DNA. It appears to be a key determinant of the survival and differentiation of B lymphocytes. After laser micro-dissection of B cells from salivary glands, analyses by quantitative RT-PCR showed that transitional B cells express high level of TLR9 mRNA unlike B cells from germinal centers. B lymphocytes from healthy donors were sorted by flow cytometry and stimulated in vitro with their TLR9. It induces survival, activation and proliferation associated with phenotypic changes. Transitional B cells exhibited characteristics of the marginal zone, whereas mature B cells expressed follicular germinal center specificities. Finally, IgM and IgG were secreted by both population, but with elevated production of autoantibodies by the transitional B cells. Increased expression of TLR9 by transitional B cells suggests that they may be highly sensitive to differentiate into autoantibody secreting cells through maturation into the marginal zone into the salivary glands. TLR9 might be a target for forthcoming biotherapies. Le syndrome de Gougerot-Sjögren est une maladie autoimmune systémique caractérisée par une infiltration lymphocytaire des glandes responsable d'une sécheresse buccale et oculaire. Une minorité des lymphocytes B infiltrants est organisée en centres germinatifs tandis que la majorité est regroupée en agrégats de lymphocytes B transitionnels et de la zone marginale. Le Toll-like receptor 9 (TLR9) reconnaît l'ADN microbien mais aussi, parfois, l'ADN du soi. Il apparaît donc comme un élément déterminant de la survie et la différenciation des lymphocytes B. Après micro-dissection laser des lymphocytes B des glandes salivaires, une analyse par RT-PCR quantitative a montré que les lymphocytes B transitionnels expriment fortement l'ARNm de TLR9 contrairement à ceux des centres germinatifs. Des lymphocytes B de donneurs sains ont été triés par cytométrie en flux puis stimulés in vitro par leur TLR9. Il s’ensuit une survie, une activation et une prolifération associées à des modifications phénotypiques. Les lymphocytes B transitionnels présentent des caractéristiques de la zone marginale, tandis que les lymphocytes B matures expriment des spécificités folliculaires des centres germinatifs. Enfin, des IgM et des IgG sont sécrétées par les deux types de population, mais avec une production d'auto-anticorps plus élevée issue de la différenciation des lymphocytes B transitionnels. L’expression accrue de TLR9 par les lymphocytes B transitionnels suggère qu'ils pourraient être particulièrement sensibles à une différenciation en cellules sécrétrices d'auto-anticorps par une maturation vers la zone marginale au sein des glandes salivaires. Le TLR9 pourrait bien devenir la cible des futures biothérapies

TOLL-LIKE RECEPTOR 9 DRIVES THE MATURATION OF B LYMPHOCYTES IN THE SALIVARY GLANDS OF PATIENTS WITH SJÖGREN’S SYNDROME

Oral Communication presented at the ";Forum des Jeunes Chercheurs";, Brest (France) 2011

A New Type of Electron Nuclear-Spin Interaction from Resistively Detected NMR in the Fractional Quantum Hall Effect Regime

Two dimensional electron gases in narrow GaAs quantum wells show huge longitudinal resistance (HLR) values at certain fractional filling factors. Applying an RF field with frequencies corresponding to the nuclear spin splittings of {69}Ga, {71}Ga and {75}As leads to a substantial decreases of the HLR establishing a novel type of resistively detected NMR. These resonances are split into four sub lines each. Neither the number of sub lines nor the size of the splitting can be explained by established interaction mechanisms.Comment: 4 pages, 3 figure

The origin of life: chemical evolution of a metabolic system in a mineral honeycomb?

For the RNA-world hypothesis to be ecologically feasible, selection mechanisms acting on replicator communities need to be invoked and the corresponding scenarios of molecular evolution specified. Complementing our previous models of chemical evolution on mineral surfaces, in which selection was the consequence of the limited mobility of macromolecules attached to the surface, here we offer an alternative realization of prebiotic group-level selection: the physical encapsulation of local replicator communities into the pores of the mineral substrate. Based on cellular automaton simulations we argue that the effect of group selection in a mineral honeycomb could have been efficient enough to keep prebiotic ribozymes of different specificities and replication rates coexistent, and their metabolic cooperation protected from extensive molecular parasitism. We suggest that mutants of the mild parasites persistent in the metabolic system can acquire useful functions such as replicase activity or the production of membrane components, thus opening the way for the evolution of the first autonomous protocells on Earth

Change of tRNA identity leads to a divergent orthogonal histidyl-tRNA synthetase/tRNAHis pair

Mature tRNAHis has at its 5′-terminus an extra guanylate, designated as G−1. This is the major recognition element for histidyl-tRNA synthetase (HisRS) to permit acylation of tRNAHis with histidine. However, it was reported that tRNAHis of a subgroup of α-proteobacteria, including Caulobacter crescentus, lacks the critical G−1 residue. Here we show that recombinant C. crescentus HisRS allowed complete histidylation of a C. crescentus tRNAHis transcript (lacking G−1). The addition of G−1 did not improve aminoacylation by C. crescentus HisRS. However, mutations in the tRNAHis anticodon caused a drastic loss of in vitro histidylation, and mutations of bases A73 and U72 also reduced charging. Thus, the major recognition elements in C. crescentus tRNAHis are the anticodon, the discriminator base and U72, which are recognized by the divergent (based on sequence similarity) C. crescentus HisRS. Transplantation of these recognition elements into an Escherichia coli tRNAHis template, together with addition of base U20a, created a competent substrate for C. crescentus HisRS. These results illustrate how a conserved tRNA recognition pattern changed during evolution. The data also uncovered a divergent orthogonal HisRS/tRNAHis pair

High Abundance Proteins Depletion vs Low Abundance Proteins Enrichment: Comparison of Methods to Reduce the Plasma Proteome Complexity

BACKGROUND: To date, the complexity of the plasma proteome exceeds the analytical capacity of conventional approaches to isolate lower abundance proteins that may prove to be informative biomarkers. Only complex multistep separation strategies have been able to detect a substantial number of low abundance proteins (<100 ng/ml). The first step of these protocols is generally the depletion of high abundance proteins by the use of immunoaffinity columns or, alternatively, the enrichment of by the use of solid phase hexapeptides ligand libraries. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a direct comparison of these two approaches. Following either approach, the plasma sample was further fractionated by SCX chromatography and analyzed by RP-LC-MS/MS with a Q-TOF mass spectrometer. The depletion of the 20 most abundant plasma proteins allowed the identification of about 25% more proteins than those detectable following low abundance proteins enrichment. The two datasets are partially overlapping and the identified proteins belong to the same order of magnitude in terms of plasma concentration. CONCLUSIONS/SIGNIFICANCE: Our results show that the two approaches give complementary results. However, the enrichment of low abundance proteins has the great advantage of obtaining much larger amount of material that can be used for further fractionations and analyses and emerges also as a cheaper and technically simpler approach. Collectively, these data indicate that the enrichment approach seems more suitable as the first stage of a complex multi-step fractionation protocol

<i>Gaia</i> Data Release 1. Summary of the astrometric, photometric, and survey properties

Context. At about 1000 days after the launch of Gaia we present the first Gaia data release, Gaia DR1, consisting of astrometry and photometry for over 1 billion sources brighter than magnitude 20.7. Aims. A summary of Gaia DR1 is presented along with illustrations of the scientific quality of the data, followed by a discussion of the limitations due to the preliminary nature of this release. Methods. The raw data collected by Gaia during the first 14 months of the mission have been processed by the Gaia Data Processing and Analysis Consortium (DPAC) and turned into an astrometric and photometric catalogue. Results. Gaia DR1 consists of three components: a primary astrometric data set which contains the positions, parallaxes, and mean proper motions for about 2 million of the brightest stars in common with the HIPPARCOS and Tycho-2 catalogues – a realisation of the Tycho-Gaia Astrometric Solution (TGAS) – and a secondary astrometric data set containing the positions for an additional 1.1 billion sources. The second component is the photometric data set, consisting of mean G-band magnitudes for all sources. The G-band light curves and the characteristics of ∼3000 Cepheid and RR-Lyrae stars, observed at high cadence around the south ecliptic pole, form the third component. For the primary astrometric data set the typical uncertainty is about 0.3 mas for the positions and parallaxes, and about 1 mas yr−1 for the proper motions. A systematic component of ∼0.3 mas should be added to the parallax uncertainties. For the subset of ∼94 000 HIPPARCOS stars in the primary data set, the proper motions are much more precise at about 0.06 mas yr−1. For the secondary astrometric data set, the typical uncertainty of the positions is ∼10 mas. The median uncertainties on the mean G-band magnitudes range from the mmag level to ∼0.03 mag over the magnitude range 5 to 20.7. Conclusions. Gaia DR1 is an important milestone ahead of the next Gaia data release, which will feature five-parameter astrometry for all sources. Extensive validation shows that Gaia DR1 represents a major advance in the mapping of the heavens and the availability of basic stellar data that underpin observational astrophysics. Nevertheless, the very preliminary nature of this first Gaia data release does lead to a number of important limitations to the data quality which should be carefully considered before drawing conclusions from the data

Massively Parallel RNA Chemical Mapping with a Reduced Bias MAP-seq Protocol

Chemical mapping methods probe RNA structure by revealing and leveraging correlations of a nucleotide's structural accessibility or flexibility with its reactivity to various chemical probes. Pioneering work by Lucks and colleagues has expanded this method to probe hundreds of molecules at once on an Illumina sequencing platform, obviating the use of slab gels or capillary electrophoresis on one molecule at a time. Here, we describe optimizations to this method from our lab, resulting in the MAP-seq protocol (Multiplexed Accessibility Probing read out through sequencing), version 1.0. The protocol permits the quantitative probing of thousands of RNAs at once, by several chemical modification reagents, on the time scale of a day using a table-top Illumina machine. This method and a software package MAPseeker (http://simtk.org/home/map_seeker) address several potential sources of bias, by eliminating PCR steps, improving ligation efficiencies of ssDNA adapters, and avoiding problematic heuristics in prior algorithms. We hope that the step-by-step description of MAP-seq 1.0 will help other RNA mapping laboratories to transition from electrophoretic to next-generation sequencing methods and to further reduce the turnaround time and any remaining biases of the protocol.Comment: 22 pages, 5 figure

A Modern Mode of Activation for Nucleic Acid Enzymes

Through evolution, enzymes have developed subtle modes of activation in order to ensure the sufficiently high substrate specificity required by modern cellular metabolism. One of these modes is the use of a target-dependent module (i.e. a docking domain) such as those found in signalling kinases. Upon the binding of the target to a docking domain, the substrate is positioned within the catalytic site. The prodomain acts as a target-dependent module switching the kinase from an off state to an on state. As compared to the allosteric mode of activation, there is no need for the presence of a third partner. None of the ribozymes discovered to date have such a mode of activation, nor does any other known RNA. Starting from a specific on/off adaptor for the hepatitis delta virus ribozyme, that differs but has a mechanism reminiscent of this signalling kinase, we have adapted this mode of activation, using the techniques of molecular engineering, to both catalytic RNAs and DNAs exhibiting various activities. Specifically, we adapted three cleaving ribozymes (hepatitis delta virus, hammerhead and hairpin ribozymes), a cleaving 10-23 deoxyribozyme, a ligating hairpin ribozyme and an artificially selected capping ribozyme. In each case, there was a significant gain in terms of substrate specificity. Even if this mode of control is unreported for natural catalytic nucleic acids, its use needs not be limited to proteinous enzymes. We suggest that the complexity of the modern cellular metabolism might have been an important selective pressure in this evolutionary process