Techniques expérimentales pour la caractérisation mécanique de maquettes in vitro de cordes vocales

National audienceLa validation des modèles élaborés en production vocale nécessite la mise au point de dispositifs in-vitro simples mais pouvant reproduire des phénomènes physiques impliqués dans la production vocale humaine. Depuis les travaux de Van den Berg (1957), de nombreuses maquettes ont été développées avec une complexité croissante. Dans cette communication, nous nous intéressons à la caractérisation mécanique des structures vibrantes, dont la connaissance est indispensable à la reproductibilité et la répétabilité des mesures ultérieures sur la maquette ainsi qu'à l'analyse des résultats. Plusieurs techniques expérimentales sont testées sur une maquette de cordes vocales. Les résultats sont comparés en fonction des différents principes de mesure (vibrométrie laser, mesure de l'ouverture glottique, accéléromètres piézo-électriques), actionneurs (pot vibrant et source acoustique) et types d'excitation (fréquence par fréquence, sinus glissant et bruit large bande)

Physical modeling of bilabial plosives production

International audienceThe context of this study is the physical modeling of speech production. The first step of our approach is to realize in-vivo measurements during the production of the vowel-consonant-vowel sequence /apa/. This measurements concerns intra-oral pressure, acoustic pressure radiated at the lips and labial parameters (aperture and width of the lips) derived from a high-speed video recording of the subject face. In a second time, theoretical models from speech production literature are under investigation to predict the air flow trough the lips. A model is validated by comparing his predictions with results obtained from measurements on a replica of phonatory system. Then, the same experimental set-up is used to introduce an aerodynamic model of supraglottal cavity expansion. Finally, we achieve numerical simulations of a vowel-bilabial plosive-vowel utterance, by using these models. Simulation results highlight the influence of the cheeks expansion during the production of bilabial plosives

Laser scanning vibrometry and modal analysis to characterize a vocal fold replica

International audienceVocal folds are composed of elastic, soft, multilayer material, and are set to various vibration regimes during phonation, while speaking or singing. To explore such vibration phenomena, a vocal folds replica has been built, allowing to control physical parameters (subglottal pressure, vocal folds stiffness, and glottal aperture) in order to understand their respective contribution. Vocal folds are imitated by latex tubes filled with water under variable pressure. The present study aims at presenting mechanical measurements performed on a single vocal fold replica by means of a shaker provided with an accelerometer in conjunction with a laser vibrometer. This vibration measurement protocol yields a series of frequency response functions over a specific area of the vocal fold. Modal analysis is then performed using an algorithm based on the least square complex exponentials (LSCE) method, which has been developed for single input-multiple output (SIMO) systems. Results are further compared with those from the rational fraction polynomial (RFP) method. Although results are in fair accordance, the observed discrepancies are quantified and discussed

A Flavor Lactone Mimicking AHL Quorum-Sensing Signals Exploits the Broad Affinity of the QsdR Regulator to Stimulate Transcription of the Rhodococcal qsd Operon Involved in Quorum-Quenching and Biocontrol Activities

In many Gram-negative bacteria, virulence, and social behavior are controlled by quorum-sensing (QS) systems based on the synthesis and perception of N-acyl homoserine lactones (AHLs). Quorum-quenching (QQ) is currently used to disrupt bacterial communication, as a biocontrol strategy for plant crop protection. In this context, the Gram-positive bacterium Rhodococcus erythropolis uses a catabolic pathway to control the virulence of soft-rot pathogens by degrading their AHL signals. This QS signal degradation pathway requires the expression of the qsd operon, encoding the key enzyme QsdA, an intracellular lactonase that can hydrolyze a wide range of substrates. QsdR, a TetR-like family regulator, represses the expression of the qsd operon. During AHL degradation, this repression is released by the binding of the γ-butyrolactone ring of the pathogen signaling molecules to QsdR. We show here that a lactone designed to mimic quorum signals, γ-caprolactone, can act as an effector ligand of QsdR, triggering the synthesis of qsd operon-encoded enzymes. Interaction between γ-caprolactone and QsdR was demonstrated indirectly, by quantitative RT-PCR, molecular docking and transcriptional fusion approaches, and directly, in an electrophoretic mobility shift assay. This broad-affinity regulatory system demonstrates that preventive or curative quenching therapies could be triggered artificially and/or managed in a sustainable way by the addition of γ-caprolactone, a compound better known as cheap food additive. The biostimulation of QQ activity could therefore be used to counteract the lack of consistency observed in some large-scale biocontrol assays

Thiacetazone, an Antitubercular Drug that Inhibits Cyclopropanation of Cell Wall Mycolic Acids in Mycobacteria

Background. Mycolic acids are a complex mixture of branched, long-chain fatty acids, representing key components of the highly hydrophobic mycobacterial cell wall. Pathogenic mycobacteria carry mycolic acid sub-types that contain cyclopropane rings. Double bonds at specific sites on mycolic acid precursors are modified by the action of cyclopropane mycolic acid synthases (CMASs). The latter belong to a family of S-adenosyl-methionine-dependent methyl transferases, of which several have been well studied in Mycobacterium tuberculosis, namely, MmaA1 through A4, PcaA and CmaA2. Cyclopropanated mycolic acids are key factors participating in cell envelope permeability, host immunomodulation and persistence of M. tuberculosis. While several antitubercular agents inhibit mycolic acid synthesis, to date, the CMASs have not been shown to be drug targets. Methodology/Principle Findings. We have employed various complementary approaches to show that the antitubercular drug, thiacetazone (TAC), and its chemical analogues, inhibit mycolic acid cyclopropanation. Dramatic changes in the content and ratio of mycolic acids in the vaccine strainMycobacterium bovis BCG, as well as in the related pathogenic speciesMycobacterium marinum were observed after treatment with the drugs. Combination of thin layer chromatography, mass spectrometry and Nuclear Magnetic Resonance (NMR) analyses of mycolic acids purified fromdrug-treated mycobacteria showed a significant loss of cyclopropanation in both the a- and oxygenated mycolate sub-types. Additionally, High-Resolution Magic Angle Spinning (HR-MAS) NMR analyses on whole cells was used to detect cell wall-associated mycolates and to quantify the cyclopropanation status of the cell envelope. Further, overexpression of cmaA2, mmaA2 or pcaA in mycobacteria partially reversed the effects of TAC and its analogue on mycolic acid cyclopropanation, suggesting that the drugs act directly on CMASs. Conclusions/Significance. This is a first report on them echanism of action of TAC, demonstrating the CMASs as its cellular targets in mycobacteria. The implications of this study may be important for the design of alternative strategies for tuberculosis treatment

Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article