Neural TTS in French: Comparing Graphemic and Phonetic Inputs Using the SynPaFlex-Corpus and Tacotron2

The SynPaFlex-Corpus is a publicly available TTS-oriented dataset, which provides phonetic transcriptions automatically produced by the JTrans transcriber, with a Phoneme Error Rate (PER) of 6.1%. In this paper, we analyze two mono-speaker Tacotron2 models trained on graphemic and phonetic inputs, provided by the SynPaFlex-Corpus. Through three subjective listening tests, we compare their pronunciation accuracy, sound quality and naturalness. Our results show significantly better pronunciation accuracy and prosody naturalness for the phoneme-based model, but no significant difference in terms of perceived sound quality. They demonstrate that a PER of 6.1% is sufficient to enhance pronunciation control by using phonetic transcripts instead of graphemes with 83 hours of recorded French read speech. They suggest that the SynPaFlex-Corpus is suitable for pre-training a model in mono-speaker fine-tuning approaches.Comment: 6 pages, 3 figure

Cyclic Di-GMP-Mediated Repression of Swarming Motility by Pseudomonas aeruginosa PA14 Requires the MotAB Stator

The second messenger cyclic diguanylate (c-di-GMP) plays a critical role in the regulation of motility. In Pseudomonas aeruginosa PA14, c-di-GMP inversely controls biofilm formation and surface swarming motility, with high levels of this dinucleotide signal stimulating biofilm formation and repressing swarming. P. aeruginosa encodes two stator complexes, MotAB and MotCD, that participate in the function of its single polar flagellum. Here we show that the repression of swarming motility requires a functional MotAB stator complex. Mutating the motAB genes restores swarming motility to a strain with artificially elevated levels of c-di-GMP as well as stimulates swarming in the wild-type strain, while overexpression of MotA from a plasmid represses swarming motility. Using point mutations in MotA and the FliG rotor protein of the motor supports the conclusion that MotA-FliG interactions are critical for c-di-GMP-mediated swarming inhibition. Finally, we show that high c-di-GMP levels affect the localization of a green fluorescent protein (GFP)-MotD fusion, indicating a mechanism whereby this second messenger has an impact on MotCD function. We propose that when c-di-GMP level is high, the MotAB stator can displace MotCD from the motor, thereby affecting motor function. Our data suggest a newly identified means of c-di-GMP-mediated control of surface motility, perhaps conserved among Pseudomonas, Xanthomonas, and other organisms that encode two stator systems

Les instruments chanteurs

Résumé Les instruments chanteurs sont nés de la rencontre entre synthèse vocale et nouvelles interfaces pour l'interaction humain-machine. La voix n'est pas un instrument de musique, car il n'y a pas d'objet externe mis en jeu par les membres ou par le souffle. La synthèse numérique permet pour la première fois une coupure entre le sujet et sa voix, en construisant des instruments chanteurs manipulés par les mains, les pieds, ou par toutes sortes d'interfaces humain-machine. Cependant, les possibilités de contrôle des instruments chanteurs sont encore limitées à certains aspects, car une transposition des gestes internes du chant effectués par l'appareil vocal en gestes externes des membres ne va pas de soi. Certains gestes sont analogues, d'autres sont médiatisés par un espace perceptif. Les travaux menés sur trois instruments chanteurs sont présentés : le contrôle de l'intonation par un stylet sur une tablette graphique et des gestes d'écriture ; le contrôle des voyelles et de la qualité vocale sur une surface ; le contrôle bimanuel de l'articulation consonantique ; le contrôle syllabique du rythme. Les modèles de synthèse sous-jacents utilisent soit la simulation du modèle source-filtre, soit la modification d'échantillons préenregistrés et étiquetés. Le contrôle des instruments chanteurs est multimodal, impliquant l'ou\"\ie ainsi que la vue, le toucher, et la kinesthésie. Cette combinaison sensorielle et motrice permet dans certains cas de rendre les instruments chanteurs plus justes et précis que la voix, la vue privilégiant les aspects mélodiques et l'audition les aspects rythmiques. Miroir de la voix, l'instrument chanteur autorise toutes sortes de spéculations : musicales bien sûr, avec le Chorus Digitalis, chœur de voix de synthèse, mais aussi pour l'analyse des pratiques vocales, pour l'éducation ou la rééducation, en renforçant l'apprentissage de gestes vocaux par des traces visuelles, des gestes manuels ou corporels. Le statut symbolique de la voix est également affecté par la possibilité de contrôler et de produire le son vocal en dehors du corps : corps augmenté, mise en scène de l'expression vocale, double de la voix, jeu de la voix d'un ou d'une autre. Abstract Singing instruments are the result of the encounter between voice synthesis and new interfaces for human-computer interaction. Voice is not a musical instrument, since it does not involve an external object stimulated by limbs or breathe. In contrast, digital synthesis allows for the first time to separate the subject from its voice, by building singing instruments manipulated by hands, feet, or any human-computer interface. However, possibilities for singing instruments control are still limited to some aspects, as the transposition from internal singing gestures realised by the vocal apparatus to external gestures is not trivial. Some gestures are analogous, while others are transposed in perceptive spaces. Related work realised on three singing instruments is introduced: the intonation control by a stylus on a graphic tablet and writing gestures; the vocalic and voice quality controls on a surface; the bi-manual control of onsonantal articulation; the rhythmic control of syllables. The underlying voice production models use either the simulation of a source-filter model, or the modification of pre-recorded and labelled samples. The control of singing instruments is multi-modal, involving hearing, sight, touch, and kinaesthesia. In some extent, this sensorimotor combination allows the singing instrument to be more accurate and precise than natural voice: the sight favouring melodic aspects while hearing being more related to rhythmic aspects. Mirror of voice, the singing instrument allows any kind of speculation: indubitably musical with Chorus Digitalis, a choir of synthesised voices, but also for the analysis of vocal practices, for education or re-education by strengthening the learning of vocal gestures through uses of visual traces, and manual and corporal gestures. Finally, the symbolic status of voice is also affected by the possibility to produce a vocal sound from outside the body: augmented body, staging of vocal expression, voice double, play of someone else's voice

Socializing, networking and development: a report from the second ‘Young Microbiologists Symposium on Microbe Signalling, Organization and Pathogenesis’

In mid-June, the second Young Microbiologists Symposium took place under the broad title of ‘Microbe signalling, organization and pathogenesis’ on the picturesque campus of University College Cork, Ireland. The symposium attracted 150 microbiologists from 15 different countries. The key feature of this meeting was that it was specifically aimed at providing a platform for junior scientists to present their work to a broad audience. The meeting was principally supported by Science Foundation Ireland with further backing from the Society for General Microbiology, the American Society for Microbiology and the European Molecular Biology Organization. Sessions focused on microbial gene expression, biogenesis, pathogenicity and host interaction. In this MicroMeeting report, we highlight some of the most significant advances and exciting developments reported during various talks and poster presentations given by the young and talented microbiologists

Coevolved mutations reveal distinct architectures for two core proteins in the bacterial flagellar motor

Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) "torque" helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity.JK was supported by Medical Research Council grant U117581331. SK was supported by seed funds from Lahore University of Managment Sciences (LUMS) and the Molecular Biology Consortium

Functioning Nanomachines Seen in Real-Time in Living Bacteria Using Single-Molecule and Super-Resolution Fluorescence Imaging

Molecular machines are examples of “pre-established” nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the genetic code, amongst many others. Much of our understanding of such nanometer length scale machines has come from in vitro studies performed in isolated, artificial conditions. Researchers are now tackling the challenges of studying nanomachines in their native environments. In this review, we outline recent in vivo investigations on nanomachines in model bacterial systems using state-of-the-art genetics technology combined with cutting-edge single-molecule and super-resolution fluorescence microscopy. We conclude that single-molecule and super-resolution fluorescence imaging provide powerful tools for the biochemical, structural and functional characterization of biological nanomachines. The integrative spatial, temporal, and single-molecule data obtained simultaneously from fluorescence imaging open an avenue for systems-level single-molecule cellular biophysics and in vivo biochemistry

Structural Insight into the Rotational Switching Mechanism of the Bacterial Flagellar Motor

Structural analysis of a clockwise-biased rotation mutant of the bacterial flagellar rotor protein FliG provides a new model for the arrangement of FliG subunits in the motor, and novel insights into rotation switching

Superresolution imaging of single DNA molecules using stochastic photoblinking of minor groove and intercalating dyes

As proof-of-principle for generating superresolution structural information from DNA we applied a method of localization microscopy utilizing photoblinking comparing intercalating dye YOYO-1 against minor groove binding dye SYTO-13, using a bespoke multicolor single-molecule fluorescence microscope. We used a full-length ∼49kbp λ DNA construct possessing oligo inserts at either terminus allowing conjugation of digoxigenin and biotin at opposite ends for tethering to a glass coverslip surface and paramagnetic microsphere respectively. We observed stochastic DNA-bound dye photoactivity consistent with dye photoblinking as opposed to binding/unbinding events, evidenced through both discrete simulations and continuum kinetics analysis. We analyzed dye photoblinking images of immobilized DNA molecules using superresolution reconstruction software from two existing packages, rainSTORM and QuickPALM, and compared the results against our own novel home-written software called ADEMS code. ADEMS code generated lateral localization precision values of 30-40nm and 60-70nm for YOYO-1 and SYTO-13 respectively at video-rate sampling, similar to rainSTORM, running more slowly than rainSTORM and QuickPALM algorithms but having a complementary capability over both in generating automated centroid distribution and cluster analyses. Our imaging system allows us to observe dynamic topological changes to single molecules of DNA in real-time, such as rapid molecular snapping events. This will facilitate visualization of fluorescently-labeled DNA molecules conjugated to a magnetic bead in future experiments involving newly developed magneto-optical tweezers combined with superresolution microscopy

Single-molecule studies of the dynamics and interactions of bacterial OXPHOS complexes

Although significant insight has been gained into biochemical, genetic and structural features of oxidative phosphorylation (OXPHOS) at the single-enzyme level, relatively little was known of how the component complexes function together in time and space until recently. Several pioneering single-molecule studies have emerged over the last decade in particular, which have illuminated our knowledge of OXPHOS, most especially on model bacterial systems. Here, we discuss these recent findings of bacterial OXPHOS, many of which generate time-resolved information of the OXPHOS machinery with the native physiological context intact. These new investigations are transforming our knowledge of not only the molecular arrangement of OXPHOS components in live bacteria, but also of the way components dynamically interact with each other in a functional state. These new discoveries have important implications towards putative supercomplex formation in bacterial OXPHOS in particular

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data