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

Stoichiometry and turnover of the bacterial flagellar switch protein FliN.

Some proteins in biological complexes exchange with pools of free proteins while the complex is functioning. Evidence is emerging that protein exchange can be part of an adaptive mechanism. The bacterial flagellar motor is one of the most complex biological machines and is an ideal model system to study protein dynamics in large multimeric complexes. Recent studies showed that the copy number of FliM in the switch complex and the fraction of FliM that exchanges vary with the direction of flagellar rotation. Here, we investigated the stoichiometry and turnover of another switch complex component, FliN, labeled with the fluorescent protein CyPet, in Escherichia coli. Our results confirm that, in vivo, FliM and FliN form a complex with stoichiometry of 1:4 and function as a unit. We estimated that wild-type motors contained 120 ± 26 FliN molecules. Motors that rotated only clockwise (CW) or counterclockwise (CCW) contained 114 ± 17 and 144 ± 26 FliN molecules, respectively. The ratio of CCW-to-CW FliN copy numbers was 1.26, very close to that of 1.29 reported previously for FliM. We also measured the exchange of FliN molecules, which had a time scale and dependence upon rotation direction similar to those of FliM, consistent with an exchange of FliM-FliN as a unit. Our work confirms the highly dynamic nature of multimeric protein complexes and indicates that, under physiological conditions, these machines might not be the stable, complete structures suggested by averaged fixed methodologies but, rather, incomplete rings that can respond and adapt to changing environments. Importance: The flagellum is one of the most complex structures in a bacterial cell, with the core motor proteins conserved across species. Evidence is now emerging that turnover of some of these motor proteins depends on motor activity, suggesting that turnover is important for function. The switch complex transmits the chemosensory signal to the rotor, and we show, by using single-cell measurement, that both the copy number and the fraction of exchanging molecules vary with the rotational bias of the rotor. When the motor is locked in counterclockwise rotation, the copy number is similar to that determined by averaged, fixed methodologies, but when locked in a clockwise direction, the number is much lower, suggesting that that the switch complex ring is incomplete. Our results suggest that motor remodeling is an important component in tuning responses and adaptation at the motor

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

Improving orthogonality in two-component biological signalling systems using feedback control

In natural biological systems, cellular responses to changing growth and environmental conditions are governed by complex signalling and control networks. A common signalling motif is that of the two component signalling systems (TCSSs), dozens of which may operate simultaneously in a single cell. When synthetic biologists create new signalling networks in living cells, achieving orthogonality of signal transmission can be difficult. One challenge is overcoming the crosstalk between pathways that arises from off-target interactions between TCSS components. In this letter we analyze a simple signalling network consisting of two parallel TCSS, demonstrating that substantial crosstalk can occur depending on induction levels of each pathway. We then propose and analyse a feedback control architecture that reduces crosstalk by expressing additional substrates depending upon the state of each pathway. We analyse this control architecture’s stability, and demonstrate that it facilitates near-orthogonal transmission of signals through each pathway

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

Load-dependent assembly of the bacterial flagellar motor

It is becoming clear that the bacterial flagellar motor output is important not only for bacterial locomotion but also for mediating the transition from liquid to surface living. The output of the flagellar motor changes with the mechanical load placed on it by the external environment: at a higher load, the motor runs more slowly and produces higher torque. Here we show that the number of torque-generating units bound to the flagellar motor also depends on the external mechanical load, with fewer stators at lower loads. Stalled motors contained at least as many stators as rotating motors at high load, indicating that rotation is unnecessary for stator binding. Mutant stators incapable of generating torque could not be detected around the motor. We speculate that a component of the bacterial flagellar motor senses external load and mediates the strength of stator binding to the rest of the motor. IMPORTANCE: The transition between liquid living and surface living is important in the life cycles of many bacteria. In this paper, we describe how the flagellar motor, used by bacteria for locomotion through liquid media and across solid surfaces, is capable of adjusting the number of bound stator units to better suit the external load conditions. By stalling motors using external magnetic fields, we also show that rotation is not required for maintenance of stators around the motor; instead, torque production is the essential factor for motor stability. These new results, in addition to previous data, lead us to hypothesize that the motor stators function as mechanosensors as well as functioning as torque-generating units

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

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