Toulouse – 16-18 rue des Pénitents Blancs

La fouille archéologique préventive de la rue des Pénitents Blancs a été conduite en 2010, préalablement à la construction de logements avec parc de stationnement en sous-sol. Elle a porté sur une parcelle d’un peu plus de 1 700 m2 située en partie orientale de la ville de Toulouse, à une trentaine de mètres de l’enceinte du Haut-Empire (intra muros). L’examen en CIRA du rapport final d’opération, remis en 2012, a souligné l’intérêt des découvertes effectuées à cette occasion, d’autant qu’ell..

Facile: a command-line network compiler for systems biology

<p>Abstract</p> <p>Background</p> <p>A goal of systems biology is the quantitative modelling of biochemical networks. Yet for many biochemical systems, parameter values and even the existence of interactions between some chemical species are unknown. It is therefore important to be able to easily investigate the effects of adding or removing reactions and to easily perform a bifurcation analysis, which shows the qualitative dynamics of a model for a range of parameter values.</p> <p>Results</p> <p>We present Facile, a Perl command-line tool for analysing the dynamics of a systems biology model. Facile implements the law of mass action to automatically compile a biochemical network (written as, for example, <monospace>E + S <-> C</monospace>) into scripts for analytical analysis (Mathematica and Maple), for simulation (XPP and Matlab), and for bifurcation analysis (AUTO). Facile automatically identifies mass conservations and generates the reduced form of a model with the minimum number of independent variables. This form is essential for bifurcation analysis, and Facile produces a C version of the reduced model for AUTO.</p> <p>Conclusion</p> <p>Facile is a simple, yet powerful, tool that greatly accelerates analysis of the dynamics of a biochemical network. By acting at the command-line and because of its intuitive, text-based input, Facile is quick to learn and can be incorporated into larger programs or into automated tasks.</p

BioJazz : In silico evolution of cellular networks with unbounded complexity using rule-based modeling

Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx

Antiferro-quadrupolar correlations in the quantum spin ice candidate Pr2Zr2O7

We present an experimental study of the quantum spin ice candidate pyrochlore coumpound \przr\ by means of magnetization measurements, specific heat and neutron scattering up to 12 T and down to 60 mK. When the field is applied along the $[111]$ and $[1\bar{1}0]$ directions, ${\bf k}=0$ field induced structures settle in. We find that the ordered moment rises slowly, even at very low temperature, in agreement with macroscopic magnetization. Interestingly, for $H \parallel [1\bar{1}0]$, the ordered moment appears on the so called $\alpha$ chains only. The spin excitation spectrum is essentially {\it inelastic} and consists in a broad flat mode centered at about 0.4 meV with a magnetic structure factor which resembles the spin ice pattern. For $H \parallel [1\bar{1}0]$ (at least up to 2.5 T), we find that a well defined mode forms from this broad response, whose energy increases with $H$, in the same way as the temperature of the specific heat anomaly. We finally discuss these results in the light of mean field calculations and propose a new interpretation where quadrupolar interactions play a major role, overcoming the magnetic exchange. In this picture, the spin ice pattern appears shifted up to finite energy because of those new interactions. We then propose a range of acceptable parameters for \przr\, that allow to reproduce several experimental features observed under field. With these parameters, the actual ground state of this material would be an antiferroquadrupolar liquid with spin-ice like excitations

Colored extrinsic fluctuations and stochastic gene expression

Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or ‘noise', is predominantly generated by interactions of the system of interest with other stochastic systems in the cell or its environment. Such extrinsic fluctuations are nonspecific, affecting many system components, and have a substantial lifetime, comparable to the cell cycle (they are ‘colored'). Here, we extend the standard stochastic simulation algorithm to include extrinsic fluctuations. We show that these fluctuations affect mean protein numbers and intrinsic noise, can speed up typical network response times, and can explain trends in high-throughput measurements of variation. If extrinsic fluctuations in two components of the network are correlated, they may combine constructively (amplifying each other) or destructively (attenuating each other). Consequently, we predict that incoherent feedforward loops attenuate stochasticity, while coherent feedforwards amplify it. Our results demonstrate that both the timescales of extrinsic fluctuations and their nonspecificity substantially affect the function and performance of biochemical networks

Les maisons du Haut-Empire de la rue de l’Oratoire à Augustonemetum / Clermont-Ferrand (Puy-de-Dôme)

Une fouille archéologique préventive a permis de reconnaître en 2010 plusieurs états d’une portion d’îlot résidentiel localisé à proximité du centre monumental d’Augustonemetum/Clermont-Ferrand. Son évolution a pu être suivie, tout comme celle de la rue qui le borde au nord. Le decumanus paraît mis en place au tout début du ier s. et les plus anciennes domus, dont une présente un riche décor (mosaïques, peintures murales), sont édifiées durant la première moitié du ier s. Elles sont détruites à la charnière des ier et iie s. et remplacées par de nouvelles demeures, après une redéfinition des propriétés à l’intérieur de l’insula, laquelle semble abandonnée dans le courant du iiie s. Le site n’est réinvesti que durant le second Moyen Âge, au cours duquel les constructions antiques sont presque systématiquement épierrées.An archaeological excavation allowed to recognize in 2010 several states of a residential tenement portion near the monumental center of Augustonemetum/Clermont-Ferrand. Its evolution has been followed, as well as the street’s one which lines it in the North. The decumanus seems to be set up at the very beginning of the 1st century and the oldest domus, which present a rich decoration (mosaics, mural paintings), are built during the first half of the 1st century. They are destroyed in the hinge of 1st and 2nd centuries and replaced by new houses, after a redefining of the properties inside the insula, which seems abandoned in the course of the 3rd century. The site is reinvested only during the Late Middle Ages. In this time, antique constructions are systematically destroyed

Les maisons du Haut-Empire de la rue de l’Oratoire à Augustonemetum / Clermont-Ferrand (Puy-de-Dôme)

Une fouille archéologique préventive a permis de reconnaître en 2010 plusieurs états d’une portion d’îlot résidentiel localisé à proximité du centre monumental d’Augustonemetum/Clermont-Ferrand. Son évolution a pu être suivie, tout comme celle de la rue qui le borde au nord. Le decumanus paraît mis en place au tout début du ier s. et les plus anciennes domus, dont une présente un riche décor (mosaïques, peintures murales), sont édifiées durant la première moitié du ier s. Elles sont détruites à la charnière des ier et iie s. et remplacées par de nouvelles demeures, après une redéfinition des propriétés à l’intérieur de l’insula, laquelle semble abandonnée dans le courant du iiie s. Le site n’est réinvesti que durant le second Moyen Âge, au cours duquel les constructions antiques sont presque systématiquement épierrées.An archaeological excavation allowed to recognize in 2010 several states of a residential tenement portion near the monumental center of Augustonemetum/Clermont-Ferrand. Its evolution has been followed, as well as the street’s one which lines it in the North. The decumanus seems to be set up at the very beginning of the 1st century and the oldest domus, which present a rich decoration (mosaics, mural paintings), are built during the first half of the 1st century. They are destroyed in the hinge of 1st and 2nd centuries and replaced by new houses, after a redefining of the properties inside the insula, which seems abandoned in the course of the 3rd century. The site is reinvested only during the Late Middle Ages. In this time, antique constructions are systematically destroyed

Current results of the PERSEE testbench: the cophasing control and the polychromatic null rate

Stabilizing a nulling interferometer at a nanometric level is the key issue to obtain deep null depths. The PERSEE breadboard has been designed to study and optimize the operation of a cophased nulling bench in the most realistic disturbing environment of a space mission. This presentation focuses on the current results of the PERSEE bench. In terms of metrology, we cophased at 0.33 nm rms for the piston and 80 mas rms for the tip/tilt (0.14% of the Airy disk). A Linear Quadratic Gaussian (LQG) control coupled with an unsupervised vibration identification allows us to maintain that level of correction, even with characteristic vibrations of nulling interferometry space missions. These performances, with an accurate design and alignment of the bench, currently lead to a polychromatic unpolarised null depth of 8.9E-6 stabilized at 3E-7 on the [1.65-2.45] \mum spectral band (37% bandwidth).Comment: 17 pages, 10 figures, proceedings of the Optics+Photonics SPIE conference, San Diego, 201

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio