Stochastic models and numerical algorithms for a class of regulatory gene networks

Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many regulatory gene networks, and study the steady state distributions of the associated Gillespie algorithm by providing efficient numerical algorithms. We also study a regulatory gene network of interest in synthetic biology and in gene therapy, using mean-field models with time delays. Convergence of the related time-nonhomogeneous Markov chain is established for a class of linear catalytic networks with feedback loop

Dynamics Of Internode And Stem Elongation In Three Cultivars Of Maize

The kinetics of elongation of individual internodes, the peduncle and panicle of maize were studied in field experiments in Gatton (Australia) using two tropical cultivars, and compared to similar data previously collected in Grignon (France) on a temperate cultivar. Data for phytomer initiation and organ extension and appearance were related to thermal time calculated from the temperature in the growing zone. Extension of internodes was analysed using a four stage framework:- an initial exponential stage, transition to rapid extension, rapid (linear) extension and transition to final length. The kinetics of internode extension were similar in Gatton and Grignon, though the rates of processes differed. Transition from stage 1 to stage 2 coincided with collar emergence. The commencement of rapid extension of the peduncle coincided with a transient reduction in the rates of extension of vegetative internodes. Further work is needed to assess whether they are effects of genotype only, or genotype and environment

Études de biomarqueurs chez la mye commune (Mya arenaria) du fjord du Saguenay : bilan de recherches (1997 à 2006)

Cet écrit se veut une synthèse des principales trouvailles afférentes aux études de terrain conduites annuellement de 1997 à 2006 en zones intertidales du fjord du Saguenay, et de celles situées autour de sa confluence avec l’estuaire du Saint-Laurent, dans le but de mieux comprendre les stress anthropiques auxquels est soumise la mye commune (Mya arenaria), bivalve ubiquiste de ces habitats sédimentaires. À l’aide d’une batterie variée de biomarqueurs, lesquels ont fait l’objet de mesures chez l’animal entier, certains de ses tissus ou cellules, nous avons pu mettre en évidence divers effets écotoxiques qui sont vraisemblablement imputables aux sources (urbaines, industrielles, portuaires, diffuses ou atmosphériques) de contamination chimique impactant le Saguenay. Dépendant du site et de ses caractéristiques pollutionnelles, nous avons noté des dérèglements de santé chez la mye qui incluent des effets sur son système reproducteur (divers types de perturbation endocrine associés aux substances estrogéniques, aux métaux ou aux TBT), sur son système immunitaire (stimulation ou dépression d’immunocompétence jaugée par la capacité de phagocytose d’hémocytes), ainsi que des effets cumulatifs de polluants qui se traduisent par des réponses, à la hausse ou à la baisse, de biomarqueurs de défenses (e.g., métallothionéines, CYP1A1, glutathione S-transférases), de dommages (e.g., augmentation de brins d’ADN, augmentation de l’activité de cyclo-oxygénase témoignant d’inflammation, peroxydation des lipides) et morphologiques (e.g., inhibition de croissance, baisse d’indice gonado-somatique). Nous démontrons aussi une plus grande dépense en énergie au niveau mitochondrial (transport d’électrons mitochondrial dans la gonade ou glande digestive) chez les myes de zones impactées, laquelle semble pouvoir être exacerbée en conditions de stress thermiques que laissent présager les changements climatiques à venir. Au final, ce bilan d’études de biomarqueurs confirme l’utilité du modèle bivalve Mya arenaria comme bio-indicateur de la qualité hydrique du Saguenay et il renseigne sur les divers affronts que subissent ces invertébrés dans ce milieu toujours aux prises avec des sources de contamination variées. D’autres études envisagées affineront nos connaissances au sujet des risques cumulatifs liés à la contamination chimique du fjord.This paper presents the major findings of annual field outings conducted from 1997 to 2006 in Saguenay Fjord intertidal areas as well as those located in proximity with the St. Lawrence River estuary. Study objectives sought to enhance our understanding of pollution pressures incurred on the soft shell clam, Mya arenaria, endemic to mud flats of these regions. By measuring the responses of a battery of biomarkers in whole animals, organs or cells, we demonstrated various adverse effects that are likely linked to chemical contamination sources (municipal, industrial, portuary, non point and atmospheric) intrinsic to the Saguenay area. Based on site and pollution features proper to each, health problems were observed in clams that included effects on their reproductive system (endocrine disruption events linked to estrogenic substances, metals or TBT), on their immune system (increase or decrease of immunocompetence assessed by phagocytic performance of hemocytes), as well as cumulative effects of pollutants, shown either by upward or downward responses of defense biomarkers ((e.g., metallothioneins, CYP1A1, glutathion S‑transferase), damage biomarkers (e.g., increase in DNA strand breaks, increase in inflammatory cyclo-oxygenase activity, lipid peroxidation) and metrics biomarkers (e.g., growth inhibition, lower gonado-somatic index). In pollution-impacted sites, clams further displayed a greater expenditure of mitochondrial energy (measured by mitochondrial electron transport in gonad or digestive gland), an energy loss that could possibly be augmented under thermic stress conditions linked to climate change. This long-term biomarker work establishes Mya arenaria as a useful bioindicator species to appraise Saguenay Fjord water quality as reflected by the diverse chemical insults to which these invertebrates are exposed in an ecosystem still struggling with multiple contamination inputs. Future studies should contribute to strengthen our knowledge related to cumulative risk issues linked to the fjord’s chemical pollution

Concepts of Static vs. Dynamic Current Transfer Length in 2G HTS coated conductors with a Current Flow Diverter Architecture

This paper uses both experimental and numerical approaches to revisit the concept of current transfer length (CTL) in second-generation high-temperature superconductor coated conductors with a current flow diverter (CFD) architecture. The CFD architecture has been implemented on eight commercial coated conductors samples from THEVA. In order to measure the 2-D current distribution in the silver stabilizer layer of the samples, we first used a custom-made array of 120 voltage taps to measure the surface potential distribution. Then, the so-called "static" CTL ($\lambda_s$) was extracted using a semi-analytical model that fitted well the experimental data. As defined in this paper, the static CTL on a 2-D domain is a generalization of the definition commonly used in literature. In addition, we used a 3-D finite element model to simulate the normal zone propagation in our CFD samples, in order to quantify their "dynamic" CTL ($\lambda_d$), a new concept introduced in this paper and defined as the CTL observed during the propagation of a quenched region. The results show that, for a CFD architecture, $\lambda_d$ is always larger than $\lambda_s$, whereas $\lambda_d = \lambda_s$ when the interfacial resistance between the stabilizer and the superconductor layers is the same everywhere. We proved that the cause of these different behaviors is related to the shape of the normal zone, which is curved for the CFD architecture, and rectangular otherwise. Finally, we showed that the NZPV is proportional to $\lambda_d$, not with $\lambda_s$, which suggests that the dynamic CTL $\lambda_d$ is the most general definition of the CTL and should always be used when current crowding and non-uniform heat generation occurs around a normal zone.Comment: 11 pages, 10 figure

OpenAlea: Scientific Workflows Combining Data Analysis and Simulation

International audienceAnalyzing biological data (e.g., annotating genomes, assembling NGS data...) may involve very complex and inter-linked steps where several tools are combined together. Scientific workflow systems have reached a level of maturity that makes them able to support the design and execution of such in-silico experiments, and thus making them increasingly popular in the bioinformatics community. However, in some emerging application domains such as system biology, developmental biology or ecology, the need for data analysis is combined with the need to model complex multi-scale biological systems, possibly involving multiple simulation steps. This requires the scientific work-flow to deal with retro-action to understand and predict the relationships between structure and function of these complex systems. OpenAlea (openalea.gforge.inria.fr) is the only scientific workflow system able to uniformly address the problem, which made it successful in the scientific community. One of its main originality is to introduce higher-order dataflows as a means to uniformly combine classical data analysis with modeling and simulation. In this demonstration paper, we provide for the first time the description of the OpenAlea system involving an original combination of features. We illustrate the demonstration on a high-throughput workflow in phenotyping, phenomics, and environmental control designed to study the interplay between plant architecture and climatic change

Quantitative and Qualitative Analysis of Dynamic Cavernosographies in Erectile Dysfunction due to Venous Leakage

Of 521 patients with erectile dysfunction in whom a multidisciplinary approach was used, 145 (27.8%) showed venous leakage as (concomitant) etiology of the impotence in dynamic cavernosography. The rate of the maintenance flow corresponded well with the response to a standardized intracavernosal injection of vasoactive drugs (p < 0.05) in patients with venous leakage. The maintenance flow increased with the age in secondary impotent men. It was not statistically different in patients with or without concomitant arterial insufficiency (p = 0.19). Fifty-one of 145 patients (32.2%) presented a pathologic cavernosal drainage via a single venous system; 94/145 (64.8%) showed a combined venous leakage. The type of leakage corresponded neither to the maintenance flow nor to the response to intracavernosal injections. Our findings show that standardized intracavernosal testing and Doppler have a high predictive value for the status of the venous occlusive system. Exact evaluation of the type of leakage can be made by bidimensional cavernosography only