Reliable flow cytometric estimation of nuclear DNA content in coffee trees

La cytométrie en flux a permis d'obtenir des mesures précises de la taille des génomes de deux taxons (#C. liberica dewevrei et #C. pseudozanguebariae). L'iodure de propidium (IP) et le #Petunia hybrida ont été utilisés, respectivement, comme fluorochrome et standard interne. La linéarité de la relation entre la quantité d'ADN et le signal fluorescent digitalisé a été vérifiée. Cinq résultats majeurs ressortent : des conditions expérimentales optimales ont été définies pour l'estimation de la position des pics (moyenne et mode), le temps de coloration (au moins deux minutes), le voltage du photomultiplicateur (557 V) et de la concentration en IP (330 microg/ml) ; les effets du voltage et de la concentration en IP ont été paramétrés ; deux biais dus aux variations de voltage et de concentration en IP ont été décelés dans l'estimation de la quantité d'ADN par noyau. Ces biais ont été minimisés ; les tailles de génome de #C. liberica dewevrei et de #C. pseudozanguebariae$ ont été estimées avec précision (respectivement 2C = 1,421 plus ou moins 0,005 pg et 2C = 1,129 plus ou moins 0,005 pg) ; des variations entre génotypes ont été mises en évidence dans chaque taxon. (Résumé d'auteur

Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis

International audienceBACKGROUND: Few genome-scale models of organisms focus on the regulatory networks and none of them integrates all known levels of regulation. In particular, the regulations involving metabolite pools are often neglected. However, metabolite pools link the metabolic to the genetic network through genetic regulations, including those involving effectors of transcription factors or riboswitches. Consequently, they play pivotal roles in the global organization of the genetic and metabolic regulatory networks. RESULTS: We report the manually curated reconstruction of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis (transcriptional, translational and post-translational regulations and modulation of enzymatic activities). We provide a systematic graphic representation of regulations of each metabolic pathway based on the central role of metabolites in regulation. We show that the complex regulatory network of B. subtilis can be decomposed as sets of locally regulated modules, which are coordinated by global regulators. CONCLUSION: This work reveals the strong involvement of metabolite pools in the general regulation of the metabolic network. Breaking the metabolic network down into modules based on the control of metabolite pools reveals the functional organization of the genetic and metabolic regulatory networks of B. subtilis

An assessment of genetic diversity within a collection of cassava (Manihot esculenta Crantz) germplasm using molecular markers

Des clones cDNA de Manioc (#Manihot esculenta Crantz) ont été utilisés pour détecter le polymorphisme de longueur des fragments de resriction (RFLP) dans une collection de germplasm de manioc conservée en culture #in vitro au centre ORSTOM de Montpellier. La collection se compose principalement de cultivars africains de #M. esculenta, ainsi que de quelques #M.glaziovii Mueller Von Argau and #M. caerulescens Pohl, et de quelques hybrides interspécifiques de #M. esculenta x #M. glaziovii$. Les sondes cDNA mettent à jour des niveaux de polymorphisme significatifs à la fois à l'intérieur et entre les espèces ; ce qui est suffisant pour créer des dendogrammes indiquant la diversité génétique à l'intérieur de la collection. (Résumé d'auteur

<i>Staphylococcus aureus </i>Transcriptome Architecture:From Laboratory to Infection-Mimicking Conditions

Staphylococcus aureus is a major pathogen that colonizes about 20% of the human population. Intriguingly, this Gram-positive bacterium can survive and thrive under a wide range of different conditions, both inside and outside the human body. Here, we investigated the transcriptional adaptation of S. aureus HG001, a derivative of strain NCTC 8325, across experimental conditions ranging from optimal growth in vitro to intracellular growth in host cells. These data establish an extensive repertoire of transcription units and non-coding RNAs, a classification of 1412 promoters according to their dependence on the RNA polymerase sigma factors SigA or SigB, and allow identification of new potential targets for several known transcription factors. In particular, this study revealed a relatively low abundance of antisense RNAs in S. aureus, where they overlap only 6% of the coding genes, and only 19 antisense RNAs not co-transcribed with other genes were found. Promoter analysis and comparison with Bacillus subtilis links the small number of antisense RNAs to a less profound impact of alternative sigma factors in S. aureus. Furthermore, we revealed that Rho-dependent transcription termination suppresses pervasive antisense transcription, presumably originating from abundant spurious transcription initiation in this A+T-rich genome, which would otherwise affect expression of the overlapped genes. In summary, our study provides genome-wide information on transcriptional regulation and non-coding RNAs in S. aureus as well as new insights into the biological function of Rho and the implications of spurious transcription in bacteria

Determination of the pressure in micrometric bubbles in irradiated nuclear fuels

In oxide nuclear fuels, at high burn-up or during high temperature periods such as ramp tests, out-of- pile heating tests, or any irradiations at high linear heat rates, fission gases can form micrometric or quasi-micrometric bubbles. During nominal operations, these bubbles participate to the pellet swelling, to the decrease of the fuel thermal conductivity and are involved in the mechanisms leading to fission gas release. During events involving a temperature increase, the resulting increase in the internal pres- sure of the bubbles might play a role in fuel fragmentation and in the opening of grain boundaries. The gas densities inside these bubbles are therefore one of the useful experimental information for the un- derstanding of the fuel behaviour, and for the fuel behaviour code progress and validation. Two methods were developed to evaluate the gas density in the quasi-micrometric bubbles, using electron probe micro analyser, secondary ion mass spectrometry and focused ion beam scanning electron microscope together. The first method provides a mean gas density for all quasi-micrometric bubbles in a given area. The sec- ond method provides a gas density in a single selected bubble. In addition to the gas density, the 3D size and shape of the selected bubble is measured and can be related to the gas density result. In this work, these methods were applied to the bubbles formed in the centre of a PWR Cr doped UO 2 at 38.8 GWd/t U after a ramp test in the Osiris reactor, with a 12 h plateau at 470 W/cm, and to the bubbles formed in a PWR Cr doped UO 2 at 62.8 GWd/t U in the centre of the pellet and on the bubbles of the high burn-up structure on the rim. Both show the high pressures reached in these bubbles.CEA-DES, EDF and Framatom

BaSysBio: Towards an understanding of dynamic transcriptional regulation at global scale in bacteria: a systems biology approach

9th International Conference on Systems Biology, ICSB 2008, 22-28 August, Goteborg, SwedenBaSysBio adopts a systems biology approach in which quantitative experimental data will be generated for each step of the information flow and will fuel computational modelling. High throughput technologies (living cell arrays, tiling DNA microarrays, MDLC proteomics and quantitative metabolomics) will be developed in conjunction with new computational modelling concepts to facilitate the understanding of biological complexity. Models will simulate the cellular transcriptional responses to environmental changes and their impact on metabolism and proteome dynamics. The iterative process of simulations and model-driven targeted experiments will generate novel hypotheses about the mechanistic nature of dynamic cellular responses, unravel emerging systems properties and ultimately provide an efficient roadmap to tackle novel, pathogenic organismsN