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157 results on '"Audit B"'

1. FORK-seq: single molecule profiling of DNA replication

Author

Hennion, Magali, Theulot, Bertrand, Arbona, Jean-Michel, Audit, B., Hyrien, Olivier, Audit, Benjamin, APPEL À PROJETS GÉNÉRIQUE 2018 - Le sequençage nanopore pour une cartographie haute-performance de la réplication de l'ADN - - NanoPoRep2018 - ANR-18-CE45-0002 - AAPG2018 - VALID, Centre épigénétique et destin cellulaire (EDC (UMR_7216)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie et modélisation de la cellule (LBMC UMR 5239), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, ANR-18-CE45-0002,NanoPoRep,Le sequençage nanopore pour une cartographie haute-performance de la réplication de l'ADN(2018), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre épigénétique et destin cellulaire (EDC), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and École normale supérieure de Lyon (ENS de Lyon)-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2022

11. Deciphering DNA replication dynamics in eukaryotic cell populations in relation with their averaged chromatin conformations

Author

Goldar, A., Arneodo, A., Audit, B., Argoul, F., Rappailles, A., Guilbaud, Guillaume, Petryk, N., Kahli, M., Hyrien, O., Goldar, A., Arneodo, A., Audit, B., Argoul, F., Rappailles, A., Guilbaud, Guillaume, Petryk, N., Kahli, M., and Hyrien, O.

Abstract

We propose a non-local model of DNA replication that takes into account the observed uncertainty on the position and time of replication initiation in eukaryote cell populations. By picturing replication initiation as a two-state system and considering all possible transition configurations, and by taking into account the chromatin's fractal dimension, we derive an analytical expression for the rate of replication initiation. This model predicts with no free parameter the temporal profiles of initiation rate, replication fork density and fraction of replicated DNA, in quantitative agreement with corresponding experimental data from both S. cerevisiae and human cells and provides a quantitative estimate of initiation site redundancy. This study shows that, to a large extent, the program that regulates the dynamics of eukaryotic DNA replication is a collective phenomenon that emerges from the stochastic nature of replication origins initiation.

Published
2016

16. Mechanical Sensing of Living Systems — From Statics to Dynamics

Author

Argoul, F., Audit, B., Arneodo, A., Argoul, F., Audit, B., and Arneodo, A.

Abstract

Living systems are fascinating sensing machines that outmatch all artificial machines. Our aim is to put a focus on the dynamics of mechanosensing in cellular systems through concepts and experimental approaches that have been developed during the past decades. By recognizing that a cellular system is not simply the intricate assembly of active and passive macromolecular actors but that it can also manifest scale-invariant and/or highly nonlinear global dynamics, biophysicists have opened a new domain of investigation of living systems. In this chapter, we review methods and techniques that have been implemented to decipher the cascade of temporal events which enable a cell to sense a mechanical stimulus and to elaborate a response to adapt or to counteract this perturbation. We mainly describe intrusive (mechanical probes) and nonintrusive (optical devices) experimental methods that have proved to be efficient for real-time characterization of stationary and nonstationary cellular dynamics. Finally, we discuss whether thermal fluctuations, which are inherent to living systems, are a source of coordination (e.g., synchronization) or randomization of the global dynamics of a cell.

Published
2015
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17. Inferring Where and When Replication Initiates from Genome-Wide Replication Timing Data (vol 108, 268101, 2012)

Author

Baker, A., Audit, B., Yang, S. C. H., Bechhoefer, J., Arneodo, A., Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université de Lyon, École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon

Subjects
[PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph], ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2012

19. A novel strategy of transcription regulation by intra-genic nucleosome ordering

Author

Vaillant, C., Palmeira, L., Chevereau, G., Audit, B., D'Aubenton-Carafa, Y., Thermes, C., Arneodo, A., Baobab, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT]
Published
2010

20. Use of Titanium and Tungsten as an Alternative to Gold in Jewellery Manufacturing.

Author

Surnam, B. Y. R., Audit, B. S., and Soopee, A.

Subjects
TITANIUM, TUNGSTEN, GOLD, JEWELRY manufacturing, TEXTILES
Abstract

In this study the use titanium and tungsten as alternatives to the noble metals in the jewellery industry was investigated. The degradation of titanium and tungsten were compared to that of gold, used as reference. Alternate immersion tests were performed in 3.5% sodium chloride and artificial perspiration. The metals' abrasion resistance with respect to textile fabrics was determined. In general, there is around 30% difference in pit density for titanium and tungsten as compared to that of gold. Pit depth and pit diameter showed a similar trend. From the abrasive test performed, it was observed that titanium and tungsten had insignificant changes in the surface reflectivity with time. Hence, it was deduced that titanium and tungsten products would have longer maintenance intervals than that of gold. New tools and techniques, however, would be required by jewellers to work with titanium and tungsten. [ABSTRACT FROM AUTHOR]

Published
2017
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22. Extracting structural and dynamical informations from wavelet-based analysis of DNA sequences

Author

Alain Arneodo, Audit, B., Vaillant, C., D Aubenton-Carafa, Y., Thermes, C., Laboratoire Joliot Curie, École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS), and Michel, Murielle

Subjects
ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2003

25. Genome sequences and great expectations

Author

Iliopoulos, I., Sophia Tsoka, Andrade, M. A., Janssen, P., Audit, B., Tramontano, A., Valencia, A., Leroy, C., Sander, C., and Ouzounis, C. A.

Subjects
Genome, Proteome, Genome, Human, Cardiovascular and Metabolic Diseases, Animals, Humans, Open Letter, Genomics, Sequence Analysis, DNA
Abstract

To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that function can be predicted for almost two-thirds of the 73,500 genes that were analyzed. Despite progress in computational biology, there will always be a great need for large-scale experimental determination of protein function.

Published
2001

26. 3D chromatin conformation correlates with replication timing and is conserved in resting cells

Author

Moindrot, B., Audit, B., Klous, P., Baker, A., Thermes, C., de Laat, W., Bouvet, P., Mongelard, F., Arneodo, A., Moindrot, B., Audit, B., Klous, P., Baker, A., Thermes, C., de Laat, W., Bouvet, P., Mongelard, F., and Arneodo, A.

Abstract

Although chromatin folding is known to be of functional importance to control the gene expression program, less is known regarding its interplay with DNA replication. Here, using Circular Chromatin Conformation Capture combined with high-throughput sequencing, we identified megabase-sized self-interacting domains in the nucleus of a human lymphoblastoid cell line, as well as in cycling and resting peripheral blood mononuclear cells (PBMC). Strikingly, the boundaries of those domains coincide with early-initiation zones in every cell types. Preferential interactions have been observed between the consecutive early-initiation zones, but also between those separated by several tens of megabases. Thus, the 3D conformation of chromatin is strongly correlated with the replication timing along the whole chromosome. We furthermore provide direct clues that, in addition to the timing value per se, the shape of the timing profile at a given locus defines its set of genomic contacts. As this timing-related scheme of chromatin organization exists in lymphoblastoid cells, resting and cycling PBMC, this indicates that it is maintained several weeks or months after the previous S-phase. Lastly, our work highlights that the major chromatin changes accompanying PBMC entry into cell cycle occur while keeping largely unchanged the long-range chromatin contacts., Although chromatin folding is known to be of functional importance to control the gene expression program, less is known regarding its interplay with DNA replication. Here, using Circular Chromatin Conformation Capture combined with high-throughput sequencing, we identified megabase-sized self-interacting domains in the nucleus of a human lymphoblastoid cell line, as well as in cycling and resting peripheral blood mononuclear cells (PBMC). Strikingly, the boundaries of those domains coincide with early-initiation zones in every cell types. Preferential interactions have been observed between the consecutive early-initiation zones, but also between those separated by several tens of megabases. Thus, the 3D conformation of chromatin is strongly correlated with the replication timing along the whole chromosome. We furthermore provide direct clues that, in addition to the timing value per se, the shape of the timing profile at a given locus defines its set of genomic contacts. As this timing-related scheme of chromatin organization exists in lymphoblastoid cells, resting and cycling PBMC, this indicates that it is maintained several weeks or months after the previous S-phase. Lastly, our work highlights that the major chromatin changes accompanying PBMC entry into cell cycle occur while keeping largely unchanged the long-range chromatin contacts.

Published
2012

49. Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

Author

Zaghloul Lamia, Lemaitre Claire, Sagot Marie-France, Gautier Christian, Arneodo Alain, Tannier Eric, and Audit Benjamin

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The Intergenic Breakage Model, which is the current model of structural genome evolution, considers that evolutionary rearrangement breakages happen with a uniform propensity along the genome but are selected against in genes, their regulatory regions and in-between. However, a growing body of evidence shows that there exists regions along mammalian genomes that present a high susceptibility to breakage. We reconsidered this question taking advantage of a recently published methodology for the precise detection of rearrangement breakpoints based on pairwise genome comparisons. Results We applied this methodology between the genome of human and those of five sequenced eutherian mammals which allowed us to delineate evolutionary breakpoint regions along the human genome with a finer resolution (median size 26.6 kb) than obtained before. We investigated the distribution of these breakpoints with respect to genome organisation into domains of different activity. In agreement with the Intergenic Breakage Model, we observed that breakpoints are under-represented in genes. Surprisingly however, the density of breakpoints in small intergenes (1 per Mb) appears significantly higher than in gene deserts (0.1 per Mb). More generally, we found a heterogeneous distribution of breakpoints that follows the organisation of the genome into isochores (breakpoints are more frequent in GC-rich regions). We then discuss the hypothesis that regions with an enhanced susceptibility to breakage correspond to regions of high transcriptional activity and replication initiation. Conclusion We propose a model to describe the heterogeneous distribution of evolutionary breakpoints along human chromosomes that combines natural selection and a mutational bias linked to local open chromatin state.

Published
2009
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50. Probabilistic annotation of protein sequences based on functional classifications

Author

Gilks Walter R, Ouzounis Christos A, Levy Emmanuel D, and Audit Benjamin

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode of protein function assignment is mostly based on the detection of sequence similarity and the premise that functional properties are conserved during evolution. Most automatic approaches developed to date rely on the identification of clusters of homologous proteins and the mapping of new proteins onto these clusters, which are expected to share functional characteristics. Results Here, we inverse the logic of this process, by considering the mapping of sequences directly to a functional classification instead of mapping functions to a sequence clustering. In this mode, the starting point is a database of labelled proteins according to a functional classification scheme, and the subsequent use of sequence similarity allows defining the membership of new proteins to these functional classes. In this framework, we define the Correspondence Indicators as measures of relationship between sequence and function and further formulate two Bayesian approaches to estimate the probability for a sequence of unknown function to belong to a functional class. This approach allows the parametrisation of different sequence search strategies and provides a direct measure of annotation error rates. We validate this approach with a database of enzymes labelled by their corresponding four-digit EC numbers and analyse specific cases. Conclusion The performance of this method is significantly higher than the simple strategy consisting in transferring the annotation from the highest scoring BLAST match and is expected to find applications in automated functional annotation pipelines.

Published
2005
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