Showing results 1281 to 1300 on 1324 in total
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Biological networks of large dimensions, with their diagram of interactions, are often well represented by a Boolean model with a family of logical rules. An advantage of Boolean and discrete modelling is the possibility of fully characterizing all qualitative dynamical trajectories of a particular network, based simply on the structure of links and interactions between nodes. A biological network may have different qualitative behaviours in response to different conditions. For instance, in response to different inputs, the system may have a single steady state, or multiple steady states, or exhibit oscillatory behaviour. In this context, using the asynchronous transition graph of the Boolean network, we have developed a method for identifying the groups of active or operational interactions that are responsible for a given dynamic behaviour.As an example, a model of an apoptosis network will be analysed. Two core groups of elements and interactions are identified: they correspond to two different mechanisms that may be used by the cell for the decision between apoptosis or cell survival.
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The turn from the 20th to the 21st Century was marked by a drastic change in the scale at which biologists study regulatory networks. In the 1990, a PhD student could spend years analysing the regulation of one particular gene by one or a few transcription factors. Microarray technologies enabled monitoring the expression of all the genes of an organism in a single experiment (transcriptome arrays), and to lead genome-wide location analysis to report supposedly exhaustive lists of transcription factor binding sites. Next Generation Sequencing amplified the movement, and many labs are now combining ChIP-seq and RNA-seq experiments to get a wide view on transcription factor binding locations, histone modifications, and transcriptional responses to a multitude of conditions, cell types, developmental stages, etc. In the first part of the talk, I will present some of the bioinformatics approaches and tools that we developed to analyse regulatory motifs from various types of high-throughput data (e.g. co-expression clusters, ChIP-seq peaks, replication origins).At the light of the evolution of the domain, I would also like to address a more general question about the insights gained from high-throughput approaches on fundamental mechanisms of regulation. Indeed, it implicitly became standard to consider that a typical high-throughput experiments should return thousands of significant features (differentially expressed genes, TF binding sites, active enhancers). This however does not fit with our classical models, were transcription factors would turn on or off specific sets of target genes ("regulatory switches"), thereby forming regulatory networks whose behaviour was understandably determined by feedback loops. How can we conciliate the undeniable robustness of regulatory networks with the apparent noisiness of binding and transcription profiles?
Thèse Cecilia Coimbra Klein - mardi 12 novembre 2013 à 14 h 30, amphithéâtre CNRS
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Queens strongly influence offspring social behaviors across the diverse eusocial taxa, suggesting that maternal influence might be involved in the origin of eusociality. Such ancestral maternal influence could have been manipulative or an honest signal, but a manipulative maternal influence could make eusociality unstable as offspring resistance evolves. Using an analytical model and individual based simulations, we show that an ancestral manipulative maternal influence becomes an honest signal under feasible conditions as maternal specialization into reproduction evolves. The reason is that specialization can move the population out of the zone of parent-offspring conflict over helping, a process that we term conflict dissolution. The key for this process is that helpers alleviate life-history trade-offs faced by mothers. Our results can simultaneously explain the origin of eusociality and its widespread association to a maternal influence via evolutionarily shifts of manipulation into honest signals.
Thèse de William Gaudry le vendredi 18 décembre 2015 à 14 h - amphithéâtre Déambulatoire 1 (Doua)
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Thèse de Julien Cattel le vendredi 16 décembre 2016 à 14 h - Amphithéâtre Dirac (Physique Nucléaire, La Doua)
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Thèse de Adrian ARELLANO DAVIN le mardi 5 décembre 2017 à 14 h, amphithéâtre CNRS (Villeurbanne)