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Stochatic interacting systems in biophysics : immunology and development

Abstract : This work presents two problems of biology requiring data analysis and models from statistical mechanics: population dynamics in immunology and gene regulation in embryo development. In immunology I study the problem of somatic evolution in the adaptive immune system: selection of and competition among cells that form a close-to-Darwinian system within one individual. First, I consider different potential hypotheses for selective dynamics: division and death signals through antigen binding or cytokines, dynamical parameters for division, death and fluctuations of the environment. I explore their impact on clone sizes. Experimentally, these clone sizes show heavy tail distributions for different species and differentpools of cells. Two families of models emerge: models where noise is consistent at the level of the clone and models where it varies from cell to cell. I show how clone size distributions help discriminate between these models and relate the shape of the distribution and the exponent of the power law to biological parameters. Second, I explore the specifics of the complex stochastic network of clones and antigens: its dimensionality, connectivity and dynamics. I study the effect of selection at different time scales and the speed of evolution of the clones. The second part of this dissertation concerns embryo development. In the fly embryo, it is crucial that nuclei can evaluate their position within the organism accurately to determine cell fate and build a healthy organism. This positional information is obtained, transferred, and maintained through diffusion of proteins and activation of genetic networks. More specifically, the patterning of the antero-posterior axis in drosophila requires the hunchback gene, activated by the Bicoid protein. I analyze data from fluorescent live imaging in the early cell cycles of the embryo. I build a tailor-made model to analyze autocorrelation functions of fluorescence time traces overcoming all biological and experimental challenges (noise, calibration, short traces, transgene construct) to extract the parameters of hunchback activation. I examine several potential types of dynamics for gene switiching (Poisson, Markovian or non-Markovian) and predict their impact on positional information and the accuracy of bicoid gradient readout.
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Submitted on : Tuesday, March 20, 2018 - 5:14:08 PM
Last modification on : Wednesday, October 14, 2020 - 4:04:29 AM
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  • HAL Id : tel-01738726, version 1


Jonathan Desponds. Stochatic interacting systems in biophysics : immunology and development. Physics [physics]. Université Paris sciences et lettres, 2016. English. ⟨NNT : 2016PSLEE037⟩. ⟨tel-01738726⟩



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