1,042 research outputs found
Artificial Gene Regulatory Networks and Spatial Computation: A Case Study
International audienceThis paper explores temporal and spatial dynamics of a population of Genetic Regulatory Networks (GRN). In order to so, a GRN model is spatially distributed to solve a multi-cellular Artificial Embryogeny problem, and Evolutionary Computation is used to optimize the developmental sequences. An in-depth analysis is provided and show that such a population of GRN display strong spatial synchronization as well as various kind of behavioral patterns, ranging from smooth diffusion to abrupt transition patterns
Chromatin dynamics in Arbidopsis development: a live cell imaging approach
Dissertation presented to obtain the Ph.D degree in BiologyThe proper development of multicellular organisms demands the distinct specification
of a variety of specialized cell types. While this is one of the oldest statements of
developmental genetics, how different patterns of gene expression are established in
genetically identical cells and maintained during somatic cell divisions is still an active topic
of research.
Chromatin structure is now recognized to regulate gene activity playing a crucial role
in cell differentiation and development. Chromatin is not simply a packaging tool but a
dynamic entity that reflects the regulatory cues necessary to program appropriate cellular
pathways. There are several ways by which chromatin structure can be remodelled. These
mechanisms include DNA-methylation, post-translational modifications of histone proteins,
histone variants and, nuclear localization. While the dynamic nature of chromatin structure
has been previously described its biological function and repercussions on development are
only now beginning to be revealed. In this work we used in vivo microscopy techniques to
assess how different aspects of chromatin organization play a role on various aspects of development.(...)A bolsa de doutoramento com a referĂȘncia SFRH/BD/23202/2005 foi atribuĂda pela
Fundação para a CiĂȘncia e Tecnologia (FCT), no Ăąmbito do Quadro ComunitĂĄrio de Apoio,
comparticipado pelo Fundo Social Europeu (FSE)
Artificial Gene Regulatory Network and Spatial Computation: A Case Study
International audienceThis paper explores temporal and spatial dynamics of a population of Genetic Regulatory Networks (GRN). In order to so, a GRN model is spatially distributed to solve a multi-cellular ArtiïŹcial Embryogeny problem, and Evolutionary Computation is used to optimize the developmental sequences. An in-depth analysis is provided and show that such a population of GRN display strong spatial synchronization as well as various kind of behavioral patterns, ranging from smooth diffusion to abrupt transition patterns
Morphogenesis by coupled regulatory networks: Reliable control of positional information and proportion regulation
Based on a non-equilibrium mechanism for spatial pattern formation we study
how position information can be controlled by locally coupled discrete
dynamical networks, similar to gene regulation networks of cells in a
developing multicellular organism. As an example we study the developmental
problems of domain formation and proportion regulation in the presence of
noise, as well as in the presence of cell flow. We find that networks that
solve this task exhibit a hierarchical structure of information processing and
are of similar complexity as developmental circuits of living cells. Proportion
regulation is scalable with system size and leads to sharp, precisely localized
boundaries of gene expression domains, even for large numbers of cells. A
detailed analysis of noise-induced dynamics, using a mean-field approximation,
shows that noise in gene expression states stabilizes (rather than disrupts)
the spatial pattern in the presence of cell movements, both for stationary as
well as growing systems. Finally, we discuss how this mechanism could be
realized in the highly dynamic environment of growing tissues in multi-cellular
organisms.Comment: Journal of Theoretical Biology, in pres
An artificial development model for cell pattern generation
La formation de structures cellulaires a un rĂŽle crucial dans le dĂ©veloppement tant artificiel que naturel. Cette thĂšse prĂ©sente un modĂšle de dĂ©veloppement artificiel pour la gĂ©nĂ©ration de structures cellulaires basĂ© sur le paradigme des automates cellulaires (AC). La croissance cellulaire est contrĂŽlĂ©e par un gĂ©nome comportant un rĂ©seau de rĂ©gulation artificiel (RRA) et une sĂ©rie de gĂšnes structurels. Ce gĂ©nome a subi une Ă©volution par algorithme gĂ©nĂ©tique (AG) afin de produire des structures cellulaires en 2D grĂące Ă l'activation et inhibition sĂ©lective des gĂšnes. De plus des gradients morphogĂ©nĂ©tiques ont Ă©tĂ© utilisĂ©s pour fournir aux cellules une information de position permettant de contraindre leur reproduction. AprĂšs Ă©volution d'un gĂ©nome par algorithme gĂ©nĂ©tique, une cellule unique est placĂ©e au milieu de la grille de lâAC oĂč sa reproduction, contrĂŽlĂ©e par le RRA, produit une structure cellulaire cible. Le modĂšle a Ă©tĂ© appliquĂ© avec succĂšs au problĂšme classique de gĂ©nĂ©ration de la structure dâun drapeau français (French flag problem).Cell pattern formation has a crucial role in both artificial and natural development. This thesis presents an artificial development model for cell pattern generation based on the cellular automata (CA) paradigm. Cellular growth is controlled by a genome consisting of an artificial regulatory network (ARN) and a series of structural genes. The genome was evolved by a genetic algorithm (GA) in order to produce 2D cell patterns through the selective activation and inhibition of genes. Morphogenetic gradients were used to provide cells with positional information that constrained cellular replication. After a genome was evolved, a single cell in the middle of the CA lattice was allowed to reproduce controlled by the ARN until a cell pattern was formed. The model was applied to the canonical problem of growing a French flag pattern.
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