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Denis Thieffry

Publications and source records attributed to Denis Thieffry.

12 recordsLinked to original sources

Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disc.

The larval development of the Drosophila melanogaster wings is organized by the protein Wingless, which is secreted by cells adjacent to the dorsal-ventral (DV) boundary. Two signaling processes acting between the second and early third instars and between the mid- and late third instar control the expression of Wingless in these boundary cells. Here, we integrate both signaling processes into a logical multivalued model encompassing four cells, i.e., a boundary and a flanking cell at each side of the boundary. Computer simulations of this model enable a qualitative reproduction of the main wild-type and mutant phenotypes described in the experimental literature. During the first signaling process, Notch becomes activated by the first signaling process in an Apterous-dependent manner. In silico perturbation experiments show that this early activation of Notch is unstable in the absence of Apterous. However, during the second signaling process, the Notch pattern becomes consolidated, and thus independent of Apterous, through activation of the paracrine positive feedback circuit of Wingless. Consequently, we propose that appropriate delays for Apterous inactivation and Wingless induction by Notch are crucial to maintain the wild-type expression at the dorsal-ventral boundary. Finally, another mutant simulation shows that cut expression might be shifted to late larval stages because of a potential interference with the early signaling process.

Animals↗

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.

MOTIVATION: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most available data on regulatory interactions are qualitative, logical modelling offers an interesting framework to delineate the main dynamical properties of the underlying networks. RESULTS: Transposing a generic model of the core network controlling the mammalian cell cycle into the logical framework, we compare different strategies to explore its dynamical properties. In particular, we assess the respective advantages and limits of synchronous versus asynchronous updating assumptions to delineate the asymptotical behaviour of regulatory networks. Furthermore, we propose several intermediate strategies to optimize the computation of asymptotical properties depending on available knowledge. AVAILABILITY: The mammalian cell cycle model is available in a dedicated XML format (GINML) on our website, along with our logical simulation software GINsim (http://gin.univ-mrs.fr/GINsim). Higher resolution state transitions graphs are also found on this web site (Model Repository page).

Animals↗

GOToolBox: functional analysis of gene datasets based on Gene Ontology.

We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license.

Animals↗

[Prediction of transcription and genomic sequences].

Technological developments have enhanced DNA sequencing at genomic scale. On the basis of the resulting sequences, computational biologists now attempt to localise the most important functional regions, starting with genes, but also importantly the regulatory motifs and conditions controlling their expression. In a recent paper published in Cell, M.A. Beer and S. Tavazoie report the results obtained by combining statistical classifications (clustering) of transcriptome data (DNA chips), software for the discovery of cis-regulatory patterns, together with a probabilistic learning method to infer regulatory rules tentatively accounting for the observed transcriptional profiles.

Forecasting↗

Introduction to 'picturing eggs, embryos and cells'.

Some twenty years ago, the historian of technology Henri Michel, who studied the history of instruments, wanted to draw our attention to the images des sciences (Michel 1977). Obviously, an instrument historian is well trained in dealing with pictorial matter, whether it may be blueprints of instruments, or detailed instructions about how to use and improve them. Further, instruments are extremely well suited media to demonstrate that theoretical knowledge has to be practically acquired, whether by making instruments, or by hand drawings. Also, historians of art have extensively worked, published and communicated on the issue of 'science and art' or 'science in art', and how their relationship shaped intellectual and technical history for several decades. As visualization denotes our ability to perceive, and to conceptualize, philosophy in general, and philosophy of science, in particular reflected about it and tried to grasp the scientists' epistemology. Over the last 25 years, an exceptional body of work was published on pictorial representation, either from a socio-cultural perspective, with an emphasis on the technology, or from the epistemic issue of how to conceptualize an eidon.

Anatomy, Comparative↗

From experimental imaging techniques to virtual embryology.

Modern embryology increasingly relies on descriptive and functional three dimensional (3D) and four dimensional (4D) analysis of physically, optically, or virtually sectioned specimens. To cope with the technical requirements, new methods for high detailed in vivo imaging, as well as the generation of high resolution digital volume data sets for the accurate visualisation of transgene activity and gene product presence, in the context of embryo morphology, were recently developed and are under construction. These methods profoundly change the scientific applicability, appearance and style of modern embryo representations. In this paper, we present an overview of the emerging techniques to create, visualise and administrate embryo representations (databases, digital data sets, 3-4D embryo reconstructions, models, etc.), and discuss the implications of these new methods on the work of modern embryologists, including, research, teaching, the selection of specific model organisms, and potential collaborators.

Computer Graphics↗

Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module.

This manuscript reports a dynamical analysis of the pair-rule cross-regulatory module controlling segmentation in Drosophila melanogaster. We propose a logical model accounting for the ability of the pair-rule module to determine the formation of alternate juxtaposed Engrailed- and Wingless-expressing cells that form the (para)segmental boundaries. This module has the intrinsic capacity to generate four distinct expression states, each characterized by the expression of a particular combination of pair-rule genes or expression mode. The selection of one of these expression modes depends on the maternal and gap inputs, but also crucially on cross-regulations among pair-rule genes. The latter are instrumental in the interpretation of the maternal-gap pre-pattern. Our logical model allows the qualitative reproduction of the patterns of pair-rule gene expressions corresponding to the wild type situation, to loss-of-function and cis-regulatory mutations, and to ectopic pair-rule expressions. Furthermore, this model provides a formal explanation for the morphogenetic role of the initial bell-shaped expression of the gene even-skipped, i.e. for the distinct effects of different levels of the Even-skipped protein on its target pair-rule genes. It also accounts for the requirement of Even-skipped for the formation of all Engrailed-stripes. Finally, it provides new insights into the roles and evolutionary origins of the apparent redundancies in the regulatory architecture of the pair-rule module.

Animals↗

Dynamical modelling of pattern formation during embryonic development.

The combination of genetic and molecular biology techniques has uncovered the intricacies of several gene networks controlling developmental processes. In the face of such complex regulatory networks, developmental geneticists cannot rely on reasoning alone; a thorough understanding of the spatio-temporal properties of these networks clearly requires the use of proper computational tools and methods.

Animals↗

Alternative epigenetic states understood in terms of specific regulatory structures.

Generally speaking, epigenetic states or epigenetic regulation refer to situations in which several states of gene expression may coexist in similar environmental conditions, despite the absence of significant changes in the genomic sequence. In one way or another, the mechanisms behind these phenomena involve vicious circles, so that each epigenetic state tends to sustain itself, even after the disappearance of the inductive signal involved in the selection of that particular state. These vicious circles constitute positive feedback circuits and are found at the core of many developmental regulatory systems. In this paper, we present a qualitative model for the regulatory network formed by maternal and gap gene cross-regulations. This network controls the initial anterior-posterior patterning during early Drosophila embryogenesis and encompasses several intertwined feedback circuits. On the basis of our model analysis, we derive interesting insights about how specific expression states of the gap genes are selected along the anterior-posterior axis, in particular in relation with the activity of one positive feedback circuit, namely that formed by giant and Krüppel cross-inhibitions. In addition, we are able to qualitatively simulate the patterns of gene expression in the wild-type, as well as to predict the phenotypes of various loss-of-function mutations at the maternal and gap genes, or cis-regulatory mutations at the gap genes, as well as the effects of ectopic expression of these genes.

Animals↗