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Christophe Godin

Publications and source records attributed to Christophe Godin.

7 recordsLinked to original sources
PubMed2006

Similarities and gradients in growth unit branching patterns during ontogeny in "Fuji" apple trees: a stochastic approach.

This study aims to explore and model the changes in growth unit (GU) branching patterns during tree ontogeny. The question was addressed in apple trees cv. "Fuji", by analysing the relative impact of GU length and within-tree position. The development of two 6-year-old trees was recorded over 6 years. The fate of axillary buds along each GU was represented as a sequence of symbols corresponding to five types of lateral growth: latent buds, short, medium, long, and floral lateral GUs. Based on an exploratory analysis of data and a priori hypotheses, a hidden semi-Markov chain was estimated from all of these GU sequences. This model was composed of six transient states representing successive branching zones along the GUs. The accuracy of this global model was a posteriori assessed by fitting the characteristic distributions computed from model parameters to the corresponding empirical characteristic distributions extracted from the observed sequences. The observed sequences were then grouped hierarchically according to the GU length, year of growth, and branching order. Comparing model parameters between these sub-groups revealed similarities between GUs. These similarities were based on particular branching zones whose composition and relative position within the GUs remained invariant across the subgroups: the latent zones, floral zone, and short-lateral zone. The probability of occurrence of the floral zone varied with the year, showing the alternate fruiting of "Fuji". It is shown that, during tree ontogeny, as GU length decreases, branching patterns tend to progressively simplify due to the disappearance of the most central zones and a progressive reduction in the length of the floral zone.

Malus↗
PubMed2006

Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in Arabidopsis.

The active transport of the plant hormone auxin plays a major role in the initiation of organs at the shoot apex. Polar localized membrane proteins of the PIN1 family facilitate this transport, and recent observations suggest that auxin maxima created by these proteins are at the basis of organ initiation. This hypothesis is based on the visual, qualitative characterization of the complex distribution patterns of the PIN1 protein in Arabidopsis. To take these analyses further, we investigated the properties of the patterns using computational modeling. The simulations reveal previously undescribed properties of PIN1 distribution. In particular, they suggest an important role for the meristem summit in the distribution of auxin. We confirm these predictions by further experimentation and propose a detailed model for the dynamics of auxin fluxes at the shoot apex.

Arabidopsis↗
PubMed2006

Definition of architectural ideotypes for good yield capacity in Coffea canephora.

BACKGROUND: Yield capacity is a target trait for selection of agronomically desirable lines; it is preferred to simple yields recorded over different harvests. Yield capacity is derived using certain architectural parameters used to measure the components of yield capacity. METHODS: Observation protocols for describing architecture and yield capacity were applied to six clones of coffee trees (Coffea canephora) in a comparative trial. The observations were used to establish architectural databases, which were explored using AMAPmod, a software dedicated to the analyses of plant architecture data. The traits extracted from the database were used to identify architectural parameters for predicting the yield of the plant material studied. CONCLUSIONS: Architectural traits are highly heritable and some display strong genetic correlations with cumulated yield. In particular, the proportion of fruiting nodes at plagiotropic level 15 counting from the top of the tree proved to be a good predictor of yield over two fruiting cycles.

Agriculture↗
PubMed2005

A protocol to analyse cellular dynamics during plant development.

In vivo microscopy generates images that contain complex information on the dynamic behaviour of three-dimensional (3D) objects. As a result, adapted mathematical and computational tools are required to help in their interpretation. Ideally, a complete software chain to study the dynamics of a complex 3D object should include: (i) the acquisition, (ii) the preprocessing and (iii) segmentation of the images, followed by (iv) a reconstruction in time and space and (v) the final quantitative analysis. Here, we have developed such a protocol to study cell dynamics at the shoot apical meristem in Arabidopsis. The protocol uses serial optical sections made with the confocal microscope. It includes specially designed algorithms to automate the identification of cell lineage and to analyse the quantitative behaviour of the meristem surface.

Anatomy, Cross-Sectional↗
PubMed2002

Hyperstructures, genome analysis and I-cells.

New concepts may prove necessary to profit from the avalanche of sequence data on the genome, transcriptome, proteome and interactome and to relate this information to cell physiology. Here, we focus on the concept of large activity-based structures, or hyperstructures, in which a variety of types of molecules are brought together to perform a function. We review the evidence for the existence of hyperstructures responsible for the initiation of DNA replication, the sequestration of newly replicated origins of replication, cell division and for metabolism. The processes responsible for hyperstructure formation include changes in enzyme affinities due to metabolite-induction, lipid-protein affinities, elevated local concentrations of proteins and their binding sites on DNA and RNA, and transertion. Experimental techniques exist that can be used to study hyperstructures and we review some of the ones less familiar to biologists. Finally, we speculate on how a variety of in silico approaches involving cellular automata and multi-agent systems could be combined to develop new concepts in the form of an Integrated cell (I-cell) which would undergo selection for growth and survival in a world of artificial microbiology.

Algorithms↗