Catherine Christophe

François Houllier

CR Biologies

C. R. Biologies 332 (2009) 935–936ForewordIntegrative animal, microbial and plant biology:Dialogue between experiment and modellingAlthough there are earlier references to integrativebiology (Bullock [1], Ng et al. [2]), it is only since the1990s, and especially since the early 2000s, that this ap-proach has been spreading (Charrier et al. [3]; Fig. 1:left). Certainly, biology is, or should be, essentially in-tegrative, but the tremendous increase in analytical andinvestigative capabilities has contributed to focusing re-search on molecular and cellular mechanisms.This reductionist and, in many respects, fruitful trendrelies primarily on ever higher throughput productionof data in structural and functional genomics and onthe development of new imaging techniques that areessential for exploring the organization and function-ing of cells or tissues. A first challenge deals thereforewith data integration, from their storage and organiza-tion to their access, analysis and traceability. Hence,the fact that recent technologies tend toward providingglobal and exhaustive molecular datasets, raises ques-tions in terms of volume of information. These tech-nologies also generate data that are increasingly diverse(e.g. from molecular data about small RNAs, genes andproteins to cellular images and integrated phenotypictraits), which raises needs for linking different types ofinformation acquired on the same organisms. Finally,these technologies are gaining in spatial and temporalresolution, thereby addressing the spatiotemporal track-ing and reconstruction of biological events, topics thatare critical in developmental biology.A second scientific challenge of integration is tocombine experimental and modelling approaches to re-construct an overall picture of the whole organism, orof some major functions. This challenge addresses theunderstanding and prediction of phenomena at nestedlevels of organization (from the finer subcellular levelsto tissues, organs, and organisms considered in their bi-otic or abiotic environment, or even to populations andcommunities) and of the spatiotemporal coordination ofevents within the organism. The study of the functioningand dynamics of networks (e.g., networks of genes ormetabolic networks within the cell, communication be-tween cells in a tissue, or signalling pathways) is there-fore seen as a central theme in biology. The analysis andprediction of the emergent properties of these networksare thus major topics of systems biology, a scientific do-main that has been growing very quickly since the early2000s (Fig. 1: centre).Fig. 1. Evolution of the number of publications, between 1980 and 2008, listed by the Web of Sciences, as of 2009 October 21st. Left: publicationswhere the topics refer to ‘integrative biology’ or ‘integrative physiology’. Centre: publications where the topics refer to ‘systems biology’. Right:publications where the topics refer to ‘synthetic biology’.1631-0691/$ – see front matter © 2009 Published by Elsevier Masson SAS on behalf of Académie des sciences.doi:10.1016/j.crvi.2009.10.006936 Foreword / C. R. Biologies 332 (2009) 935–936Mass production of data also renews comparativeapproaches. A third scientific challenge of integrationrefers therefore to the study of the diversity of individu-als and species, to the analysis of phenotypic plasticityand of the genotype–environment interactions, as wellas to evolutionary approaches, such as phylogenomics.This challenge leads naturally to a particular reflectionon the choice of species and systems that are studied.After a period where some model systems benefitedfrom huge scientific investments, there is a strong devel-opment of structural and functional genomics in otherbiological systems, e.g. in species that are critical inagriculture and for food production, for chemical, ener-getic and other non-food uses of biomass, or in naturalecosystems. The concept of model species is thus evolv-ing under the joint effect of the accelerated renewal oftechnology, and of comparative and translational ap-proaches.Whatever the challenge, integrative biology involvesthe ability to articulate experimental approaches, largescale data acquisition, and formal or quantitative dataanalysis and modelling approaches. This issue of theC. R. Biologies illustrates this movement towards amore predictive biology that should finally result notonly in a better understanding of living organisms, butalso in a greater capability to control and engineer them(Fig. 1: right). They also illustrate the diversity of ap-proaches in animal, microbe and plant integrative biol-ogy, as well as the traits and species that are important inagronomy. To a large extent, these approaches could betransposed to higher levels of organization, populationsand communities (Thellier [4]). Here, the choice was,however, made to focus on levels of organization thatrange from the gene to the organism, and to present ap-proaches at the intra-cellular level or involving systemsbiology, approaches in developmental biology, mainlyat the level of tissues and organs, and approaches of sys-tems where organisms interact with their environment.Catherine ChristopheINRA DSPPV, Direction Scientifique,Plantes et Produits du Végétal,147, rue de l’Université,75338 Paris cedex 07, FranceE-mail address: cchristophe@paris.inra.frFrançois HoullierINRA DSPPV, Direction Scientifique,Plantes et Produits du Végétal,147, rue de l’Université,75338 Paris cedex 07, FranceE-mail address: houllier@paris.inra.frReferences[1] T. Bullock, In search of principles in integrative biology, Ameri-can Zoologist 5 (4) (1965) 745–755.[2] E. Ng, R.S. Loomis, W.F. Hunt, Integrative physiology ofsugar beet. Developmental control of partitioning, Plant Physiol-ogy 56 (2) (1975) 77.[3] A. Charrier (coordinator), La biologie intégrative végétale, INRA,Conseil scientifique, Paris, 2005, 43 pages.[4] M. Thellier, Modelling of complex systems in agronomy and en-vironment, C. R. Biologies 329 (2006) 1–2.

Integrative animal, microbial and plant biology: Dialogue between experiment and modelling

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Integrative animal, microbial and plant biology: Dialogue between experiment and modelling

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