In Toulouse there is solid research network with groups in the areas of the Biology of Organisms, Ecology and Veterinary science and Agronomy sciences (UPS, INRA, INPT, Veterinary School). This touches on a good number of evolving ecological problems linked to an appreciation of the diversity of biological resources. By stimulating interactions and collaborations, this theme has helped to bring together researchers and teaching staff coming from different areas of life sciences (eg genetics and ecology of populations, ecology of communities, theoretical biology, agronomy and animal science) as well as from other scientific disciplines (eg mathematics and physics)
Three major themes are presented that aim to cover conceptual and theoretical objectives and their applications:
1- The origins and evolution of biological resources. This theme deals with the problems relating (i) the evolving process and mechanisms in the diversity of living organisms and (ii) the mechanisms of adaptation and formation of species. An understanding in these fields backs-up research areas such as systematics, evolving biogeography, evolutionary genetics, and molecular evolution.
2- Current dynamics of biodiversity. The emphasis here is on the factors that regulate the evolution of populations and communities, like environmental changes, unstable and long-lasting interactions between species, genetic and demographic factors. An understanding in these fields backs-up research areas such as the ecology of communities and the genetics and ecology of populations.
3- The protection, restoration and management of biological resources. The objectives of the research in the framework of this theme are (i) to test and perfect methods for recording and characterising organisms, populations and communities in order to deepen, enrich and improve biodiversity management strategies and (ii) to evaluate the priorities for the conservation and restoration of genetic resources, habitats and species, in order to better understand the consequence of biodiversity management practices.
The objective of these themes is to give the graduate students a conceptual and experimental mastery of the mechanisms that determine the origin, establishment, the maintenance, the regulation and the evolution of biological diversity within communities. The wide diversity of the research groups involved in this theme as well as the tools and approaches used to understand the dynamics of this biodiversity, should enable the students to be educated in a multidisciplinary spirit. For example the students will have the chance to use the latest mathematical and computational tools to profit from the wealth of information stemming from modern molecular biology. Finally, in parallel with the fundamental aspects of ecology and evolutionary biology, the training will also bring an awareness of how research and initiatives in microbial, plant and animal biodiversity are applied in management, conservation and promotion, in order to help students with their move into the professional world.
The research groups involved work essentially on understanding the role of cell surfaces or signalling pathways in the processes of differentiation (formation of xylem in woody plants; fruit ripening, etc.) and the adaptation of plants to abiotic environment factors (drought, cold, gravity). The themes to be covered are the following:
- The role of cell wall cell signalling in xylem formation;
- Control of transcription in xylem formation;
- Structure and function of plant cell walls;
- Cytosolic and nuclear calcium signalling in plants;
- Calcium signalling in plant adaptation to the environment;
- Control of transcription in fruit ripening and the interplay between hormone signalling pathways;
- The role of ethylene in fruit ripening and the biogenesis of flavours.
In terms of the their final applications, this research is aimed at improving plant production, particularly the quality of wood, the taste and nutritional quality of fruit, and plant adaptation to adverse environmental conditions.
The aim of the research is to understand and to model agricultural ecosystems to be able to propose management strategies that fit within the current issues of sustainable development (the social, environmental and economic impacts). It also concerns the analysing and modelling of the effects of agriculture on the countryside and on managing the natural resources (water, land). The studies are carried out at different levels of scale: small fields, groups of fields, very large fields, catchment areas, territory.
The research areas within this main theme take in several disciplines: (i) ecophysiology of plants (ii) systemic agronomy and animal science (iii) functional ecology and ecology of landscapes (iv) mathematics, statistics and computing applied to biological modelling and decision-making systems (v) geomatics (vi) chemistry and biochemistry. The areas covered by the different research groups are:
• Measurement of the transfer of pesticides used in viticulture into the aqueous environment and their detoxification by soil organisms.
• The development of spatio-temporal models applied to agro-ecosystems and decision making in agriculture.
• Modelling applied to the management of renewable natural resources in the rural setting, notably of the diversity of the fauna and flora, and of water, from the field level to the territory.
• The study and modelling of the effects of plant variety on the durability of large-scale farming in situations where the availability of water and nitrogen are limited.
• The study and modelling of the effects of farming practices (fertilisation, pastures, mowing) on agricultural priorities (productivity and quality) and on the environment (biodiversity), that is on the genotypes of native plants, for conservation, and on the natural areas, that are promoted by animal grazing.
• The analysis and modelling of land-use changes in agricultural and forest areas applied to prospective and spacio-temporal dynamic studies of the ecosytems and landscape and the support of the land management.
The research groups carry out the research with applications to linked to farming practices in conjunction with ecological issues and are therefore involved with different players from the agricultural world, such as institutes of plant technology (CETIOM, ARVALIS, Institut de l’Elevage, etc), the Chambers of Agriculture, and Departmental agencies for Agriculture and Forest, or environmental management bodies (DIREN, Agence de Bassin, Parc National des Pyrénées, Conservatoire Botanique).
The field of bioengineering is multidisciplinary and requires the integration of biological concepts and technologies with rigorous production methods that are constantly advancing. The success of this integration depends largely on efficiently marrying the quantitative analysis with the phenomena under study. The mastery and development of the necessary tools (eg biomathematics and biostatistics) is required to integrate the vast amount of experimental data. The students passing this training will be highly suited not only to the needs of the public sector in areas of wide social importance, but also in the socio/economic sector that requires more and more a global view of the applied problems of science technology.
The demands of bioengineering require more and more a pluridisciplinary and integrated approach, but without neglecting the knowledge of the basic subject areas. This demands an excellent mastery of all the important phenomena that determine the overall success of the experimental approach and its applications. Research in this field is based on the identification of the fundamental activities and the bottlenecks encountered and the behaviour of the biological systems within the specific constraints of their applications. The research groups involved in this theme have for a long time carried out high-level research in real applications. They are heavily involved in regional, national and international research projects, and with new technological platforms (the biochips of the Génopole de Toulouse, protein engineering, metabolomics).
A training does not come into its own unless the students are fully equipped to enter professional life, either in the public or industrial sectors. At the moment, there is a shortage of young researchers/managers able to work at the interface of different disciplines due to their narrow subject-specific education, and consequent narrow vision of complex events. There is therefore a need , if not an obligation, to train young researchers with a broad view who will be able to develop during their careers not only in response to the demands of society, but also to apply technological development in other fields than their own. By their adaptability, such professionals will assure our socio-economic competitiveness, and will be less subject to follow the approach of developing research and strategies based on foreign technologies, that in fact lead to a falling behind technologically.
Important advances have been made with microorganisms in analysing what determines their pathogenesis or their ability to establish symbiosis. Thus, thanks to the use of post-genomic techniques, it is now possible to unravel the mechanisms that govern plant-microrganism interactions, such as colonisation of plants. The discovery of a number of effectors of pathogenesis and the control of their expression is currently a major research area. Equally important are an understanding and the tools resulting from a functional analyses of the symbiotic partner for elucidating the genetic control by the plant of the symbiotic process.
In the case of the plant partner of the interaction, considerable progress has been made in recent years thanks to the molecular genetic techniques developed using Arabidopsis, and more recently, Medicago. In the case of pathogenic interactions, these advances have particularly led to the characterisation of resistance genes, and to the unravelling of the signalling networks linked to the Hypersensitive Response, a type of cell death associated with resistance. Most recently, studies have been developed to identify the plant targets of the pathogenesis factors and more broadly, the mechanisms of sensitivity. Equally, another major area off research is the understanding of the symbiotic process, either bacterial or mycorrhizal, from the initial perception of the microorganism (signals, receptors) up to the development of specific symbiotic cells and organs (nodules, microrhizomes). All this research depends on the approaches of genetics, genomics, cell and molecular biology and biochemistry. This is carried out in the Institute IFR 40, which brings together a number of research groups who work in a coordinated way on this theme, and on the same models.
The main objective of the research in this theme is to understand the biological mechanisms involved in the production of healthy and good quality food, and the raising of stock in optimal and sustainable conditions. The main areas in this theme are:
- The toxicology of xenobiotics and their impact on the quality and safety of food. The main xenobiotics are mycotoxins, endocrine disruptors (pollutants, drugs) and substances formed during processing. The effects are studied in rodents, farm animals and consumers.
- Pathophysiology and microbial genetics, co-evolution between pathogenic agents and hosts, studies on beneficial bacteria(probiotics, digestive symbionts) new anti-parasitics (macrocyclic lactones, tannins extracted from plants): application in the health and safety of food and durable agriculture
- The genetics and nutrition of herbivores and the impact of the raising and slaughter of animals on the structure of tissues and their metabolism, and the technological and organoleptic qualities of animal products, and their "health value" for the consumer.
The lecturers aim to give the students the scientific basis necessary to understand the processes that ensure the technological, organoleptic, nutritional and hygienic qualities of animal output. The originality lies in the fact that (1) they call upon the most recent scientific advances common to the living world whether it be animal, plant or microbes (2) they show the specifics of each of these kingdoms but also their interactions (3) they are concerned with studying different levels of scale from molecules to populations, using the latest techniques of cell and molecular biology and experimental models in silico and in vivo, as well as emphasising integrated approaches to problems (4) they take into account the applied aspects of these scientific advances in the agro-veterinary and agro-industrial setting.
The lecturers involved have several objectives: (1) to educate the students in the most advanced concepts and tools in Biology (2) to give the students a broad multidisciplinary view of scientific research, including the socio-economic consequences and the demands of society (3) to enable the students to go into a research area in depth, with the realisation of both the fundamental and applied aspects.
The training to be a researcher necessitates a solid background in the science and the technology, but this must be accompanied by an open-mindedness that will enable the person to evolve during their career. This proposed theme covers diverse aspects of veterinary and agronomical research by the materials studied and much by the organisation of the materials. As such, it is appropriate as it gives the future Ph.Ds a broad vision of the work of a researcher and considerable adaptability.
A group of students to whom this course is aimed, namely specialists in agronomy and vetinerary science, will have already been taught by case-studies and the approach of "diagnosis, prognosis, treatment". The research training of these students will create a pool of future professionals for agriculture and the agro-industry, who will be equipped with a high level biological culture, practical skills and the rigour of the scientific approach. The diffusion of the way of thinking and approaches that these students will bring should enrich other French or foreign postgraduates who come into course with a more academic background.