L3 - Plant Biology for the Agro-Environment

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Bioinformatics is a discipline at the crossroads of computer science, mathematics and the life sciences. It is based in particular on the use and development of computer tools for the analysis of massive biological data. Eventually, these megadata can be organized into searchable online databases, enabling users to extract data relevant to a biological problem.

The aim of the "Bioinformatics applied to plant biology" teaching unit is to introduce students to the use of databases and to offer a first approach to data mining using R software.

Virtually all teaching will take the form of practical case studies in the computer room, in student sub-groups.

In the first part, students will learn the rudiments of the R computer language, enabling them to organize and clean up their raw data to make it fully exploitable for further analysis. They will then learn how to propose explicit graphical representations based on biological data. Particular attention will be paid to writing reusable scripts and choosing the graphics associated with the calculations according to the biological question at hand.

In the second part, students will use general databases such as NCBI, or databases devoted exclusively to the model plant Arabidopsis (TAIR), to carry out data mining.

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In this course, students work in groups to carry out bibliographical research on a selection of medicinal plants during tutorials, in order to identify plant biomolecules with potential biological or pharmacological properties. Using the documents provided, each group identifies, proposes and implements an extraction protocol and a simple biological activity test protocol to test the biostatic, antibiotic or antioxidant activity of the targeted molecules. The bibliographic monitoring approach and the results obtained during the practical work, together with their analysis and interpretation, will be discussed during a poster presentation session, which will lead to an assessment.

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This UE is a specialization module in Functional Plant Biology, covering the mechanisms underlying the major stages in plant development.

It is based on knowledge derived mainly from the model plant Arabidopsis thaliana and covers the following concepts from a molecular, cellular and physiological point of view:

• Roles and functions of the main phytohormones.
• Development of male and female gametes, fertilization.
• Embryo, seed and fruit development.
• Functioning of root and stem meristems (vegetative and floral).
• Flower architecture.
• Adaptive development mechanisms in response to abiotic factors: light, gravity, cold.

Certain aspects of development will also be analyzed from an evolutionary perspective, by studying the role of developmental genes in the diversification and evolution of developmental processes in land plants (evolution of the root system, floral architecture, etc.).

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This course describes the methodology used by life science researchers to communicate the results of their experiments, both orally and in writing. As English is the common language of international researchers, a large part of this course is taught in this language.

Written communication is addressed through the study of the (macro) structuring of a research article, as well as through a study of the publication process in scientific journals. Several elements of written structuring (micro) are examined in order to understand the differences between scientific and literary English: clarity, cohesion, coherence.

These studies are supplemented by a tutored project during the semester, during which students analyze a research article recently published in the scientific literature and transcribe it into an oral presentation (conference) in English.

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Molecular biology is a fascinating subject of study in its own right, but it also provides other disciplines in biology (cell biology, genetics, physiology...) with fantastic tools for modifying and quantifying genes and their products.

The EU provides a deeper understanding of the mechanisms of organization, maintenance, replication and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, we'll be exploring the properties of information-carrying macromolecules (DNA, RNA, proteins), and how transactions between them explain how eukaryotic cells function and adapt to the environment and to the development of organisms.

At the same time, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and analyzed in greater depth in practical sessions.

TDs will address these topics in the form of (1) exercises enabling students to check their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. In this way, the fundamentals of scientific reasoning and the critical analysis of results are acquired and/or deepened.

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This teaching unit covers the different categories of biotechnologies according to their field of application:

• Plant biotechnologies concern the agri-food industry and encompass a range of technologies that use plant organisms and their cells to produce and transform food products, biomaterials and energy, as well as recombinant proteins for therapeutic purposes.

• Animal biotechnology covers the fields of health, drugs, diagnostics and tissue engineering, as well as the development of genetic or molecular processes for therapeutic purposes.
• Microbial biotechnologies involve the use of micro-organisms (viruses or bacteria) and their cultivation in the agri-food/pharmaceutical industry, as well as their use in environmental protection.

The teaching offered to students in the Licence 3 Life Sciences is designed to enable them to discover or deepen their theoretical knowledge of the various biotechnologies, and to master the associated tools/applications.

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Functional genetics aims to better understand the relationships between genotype and phenotype. This course integrates various aspects of the analysis of gene and genome function at the whole-genome level using in vivo approaches, as well as transcriptional and expression regulation of eukaryotic genomes. The course is illustrated by concrete examples of developmental genetics in physiological and pathological contexts.

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After defining intensive agriculture and analyzing its risks/benefits, this module will enable students to reflect on the various possible ways of moving agriculture towards an agroecological approach. Examples include biopesticides, ecological intensification and soil management. A visit to a company involved in sustainable agriculture is also organized. The sites visited vary from year to year, depending on the wishes of the students and the availability of the companies. Examples of visits made as part of this module: Bayer, Vilmorin, Geves, CTIFL, sudExpé...

Licenciales.

Students will be asked to present a project or business start-up developing innovative proposals for changing cultivation practices, or any other use of plant products to reduce environmental impact.

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This course presents the major functions of carbon, mineral and water nutrition in plants, which ensure their autotrophy (the production of their own biomass). It will provide the basis for understanding the fundamental mechanisms of nutrient absorption, distribution and assimilation. The course will be divided into two main parts, one dedicated to mineral nutrition and the other to carbon nutrition.

After a review of the properties of plant membranes and walls and the concepts of transmembrane transport, the part of the course dedicated to mineral nutrition will teach the mechanisms of water absorption and circulation, root uptake, subcellular compartmentalization and mineral distribution, as well as nitrogen assimilative metabolism.

The chapter dedicated to carbon nutrition will present the functioning of the chloroplast in the plant cell, photosynthesis (capture of light energy and synthesis of the first carbon compounds), the production of organic compounds and their allocation in the plant.

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This UE is a module designed to introduce students to scientific research in fundamental or applied plant agro-sciences. Students must complete an internship of 10 weeks or more (which may continue over the summer) in a research laboratory (CNRS, INRAE, IRD, CIRAD), in an applied research organization such as GEVES, CTIFL, SudExpe, Serfel, IFV or in a private company such as Staphyt, AgroXp, Vilmorin. Montpellier offers a wide range of internship opportunities in this field.

This is a module for integration into the professional world, enabling students to make contact with players in the world of plant-based Agro-Sciences:

• apply the techniques learned in the various courses of the BiPAgro Bachelor's degree.
• exposure to the professional world
• develop your own professional project and enhance your CV

Students write a dissertation which they defend in front of a jury made up of teacher-researchers, researchers and/or field technicians/engineers. 

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 In this course, students deepen their knowledge of the different methods of plant transgenesis using biological, chemical or physical vectors, their acceptability and their applications in fields as varied as plant improvement, the production of biomolecules or therapeutic recombinant proteins. In tutorials, students are encouraged to document, reflect, argue and debate on transgenesis and its alternatives through a plant improvement scenario. In practical work, students are involved in improving a protocol for obtaining root hairs, using the knowledge they have acquired in class.

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The modalities of this UE are specifically adapted to the different L3 courses. Nevertheless, the objectives are the same: to give students an insight into the professional world of life science research.

Students will be offered a short internship in a laboratory/company or a tutored project with a tutor working in a laboratory or company associated with biology.

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