L3 - Plant Biology for the Agro-Environment

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Bioinformatics is a discipline at the crossroads of computer science, mathematics and 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 so that a user can extract data relevant to a biological problem.

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

Almost all the teaching will be done in the form of practical cases in the computer room in sub-groups of students.

In the first part, students will learn the basics of the R language to organize and clean their raw data in order to make them fully exploitable for further analysis. Then, they will learn how to propose explicit graphical representations from biological data. Particular attention will be given to the writing of reusable scripts and the choice of graphs associated with the calculations according to the biological question.

In a second part, students will exploit generalist databases such as NCBI or exclusively dedicated to the model plant Arabidopsis (TAIR) to perform data mining.

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In this course, students will conduct bibliographic research on a selection of medicinal plants during tutorials in order to identify the biomolecules of the plant that may have biological or pharmacological properties. Each group will use documents provided to them to identify, propose and implement 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, as well as their analysis and interpretation, will be discussed during a poster presentation session, which will result in an evaluation.

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This course is a specialization module in Functional Plant Biology that deals with the mechanisms underlying the major stages of plant development.

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

• Roles and function of the main phytohormones.
• Development of male and female gametes, fertilization.
• Development of the embryo, the seed and the fruit.
• Functioning of root and stem meristems (vegetative and floral).
• Architecture of the flower.
• Mechanisms of adaptive development in response to abiotic factors: light, gravity, cold.

Some 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, ...).

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This course describes the methodology used by researchers in the life sciences to communicate the results of their experiments, both in writing and orally. 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 structuring (macro) 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 complemented by a tutored project during the semester during which students are required to analyze a recently published research article in the scientific literature and to transcribe it into an oral presentation (conference) in English.

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Molecular biology is both 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, the properties of information-carrying macromolecules (DNA, RNA, proteins) will be explored, and how the transactions between them explain the functioning of eukaryotic cells and their adaptation to the environment and to the development of organisms.

In parallel, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and further developed in class by analyzing results.

Thus, the tutorials approach these subjects in the form of (1) exercises leading the students to verify their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. Thus, the basics of scientific reasoning and critical analysis of results will be 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 include a series of technologies using the organism of plants and their cells to produce and transform food products, biomaterials and energy, but also recombinant proteins for therapeutic purposes

• Animal biotechnologies concern the fields of health, medicine, diagnosis, tissue engineering as well as the development of genetic or molecular processes with a therapeutic purpose.
• Microbial biotechnologies concern the use of micro-organisms (viruses or bacteria) and their cultivation within the agro-food/pharmaceutical industry or their interest in environmental protection.

The teaching offered to students in the Bachelor 3 Life Sciences is to enable them to discover or deepen their theoretical knowledge of the various biotechnologies as well as 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 the different aspects of the analysis of gene and genome function at the whole genome level by in vivo approaches, as well as transcriptional regulation and expression regulation of eukaryotic genomes. The course is illustrated by concrete examples in developmental genetics in physiological and pathological contexts.

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After defining intensive agriculture and analyzing its risks/benefits, this module will allow students to reflect on the different possible ways to make agriculture evolve in an agroecological approach. Examples such as biopesticides, ecological intensification and soil management will be developed. A visit of a company working for a sustainable agriculture is also organized. The site visited varies from year to year depending on the students' wishes and the availability of the companies. Example of visits made within the framework of this module: Bayer, Vilmorin, Geves, CTIFL, sudExpé...

Licenciales.

The students will be asked to present a project or a business creation developing innovative proposals to change cultivation practices, or any other use of plant products in order to reduce the environmental impact.

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This course presents the main functions of carbon, mineral and water nutrition of the plant that ensure its autotrophy (the production of its biomass). It will give the necessary basis for the understanding of the fundamental mechanisms of absorption, distribution and assimilation of nutrients. 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 uptake 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 of discovery of scientific research in fundamental or applied plant agrosciences. The student must do an internship of 10 weeks or more (which can 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. There are many internship sites in Montpellier in this field.

It is a module of insertion in the professional world allowing to enter in relation with the actors of the world of the plant Agro-Sciences giving to the student the opportunity

• to apply the techniques learned in the different courses of the Bachelor's degree course BiPAgro.
• to be confronted with the professional environment
• to develop one's own professional project and enrich one's CV

The student writes a dissertation and defends it in front of a jury composed of teacher-researchers, researchers and/or field technicians/engineers. 

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 In this course, students learn about 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 asked to document, reflect, argue and debate on transgenesis and its alternatives through a scenario related to plant improvement. In practical work, students are involved in the improvement of a protocol aimed at 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 courses of the L3. Nevertheless, the objectives are common: to give students an overview of the professional world related to research in life sciences.

The student 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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