L3 - Plant Biology for Agro-Environment

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Bioinformatics is a discipline at the crossroads of computer science, mathematics, and life sciences. It relies in particular on the use and development of computer tools for analyzing massive amounts of biological data. Ultimately, this big data can be organized into online searchable databases so that users can extract data relevant to a biological problem.

The "Bioinformatics Applied to Plant Biology" teaching unit aims to familiarize students with the use of databases and offer an introduction to data exploration using R software.

Almost all of the teaching will take the form of practical case studies in the computer lab in small groups of students.

In the first part, students will learn the basics of the R programming language, enabling them to organize and clean their raw data so that it can be fully exploited for subsequent analysis. They will then learn how to produce clear graphical representations based on biological data. Particular attention will be paid to writing reusable scripts and choosing the appropriate graphics for the calculations, depending on the biological question.

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

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In this EU, students work in groups to conduct bibliographic research on a selection of medicinal plants during supervised tutorials in order to identify the plant's biomolecules that may have biological or even pharmacological properties. Using documents provided to them, each group identifies, proposes, and implements in practical work an extraction protocol and a simple biological activity test protocol to test the biostatic, antibiotic, or antioxidant activity of the targeted molecules. The literature review process and the results obtained in practical work, along with their analysis and interpretation, will be discussed during a poster presentation session, which will be assessed.

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

It draws on knowledge derived mainly from the model plant Arabidopsis thaliana and addresses the following concepts from a molecular, cellular, and physiological perspective:

• Roles and functioning of the main plant hormones.
• Development of male and female gametes, fertilization.
• Development of the embryo, seed, and fruit.
• Functioning of root and shoot 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 terrestrial 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 in writing and orally. As English is the common language of international researchers, a large part of this course is taught in English.

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

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

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Molecular biology is not only a fascinating subject in its own right, but it also provides other biological disciplines (cell biology, genetics, physiology, etc.) with fantastic tools for modifying and quantifying genes and their products.

The EU is deepening its understanding of the mechanisms involved in the organization, maintenance, replication, and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, we will explore the properties of information-carrying macromolecules (DNA, RNA, proteins) and how interactions between them explain the functioning of eukaryotic cells and their adaptation to the environment and the development of organisms.

At the same time, the main techniques used to monitor or modify gene expression, or to study the mechanisms of this expression, will be presented in lectures and explored in greater depth in tutorials through the analysis of results.

Thus, the tutorials address these topics in the form of (1) exercises that allow students to test their understanding of the knowledge described above, and (2) experiments taken from scientific articles for analysis. In this way, the fundamentals of scientific reasoning and critical analysis of results will be acquired and/or further developed.

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

• Plant biotechnology concerns the agri-food industry and encompasses a range of technologies that use plants and plant 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, medicine, diagnostics, tissue engineering, and the development of genetic or molecular processes for therapeutic purposes.
• Microbial biotechnology involves the use of microorganisms (viruses or bacteria) and their cultivation in the agri-food/pharmaceutical industry, as well as their role in environmental protection.

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

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After defining intensive agriculture and analyzing its risks and benefits, this module will enable students to reflect on the various possible avenues for developing agriculture using an agroecological approach. Examples such as biopesticides, ecological intensification, and soil management will be explored. A visit to a company working towards sustainable agriculture is also organized. The site visited varies from year to year depending on student preferences and company availability. Examples of visits made as part of this module include Bayer, Vilmorin, Geves, CTIFL, and sudExpé.

Licensed.

Students will be asked to present a project or business plan that develops innovative proposals to change farming practices or any other use of plant products in order to reduce environmental impact.

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

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

The chapter on carbon nutrition will present how chloroplasts function in plant cells, photosynthesis (capturing light energy and synthesizing the first carbon compounds), the production of organic compounds, and their allocation within the plant.

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This EU is a module for discovering scientific research in fundamental or applied plant sciences. Students must complete an internship of 10 weeks or more (which may continue into 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, or Vilmorin. CIRAD), an applied research organization such as GEVES, CTIFL, SudExpe, Serfel, IFV, or a private company such as Staphyt, AgroXp, or Vilmorin. There are many internship opportunities in this field in the Montpellier area.

This is a module designed to help students enter the professional world by connecting them with key players in the field of plant agricultural sciences, giving students the opportunity to:

• apply the techniques learned in the various courses of the BiPAgro Bachelor's degree program.
• to face the professional environment
• to develop your own career plan and enhance your resume

Students write a thesis that they defend before a panel composed of faculty members, researchers, and/or field technicians/engineers. 

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 In this course, students deepen their knowledge of the various methods of plant transgenesis using biological, chemical, or physical vectors, their acceptability, and their applications in fields as varied as plant improvement, biomolecule production, and recombinant therapeutic proteins. In tutorials, students are encouraged to research, reflect, argue, and debate transgenesis and its alternatives through a scenario related to plant breeding. 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 terms and conditions of this course unit are specifically tailored to the different L3 programs. However, the objectives are the same: to give students an overview of the professional world related to life sciences research.

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

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