L2 - Plant Biology for Agro-Environment

This compulsory S3 course allows students to consolidate and deepen the foundations of molecular biology and cell biology acquired in L1.

Molecular Biology Section: The molecular and structural bases of nucleic acids will be developed and explored in depth in order to understand the physicochemical properties of nucleic acids, which open up various prospects for technological applications, and the molecular mechanisms of the main stages of molecular biology, such as DNA replication, gene transcription into mRNA, and their translation into proteins. These stages, illustrated by experimental evidence drawn from various historical studies, will be studied in depth in prokaryotes. Comparisons with eukaryotes will also be discussed. The molecular mechanisms of DNA repair will also be described and developed.

Cell Biology section: The major concepts of membrane and cytosolic protein complex formation will be addressed, particularly in the context of cell signaling pathways. The concepts of ligands, receptors, scaffold proteins, signaling enzyme proteins, intracellular second messengers, and response kinetics will be presented. Biochemistry and cell biology techniques used to detect the presence and location of proteins in cells and tissues will be discussed.

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Description of the EU (max. 10 lines):

The aim of this EU is to explain how to measure variation in biology and how it can be represented. It is based on concrete examples from various disciplines of biology (ecology, developmental biology, evolution, genetics, physiology) and provides the statistical tools to measure this variation and the graphical methods to represent it. The statistical concepts of sampling, inference, distribution, central tendency, dispersion, distribution function, parameters, confidence interval, and dependence between variables for different types of variables (binomial, discrete, continuous) are explained using tutorials based on biological problems.

Skills targeted by the EU (see skills reference framework):

- Descriptive analytical tools in biology, introduction to biostatistics through the analysis of biological patterns

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This course provides students with a fundamental understanding of microbiology. It will detail the structures of microorganisms, prokaryotes, eukaryotes, and viruses. It will provide an overview of the diversity of these microorganisms and describe how they reproduce.

For bacteria, trophic types and factors influencing growth will be developed, as well as the study of growth in non-renewed environments. Genetics and horizontal transfers between bacteria will be addressed.
Some eukaryotic microorganisms will be studied: habitat, lifestyles, ecological role or parasitism, as well as their mode of development.
In virology, the main cycles of virus multiplication will be detailed, and modes of transmission and the concept of viral pathogenesis will be addressed. The principle of antiviral vaccination and antiviral treatments will be presented and illustrated with concrete examples. 
The principle of antiviral vaccination and antiviral treatments will be presented and illustrated using concrete examples.
Practical work will provide an introduction to sterile techniques for handling microorganisms, counting bacteria, and conjugation.

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This module should enable students to acquire:

Basic concepts in physiology: Concept of homeostasis; levels of organization of the human body; compartments of the internal environment; study of the endocrine system; acid-base and water-mineral balance; anatomical and functional studies of the central and peripheral nervous systems.

Basic concepts in immunology:

General overview of the immune system; study of T and B lymphocytes, antigen-presenting cells; study of antimicrobial immunity and complement.

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This compulsory course allows students to consolidate the fundamentals of biochemistry acquired in the first year by approaching this discipline through a cross-disciplinary study of enzymes involved in cellular metabolism, particularly glycolysis. Several areas of biochemistry will be covered: the fundamentals of Michaelian enzymology and a description of the metabolic reactions involved in glycolysis. Finally, the technical aspect will be addressed through the presentation and analysis of techniques for measuring enzyme activity and purifying, quantifying, and detecting proteins.

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Description*: This second general chemistry course aims to consolidate and deepen the study of reactions in aqueous solution, particularly those involving the formation of metal complexes. The principles of thermodynamics will be presented and applied to the study of chemical equilibria of biological interest. Rather than giving a presentation using mathematical formalism, which would require a much greater number of hours, students will be asked to understand the physical meaning of these principles and the main thermodynamic functions and their applications to chemical systems, often of biological interest. In particular, resting membrane potentials and the use of pH potential diagrams in biology will be presented.

Students will work on course materials (written and audio) ahead of certain lectures and tutorials, enabling them to fully participate in face-to-face teaching in lectures and tutorials, understand the concepts presented, and acquire the necessary skills.

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1- Linux basics (1.5 hours lecture + 3 hours tutorial): Basic commands for navigating Linux and understanding the logic of this language. Short exercises on extracting information in bash/shell. Element revisited for the analysis of alignment files.

2- Databases (3 hours of lectures + 4.5 hours of tutorials): knowledge of the main bibliographic and biological databases (NCBI, Ensembl, Galaxie, etc.). Ability to perform relevant and effective queries, exploit, sort, and describe different formats.

3- Sequence analysis (1.5 hours lecture + 4.5 hours tutorial): Sequence alignment and comparison with a brief introduction to phylogenetics (dot plot, Blast, etc.)

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This compulsory S4 course allows students to consolidate and deepen the foundations of molecular biology and cell biology acquired in L1.

- Cell biology: The course will cover four major topics: 1) The functioning of the cellular cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation to highlight protein interactions, fluorescence videomicroscopy to track cell distribution dynamics, and evaluation of the importance of proteins of interest in a cellular process using strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology: After acquiring knowledge about transcription and translation mechanisms in semester 3, we will address gene expression regulation: transcriptional regulation (repressors, activators) and attenuation in prokaryotes, and the basics of expression regulation mechanisms in eukaryotes.

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Learn about the major families of plant molecules and their properties, the biosynthesis pathways of these molecules, and the mechanisms regulating biosynthesis in plants and microorganisms. In this module, the major families of molecules derived from secondary plant metabolism (terpenes, flavonoids, alkaloids, saponins) are studied through their biosynthesis in plants and the differentiation of structures or groups of specialized cells. Based on this knowledge, biotechnological approaches for metabolic engineering are presented. The role of these molecules in plant life is discussed, as well as their properties used by industry as dyes, flavorings, perfumes, medicines, and biofuels. The use of natural polymers for the manufacture of industrial materials is addressed (paper pulp, rubber, plastics) and the production chains are described. Understanding the major families of plant molecules and their properties, the biosynthesis pathways of these molecules, and the mechanisms regulating these biosyntheses in plants remains a major challenge for the development of biorefineries in Europe.                                              

Keywords: secondary metabolism, metabolic engineering, biomolecule valorization, cellular and metabolic differentiation, regulation of secondary metabolism.

Additional information:

Visits to two analytical platforms are planned at the Montpellier hub (each lasting 1.5 hours).

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The objective of this EU is to understand evolutionary processes at both the micro- and macro-evolutionary scales.

Using examples, manipulations, and accessible modeling, the lessons will aim to present in a concrete and quantitative manner the effects of the four evolutionary forces operating at the individual and population levels (mutation, migration, selection, and drift). The integration of these microevolutionary processes on larger time scales (e.g., differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to phylogenetics tools (reading and constructing trees) for studying macroevolutionary events (diversification, extinction) and tracing changes in character states, in particular by integrating fossil data.

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The Physiology of Major Functions course (semester 4) aims to describe the role and interactions of the different systems in the body that work together to maintain a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive, and renal systems and their nervous and hormonal controls. Understanding the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac failure; hemorrhage; exposure to extreme environments.

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This compulsory course will enable students to deepen the skills they acquired in "Biochemistry S3." It will enable them to understand cellular metabolism by:

-understanding bioenergetics in order to study the processes by which living cells convey, transmit, use, accumulate, and release energy;
-the study of catabolism and anabolism of carbohydrates, lipids, nucleotides, amino acids, and the metabolic interactions between these pathways.

- the description of metabolic disorders.

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In this introductory course to genetic analysis, the objectives are to learn the terms, principles, concepts, and methods used in formal genetics, as well as their fields of application, particularly in human and medical genetics. This course covers the genetics of transmission (Mendelian and non-Mendelian), quantitative genetics, and concepts of population genetics. Throughout the course, close links are established between classical genetics and molecular genetics.

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Plants interact with a multitude of microorganisms in their environment. These microorganisms act alone or in communities. They can have negative or positive effects on plants, their growth, nutrition, and health. In this module, we will present the different forms that these biotic interactions can take (symbiosis, parasitism, pathogenicity) based on popular biological models (mycorrhizal or nitrogen-fixing symbiosis, diseases caused by different microorganisms). This will also be an opportunity to introduce emerging concepts in the field, such as the microbiome and holobiont.

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1- Linux basics (1.5 hours lecture + 3 hours tutorial): Basic commands for navigating Linux and understanding the logic of this language. Short exercises on extracting information in bash/shell. Element revisited for the analysis of alignment files.

2- Databases (3 hours of lectures + 4.5 hours of tutorials): knowledge of the main bibliographic and biological databases (NCBI, Ensembl, Galaxie, etc.). Ability to perform relevant and effective queries, exploit, sort, and describe different formats.

3- Sequence analysis (1.5 hours lecture + 4.5 hours tutorial): Sequence alignment and comparison with a brief introduction to phylogenetics (dot plot, Blast, etc.)

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This compulsory S4 course allows students to consolidate and deepen the foundations of molecular biology and cell biology acquired in L1.

- Cell biology: The course will cover four major topics: 1) The functioning of the cellular cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation to highlight protein interactions, fluorescence videomicroscopy to track cell distribution dynamics, and evaluation of the importance of proteins of interest in a cellular process using strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology: After acquiring knowledge about transcription and translation mechanisms in semester 3, we will address gene expression regulation: transcriptional regulation (repressors, activators) and attenuation in prokaryotes, and the basics of expression regulation mechanisms in eukaryotes.

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This course aims to broaden the knowledge acquired previously to different areas of microbiology, particularly microbial ecology.

It will address pathogenic relationships, but will also present examples of symbiotic associations. It will discuss the applications of microorganisms in biotechnology. It will describe how antibiotics work and the associated resistance phenomena, as well as their impact.

The EU will address the concept of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be addressed more specifically, and the mechanisms of bacterial resistance to phage infection will be detailed. The different types of viral infection in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

Knowledge about microorganisms will be expanded through the study of Archaea and a model eukaryotic organism, yeast.

The practical work will focus on performing and interpreting an antibiogram, and on titrating bacteriophages.

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Learn about the major families of plant molecules and their properties, the biosynthesis pathways of these molecules, and the mechanisms regulating biosynthesis in plants and microorganisms. In this module, the major families of molecules derived from secondary plant metabolism (terpenes, flavonoids, alkaloids, saponins) are studied through their biosynthesis in plants and the differentiation of structures or groups of specialized cells. Based on this knowledge, biotechnological approaches for metabolic engineering are presented. The role of these molecules in plant life is discussed, as well as their properties used by industry as dyes, flavorings, perfumes, medicines, and biofuels. The use of natural polymers for the manufacture of industrial materials is addressed (paper pulp, rubber, plastics) and the production chains are described. Understanding the major families of plant molecules and their properties, the biosynthesis pathways of these molecules, and the mechanisms regulating these biosyntheses in plants remains a major challenge for the development of biorefineries in Europe.                                              

Keywords: secondary metabolism, metabolic engineering, biomolecule valorization, cellular and metabolic differentiation, regulation of secondary metabolism.

Additional information:

Visits to two analytical platforms are planned at the Montpellier hub (each lasting 1.5 hours).

See the full page

The objective of this EU is to understand evolutionary processes at both the micro- and macro-evolutionary scales.

Using examples, manipulations, and accessible modeling, the lessons will aim to present in a concrete and quantitative manner the effects of the four evolutionary forces operating at the individual and population levels (mutation, migration, selection, and drift). The integration of these microevolutionary processes on larger time scales (e.g., differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to phylogenetics tools (reading and constructing trees) for studying macroevolutionary events (diversification, extinction) and tracing changes in character states, in particular by integrating fossil data.

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The Physiology of Major Functions course (semester 4) aims to describe the role and interactions of the different systems in the body that work together to maintain a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive, and renal systems and their nervous and hormonal controls. Understanding the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac failure; hemorrhage; exposure to extreme environments.

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This compulsory course will enable students to deepen the skills they acquired in "Biochemistry S3." It will enable them to understand cellular metabolism by:

-understanding bioenergetics in order to study the processes by which living cells convey, transmit, use, accumulate, and release energy;
-the study of catabolism and anabolism of carbohydrates, lipids, nucleotides, amino acids, and the metabolic interactions between these pathways.

- the description of metabolic disorders.

See the full page

In this introductory course to genetic analysis, the objectives are to learn the terms, principles, concepts, and methods used in formal genetics, as well as their fields of application, particularly in human and medical genetics. This course covers the genetics of transmission (Mendelian and non-Mendelian), quantitative genetics, and concepts of population genetics. Throughout the course, close links are established between classical genetics and molecular genetics.

See the full page