L2 - Plant Biology for the Agro-Environment

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

Molecular Biology part: The molecular and structural bases of nucleic acids will be developed and deepened to understand the physicochemical properties of nucleic acids, which open up various prospects for technological applications, and the molecular mechanisms of the main steps in Molecular Biology, such as DNA replication, transcription of genes into mRNA and translation of these into proteins. These steps, illustrated by experimental evidence deduced 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: This section covers the major concepts of membrane and cytosolic protein complex formation, particularly in the context of cell signaling pathways. The notions of ligands, receptors, scaffolding proteins, enzymatic signaling proteins, intracellular second messengers and response kinetics will be presented. Biochemistry and cell biology techniques for demonstrating the presence and localization of proteins in cells and tissues will be presented.

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EU description (max 10 lines):

The aim of this course is to help students understand how to measure variation in biology, and how it can be represented. It is based on concrete examples drawn from various disciplines in biology (ecology, developmental biology, evolution, genetics, physiology) and gives the statistical tools for measuring this variation and the graphical methods for representing it. The statistical concepts of sampling, inference, distribution, central tendency, dispersion, distribution function, parameters, confidence intervals and dependence between variables for different types of variables (binomial, discrete, continuous) are explained with the help of practical exercises based on biological problems.

Competencies targeted by the EU (see competency framework):

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

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This course provides a basic understanding of microbiology. It will detail the structures of microorganisms, prokaryotes and eukaryotes, and viruses. It will give an overview of the diversity of these microorganisms and describe their mode of multiplication.

For bacteria, trophic types and factors influencing growth will be developed, as well as the study of growth in a non-renewed environment. Genetics and horizontal transfer between bacteria will also be covered.
A number of eukaryotic microorganisms will be studied: habitat, lifestyle, ecological role or parasitism, as well as their mode of development.
In virology, the main multiplication cycles of viruses will be detailed, and modes of transmission and the notion of viral pathogenesis will be covered. The principles of anti-viral vaccination and anti-viral treatments will be presented and illustrated with concrete examples.
The principles of antiviral vaccination and treatment will be presented and illustrated with concrete examples.
Practical work will introduce students to techniques for sterile handling of microorganisms, bacterial counting and conjugation.

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This module will enable students to acquire :

Physiology basics : concept of homeostasis; levels of organization of the human body; compartments of the internal environment; study of the endocrine system; acid-base and hydro-mineral balance; anatomical and functional studies of the central and peripheral nervous systems.

Immunology basics :

General presentation 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 enables students to consolidate the foundations of biochemistry acquired in L1 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 basics of Michael enzymology, description of the metabolic reactions involved in glycolysis. Finally, the technical aspect will be addressed through the presentation and analysis of techniques for measuring enzymatic activity, purifying, quantifying and detecting proteins.

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Description*: This second general chemistry teaching unit 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 a presentation using mathematical formalism, which would require a much greater time commitment, the student will be asked to understand the physical meaning of these principles and the main thermodynamic functions, and to apply them to chemical systems, often of biological interest. In particular, resting membrane potentials and the use of pH potential diagrams in biology will be presented.

In advance of certain courses and tutorials, students will work on written and audio course documents, to ensure that classroom teaching and tutorials enable them to play a full part in the training, understand the concepts presented and the skills to be acquired.

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1- Linux basics (1.5h CM + 3hTD) : Basic commands to navigate under Linux and understand the logic of this language. Small information extraction exercises in bash/shell. Element used to analyze alignment files.

2- Database (3h CM + 4,5hTD): knowledge of the main bibliographic and biological databases (NCBI, Ensembl, Galaxie...). Relevant and efficient queries, exploitation, sorting, description of different formats.

3- Sequence analysis (1.5hCM + 4.5H TD): Alignment and comparison of sequences with a short introduction to phylogeny (dot plot, Blast ...).

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

- Cell biology: 4 major themes will be covered: 1) Cell cytoskeleton function, 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 monitor cell distribution dynamics, assessment of the importance of proteins of interest in a cellular process by strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology : After acquiring knowledge of transcription and translation mechanisms in Semester 3, we'll move on to the regulation of gene expression: transcriptional regulation (repressor, activator) and attenuation in prokaryotes, the basics of expression regulation mechanisms in eukaryotes.

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Learn about the major families of plant molecules and their properties, the biosynthetic pathways of these molecules, and the mechanisms regulating these biosyntheses in plants and microorganisms. In this module, the major families of molecules resulting from secondary plant metabolism (terpenes, flavonoids, alkaloids, saponins) are studied through their biosynthesis in the plant and the differentiation of specialized cell structures or groups. Based on this knowledge, biotechnological approaches for metabolic engineering are presented. The role of these molecules in plant life is discussed, as are their properties for industrial use as colorants, aromas, perfumes, medicines and biofuels. The use of natural polymers in the manufacture of industrial materials (paper pulp, rubber, plastics) is discussed, and production channels are described. Knowledge of the major families of plant molecules and their properties, the biosynthesis pathways of these molecules, and the mechanisms regulating these biosyntheses in the plant remains a major challenge for the development of biorefining in Europe.                                              

Key words: secondary metabolism, metabolic engineering, valorization of biomolecules, cellular and metabolic differentiation, regulation of secondary metabolism.

Additional information :

Visits to 2 analytical platforms are planned at the Montpellier site (duration 1h30 each).

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The aim of this course is to understand evolutionary processes on both micro- and macro-evolutionary scales.

Using examples, manipulations and accessible modeling, the aim of the lessons is to present, in a concrete and quantitative way, the effects of the 4 evolutionary forces operating on the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes on larger time scales (e.g. differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to the tools of phylogeny (tree reading and construction), making it possible to study macro-evolutionary events (diversification, extinction) and trace changes in character states, notably by integrating fossil data.

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Physiology of major functions (semester 4) aims to describe the role and interactions of the body's various systems in maintaining a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive and renal systems and their nervous and hormonal controls. Understand the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac insufficiency; hemorrhage; exposure to extreme environments.

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This compulsory UE will enable students to deepen their skills acquired in "S3 biochemistry". It will enable them to understand cellular metabolism through:

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

- description of metabolic pathologies.

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In this introductory course to genetic analysis, the objectives are to learn about the terms, principles, concepts and methods used in formal genetics, as well as their fields of application, particularly in human and medical genetics. The course covers the genetics of transmission (Mendelian or non-Mendelian), quantitative genetics and notions 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 community. 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 (symbioses, parasitism-pathogenicity), using popular biological models (mycorrhizal or nitrogen-fixing symbioses, diseases caused by different microorganisms). This will also be an opportunity to present emerging concepts in the field, such as the microbiome or the holobiont.

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1- Linux basics (1.5h CM + 3hTD) : Basic commands to navigate under Linux and understand the logic of this language. Small information extraction exercises in bash/shell. Element used to analyze alignment files.

2- Database (3h CM + 4,5hTD): knowledge of the main bibliographic and biological databases (NCBI, Ensembl, Galaxie...). Relevant and efficient queries, exploitation, sorting, description of different formats.

3- Sequence analysis (1.5hCM + 4.5H TD): Alignment and comparison of sequences with a short introduction to phylogeny (dot plot, Blast ...).

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

- Cell biology: 4 major themes will be covered: 1) Cell cytoskeleton function, 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 monitor cell distribution dynamics, assessment of the importance of proteins of interest in a cellular process by strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology : After acquiring knowledge of transcription and translation mechanisms in Semester 3, we'll move on to the regulation of gene expression: transcriptional regulation (repressor, activator) and attenuation in prokaryotes, the basics of expression regulation mechanisms in eukaryotes.

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The aim of this course is to broaden previously acquired knowledge in various areas of microbiology, in particular microbial ecology.

She will focus on pathogenic relationships, but will also present examples of symbiotic associations. Applications of microorganisms in biotechnology will be discussed. It will describe the mode of action of antibiotics and associated resistance phenomena, as well as their impact.

This course will introduce the notion of viral ecology, presenting the place and role of viruses in ecosystems. The case of bacteriophages will be dealt with more specifically, and the mechanisms of bacterial resistance to phagic infection will be detailed. The different types of viral infection in animals will be presented (acute and persistent infections) and illustrated by studying the pathogenesis of selected viral infections.

Our knowledge of microorganisms will be extended by the study of Archaea and a model eukaryotic organism, yeast.

Practical work will focus on carrying out an antibiogram and its interpretation, and on bacteriophage titration.

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Learn about the major families of plant molecules and their properties, the biosynthetic pathways of these molecules, and the mechanisms regulating these biosyntheses in plants and microorganisms. In this module, the major families of molecules resulting from secondary plant metabolism (terpenes, flavonoids, alkaloids, saponins) are studied through their biosynthesis in the plant and the differentiation of specialized cell structures or groups. Based on this knowledge, biotechnological approaches for metabolic engineering are presented. The role of these molecules in plant life is discussed, as are their properties for industrial use as colorants, aromas, perfumes, medicines and biofuels. The use of natural polymers in the manufacture of industrial materials (paper pulp, rubber, plastics) is discussed, and production channels are described. Knowledge of the major families of plant molecules and their properties, the biosynthesis pathways of these molecules, and the mechanisms regulating these biosyntheses in the plant remains a major challenge for the development of biorefining in Europe.                                              

Key words: secondary metabolism, metabolic engineering, valorization of biomolecules, cellular and metabolic differentiation, regulation of secondary metabolism.

Additional information :

Visits to 2 analytical platforms are planned at the Montpellier site (duration 1h30 each).

See full page

The aim of this course is to understand evolutionary processes on both micro- and macro-evolutionary scales.

Using examples, manipulations and accessible modeling, the aim of the lessons is to present, in a concrete and quantitative way, the effects of the 4 evolutionary forces operating on the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes on larger time scales (e.g. differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to the tools of phylogeny (tree reading and construction), making it possible to study macro-evolutionary events (diversification, extinction) and trace changes in character states, notably by integrating fossil data.

See full page

Physiology of major functions (semester 4) aims to describe the role and interactions of the body's various systems in maintaining a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive and renal systems and their nervous and hormonal controls. Understand the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac insufficiency; hemorrhage; exposure to extreme environments.

See full page

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This compulsory UE will enable students to deepen their skills acquired in "S3 biochemistry". It will enable them to understand cellular metabolism through:

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

- description of metabolic pathologies.

See full page

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

See full page