L2 - Plant Biology for the Agro-Environment

This compulsory UE in S3 allows students to consolidate and deepen the basics 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 various perspectives of technological applications, and the molecular mechanisms of the main steps of Molecular Biology, such as DNA replication, transcription of genes into mRNAs and translation of these into proteins. These steps, illustrated by experimental evidence 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 Part: Major concepts of membrane and cytosolic protein complex formation will be discussed, particularly in the context of cell signaling pathways. The notions of ligands, receptors, scaffolding proteins, enzymatic signaling proteins, intracellular second messengers, response kinetics will be presented. Biochemistry and cell biology techniques to demonstrate the presence and localization of proteins in cells and tissues will be presented.

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Description of the EU (max 10 lines):

The objective of this course is to understand 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 gives 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 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.

Competences aimed at by the UE (see reference frame of competences):

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

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This course provides the fundamental basis 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 transfers between bacteria will be discussed.
Some eukaryotic microorganisms will be studied: habitat, life style, ecological role or parasitism as well as their mode of development.
In virology, the main multiplication cycles of viruses will be detailed, the modes of transmission and the notion of viral pathogenesis will be discussed. The principle of anti-viral vaccination and anti-viral treatments will be presented and illustrated with concrete examples.
The principle of anti-viral vaccination and anti-viral treatments will be presented and illustrated with concrete examples.
The practical work will allow the initiation to the techniques of sterile manipulation of microorganisms, to the counting of bacteria and to conjugation.

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This module should enable students to acquire:

Basic notions 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 hydro-mineral balance; anatomical and functional studies of the central and peripheral nervous system.

Basic concepts in Immunology:

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 allows students to consolidate the basics of biochemistry acquired in L1 by approaching this discipline through a transversal study of enzymes involved in cellular metabolism, particularly glycolysis. Several areas of biochemistry will be covered: the basics of Michaelian enzymology, the description of metabolic reactions involved in glycolysis. Finally, the technical aspect will be approached by the presentation and the analysis of the techniques allowing to measure an enzymatic activity, to purify, to quantify and to detect proteins.

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Description*: This second unit of general chemistry aims to consolidate and deepen the study of reactions in aqueous solution, especially 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 that would require a much larger 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.

The students will work before certain courses and tutorials on course documents (written and audio) so that the classroom teaching in courses and tutorials can allow them to be fully involved in the training, to 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 exercises to extract information in bash/shell. Element used for the analysis of alignment files.

2- Database (3h CM + 4,5hTD): know the main bibliographic and biological databases (NCBI, Ensembl, Galaxie...). Know how to make relevant and efficient queries, exploit, sort, description of the different formats

3- Sequence analysis (1,5hCM + 4,5H TD): Alignment and comparison of sequences with a small introduction to phylogeny (dot plot, Blast ...)

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This compulsory UE of S4 allows students to consolidate and deepen the bases of molecular and cellular biology acquired in L1.

- Cell biology: The teaching will focus on 4 major themes: 1) The functioning of the cell cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation for the detection of protein interactions, fluorescence videomicroscopy to follow the dynamics of cell distribution, evaluation of the importance of proteins of interest in a cellular process by strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology : After acquiring in semester 3 knowledge concerning the mechanisms of transcription and translation, we will approach the regulation of gene expression: transcriptional regulation (repressor, activator) and attenuation in prokaryotes, the bases of the mechanisms of regulation of expression in eukaryotes.

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To know the major families of plant molecules and their properties, the biosynthetic pathways of these molecules, the mechanisms of regulation of these biosyntheses in the plant and microorganisms. In this module, the major families of molecules from secondary plant metabolism (terpenes, flavonoids, alkaloids, saponins) are studied through their biosynthesis in the plant and the differentiation of specialized structures or groups of 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, flavors, fragrances, drugs, biofuels. The use of natural polymers in the manufacture of industrial materials is discussed (paper pulp, rubber, plastics) and the production channels are described. Knowledge of the major families of plant molecules and their properties, the biosynthesis pathways of these molecules, and the mechanisms of regulation of these biosyntheses in the plant 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 of 2 analytical platforms are planned on the Montpellier pole (duration 1h30 each)

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

Based on examples, manipulations and accessible modeling, the lessons will aim at presenting in a concrete and quantitative way the effects of the 4 evolutionary forces operating at the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes at 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 (reading and construction of trees) allowing the study of macro-evolutionary events (diversification, extinction) and the tracing of changes in character states, notably by integrating fossil data.

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The Physiology of major functions (semester 4) aims to describe the role and interactions of the various systems of the organism that contribute to 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 course will allow students to deepen their skills acquired in "S3 biochemistry". It will allow them to understand cellular metabolism through:

-The understanding of bioenergetics in order to study the processes by which living cells carry, transmit, use, store and release energy;
-the study of catabolism and anabolism of carbohydrates, lipids, nucleotides, 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 the terms, principles, concepts and methods used in formal genetics, as well as their application in human and medical genetics. This 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 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, their nutrition, their health. In this module, we will present the different forms that these biotic interactions can take (symbioses, parasitism-pathogenicity) based on popular biological models (mycorrhizal or nitrogen-fixing symbioses, diseases caused by different microorganisms). It 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 exercises to extract information in bash/shell. Element used for the analysis of alignment files.

2- Database (3h CM + 4,5hTD): know the main bibliographic and biological databases (NCBI, Ensembl, Galaxie...). Know how to make relevant and efficient queries, exploit, sort, description of the different formats

3- Sequence analysis (1,5hCM + 4,5H TD): Alignment and comparison of sequences with a small introduction to phylogeny (dot plot, Blast ...)

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This compulsory UE of S4 allows students to consolidate and deepen the bases of molecular and cellular biology acquired in L1.

- Cell biology: The teaching will focus on 4 major themes: 1) The functioning of the cell cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation for the detection of protein interactions, fluorescence videomicroscopy to follow the dynamics of cell distribution, evaluation of the importance of proteins of interest in a cellular process by strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology : After acquiring in semester 3 knowledge concerning the mechanisms of transcription and translation, we will approach the regulation of gene expression: transcriptional regulation (repressor, activator) and attenuation in prokaryotes, the bases of the mechanisms of regulation of expression in eukaryotes.

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

It will deal with pathogenic relationships, but will also present examples of symbiotic associations. It will address the applications of microorganisms in biotechnology. It will describe the mode of action of antibiotics and the associated resistance phenomena and their impact.

The EU will approach the notion of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be treated more specifically and the mechanisms of resistance of bacteria to phagic infection will be detailed. The different types of viral infections in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

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

The practical work will focus on the realization of an antibiogram and its interpretation, and on the titration of bacteriophages.

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To know the major families of plant molecules and their properties, the biosynthetic pathways of these molecules, the mechanisms of regulation of these biosyntheses in the plant and microorganisms. In this module, the major families of molecules from secondary plant metabolism (terpenes, flavonoids, alkaloids, saponins) are studied through their biosynthesis in the plant and the differentiation of specialized structures or groups of 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, flavors, fragrances, drugs, biofuels. The use of natural polymers in the manufacture of industrial materials is discussed (paper pulp, rubber, plastics) and the production channels are described. Knowledge of the major families of plant molecules and their properties, the biosynthesis pathways of these molecules, and the mechanisms of regulation of these biosyntheses in the plant 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 of 2 analytical platforms are planned on the Montpellier pole (duration 1h30 each)

See full page

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

Based on examples, manipulations and accessible modeling, the lessons will aim at presenting in a concrete and quantitative way the effects of the 4 evolutionary forces operating at the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes at 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 (reading and construction of trees) allowing the study of macro-evolutionary events (diversification, extinction) and the tracing of changes in character states, notably by integrating fossil data.

See full page

The Physiology of major functions (semester 4) aims to describe the role and interactions of the various systems of the organism that contribute to 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 course will allow students to deepen their skills acquired in "S3 biochemistry". It will allow them to understand cellular metabolism through:

-The understanding of bioenergetics in order to study the processes by which living cells carry, transmit, use, store and release energy;
-the study of catabolism and anabolism of carbohydrates, lipids, nucleotides, 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 the terms, principles, concepts and methods used in formal genetics, as well as their application in human and medical genetics. This 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 and molecular genetics.

See full page