CHOICE HAV415V

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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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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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