SV S5 Profile Selection

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This practical work unit aims to apply students' knowledge of microbiology and molecular biology to identify bacteria in the environment.

Quantitative and qualitative analysis of the bacterial population present in a soil sample is typically performed by identifying species using conventional bacteriological methods in successive stages: 1) isolation of the bacterial flora; 2) diagnosis of family and genus using conventional media and tests; 3) diagnosis of species using API System galleries.

Molecular biology techniques now make it possible to identify bacteria present in a sample without the need for culture. This approach requires access to a sequencing platform and will also be carried out in practical work, allowing the two approaches to be compared. The sequencing results obtained will enable bioinformatic analysis of the rrsA gene specifying the 16S RNA of the isolated bacteria.

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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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This EU is a logical continuation of the S4 EU (Fundamentals of Physiology and Immunology) and aims to deepen knowledge of fundamental, applied, and clinical immunology. We will also address "unconventional" concepts in immunology and develop innovative immunotherapy strategies. This course unit will cover all topics related to modern immunology and will be strongly oriented towards the clinical aspects of this discipline.

 Keywords

Fundamental immunology, Anti-infectious immunity, Immunotherapy, Vaccination, Autoimmunity, Immune deficiencies, Anti-cancer immunity, Non-conventional immunity

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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 course unit aims to deepen students' knowledge of microbiology for those who wish to pursue further studies in this discipline.

She will discuss molecular genetics applied to prokaryotes (mobile genetic elements and resistance, CRISPR, 2-component system, quorum sensing, horizontal transfers, etc.) and the specificities of bacterial metabolism.

Bacteria with a particular morphology will be presented.  

In virology, the pathophysiology of viral infections, as well as the prevention and control of viral diseases, will be presented. Mechanisms of immune evasion will be detailed. Mechanisms of viral evolution will be described and linked to viral emergence.

The parasitic lifestyle of certain eukaryotic microorganisms will be illustrated by describing their obligatory intracellular development and the changes in the host cell induced by these parasites.

Finally, the EU will address the concept of microbiota and present the latest data on the nature of human microbiota and its role in health.

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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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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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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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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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This course offers an in-depth study of the structural biochemistry of biomolecules, particularly proteins and nucleic acids.

The basic concepts and nomenclature used for analyzing 3D protein structures are briefly reviewed (Ramachandran diagram, structural motifs and domains, folding, family, superfamily, etc.). These concepts are supplemented by a study of the stability and dynamics of biomolecules.

The structural classification of proteins is detailed according to the four main types of folding. Structure-function relationships are illustrated using examples of proteins. The specific characteristics of membrane protein structures (integral proteins, membrane-bound proteins) are discussed.

The main tools for modeling and predicting secondary and tertiary structures are presented.

The different structures and functions of nucleic acids are studied. Protein-nucleic acid complexes are described from a structural point of view (main recognition motifs, etc.) and the concepts of recognition specificity are detailed.

This teaching is illustrated in tutorials. These tutorials consist of familiarizing students with the main databases used in structural biology, as well as with the PyMol software for analyzing 3D structures.

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This course provides fundamental knowledge in formal and structural enzymology.

- The first part of this course deals with formal kinetics (study of reaction rates, determination of the order of a reaction, equilibrium and kinetics, reversible and balanced reactions). The experimental aspects are presented in parallel (determination of kinetic constants by spectrophotometry, fluorescence, radioactivity, immunoassays, etc.).

- The second part of the course focuses on the study of single-substrate enzyme kinetics.

Definition of an enzyme, catalyst. Enzyme nomenclature (EC)

Michaelis kinetics. Michaelis-Menten equation. Definition of enzyme parameters,_KM, maximum velocity, catalytic constant, turnover. Different graphical representations (Lineweaer-Burk, Eadie-Hofstee). 

The different types of inhibition are also studied (competitive, noncompetitive, mixed) as well as their graphical representation.

Determination of inhibition constancy. Irreversible inhibitors.

Reaction rate. Arrhenius law.

- The third section focuses on describing multi-substrate enzyme kinetics from a formal perspective. With ternary complexes. Random or ordered mechanism.

Without ternary complex. Ping-Pong mechanism, Theorell-Chance. Cleland representation.

Graphical determination.

- The fourth part concerns equilibrium bonds and allostery.

Receptor-ligand/enzyme-substrate binding. Determination of the dissociation (or association) constant. Specific and non-specific binding.

Demonstration and graphical representation of Scatchard. Allosteric receptors (or enzymes). Non-Michaelian enzyme. Concept of cooperativity. Positive and negative cooperativity. Hill number, Hill graph.

Allosteric regulation models are presented. Allostery. Cooperative models: concerted (Monod-Wyman-Changeux) and sequential (Koshland-Nemethy-Filmer). Role of effectors, activators, or inhibitors. Example of hemoglobin and oxygen binding.

- The fifth part of the course links enzyme structures and their function using several examples. Description of the 3D structures and catalytic mechanisms of acetylcholinesterase, proteases, and nucleoside diphosphate kinase. Concept of catalytic triad, binding pocket, 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.

See the full page

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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This course unit allows students to deepen their knowledge of metabolism. It provides a comprehensive overview of human metabolism, emphasizing the links between different metabolic pathways. It also shows how different tissues communicate to maintain overall energy homeostasis. Disruptions in this metabolism that cause certain diseases will be presented.

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Students will be required to conduct a bibliographic analysis on a topic of their choice, approved by the EU officials. Under the supervision of a teacher-researcher, students will have to answer the questions they raise through an analysis of the available bibliography. They will have to review the state of the art in their field of work, identify areas of uncertainty and controversy, and open questions that remain to be resolved. They will be required to carry out a genuine critical scientific analysis of the available bibliography, rather than simply summarizing it. They will be required to follow the conventions for writing a scientific article, which involves citing sources, synthesizing information through illustration, problematization, and summarizing scientific results.

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This course builds on the Evolutionary Foundations course to introduce key concepts in evolutionary ecology in order to understand and formalize, in a simple way, the evolutionary and ecological mechanisms that shape biodiversity at different scales of integration.

This course unit is designed as a coherent whole, with lectures, tutorials, and practicals complementing each other. Concepts are introduced through examples and then formalized using mathematical models, which are tested against experiments and real-world data.

It will cover population dynamics (intra- and interspecific competition) and ecological niche, and will detail the mechanisms of evolution and their genetic consequences at the population level: natural selection (including sexual selection), the influence of reproductive regimes, and genetic drift. The tutorials will enable students to grasp the mathematical formalization of concepts covered in class and their simple computer modeling, as well as data set analysis. The practicals will enable small groups to carry out and analyze two experiments, each lasting one month (with a report and oral presentation), in order to develop scientific methodology and reasoning.

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The EU is organized into five main themes:

Topic 1: Genetic mapping and recombination. Concepts of molecular biology related to gene expression, DNA repair, and epigenetic processes.

Theme 2: Introduction to molecular evolution: Measuring the intensity of selection in genetic divergence. Molecular clock and variation in rates of evolution created by the action of natural selection. Neutral theory of evolution.

Theme 3: Introduction to genomics: composition and size of genomes. Importance of repeated elements. Concept of genetic linkage and local selection effects. Influence of demography.

Theme 4: Molecular tools for biodiversity: Barcoding, eDNA, metabarcoding. Molecular taxonomy. Limitations related to hybridization. Applications in conservation.

Theme 5: Extranuclear heredity . Symbiosis, parasitism, and co-evolution (intracellular: e.g., Wolbachia). Extended concept of phenotype.

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This teaching unit will aim to address the elements necessary for understanding the lifestyle of large groups of single-celled organisms that form the basis of ecosystem functioning (viruses, bacteria, archaea, and single-celled eukaryotes, etc.). The courses cover the biological organization of each type of organism, their modes of reproduction, and their diversity, leading to concepts of ecology. We will discuss the role of these microorganisms in the functioning and dynamics of ecosystems, considering the interactions that these organisms have with other living beings (the concept of "symbiosis" in all its forms).

The practical work will enable:

 - the implementation of techniques enabling bacterial enumeration (CFU) and the identification of a particular strain from an environmental sample

 - highlighting the diversity of phytoplankton (single-celled algae) in aquatic environments (freshwater)

 - highlighting the specificity of interactions between bacteria and bacteriophages

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The main objective is to learn the basics of comparative anatomy of chordates, so that they can be compared and classified, before tracing the key stages of their evolutionary history. The lessons are integrative in that they draw on both current organisms and the fossil record to document the evolutionary history of the clade in its entirety and in all its aspects. Anatomical, biomechanical, phylogenetic, and ecomorphological approaches will be addressed in lectures to illustrate the diversity and major characteristics of chordates. Practical work (and tutorials) will illustrate the evolution of the diversity of integuments, the skeleton, musculature, and the digestive and respiratory systems over long periods of time.

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This course is a natural continuation of the course " Quantification of Risk " (HAV424B) presented in S4. It aims to provide the concepts for constructing experimental protocols that answer biological questions and to associate them with appropriate models for analyzing variability. The first part will be devoted to the construction of experimental protocols that can answer a multitude of questions in the life sciences, i.e., taking into account the inevitable dependence of statistical individuals, such as kinship, spatial or temporal structure of populations. This part will provide an opportunity to address the concepts of fluctuation, replication, and pseudo-replication, which will be taken into account in the models constructed in the second part of the course. The second part will focus on demonstrating the link between the experimental protocol carried out and the modeling of the variability of a quantitative response variable, through the construction of models including several qualitative or quantitative variables. Particular attention will be paid to the conditions for applying these methods, type I and II errors, methods for estimating the parameters of the models constructed (including likelihood), and the interpretation of the estimated parameters. Each concept will be illustrated by the analysis of real biological data from several topics, helping students to discover not only modern and current biological issues but also the tools developed to address them. Practical work using R will enable students to independently perform analyses on published biological cases.

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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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Through practical work sessions, study of different physiological regulations in animals.

Acquisition of surgical techniques in rats to determine blood volume, osmotic diuresis and renal permeability, the action of adrenaline and insulin on blood sugar levels, inulin clearance, and the mechanisms of glucose transport across the intestinal wall.

Study of the mechanical and electrical functioning of the frog heart.

Learning all the elements necessary to successfully complete the required practical work protocol in order to obtain results and compile a report.

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This EU is a logical continuation of the S4 EU (Fundamentals of Physiology and Immunology) and aims to deepen knowledge of fundamental, applied, and clinical immunology. We will also address "unconventional" concepts in immunology and develop innovative immunotherapy strategies. This course unit will cover all topics related to modern immunology and will be strongly oriented towards the clinical aspects of this discipline.

 Keywords

Fundamental immunology, Anti-infectious immunity, Immunotherapy, Vaccination, Autoimmunity, Immune deficiencies, Anti-cancer immunity, Non-conventional immunity

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The objective of this teaching unit is to provide an integrated approach to the functioning of the nervous system, drawing on several disciplines within neuroscience (neurodevelopment, functional neuroanatomy, neuroimaging, cognitive neuroscience) and focusing on complex brain functions.

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The objective of this EU is the morpho-functional study of cells in the nervous system (neurons, glial cells), namely: the description of the mechanisms involved in neuronal excitability (generation and propagation of action potentials) and neurotransmission (mechanisms of neurotransmitter release and synthesis, and the structure and function of neurotransmitter receptors). The concepts of synaptic plasticity are also developed.

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The cardiovascular physiology course aims to describe and acquire knowledge about the functioning of the cardiovascular system of the whole animal at the molecular and cellular levels. Topics covered will include cardiac contraction, regulation of cardiac electrical activity (electrocardiogram and ion channels), regulation of blood pressure and baroreflex, and regulation of cardiovascular functions by the autonomic nervous system.

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