SV S5 Profile Selection

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This laboratory session is designed to help students apply their 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 steps: 1) isolation of the bacterial flora; 2) identification of the family and genus using conventional media and tests; 3) identification of the species using API System galleries.

Molecular biology techniques now make it possible to identify the bacteria present in a sample without the need for culture. This approach requires access to a sequencing platform and will also be carried out during lab sessions, which will allow for a comparison of the two approaches. The sequencing results obtained will enable a bioinformatics analysis of the rrsA gene encoding the 16S rRNA of the isolated bacteria.

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This course describes the methodology used by life sciences researchers to communicate the results of their experiments, both in writing and orally. Since English is the common language of international researchers, a large portion of this course is taught in English.

Written communication is addressed through an examination of the (macro) structure of a research article, as well as through an examination of the publication process in scientific journals. Several elements of written (micro) structure are examined in order to understand the differences between scientific English and literary English: clarity, cohesion, and coherence.

These courses are supplemented by a supervised project during the semester, in which students are required to analyze a research article recently published in the scientific literature and present it as an oral presentation (lecture) in English.

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This course unit serves as a logical continuation of the S4 course unit (Fundamentals of Physiology and Immunology) and aims to deepen students’ knowledge of basic, applied, and clinical immunology. We will also explore “non-conventional” concepts in immunology and discuss innovative immunotherapy strategies. This course will cover all topics related to modern immunology and will have a strong focus on the clinical aspects of this discipline.

 Keywords

Basic Immunology, Anti-infectious Immunity, Immunotherapy, Vaccination, Autoimmunity, Immunodeficiencies, Anti-cancer Immunity, Non-conventional Immunity

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Molecular biology is not only a fascinating field of study in its own right, but it also provides other branches of biology (cell biology, genetics, physiology, etc.) with fantastic tools for modifying and quantifying genes and their products.

The EU is deepening our understanding of the mechanisms underlying 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 the interactions between them account for the functioning of eukaryotic cells and their adaptation to the environment and to the development of organisms.

At the same time, the main techniques used to monitor or modify gene expression—or to study the mechanisms underlying gene expression—will be covered in lectures and explored in greater depth in tutorials through the analysis of results.

Thus, the tutorials address these topics through (1) exercises that allow students to assess their understanding of the concepts described above, and (2) experiments drawn from scientific articles for analysis. In this way, students will acquire and/or deepen their understanding of the fundamentals of scientific reasoning and the critical analysis of results.

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This course unit is designed to deepen students' knowledge of microbiology for those who wish to continue their studies in this field.

It will cover molecular genetics as applied to prokaryotes (mobile genetic elements and resistance, CRISPR, the two-component system, quorum sensing, horizontal gene transfer, etc.) and the specific characteristics of bacterial metabolism.

Bacteria with distinctive morphologies will be presented.  

In virology, the pathophysiology of viral infections, as well as the prevention and control of viral diseases, will be presented. The mechanisms by which viruses evade the immune system will be discussed in detail. The 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 obligate intracellular development and the changes in the host cell induced by these parasites.

The EU will finally address the concept of the microbiome and present the latest data on the nature of the human microbiome and its role in health.

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This course is a specialization module in Functional Plant Biology that explores the mechanisms underlying the major stages of plant development.

It draws on knowledge derived primarily from the model plant Arabidopsis thaliana and addresses the following concepts from molecular, cellular, and physiological perspectives:

• Roles and Functions of the Major Phytohormones.
• Development of male and female gametes; fertilization.
• Development of the embryo, seed, and fruit.
• Function of root and stem meristems (vegetative and floral).
• The Architecture of the Flower.
• Mechanisms of adaptive development in response to abiotic factors: light, gravity, and 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 land plants (evolution of the root system, floral architecture, etc.).

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This course describes the methodology used by life sciences researchers to communicate the results of their experiments, both in writing and orally. Since English is the common language of international researchers, a large portion of this course is taught in English.

Written communication is addressed through an examination of the (macro) structure of a research article, as well as through an examination of the publication process in scientific journals. Several elements of written (micro) structure are examined in order to understand the differences between scientific English and literary English: clarity, cohesion, and coherence.

These courses are supplemented by a supervised project during the semester, in which students are required to analyze a research article recently published in the scientific literature and present it as an oral presentation (lecture) in English.

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Bioinformatics is a discipline at the intersection of computer science, mathematics, and the life sciences. It relies in particular on the use and development of computational 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 course unit “Bioinformatics Applied to Plant Biology” aims to familiarize students with the use of databases and provide an introduction to data exploration using the R software.

Virtually all instruction will take the form of practical exercises in the computer lab in small groups of students.

In the first part, students will learn the basics of the R programming language, which will enable them to organize and clean their raw data so that it can be fully utilized for subsequent analyses. Next, they will learn how to create clear graphical representations based on biological data. Particular attention will be given to writing reusable scripts and selecting appropriate graphics for the calculations based on the biological question at hand.

In the second part of the course, students will use general-purpose databases such as NCBI or those dedicated exclusively to the model plant Arabidopsis (TAIR) to conduct data mining.

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Molecular biology is not only a fascinating field of study in its own right, but it also provides other branches of biology (cell biology, genetics, physiology, etc.) with fantastic tools for modifying and quantifying genes and their products.

The EU is deepening our understanding of the mechanisms underlying 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 the interactions between them account for the functioning of eukaryotic cells and their adaptation to the environment and to the development of organisms.

At the same time, the main techniques used to monitor or modify gene expression—or to study the mechanisms underlying gene expression—will be covered in lectures and explored in greater depth in tutorials through the analysis of results.

Thus, the tutorials address these topics through (1) exercises that allow students to assess their understanding of the concepts described above, and (2) experiments drawn from scientific articles for analysis. In this way, students will acquire and/or deepen their understanding of the fundamentals of scientific reasoning and the critical analysis of results.

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Functional genetics aims to better understand the relationships between genotype and phenotype. This course covers various aspects of analyzing gene and genome function at the whole-genome level using in vivo approaches, as well as transcriptional regulation and the regulation of gene expression in eukaryotic genomes. The course is illustrated with concrete examples from developmental genetics in both physiological and pathological contexts.

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

The basic concepts and terminology used in the analysis of 3D protein structures are briefly reviewed here (Ramachandran plot, 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 described in detail based on 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 various structures and functions of nucleic acids are studied. Protein-nucleic acid complexes are described from a structural perspective (main recognition motifs, etc.), and the concepts of recognition specificity are explained in detail.

This course is supplemented by tutorials. These tutorials are designed to familiarize 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 of formal and structural enzymology.

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

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

Definition of an enzyme, a catalyst. Enzyme classification (EC)

Michaelis kinetics. Michaelis-Menten equation. Definition of enzymatic parameters:_KM, maximum velocity, catalytic constant, turnover. Various graphical representations (Lineweaver-Burk, Eadie-Hofstee). 

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

Determination of the inhibition constant. Irreversible inhibitors.

Reaction rate. Arrhenius's law.

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

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

Graphical determination.

- Part 4 covers equilibrium binding and allosterism.

Receptor-Ligand / Enzyme-Substrate Binding. Determination of the dissociation (or association) constant. Specific and nonspecific binding.

Scatchard's demonstration and graphical representation. Allosteric receptors (or enzymes). Non-Michaelis enzyme. Concept of cooperativity. Positive and negative cooperativity. Hill number, Hill plot.

Allosteric regulation models are presented. Allostery. Models of cooperativity: 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 explores the relationship between enzyme structures and their functions using several examples. It describes the 3D structures and catalytic mechanisms of acetylcholine esterase, proteases, and nucleoside diphosphate kinase. It also covers concepts such as the catalytic triad, the binding pocket, and more. 

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This course describes the methodology used by life sciences researchers to communicate the results of their experiments, both in writing and orally. Since English is the common language of international researchers, a large portion of this course is taught in English.

Written communication is addressed through an examination of the (macro) structure of a research article, as well as through an examination of the publication process in scientific journals. Several elements of written (micro) structure are examined in order to understand the differences between scientific English and literary English: clarity, cohesion, and coherence.

These courses are supplemented by a supervised project during the semester, in which students are required to analyze a research article recently published in the scientific literature and present it as an oral presentation (lecture) in English.

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Molecular biology is not only a fascinating field of study in its own right, but it also provides other branches of biology (cell biology, genetics, physiology, etc.) with fantastic tools for modifying and quantifying genes and their products.

The EU is deepening our understanding of the mechanisms underlying 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 the interactions between them account for the functioning of eukaryotic cells and their adaptation to the environment and to the development of organisms.

At the same time, the main techniques used to monitor or modify gene expression—or to study the mechanisms underlying gene expression—will be covered in lectures and explored in greater depth in tutorials through the analysis of results.

Thus, the tutorials address these topics through (1) exercises that allow students to assess their understanding of the concepts described above, and (2) experiments drawn from scientific articles for analysis. In this way, students will acquire and/or deepen their understanding of the fundamentals of scientific reasoning and the critical analysis of results.

View the full page

Functional genetics aims to better understand the relationships between genotype and phenotype. This course covers various aspects of analyzing gene and genome function at the whole-genome level using in vivo approaches, as well as transcriptional regulation and the regulation of gene expression in eukaryotic genomes. The course is illustrated with concrete examples from developmental genetics in both physiological and pathological contexts.

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This course unit enables students to deepen their understanding of metabolism. It provides a comprehensive overview of human metabolism. It will emphasize the connections between various metabolic pathways. It will also demonstrate how different tissues communicate with one another to maintain overall energy homeostasis. Disruptions in this metabolic process that lead to certain diseases will be discussed.

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Students will be required to conduct a literature review on a topic of their choice, which must be approved by the course instructors. Under the guidance of a faculty member, students must address the research question they have identified through an analysis of the available literature. They must provide a review of the current state of the art in their field, identifying areas of uncertainty, controversy, and unresolved questions. They must conduct a genuine critical scientific analysis of the available literature, rather than merely summarizing it. They must adhere to the conventions for writing a scientific article, including citing sources, synthesizing information through illustrations, framing the research question, and synthesizing scientific results.

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This unit builds on the "Basics of Evolution" unit to introduce the main concepts in evolutionary ecology, with the aim of understanding and formally describing, in a straightforward manner, the evolutionary and ecological mechanisms that shape biodiversity at various levels of integration.

This course unit is designed as a coherent whole in which lectures, tutorials, and lab sessions complement one another. Concepts are introduced through examples and then formalized using mathematical models, which are then tested against experimental results and real-world data.

It will cover population dynamics (intra- and interspecific competition) and ecological niches, and will detail the mechanisms of evolution and their genetic consequences at the population level: natural selection (including sexual selection), the influence of reproductive strategies, and genetic drift. The tutorials will enable students to master the mathematical formalization of concepts covered in class, their simple computer modeling, and the analysis of datasets. The lab sessions will involve conducting and analyzing, in small groups, two experiments lasting one month each (including the writing of a report and an oral presentation) in order to develop scientific methodology and reasoning.

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The EU is organized into five major areas:

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

Topic 2: Introduction to Molecular Evolution: Measuring the intensity of selection in genetic divergence. The molecular clock and variation in evolutionary rates caused by natural selection. The neutral theory of evolution.

Topic 3: Introduction to Genomics: Composition and Size of Genomes. Importance of Repeated Elements. Concepts of Genetic Linkage and Local Selection Effects. Influence of Demographics.

Topic 4: Molecular Tools for Biodiversity: Barcoding, eDNA, metabarcoding. Molecular taxonomy. Limitations related to hybridization. Applications in conservation.

Topic 5: Extranuclear inheritance . Symbiosis, parasitism, and coevolution (intracellular: e.g., Wolbachia). The concept of the extended phenotype.

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This course will cover the concepts necessary for understanding the way of life of the major groups of single-celled organisms that form the basis of ecosystem functioning (viruses, bacteria, archaea, and single-celled eukaryotes, etc.). The lectures will cover the biological organization of each type of organism, their modes of reproduction, and their diversity, leading to an understanding of ecological concepts. We will examine the role of these microorganisms in the functioning and dynamics of ecosystems, considering the interactions these organisms have with other living beings (the concept of “symbiosis” in all its forms).

The hands-on exercises will allow students to:

 - the implementation of techniques for bacterial counting (CFU) and the identification of a specific strain from an environmental sample

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

 - identifying the unique characteristics of interactions between bacteria and bacteriophages

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The main objective is to learn the basics of the comparative anatomy of chordates so that we can compare and classify them, before tracing the key stages of their evolutionary history. The course is integrative in that it draws on both extant organisms and the fossil record to document the evolutionary history of the clade in its entirety and from all angles. Anatomical, biomechanical, phylogenetic, and ecomorphological approaches will be covered in lectures to illustrate the diversity and major characteristics of chordates. The lab sessions (and tutorials) will illustrate the evolution of diversity in the integument, skeleton, musculature, and digestive and respiratory systems over long time scales.

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This course is a natural continuation of the course “Quantification of Randomness” (HAV424B) offered in Semester 4. It is designed to provide students with the concepts needed to develop experimental protocols that address biological questions and to apply appropriate models for analyzing variability. The first part will focus on designing experimental protocols capable of addressing a wide range of questions in the life sciences, specifically by taking into account the inevitable dependencies among statistical individuals, such as kinship and the spatial or temporal structure of populations. This section will thus provide an opportunity to address the concepts of fluctuation, replication, and pseudo-replication, which will be incorporated into the models developed in the second part of the course. The second part will focus on demonstrating the link between the experimental protocol implemented and the modeling of the variability of a quantitative response variable, through the development of models that include several qualitative or quantitative variables. Particular attention will be paid to the conditions under which these methods are applicable, to Type I and Type II errors, to methods for estimating the parameters of the constructed models (including likelihood), and to the interpretation of the estimated parameters. Each concept will be illustrated through the analysis of real biological data from various fields, thereby helping students discover not only current and common biological questions but also the tools developed to address them. Hands-on exercises using R will enable students to independently perform analyses on published biological case studies.

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This course describes the methodology used by life sciences researchers to communicate the results of their experiments, both in writing and orally. Since English is the common language of international researchers, a large portion of this course is taught in English.

Written communication is addressed through an examination of the (macro) structure of a research article, as well as through an examination of the publication process in scientific journals. Several elements of written (micro) structure are examined in order to understand the differences between scientific English and literary English: clarity, cohesion, and coherence.

These courses are supplemented by a supervised project during the semester, in which students are required to analyze a research article recently published in the scientific literature and present it as an oral presentation (lecture) in English.

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Through hands-on laboratory sessions, students will study various physiological regulatory mechanisms in animals.

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

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

Learning all the elements necessary to successfully carry out the required lab protocol in order to obtain results and write a lab report.

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This course unit serves as a logical continuation of the S4 course unit (Fundamentals of Physiology and Immunology) and aims to deepen students’ knowledge of basic, applied, and clinical immunology. We will also explore “non-conventional” concepts in immunology and discuss innovative immunotherapy strategies. This course will cover all topics related to modern immunology and will have a strong focus on the clinical aspects of this discipline.

 Keywords

Basic Immunology, Anti-infectious Immunity, Immunotherapy, Vaccination, Autoimmunity, Immunodeficiencies, Anti-cancer Immunity, Non-conventional Immunity

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

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

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

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