Bachelor's Degree (3rd Year) in CPES: Modeling and Numerical Methods in the Life Sciences

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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.

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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 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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This course builds on the Structural Biochemistry course taken in S5. Students will learn the basic concepts of the various approaches used for multiscale structural characterization, as well as the analysis of macromolecular interactions. The advantages and limitations of all these tools will be highlighted so that students can understand how they complement one another and learn to use them in an integrated manner to address a given biological question. 

The lab sessions will combine the application of structural analysis using visualization tools (such as PyMOL) with the analysis of research articles that employ a combination of the approaches covered in the lecture series. Students will then be required to design their own experimental project to address a specific research question.

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This course provides a concise overview of the concepts necessary for mathematical modeling in biology. The focus is on linear and nonlinear dynamical systems in one and two dimensions. The course begins with essential concepts in linear algebra: matrices, systems of linear equations, and the geometric interpretation of the solutions to these systems as vectors and subspaces (lines, planes, etc.). The theory of vectors and eigenvalues of matrices is introduced in relation to linear dynamical systems. For nonlinear dynamical systems, the qualitative theory of differential equations (attractors, phase portraits, zero-level isoclines) is presented as an alternative to the often complicated calculation of solutions. The tutorial covers a wide range of biological models used in ecology, epidemiology, oncology, and systems biology.

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This course unit enables students to consolidate and deepen their understanding of the practical management of large amounts of experimental data collected during a one-week block of lab work (5 consecutive days). This data is collected through the implementation of numerous different protocols, with a focus on ensuring the best possible reproducibility of the experiments and maximizing efficiency in the preparation, execution, and analysis of the various experiments. A high degree of autonomy in setting up the protocols will be encouraged, ultimately leading to experimental proficiency and independence. These lab sessions also provide opportunities for group work (in pairs or groups of three, depending on facility capacity and class size) and for writing a report that thoroughly documents the protocols carried out, all experimental data obtained, and their analyses in order to determine a wide range of biochemical parameters. A significant portion of the evaluation will be based on the students’ ability to generate, manage, utilize, and analyze raw experimental data with the utmost rigor.

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As part of this course unit, students will learn the experimental principles involved in working with nucleic acids. The lectures will focus on two main areas:

1. Development of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, the CRISPR/Cas9 system, etc.) and reflection on ethical issues in biology.

The tutorials will consist of:

- Analysis of articles presenting problems to be solved using the knowledge gained in the course. The chosen topics will, as much as possible, relate to parallel course units in the third year of the bachelor’s program. Students will present these articles in the form of oral presentations, in groups of 3 to 4 students, to the entire class.

- Sessions dedicated to using basic bioinformatics tools in the computer lab.

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Systems biology offers the opportunity to understand how living organisms function at different organizational scales. This course will focus primarily on the subcellular scale. At this scale, systems biology models integrate multiple levels of interaction involving the transcriptome, proteome, and metabolome. Predictions from in silico models can be used in biomedical research to understand multifactorial diseases and optimize drug treatments; in bioengineering to synthesize genomes with optimized properties and functions (synthetic biology); and to guide basic research into the principles of how living systems function. The course consists of a theoretical component (lectures and tutorials on the modeling of gene, signaling, and metabolic networks) and a practical component (computer labs using MATLAB software).

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After defining intensive agriculture and analyzing its risks and benefits, this module will enable students to reflect on various possible approaches to transitioning agriculture toward an agroecological model. Examples such as biopesticides, ecological intensification, and soil management will be explored. A field trip to a company committed to sustainable agriculture is also organized. The site visited varies from year to year depending on student preferences and company availability. Examples of field trips conducted as part of this module include visits to Bayer, Vilmorin, Geves, CTIFL, and sudExpé.

Bachelor's degrees.

Students will be asked to present a project or business plan that develops innovative proposals to advance farming practices or any other use of plant products in order to reduce environmental impact.

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This course unit presents the major functions of carbon, mineral, and water nutrition in plants that enable their autotrophy (the production of their biomass). It will provide the necessary foundation for understanding the fundamental mechanisms of nutrient absorption, distribution, and assimilation. The course unit will consist of two main parts: one dedicated to mineral nutrition and the other to carbon nutrition.

After reviewing the properties of membranes and plant cell walls and the concepts of transmembrane transport, the section of the course devoted to mineral nutrition will cover the mechanisms of water absorption and circulation, root absorption, subcellular compartmentalization, and mineral distribution, as well as nitrogen assimilation metabolism.

The chapter on carbon nutrition will discuss how chloroplasts function in plant cells, photosynthesis (the capture of light energy and the synthesis of primary carbon compounds), the production of organic compounds, and their distribution within the plant.

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This course unit is an introductory module to scientific research in fundamental or applied plant agricultural sciences. Students must complete an internship of 10 weeks or more (which may continue through the summer) in a research laboratory (CNRS, INRAE, IRD, CIRAD), at an applied research organization such as GEVES, CTIFL, SudExpe, Serfel, or IFV, or at a private company such as Staphyt, AgroXp, or Vilmorin. There are numerous internship opportunities in this field in the Montpellier area.

This is a module designed to prepare students for the professional world by connecting them with key players in the field of plant agricultural sciences, giving students the opportunity to:

• to apply the techniques learned in the various course units of the BiPAgro track of the bachelor’s degree program.
• to gain experience in the professional world
• to develop your own career plan and enhance your resume

The student writes a thesis, which he or she defends before a committee composed of faculty members, researchers, and/or field technicians or engineers. 

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Bacteriology:

Through various examples, students will gain a better understanding of the concept of pathogenicity in relation to bacterial virulence. The methods and mechanisms used to manipulate the body’s cells at the mucosal level in order to penetrate the internal environment—that is, invasive potential—will be discussed, as well as the perception of environmental signals and the integration of these signals to coordinate the response of prokaryotes so that they exhibit collective behavior. A description of several examples of toxins and modulins associated with colonization and/or invasion will provide a better understanding of the differences in strategies among prokaryotic pathogens. Finally, we will address the concept of the microbiota and its influence on the body’s functioning, as well as its role in the development of certain diseases.

Immunology:

The Immunology section provides an overview of how the immune system functions during infection. From the initiation and progression of the inflammatory response upon the recognition of non-self signals by the innate immune system (PRR-PAMP) to the mechanisms of cell activation and the resulting cellular responses, we can appreciate the diversity of possibilities offered by the various components of the immune system. Furthermore, the sequence of events leading to the direction of the immune response and the acquisition of lasting protection during the adaptive phase will provide a better understanding of vaccine strategy. Finally, intestinal mucosal immunity will be discussed in the context of the relationship between the host and the microbiota.

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The molecular biology practical training course aims to enable students to work independently on a molecular biology protocol and to introduce them to hypothesis-driven research. Students will have six days to address a biological problem that will be presented to them. This will allow them to apply, under laboratory conditions, some of the techniques covered in their theoretical coursework, thereby gaining a better understanding of them.

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The course will cover the fundamentals and principles of microbial ecology (microbial biodiversity; cultivable and non-cultivable microorganisms;   major microbial groups, key microbial functions and biogeochemical cycles, microbial metabolism in the environment and environmental applications, and the fundamentals of ecology as they apply to microorganisms (microbial interactions, free-living organisms, competition, collaboration, symbiosis, parasitism, and their applications). The following topics will be specifically addressed as examples:

- Viruses: the concepts of emergence and re-emergence

-Vibrios: virulence factors, adaptation to the host, and horizontal transfer

-streptococci, comparative genomics, genomic reduction, specialization

 Applications of microbial ecology to biotechnology will include: detection, production of inocula, bioproductions, bioremediation, and water treatment, using concrete examples (development of multipathogen detection tools that account for mutation; production of a flavor enhancer by a soil corynebacterium; applications of microbial interaction studies to the selection of cheese flavors; a quality index for vineyard soil, etc.)

Practical Course: Water Analysis—Principles, Standards, and Applications: 6 hours total

Tutorial/independent work based on the results of the lab: design of a water treatment model for a real-world scenario (cadastral data, topographic survey, total fecal coliform and streptococcal load from the lab, student presentations on the various types of (micro) wastewater treatment plants, etc.) The goal is to propose a conceptual solution tailored to the specific site conditions.

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As part of this course unit, students will learn the experimental principles involved in working with nucleic acids. The lectures will focus on two main areas:

1. Development of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, the CRISPR/Cas9 system, etc.) and reflection on ethical issues in biology.

The tutorials will consist of:

- Analysis of articles presenting problems to be solved using the knowledge gained in the course. The chosen topics will, as much as possible, relate to parallel course units in the third year of the bachelor’s program. Students will present these articles in the form of oral presentations, in groups of 3 to 4 students, to the entire class.

- Sessions dedicated to using basic bioinformatics tools in the computer lab.

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The EU aims to advance knowledge in fundamental and applied virology, with an emphasis on an integrative approach to the discipline. It will present the specific characteristics of host-virus interactions and the pathophysiology of viral infections in different types of hosts (vertebrates, insects, and plants). It will address aspects of viral ecology, virus emergence, and associated risks to human and animal health. Finally, the course will cover research methods, virological detection and diagnostic tools, and the applications of viruses in biotechnology.

The course will consist of lectures, tutorials (analysis of current scientific articles and oral presentations), and practical exercises that illustrate the material covered in the lectures and tutorials (virus amplification and purification, and quantification using standard techniques).

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The objective of this EU is to provide an overview of the diversity of angiosperms, examined through the lens of the most recent phylogenies proposed bythe Angiosperm Phylogeny Group ( APG). This phylogenetic framework will be supported throughout the course by the practical observation of vegetative and floral characters in a selection of taxa spanning the entire phylogeny, in order to identify the synapomorphies of the major clades, any homoplasies, as well as adaptations (floral biology, pollination, trophic interactions, etc.).

Students also explore the diversity of angiosperms from a floristic perspective by creating a herbarium of species that are generally Mediterranean in origin. In the process, they become familiar with the use of a flora and digital identification tools (such as Pl@ntNet and Tela Botanica’s e-Flore).

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Through five major themes, we will explore the fundamental connections between the principles of evolution and evolutionary ecology—as covered in previous course units—and their current societal applications.

These five major themes are: human evolution, biodiversity conservation, the domestication of animal and plant species, evolutionary medicine, and major global crises and disruptions

Two sessions on understanding and summarizing scientific articles are held in conjunction with the course unit "Evolutionary Ecology and Its Applications."

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By the end of this course, students will have acquired the essential basic knowledge needed to properly prepare and carry out a science communication initiative tailored to a specific target audience, both orally and in writing. They will also be able to design educational materials and outreach workshops for the general public.

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Universities are often perceived as inaccessible to a large segment of society. As part of the UniverlaCité initiative, which aims to bring the university experience to priority neighborhoods, students will develop science workshops designed for students in REP schools. 

The EU will offer students the opportunity to:

1- share their own experiences and apply the knowledge they have acquired at the university in order to best meet the needs of society.

2- Identify and develop skills in science communication through the design and production of educational materials tailored to the target audience.

The course will consist of tutorials and project monitoring (SPS) on predefined topics. The sociocultural situation in vulnerable urban areas will be addressed during the first tutorial. This first tutorial will also serve to lay the groundwork for the course, provide a detailed overview of the UniverlaCité program, and offer a broad introduction to science communication.

The following tutorials will serve as sessions during which students, divided into groups, will be asked to propose activities to be implemented. The constraints provided by the teaching team will be: the target audience, the theme (which will be defined by the teaching team and updated each year), and the requirement to propose “off-campus” activities.

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Major human and animal health challenges related to global changes, namely:

• the degradation of natural environments, leading to a decline in the quality of natural resources (various forms of pollution) and a loss of biodiversity
• climate change
• the urbanization of living environments
• new treatment approaches
• the globalization of trade
• the standardization of lifestyles

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Through five major themes, we will explore the fundamental connections between the principles of evolution and evolutionary ecology—as covered in previous course units—and their current societal applications.

These five major themes are: human evolution, biodiversity conservation, the domestication of animal and plant species, evolutionary medicine, and major global crises and disruptions.

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This course provides an introduction to the ecology of continental freshwater ecosystems and marine ecosystems, as well as to the transitional environments between these two compartments—namely, mangroves, estuaries, and deltas.  These ecosystems will be examined from both structural and functional perspectives, with an emphasis on their similarities and differences, as well as on the abiotic and biotic factors that govern the organization of the communities of organisms that inhabit them.

They should provide an overview of these ecosystems or hydrosystems and how they function at various scales.

The first part of the course is devoted entirely to theoretical instruction; the second part consists of introductory sessions for field trips, the field trips themselves, and laboratory sessions in which the data collected in the field are analyzed and discussed as a group.

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Molecular tools are an integral part of studies aimed at describing and characterizing biodiversity. The course will aim to introduce various molecular approaches (barcoding, metabarcoding, and environmental DNA, etc.) that enable (1) the description, characterization, and quantification of this diversity at the intra- or interspecific levels, as well as at the population and ecosystem levels, and (2) the presentation of their areas of application across different temporal and spatial scales. The course will incorporate practical components designed to introduce students to these techniques, help them implement them, analyze the resulting data, and report on their findings. Emphasis will be placed on group work in collaboration with researchers and faculty members.

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ORPAL is an ecology course offered as an APP (1/3 fieldwork and 2/3 laboratory practicals). Drawing on concepts and methods from ecology, this course aims to introduce students to historical ecology (the study of interactions between humans and their environment over varying time periods) and its main applications in paleoecology, from defining the research question, field sampling, and data collection, all the way through to interpretation and the writing of a scientific paper (see https://biologie-ecologie.com/exemples-travaux/). This course serves as an interesting theoretical and experimental prerequisite for the ACCES, CEPAGE, PALEONTOLOGY, ECOSYSTEMS, or BIOGET tracks.

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Adaptations to a “parasitic” lifestyle are studied across all parasitic organisms (viruses, bacteria, eukaryotes), encompassing various scales of analysis “from molecules to populations.”

Thus, the coevolution between hosts and parasites will be examined from the perspective of host–parasite molecular and cellular interactions (immunity, evasion, exploitation of host resources, etc.), as well as the morpho-anatomical structures involved in adaptation to the sub-host site or in survival in the external environment, and finally from the perspective of behavioral adaptations for encountering the host (facilitation).

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One of the goals of this course unit is to synthesize concepts and knowledge acquired in animal biology (anatomy, systematics) and ecology to describe and understand the morphology and evolutionary changes in vertebrate morphology. In addition to covering extant groups, this course unit will focus heavily on extinct fossil groups, particularly their contribution to our understanding of the various eco-morphological adaptations (e.g., the acquisition or return to an aquatic lifestyle, the acquisition of flight) that have shaped the evolutionary history of clades.

This course unit also aims to provide theoretical and practical foundations in phylogenetics (cladistics) for tracing the evolution of a clade (using distance, parsimony, and likelihood methods), based on both molecular and phenotypic characters (both modern and fossil).

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Introduce students to an integrated approach to plant biology through the study of the morpho-anatomical characteristics of stems and roots. Help them discover the coordinated spatio-temporal development of root and stem architectures through the adaptations of Mediterranean and tropical species. Reproductive structures and the diversity of biological types will also be addressed. This course unit serves as preparation for the BioGET track of the BE Master’s program and draws on the natural environment as well as local and regional facilities (Amazonian Greenhouse, Villa Thuret, Château La Pérouse Garden).

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The mechanism of action of drugs is based on an interaction with a target cellular structure in the body, leading to the modulation of its function. Thus, this course unit consists of two main components. The^first component aims to familiarize students with the various modes of cellular communication, the different chemical messengers, their targets, and their modes of action. The second component will aim to provide students with a basic understanding of pharmacology, specifically how drugs work and their fate within the body. To this end, the concepts of pharmacodynamics (ligand-receptor interaction, dose-response relationship) and pharmacokinetics (ADME: absorption, distribution, metabolism, and excretion) will be covered. In addition, drug targets, their intracellular signaling, and their therapeutic indications will be discussed.

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The EU course provides an introduction to the key issues surrounding the major diseases affecting the nervous system, whether neurological or psychiatric. These conditions are addressed from a multidisciplinary perspective, ranging from the molecular level to symptoms. This foundational knowledge of neuropathology will serve as a basis for the research areas covered later in the master’s program.

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The course on Muscular and Cardiac Disorders builds on the knowledge gained in the previous semester on cardiovascular physiology to explore the molecular and cellular mechanisms that lead to cardiac disorders (various arrhythmias, including atrial fibrillation, heart failure, etc.) and muscular disorders (myopathies, etc.).

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The course on Sensory and Motor Neurophysiology offered in the EU covers, on the one hand, the anatomical and functional organization of the major sensory systems—vision, hearing, and somatosensation. On the other hand, it addresses motor function and its central control at the spinal and supraspinal levels: the brainstem, motor cortex, cerebellum, and basal ganglia.

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The objective of this course unit is to provide students with fundamental and in-depth knowledge and skills regarding the physiology of the endocrine system. By studying the morphological and functional organization of the endocrine system, students will gain an understanding of the various hormonal systems (endocrine glands, hypothalamic-pituitary axis, reproductive system) and their essential roles in carrying out major physiological functions and maintaining homeostasis.

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