L2 - Microbiology

This compulsory S3 course allows students to consolidate and deepen the foundations of molecular biology and cell biology acquired in L1.

Molecular Biology Section: The molecular and structural bases of nucleic acids will be developed and explored in depth in order to understand the physicochemical properties of nucleic acids, which open up various prospects for technological applications, and the molecular mechanisms of the main stages of molecular biology, such as DNA replication, gene transcription into mRNA, and their translation into proteins. These stages, illustrated by experimental evidence drawn from various historical studies, will be studied in depth in prokaryotes. Comparisons with eukaryotes will also be discussed. The molecular mechanisms of DNA repair will also be described and developed.

Cell Biology section: The major concepts of membrane and cytosolic protein complex formation will be addressed, particularly in the context of cell signaling pathways. The concepts of ligands, receptors, scaffold proteins, signaling enzyme proteins, intracellular second messengers, and response kinetics will be presented. Biochemistry and cell biology techniques used to detect the presence and location of proteins in cells and tissues will be discussed.

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This course is a cross-disciplinary course in L2 SV aimed at providing biology students with a fundamental knowledge base on plant functioning, enabling them to understand current issues in plant agricultural sciences.

The following basic concepts of Plant Physiology/Functional Biology will be studied: 

Essential experimental approaches: plant transgenesis, forward and reverse genetics

basics of autotrophy

mechanisms underlying the major stages of angiosperm development: meristem function, floral transition, fertilization.

auxin, a major hormone for plant development and their response to the abiotic environment

The practical sessions will enable students to manipulate the regulation of plant water nutrition and analyze their mineral nutrition using various biochemical assays (flame photometry, spectrophotometry). 

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Description of the EU (max. 10 lines):

The aim of this EU is to explain how to measure variation in biology and how it can be represented. It is based on concrete examples from various disciplines of biology (ecology, developmental biology, evolution, genetics, physiology) and provides the statistical tools to measure this variation and the graphical methods to represent it. The statistical concepts of sampling, inference, distribution, central tendency, dispersion, distribution function, parameters, confidence interval, and dependence between variables for different types of variables (binomial, discrete, continuous) are explained using tutorials based on biological problems.

Skills targeted by the EU (see skills reference framework):

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

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This course provides students with a fundamental understanding of microbiology. It will detail the structures of microorganisms, prokaryotes, eukaryotes, and viruses. It will provide an overview of the diversity of these microorganisms and describe how they reproduce.

For bacteria, trophic types and factors influencing growth will be developed, as well as the study of growth in non-renewed environments. Genetics and horizontal transfers between bacteria will be addressed.
Some eukaryotic microorganisms will be studied: habitat, lifestyles, ecological role or parasitism, as well as their mode of development.
In virology, the main cycles of virus multiplication will be detailed, and modes of transmission and the concept of viral pathogenesis will be addressed. The principle of antiviral vaccination and antiviral treatments will be presented and illustrated with concrete examples. 
The principle of antiviral vaccination and antiviral treatments will be presented and illustrated using concrete examples.
Practical work will provide an introduction to sterile techniques for handling microorganisms, counting bacteria, and conjugation.

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This module should enable students to acquire:

Basic concepts in physiology: Concept of homeostasis; levels of organization of the human body; compartments of the internal environment; study of the endocrine system; acid-base and water-mineral balance; anatomical and functional studies of the central and peripheral nervous systems.

Basic concepts in immunology:

General overview of the immune system; study of T and B lymphocytes, antigen-presenting cells; study of antimicrobial immunity and complement.

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This compulsory course allows students to consolidate the fundamentals of biochemistry acquired in the first year by approaching this discipline through a cross-disciplinary study of enzymes involved in cellular metabolism, particularly glycolysis. Several areas of biochemistry will be covered: the fundamentals of Michaelian enzymology and a description of the metabolic reactions involved in glycolysis. Finally, the technical aspect will be addressed through the presentation and analysis of techniques for measuring enzyme activity and purifying, quantifying, and detecting proteins.

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This second general chemistry course aims to consolidate and deepen students' understanding of reactions in aqueous solution, particularly those involving the formation of metal complexes. The principles of thermodynamics will be presented and applied to the study of chemical equilibria of biological interest. Rather than giving a presentation using mathematical formalism, which would require a much greater number of hours, students will be asked to understand the physical meaning of these principles and the main thermodynamic functions and their applications to chemical systems, often of biological interest. In particular, resting membrane potentials and the use of pH potential diagrams in biology will be presented.

Students will work on course materials (written and audio) ahead of certain lectures and tutorials, enabling them to fully participate in face-to-face teaching in lectures and tutorials, understand the concepts presented, and acquire the necessary skills.

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The first part (approximately 1/3) of the module will address (biological) processes with a temporal evolution described by an exponential law (growth or decay).

Radioactivity will be discussed as an illustration of such a process and for its applications in the fields of biology, health, and the environment (dating, tracing, etc.).

The second part (approximately 2/3) of the module will introduce the concepts of fluid and pressure, and present the laws of hydrostatics (fundamental law of fluid statics, Archimedes' theorem).

Fluid dynamics will be introduced, including the concepts of flow, viscosity, sedimentation, and centrifugation, in relation to the Biology-Health sector.

List of Chapter Titles in the Module:

- Exponential variations

- Radioactivity (radioactive decay, activity)

- Fluids: definition, properties, concept of pressure

- Hydrostatics: fundamental law of fluid statics, Archimedes' theorem.

- Elements of hydrodynamics: flows, Bernoulli's theorem

- Viscosity; Sedimentation and centrifugation

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In a context where nutrition has become the focus of interest for an increasingly wide audience, the objective of this EU is to establish food consumption benchmarks using a scientific approach.

This course introduces students to the basics of food and nutrition by describing nutrients (proteins, carbohydrates, lipids, fiber, vitamins, and minerals), nutritional requirements, and different food groups. Certain food processes and technologies will also be covered. 

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This course unit is offered to second-year Life Sciences students who wish to explore or deepen their understanding of how biotechnology can help address current and future challenges in the sustainable production of agricultural and agri-food resources.

Humans use the properties of photosynthetic organisms and microorganisms to obtain and transform multiple resources and services: food products for humans or livestock, therapeutic molecules, construction materials, etc. This use depends on natural conditions and its impact is likely to affect the environment in return, for example through the extraction or deterioration of limited and/or non-renewable resources (water, soil, etc.). It is therefore important, in order for this production of resources to be sustainable, that its organization (the concept of agronomy) incorporates knowledge of these impacts and draws on an understanding of the properties of plants and microorganisms to address these issues. The development and use of new biotechnologies in the fields of applied genetics and plant physiology, the use of microorganisms, and the favorable or unfavorable interactions between these microorganisms and plants are key components of these sustainable agronomy strategies.

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The aim of this teaching unit is to understand animal behavior in an integrative way, in light of Tinbergen's four "whys": from its ontogenesis and neurobiological causes to its evolution and biological functions. In addition to historical, conceptual, and methodological contributions, students will be guided in understanding the diversity of traits involved, as well as the diversity of approaches and associated scientific questions. This teaching unit will thus highlight, through various examples, the diversity of disciplines studying animal behavior: neuroscience, ethology, behavioral ecology, and will enable students to pursue their studies in the appropriate fields: animal physiology and neuroscience/evolutionary biology and ecology/others, etc.

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Computer database:

1- Information and data

Conduct research and monitor information (search engines, social media, etc.)

Manage data (file manager, databases, etc.)

Processing data (spreadsheet)

2- Communication and collaboration

Interact (email, videoconferencing, etc.)

Share and publish (sharing platforms, forum and comment sections, etc.)

Collaborate in a group (collaborative work platform and document sharing, etc.)

Becoming part of the digital world (developing a public presence on the web, etc.)

3- Content creation

Developing text documents (word processing, presentations, etc.)

Develop multimedia documents (capture and editing of images/sound/video/animation, etc.)

Adapt documents to their purpose (format conversion tools, etc.)

Programming (simple computer development, solving logical problems, etc.)

4- Protection and safety

Securing the digital environment (protection software, encryption, etc.)

Protect personal data and privacy (privacy settings, etc.)

Protecting health, well-being, and the environment

5- Environment and digital technology

Solve technical problems (software configuration and maintenance, etc.)

Building a digital environment (operating system, installing new software, etc.)

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1- Linux basics (1.5 hours lecture + 3 hours tutorial): Basic commands for navigating Linux and understanding the logic of this language. Short exercises on extracting information in bash/shell. Element revisited for the analysis of alignment files.

2- Databases (3 hours of lectures + 4.5 hours of tutorials): knowledge of the main bibliographic and biological databases (NCBI, Ensembl, Galaxie, etc.). Ability to perform relevant and effective queries, exploit, sort, and describe different formats.

3- Sequence analysis (1.5 hours lecture + 4.5 hours tutorial): Sequence alignment and comparison with a brief introduction to phylogenetics (dot plot, Blast, etc.)

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This compulsory S4 course allows students to consolidate and deepen the foundations of molecular biology and cell biology acquired in L1.

- Cell biology: The course will cover four major topics: 1) The functioning of the cellular cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation to highlight protein interactions, fluorescence videomicroscopy to track cell distribution dynamics, and evaluation of the importance of proteins of interest in a cellular process using strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology: After acquiring knowledge about transcription and translation mechanisms in semester 3, we will address gene expression regulation: transcriptional regulation (repressors, activators) and attenuation in prokaryotes, and the basics of expression regulation mechanisms in eukaryotes.

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

It will address pathogenic relationships, but will also present examples of symbiotic associations. It will discuss the applications of microorganisms in biotechnology. It will describe how antibiotics work and the associated resistance phenomena, as well as their impact.

The EU will address the concept of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be addressed more specifically, and the mechanisms of bacterial resistance to phage infection will be detailed. The different types of viral infection in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

Knowledge about microorganisms will be expanded through the study of Archaea and a model eukaryotic organism, yeast.

The practical work will focus on performing and interpreting an antibiogram, and on titrating bacteriophages.

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

Using examples, manipulations, and accessible modeling, the lessons will aim to present in a concrete and quantitative manner the effects of the four evolutionary forces operating at the individual and population levels (mutation, migration, selection, and drift). The integration of these microevolutionary processes on larger time scales (e.g., differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to phylogenetics tools (reading and constructing trees) for studying macroevolutionary events (diversification, extinction) and tracing changes in character states, in particular by integrating fossil data.

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The Physiology of Major Functions course (semester 4) aims to describe the role and interactions of the different systems in the body that work together to maintain a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive, and renal systems and their nervous and hormonal controls. Understanding the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac failure; hemorrhage; exposure to extreme environments.

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This course aims to explore in greater depth, in small groups through tutorials and practical sessions, the fundamental molecular and cellular processes covered in the BMC2 and BMC3 courses, approaching them through more concrete concepts. The lessons will be based on real data (experimental results, scientific articles) to explain the main scientific approaches in simple terms and teach students how to analyze and interpret results (Example 1: showing an in cellulo interaction by expressing labeled proteins in cell lines followed by immunoprecipitation and western blot. Example 2: principle of immunofluorescence, intracellular distribution of an antigen. Example 3: in vitro transcription and translation and interaction study by GST pull-down). Practical work will illustrate some of these basic approaches: cell culture, construction of expression vectors, transfection, immunolabeling, fluorescence microscopy.   

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This compulsory course will enable students to deepen the skills they acquired in "Biochemistry S3." It will enable them to understand cellular metabolism by:

-understanding bioenergetics in order to study the processes by which living cells convey, transmit, use, accumulate, and release energy;
-the study of catabolism and anabolism of carbohydrates, lipids, nucleotides, amino acids, and the metabolic interactions between these pathways.

- the description of metabolic disorders.

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In this introductory course to genetic analysis, the objectives are to learn the terms, principles, concepts, and methods used in formal genetics, as well as their fields of application, particularly in human and medical genetics. This course covers the genetics of transmission (Mendelian and non-Mendelian), quantitative genetics, and concepts of population genetics. Throughout the course, close links are established between classical genetics and molecular genetics.

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1- Linux basics (1.5 hours lecture + 3 hours tutorial): Basic commands for navigating Linux and understanding the logic of this language. Short exercises on extracting information in bash/shell. Element revisited for the analysis of alignment files.

2- Databases (3 hours of lectures + 4.5 hours of tutorials): knowledge of the main bibliographic and biological databases (NCBI, Ensembl, Galaxie, etc.). Ability to perform relevant and effective queries, exploit, sort, and describe different formats.

3- Sequence analysis (1.5 hours lecture + 4.5 hours tutorial): Sequence alignment and comparison with a brief introduction to phylogenetics (dot plot, Blast, etc.)

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This compulsory S4 course allows students to consolidate and deepen the foundations of molecular biology and cell biology acquired in L1.

- Cell biology: The course will cover four major topics: 1) The functioning of the cellular cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation to highlight protein interactions, fluorescence videomicroscopy to track cell distribution dynamics, and evaluation of the importance of proteins of interest in a cellular process using strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology: After acquiring knowledge about transcription and translation mechanisms in semester 3, we will address gene expression regulation: transcriptional regulation (repressors, activators) and attenuation in prokaryotes, and the basics of expression regulation mechanisms in eukaryotes.

See the full page

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

It will address pathogenic relationships, but will also present examples of symbiotic associations. It will discuss the applications of microorganisms in biotechnology. It will describe how antibiotics work and the associated resistance phenomena, as well as their impact.

The EU will address the concept of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be addressed more specifically, and the mechanisms of bacterial resistance to phage infection will be detailed. The different types of viral infection in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

Knowledge about microorganisms will be expanded through the study of Archaea and a model eukaryotic organism, yeast.

The practical work will focus on performing and interpreting an antibiogram, and on titrating bacteriophages.

See the full page

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

Using examples, manipulations, and accessible modeling, the lessons will aim to present in a concrete and quantitative manner the effects of the four evolutionary forces operating at the individual and population levels (mutation, migration, selection, and drift). The integration of these microevolutionary processes on larger time scales (e.g., differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to phylogenetics tools (reading and constructing trees) for studying macroevolutionary events (diversification, extinction) and tracing changes in character states, in particular by integrating fossil data.

See the full page

The Physiology of Major Functions course (semester 4) aims to describe the role and interactions of the different systems in the body that work together to maintain a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive, and renal systems and their nervous and hormonal controls. Understanding the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac failure; hemorrhage; exposure to extreme environments.

See the full page

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This compulsory course will enable students to deepen the skills they acquired in "Biochemistry S3." It will enable them to understand cellular metabolism by:

-understanding bioenergetics in order to study the processes by which living cells convey, transmit, use, accumulate, and release energy;
-the study of catabolism and anabolism of carbohydrates, lipids, nucleotides, amino acids, and the metabolic interactions between these pathways.

- the description of metabolic disorders.

See the full page

In this introductory course to genetic analysis, the objectives are to learn the terms, principles, concepts, and methods used in formal genetics, as well as their fields of application, particularly in human and medical genetics. This course covers the genetics of transmission (Mendelian and non-Mendelian), quantitative genetics, and concepts of population genetics. Throughout the course, close links are established between classical genetics and molecular genetics.

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Plants interact with a multitude of microorganisms in their environment. These microorganisms act alone or in communities. They can have negative or positive effects on plants, their growth, nutrition, and health. In this module, we will present the different forms that these biotic interactions can take (symbiosis, parasitism, pathogenicity) based on popular biological models (mycorrhizal or nitrogen-fixing symbiosis, diseases caused by different microorganisms). This will also be an opportunity to introduce emerging concepts in the field, such as the microbiome and holobiont.

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1- Linux basics (1.5 hours lecture + 3 hours tutorial): Basic commands for navigating Linux and understanding the logic of this language. Short exercises on extracting information in bash/shell. Element revisited for the analysis of alignment files.

2- Databases (3 hours of lectures + 4.5 hours of tutorials): knowledge of the main bibliographic and biological databases (NCBI, Ensembl, Galaxie, etc.). Ability to perform relevant and effective queries, exploit, sort, and describe different formats.

3- Sequence analysis (1.5 hours lecture + 4.5 hours tutorial): Sequence alignment and comparison with a brief introduction to phylogenetics (dot plot, Blast, etc.)

See the full page

This compulsory S4 course allows students to consolidate and deepen the foundations of molecular biology and cell biology acquired in L1.

- Cell biology: The course will cover four major topics: 1) The functioning of the cellular cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation to highlight protein interactions, fluorescence videomicroscopy to track cell distribution dynamics, and evaluation of the importance of proteins of interest in a cellular process using strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology: After acquiring knowledge about transcription and translation mechanisms in semester 3, we will address gene expression regulation: transcriptional regulation (repressors, activators) and attenuation in prokaryotes, and the basics of expression regulation mechanisms in eukaryotes.

See the full page

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

It will address pathogenic relationships, but will also present examples of symbiotic associations. It will discuss the applications of microorganisms in biotechnology. It will describe how antibiotics work and the associated resistance phenomena, as well as their impact.

The EU will address the concept of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be addressed more specifically, and the mechanisms of bacterial resistance to phage infection will be detailed. The different types of viral infection in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

Knowledge about microorganisms will be expanded through the study of Archaea and a model eukaryotic organism, yeast.

The practical work will focus on performing and interpreting an antibiogram, and on titrating bacteriophages.

See the full page

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

Using examples, manipulations, and accessible modeling, the lessons will aim to present in a concrete and quantitative manner the effects of the four evolutionary forces operating at the individual and population levels (mutation, migration, selection, and drift). The integration of these microevolutionary processes on larger time scales (e.g., differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to phylogenetics tools (reading and constructing trees) for studying macroevolutionary events (diversification, extinction) and tracing changes in character states, in particular by integrating fossil data.

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This EU is dedicated to biological markers. It is a preliminary introduction to detection and diagnostic techniques. It covers various aspects of biomarking:

Molecular markers/techniques for identification through genomic analysis in medicine and agronomy.

1) Concept of polymorphism and detection technique: RFLP/ER nucleic acid probes

2) RFLP markers and other genetic markers: SNP, STR.

3) Search for new molecular markers: differential screening of cDNA libraries / subtractive libraries / Transcriptomics

4) Other genomic analyses of polymorphism: AFLP / DNA fingerprinting.

Identification techniques in the food industry using immunological techniques

1) Basic concepts in immunological techniques
2) Agglutination reactions
3) Immunoenzymatic assay methods
Case studies of applications in the agri-food industry:
- study of the beet rhizomania diagnostic kit (sandwich ELISA)
- determination of ochratoxin A in cereals (competitive ELISA)
- assessment of fish freshness by histamine determination (competitive ELISA)

Biochemical identification of protein markers and others (metabolites)

1) Fundamentals of chromatography and physical characterization of a spectrum (the interactions involved in each case and the solvents used to implement them).

2) Affinity chromatography

2.1) Principle of this type of analysis

2.2) Search for the best tag for the preparation of a specific gel. 

2.3) Their usefulness for different fields of research investigation.

3) Study of protein-protein, protein-DNA, and other interactions...

4) HPLC, FPLC, and gas chromatography.

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The Physiology of Major Functions course (semester 4) aims to describe the role and interactions of the different systems in the body that work together to maintain a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive, and renal systems and their nervous and hormonal controls. Understanding the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac failure; hemorrhage; exposure to extreme environments.

See the full page

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This compulsory course will enable students to deepen the skills they acquired in "Biochemistry S3." It will enable them to understand cellular metabolism by:

-understanding bioenergetics in order to study the processes by which living cells convey, transmit, use, accumulate, and release energy;
-the study of catabolism and anabolism of carbohydrates, lipids, nucleotides, amino acids, and the metabolic interactions between these pathways.

- the description of metabolic disorders.

See the full page

In this introductory course to genetic analysis, the objectives are to learn the terms, principles, concepts, and methods used in formal genetics, as well as their fields of application, particularly in human and medical genetics. This course covers the genetics of transmission (Mendelian and non-Mendelian), quantitative genetics, and concepts of population genetics. Throughout the course, close links are established between classical genetics and molecular genetics.

See the full page