L2 - Microbiology

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

Molecular Biology part: The molecular and structural bases of nucleic acids will be developed and deepened to understand the physicochemical properties of nucleic acids, which open various perspectives of technological applications, and the molecular mechanisms of the main steps of Molecular Biology, such as DNA replication, transcription of genes into mRNAs and translation of these into proteins. These steps, illustrated by experimental evidence 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 Part: Major concepts of membrane and cytosolic protein complex formation will be discussed, particularly in the context of cell signaling pathways. The notions of ligands, receptors, scaffolding proteins, enzymatic signaling proteins, intracellular second messengers, response kinetics will be presented. Biochemistry and cell biology techniques to demonstrate the presence and localization of proteins in cells and tissues will be presented.

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This UE is a transversal UE of L2 SV aiming at giving to the students in Biology a basic knowledge on the functioning of plants allowing to understand the current stakes of the plant Agro-sciences.

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

essential experimental approaches: plant transgenesis, direct and reverse genetics

basics of autotrophy

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

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

The practical sessions will allow students to manipulate the regulation of water nutrition in plants and to analyze their mineral nutrition using different biochemical assays (flame photometry, spectrophotometry). 

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Description of the EU (max 10 lines):

The objective of this course is to understand 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 gives 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 intervals and dependence between variables for different types of variables (binomial, discrete, continuous) are explained with the help of practical exercises based on biological problems.

Competences aimed at by the UE (see reference frame of competences):

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

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This course provides the fundamental basis of microbiology. It will detail the structures of microorganisms, prokaryotes and eukaryotes, and viruses. It will give an overview of the diversity of these microorganisms and describe their mode of multiplication.

For bacteria, trophic types and factors influencing growth will be developed, as well as the study of growth in a non-renewed environment. Genetics and horizontal transfers between bacteria will be discussed.
Some eukaryotic microorganisms will be studied: habitat, life style, ecological role or parasitism as well as their mode of development.
In virology, the main multiplication cycles of viruses will be detailed, the modes of transmission and the notion of viral pathogenesis will be discussed. The principle of anti-viral vaccination and anti-viral treatments will be presented and illustrated with concrete examples.
The principle of anti-viral vaccination and anti-viral treatments will be presented and illustrated with concrete examples.
The practical work will allow the initiation to the techniques of sterile manipulation of microorganisms, to the counting of bacteria and to conjugation.

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This module should enable students to acquire:

Basic notions 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 hydro-mineral balance; anatomical and functional studies of the central and peripheral nervous system.

Basic concepts in Immunology:

General presentation 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 basics of biochemistry acquired in L1 by approaching this discipline through a transversal study of enzymes involved in cellular metabolism, particularly glycolysis. Several areas of biochemistry will be covered: the basics of Michaelian enzymology, the description of metabolic reactions involved in glycolysis. Finally, the technical aspect will be approached by the presentation and the analysis of the techniques allowing to measure an enzymatic activity, to purify, to quantify and to detect proteins.

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This second unit of general chemistry aims to consolidate and deepen the study of reactions in aqueous solution, especially 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 a presentation using mathematical formalism that would require a much larger time commitment, the student will be asked to understand the physical meaning of these principles and the main thermodynamic functions and to apply them to chemical systems, often of biological interest. In particular, resting membrane potentials and the use of pH potential diagrams in biology will be presented.

The students will work before certain courses and tutorials on course documents (written and audio) so that the classroom teaching in courses and tutorials can allow them to be fully involved in the training, to understand the concepts presented and the skills to be acquired.

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

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

The second part (about 2/3) of the module will introduce the notions 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 connection with the Biology-Health sector.

List of Chapters in the module :

- Exponential variations

- Radioactivity (radioactive decay, activity)

- Fluids: definition, properties, notion of pressure

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

- Elements of hydrodynamics: flows, Bernouilli's theorem

- Viscosity; Sedimentation and centrifugation

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In a context where nutrition has become the center of interest of an increasingly large public, the objective of this EU is the establishment of benchmarks for food consumption with a scientific approach.

This course will introduce the basics of food and nutrition through the description of nutrients (proteins, carbohydrates, fats, fibers, vitamins and minerals), nutritional requirements and the different food groups. Some food processes and technologies will also be discussed. 

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This course is offered to L2 Life Sciences students wishing to learn more about how biotechnologies can contribute to the current and future challenges of sustainable production of agricultural and agri-food resources.

Man uses 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 is dependent on natural conditions and its impact on the environment is likely to be reversed, for example via the withdrawal or deterioration of limited and/or non-renewable resources (water, soil, etc.). It is therefore important, for this production of resources to be sustainable, that its organization (notion of agronomy) integrates the knowledge of these impacts and relies on the understanding of the properties of plants and microorganisms to meet these challenges. 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, contribute greatly to these sustainable agronomy strategies.

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The aim of this course is to understand animal behavior in an integrative way, in the light of Tinbergen's four 'whys': from its ontogeny, its neurobiological causes to its evolution and its biological functions. In addition to historical, conceptual and methodological contributions, the students will be accompanied in order to apprehend the diversity of the features involved as well as the diversity of the approaches and the associated scientific questionings. This course will thus highlight, through different examples, the diversity of disciplines studying animal behavior: Neurosciences, Ethology, Behavioral Ecology and will help students to pursue their studies in the appropriate fields of Animal Physiology and Neurosciences/ Evolutionary Biology and Ecology/ Others....

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Computer base:

1- Information and data

Conducting research and monitoring information (search engine, social networks...)

Manage data (file manager, databases...)

Process data (spreadsheet)

2- Communication and collaboration

Interact (e-mail, video-conferencing, etc.)

Share and publish (sharing platforms, forum and comment space...)

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

Enter the digital world (develop a public presence on the web...)

3- Content creation

Develop text documents (word processing, presentation...)

Develop multimedia documents (image/sound/video/animation capture and editing...)

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

Programming (simple computer development, solving a logical problem...)

4- Protection and security

Secure the digital environment (protection software, encryption...)

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

Protecting health, well-being and the environment

5- Environment and digital

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

Build a digital environment (operating system, installation of new software...)

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1- Linux basics (1,5h CM + 3hTD): Basic commands to navigate under Linux and understand the logic of this language. Small exercises to extract information in bash/shell. Element used for the analysis of alignment files.

2- Database (3h CM + 4,5hTD): know the main bibliographic and biological databases (NCBI, Ensembl, Galaxie...). Know how to make relevant and efficient queries, exploit, sort, description of the different formats

3- Sequence analysis (1,5hCM + 4,5H TD): Alignment and comparison of sequences with a small introduction to phylogeny (dot plot, Blast ...)

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This compulsory UE of S4 allows students to consolidate and deepen the bases of molecular and cellular biology acquired in L1.

- Cell biology: The teaching will focus on 4 major themes: 1) The functioning of the cell cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation for the detection of protein interactions, fluorescence videomicroscopy to follow the dynamics of cell distribution, evaluation of the importance of proteins of interest in a cellular process by strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology : After acquiring in semester 3 knowledge concerning the mechanisms of transcription and translation, we will approach the regulation of gene expression: transcriptional regulation (repressor, activator) and attenuation in prokaryotes, the bases of the mechanisms of regulation of expression in eukaryotes.

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

It will deal with pathogenic relationships, but will also present examples of symbiotic associations. It will address the applications of microorganisms in biotechnology. It will describe the mode of action of antibiotics and the associated resistance phenomena and their impact.

The EU will approach the notion of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be treated more specifically and the mechanisms of resistance of bacteria to phagic infection will be detailed. The different types of viral infections in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

The knowledge on microorganisms will be extended by the study of Archaea and a model eukaryotic organism, the yeast.

The practical work will focus on the realization of an antibiogram and its interpretation, and on the titration of bacteriophages.

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

Based on examples, manipulations and accessible modeling, the lessons will aim at presenting in a concrete and quantitative way the effects of the 4 evolutionary forces operating at the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes at larger time scales (e.g. differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to the tools of phylogeny (reading and construction of trees) allowing the study of macro-evolutionary events (diversification, extinction) and the tracing of changes in character states, notably by integrating fossil data.

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The Physiology of major functions (semester 4) aims to describe the role and interactions of the various systems of the organism that contribute to maintaining a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive and renal systems and their nervous and hormonal controls. Understand the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac insufficiency; hemorrhage; exposure to extreme environments.

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This course is designed to deepen in small groups the fundamental molecular and cellular processes seen in the BMC2 and BMC3 courses by approaching them through more concrete notions. The lessons will be based on real data (experimental results, scientific articles) to simply explain the main scientific approaches and to learn how to analyze and interpret the results (Example 1: show an interaction in cellulo by expression of tagged proteins in cell lines followed by immunoprecipitation and western-blot. Example 2: principle of immunofluorescence, intracellular distribution of an antigen. Example 3: transcription and translation in vitro and study of interaction by GST-pull down). The practical exercises 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 allow students to deepen their skills acquired in "S3 biochemistry". It will allow them to understand cellular metabolism through:

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

- description of metabolic pathologies.

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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 application in human and medical genetics. This course covers the genetics of transmission (Mendelian or non-Mendelian), quantitative genetics and notions of population genetics. Throughout the course, close links are established between classical and molecular genetics.

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1- Linux basics (1,5h CM + 3hTD): Basic commands to navigate under Linux and understand the logic of this language. Small exercises to extract information in bash/shell. Element used for the analysis of alignment files.

2- Database (3h CM + 4,5hTD): know the main bibliographic and biological databases (NCBI, Ensembl, Galaxie...). Know how to make relevant and efficient queries, exploit, sort, description of the different formats

3- Sequence analysis (1,5hCM + 4,5H TD): Alignment and comparison of sequences with a small introduction to phylogeny (dot plot, Blast ...)

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This compulsory UE of S4 allows students to consolidate and deepen the bases of molecular and cellular biology acquired in L1.

- Cell biology: The teaching will focus on 4 major themes: 1) The functioning of the cell cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation for the detection of protein interactions, fluorescence videomicroscopy to follow the dynamics of cell distribution, evaluation of the importance of proteins of interest in a cellular process by strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology : After acquiring in semester 3 knowledge concerning the mechanisms of transcription and translation, we will approach the regulation of gene expression: transcriptional regulation (repressor, activator) and attenuation in prokaryotes, the bases of the mechanisms of regulation of expression in eukaryotes.

See full page

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

It will deal with pathogenic relationships, but will also present examples of symbiotic associations. It will address the applications of microorganisms in biotechnology. It will describe the mode of action of antibiotics and the associated resistance phenomena and their impact.

The EU will approach the notion of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be treated more specifically and the mechanisms of resistance of bacteria to phagic infection will be detailed. The different types of viral infections in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

The knowledge on microorganisms will be extended by the study of Archaea and a model eukaryotic organism, the yeast.

The practical work will focus on the realization of an antibiogram and its interpretation, and on the titration of bacteriophages.

See full page

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

Based on examples, manipulations and accessible modeling, the lessons will aim at presenting in a concrete and quantitative way the effects of the 4 evolutionary forces operating at the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes at larger time scales (e.g. differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to the tools of phylogeny (reading and construction of trees) allowing the study of macro-evolutionary events (diversification, extinction) and the tracing of changes in character states, notably by integrating fossil data.

See full page

The Physiology of major functions (semester 4) aims to describe the role and interactions of the various systems of the organism that contribute to maintaining a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive and renal systems and their nervous and hormonal controls. Understand the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac insufficiency; hemorrhage; exposure to extreme environments.

See full page

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This compulsory course will allow students to deepen their skills acquired in "S3 biochemistry". It will allow them to understand cellular metabolism through:

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

- description of metabolic pathologies.

See 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 application in human and medical genetics. This course covers the genetics of transmission (Mendelian or non-Mendelian), quantitative genetics and notions of population genetics. Throughout the course, close links are established between classical and molecular genetics.

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

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1- Linux basics (1,5h CM + 3hTD): Basic commands to navigate under Linux and understand the logic of this language. Small exercises to extract information in bash/shell. Element used for the analysis of alignment files.

2- Database (3h CM + 4,5hTD): know the main bibliographic and biological databases (NCBI, Ensembl, Galaxie...). Know how to make relevant and efficient queries, exploit, sort, description of the different formats

3- Sequence analysis (1,5hCM + 4,5H TD): Alignment and comparison of sequences with a small introduction to phylogeny (dot plot, Blast ...)

See full page

This compulsory UE of S4 allows students to consolidate and deepen the bases of molecular and cellular biology acquired in L1.

- Cell biology: The teaching will focus on 4 major themes: 1) The functioning of the cell cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) Introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation for the detection of protein interactions, fluorescence videomicroscopy to follow the dynamics of cell distribution, evaluation of the importance of proteins of interest in a cellular process by strategies to modulate their expression (RNA interference, overexpression).

- Molecular biology : After acquiring in semester 3 knowledge concerning the mechanisms of transcription and translation, we will approach the regulation of gene expression: transcriptional regulation (repressor, activator) and attenuation in prokaryotes, the bases of the mechanisms of regulation of expression in eukaryotes.

See full page

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

It will deal with pathogenic relationships, but will also present examples of symbiotic associations. It will address the applications of microorganisms in biotechnology. It will describe the mode of action of antibiotics and the associated resistance phenomena and their impact.

The EU will approach the notion of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be treated more specifically and the mechanisms of resistance of bacteria to phagic infection will be detailed. The different types of viral infections in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

The knowledge on microorganisms will be extended by the study of Archaea and a model eukaryotic organism, the yeast.

The practical work will focus on the realization of an antibiogram and its interpretation, and on the titration of bacteriophages.

See full page

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

Based on examples, manipulations and accessible modeling, the lessons will aim at presenting in a concrete and quantitative way the effects of the 4 evolutionary forces operating at the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes at larger time scales (e.g. differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to the tools of phylogeny (reading and construction of trees) allowing the study of macro-evolutionary events (diversification, extinction) and the tracing of changes in character states, notably by integrating fossil data.

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This course is dedicated to biological markers. It is a pre-introduction to detection and diagnostic techniques. It deals with different aspects of biomarkers :

Molecular markers / techniques of identification by genomic analysis in medicine and agronomy.

1) Concept of polymorphism and detection technique: The RFLP / ER-probe nucleic acid

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) Basics of immunological techniques
2) Agglutination reactions
3) Enzyme-linked immunosorbent assay methods
Studies of examples of application in the food industry:
- study of the diagnostic kit for rhizominia in beet (sandwich ELISA)
- determination of ochratoxin A in cereals (competitive ELISA)
- evaluation of the freshness of fish by determination of histamine (competitive ELISA)

Biochemical identification of protein and other markers (metabolites)

1) Basics of chromatography and the 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 (label) for the preparation of a specific gel. 

2.3) Their usefulness for the different fields of investigation in research.

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

4) HPLC and FPLC and Gas Chromatography.

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The Physiology of major functions (semester 4) aims to describe the role and interactions of the various systems of the organism that contribute to maintaining a constant internal environment. Acquisition of anatomical and functional knowledge of the cardiovascular, respiratory, digestive and renal systems and their nervous and hormonal controls. Understand the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac insufficiency; hemorrhage; exposure to extreme environments.

See full page

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This compulsory course will allow students to deepen their skills acquired in "S3 biochemistry". It will allow them to understand cellular metabolism through:

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

- description of metabolic pathologies.

See 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 application in human and medical genetics. This course covers the genetics of transmission (Mendelian or non-Mendelian), quantitative genetics and notions of population genetics. Throughout the course, close links are established between classical and molecular genetics.

See full page