Choice Profile SV S5

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This practical course aims to apply students' knowledge of microbiology and molecular biology to the identification of environmental bacteria.

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

Molecular biology techniques now make it possible to identify the bacteria present in a sample without the need for cultivation. This approach requires access to a sequencing platform and will also be carried out as part of the practical work, enabling the two approaches to be compared. The sequencing results obtained will enable bioinformatic analysis of the rrsA gene specifying the RNA16S of isolated bacteria.

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

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

These studies are supplemented by a tutored project during the semester, during which students analyze a research article recently published in the scientific literature and transcribe it into an oral presentation (conference) in English.

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This EU is the logical continuation of the S4 EU (Basics of physiology and immunology) and aims to deepen knowledge of fundamental, applied and clinical immunology. We will also cover "unconventional" immunology and develop innovative immunotherapy strategies. The course will cover all aspects of modern immunology, with a strong emphasis on clinical aspects.

 Key words

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

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Molecular biology is a fascinating subject of study in its own right, but it also provides other disciplines in biology (cell biology, genetics, physiology...) with fantastic tools for modifying and quantifying genes and their products.

The EU provides a deeper understanding of the mechanisms of organization, maintenance, replication and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, we'll be exploring the properties of information-carrying macromolecules (DNA, RNA, proteins), and how transactions between them explain how eukaryotic cells function and adapt to the environment and to the development of organisms.

At the same time, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and analyzed in greater depth in practical sessions.

TDs will address these topics in the form of (1) exercises enabling students to check their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. In this way, the fundamentals of scientific reasoning and the critical analysis of results are acquired and/or deepened.

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This course is designed to deepen the knowledge of microbiology for students wishing to continue their studies in this discipline.

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

Bacteria with special morphology will be presented.  

In virology, the pathophysiology of viral infections and the prevention and control of viral diseases will be presented. Mechanisms of escape from the immune system will be detailed. Viral evolution mechanisms will be described and related to viral emergence.

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

Lastly, the EU will look at the concept of the microbiota and present the latest data on the nature of the human microbiota and its role in health.

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This UE is a specialization module in Functional Plant Biology, covering the mechanisms underlying the major stages in plant development.

It is based on knowledge derived mainly from the model plant Arabidopsis thaliana and covers the following concepts from a molecular, cellular and physiological point of view:

• Roles and functions of the main phytohormones.
• Development of male and female gametes, fertilization.
• Embryo, seed and fruit development.
• Functioning of root and stem meristems (vegetative and floral).
• Flower architecture.
• Adaptive development mechanisms in response to abiotic factors: light, gravity, cold.

Certain aspects of development will also be analyzed from an evolutionary perspective, by studying the role of developmental genes in the diversification and evolution of developmental processes in land plants (evolution of the root system, floral architecture, etc.).

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

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

These studies are supplemented by a tutored project during the semester, during which students analyze a research article recently published in the scientific literature and transcribe it into an oral presentation (conference) in English.

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Bioinformatics is a discipline at the crossroads of computer science, mathematics and the life sciences. It is based in particular on the use and development of computer tools for the analysis of massive biological data. Eventually, these megadata can be organized into searchable online databases, enabling users to extract data relevant to a biological problem.

The aim of the "Bioinformatics applied to plant biology" teaching unit is to introduce students to the use of databases and to offer a first approach to data mining using R software.

Virtually all teaching will take the form of practical case studies in the computer room, in student sub-groups.

In the first part, students will learn the rudiments of the R computer language, enabling them to organize and clean up their raw data to make it fully exploitable for further analysis. They will then learn how to propose explicit graphical representations based on biological data. Particular attention will be paid to writing reusable scripts and choosing the graphics associated with the calculations according to the biological question at hand.

In the second part, students will use general databases such as NCBI, or databases devoted exclusively to the model plant Arabidopsis (TAIR), to carry out data mining.

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Molecular biology is a fascinating subject of study in its own right, but it also provides other disciplines in biology (cell biology, genetics, physiology...) with fantastic tools for modifying and quantifying genes and their products.

The EU provides a deeper understanding of the mechanisms of organization, maintenance, replication and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, we'll be exploring the properties of information-carrying macromolecules (DNA, RNA, proteins), and how transactions between them explain how eukaryotic cells function and adapt to the environment and to the development of organisms.

At the same time, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and analyzed in greater depth in practical sessions.

TDs will address these topics in the form of (1) exercises enabling students to check their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. In this way, the fundamentals of scientific reasoning and the critical analysis of results are acquired and/or deepened.

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

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This course offers an in-depth look at the structural biochemistry of biomolecules, with a particular focus on proteins and nucleic acids.

The basic concepts and nomenclature used to analyze 3D protein structures are briefly reviewed (Ramachandran diagram, structural motif and domain, folding, family, superfamily, etc......). These notions are complemented by a study of the stability and dynamics of biomolecules.

The structural classification of proteins is detailed according to the 4 main types of folding. Structure-function relationships are illustrated using examples of proteins. Specificities of membrane protein structures (integral proteins, membrane-bound proteins) are discussed.

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

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

This course is illustrated by tutorials. These involve familiarizing students with the main databases used in structural biology, as well as with PyMol software for 3D structure analysis.

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This course provides fundamental knowledge of formal and structural enzymology.

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

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

Definition of an enzyme, catalyst. Enzyme nomenclature (E.C)

Michaelian kinetics. Michaelis-Menten equation. Definition of enzymatic parameters,_KM, maximum speed, catalytic constant, turn-over. Various graphical representations (Lineweaer-Burk, Eadie-Hofstee). 

The different types of inhibition (competitive, incompetent, non-competitive, mixed) and their graphical representation are also studied.

Determining inhibition constancy. Irreversible inhibitors.

Reaction speed. Arrhenius' law.

- The third section describes multi-substrate enzymatic kinetics from a formal point of view. With ternary complex. Random or ordered mechanism.

No ternary complex. Ping-Pong, Theorell-Chance mechanism. Cleland representation.

Graphical determination.

- The fourth part deals with equilibrium bonding and allostery.

Receptor-Ligand / Enzyme-Substrate binding. Determination of dissociation (or association) constant. Specific and non-specific binding.

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

Models of allosteric regulation are presented. Allostery. Cooperative models, concerted (Monod-Wyman-Changeux), sequential (Koshland-Nemethy-Filmer). Role of effectors: activator or inhibitor. Example of hemoglobin and oxygen uptake.

- The fifth part of the course relates enzyme structures to their function, using several examples. Description of the 3D structures and catalytic mechanisms of acetylcholine esterase, proteases and nucleoside diphosphate kinase. Notion of catalytic triad, binding pocket, etc. 

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

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

These studies are supplemented by a tutored project during the semester, during which students analyze a research article recently published in the scientific literature and transcribe it into an oral presentation (conference) in English.

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Molecular biology is a fascinating subject of study in its own right, but it also provides other disciplines in biology (cell biology, genetics, physiology...) with fantastic tools for modifying and quantifying genes and their products.

The EU provides a deeper understanding of the mechanisms of organization, maintenance, replication and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, we'll be exploring the properties of information-carrying macromolecules (DNA, RNA, proteins), and how transactions between them explain how eukaryotic cells function and adapt to the environment and to the development of organisms.

At the same time, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and analyzed in greater depth in practical sessions.

TDs will address these topics in the form of (1) exercises enabling students to check their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. In this way, the fundamentals of scientific reasoning and the critical analysis of results are acquired and/or deepened.

See full page

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

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This course enables students to deepen their knowledge of metabolism. This course provides a global vision of human metabolism. It will emphasize the links between the different metabolic pathways. It will also show how different tissues communicate to maintain overall energy homeostasis. Dysregulation of this metabolism, at the origin of certain pathologies, will be presented.

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Students will be asked to carry out a bibliographical analysis on a topic of their choice, validated by the UE supervisors. Under the tutelage of a teacher-researcher, students will have to answer the problem they have set themselves by analyzing the available bibliography. They will have to assess the state of the art in the field they are working on, identifying areas of uncertainty and controversy, and open questions that remain to be resolved. They will have to carry out a genuine critical scientific analysis of the available bibliography, and not simply report on it. They will have to follow the conventions of scientific article writing, involving citation of sources, synthesis of information through illustration, problematization and synthesis of scientific results.

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This course is an extension of the "Fundamentals of Evolution" course, and introduces the main concepts of evolutionary ecology in order to understand and formalize in a simple way the evolutionary and ecological mechanisms that shape biodiversity at different scales of integration.

This course is designed as a coherent whole, with lectures, tutorials and practical work complementing each other. Notions are approached by example, then formalized using mathematical models, which are compared with experience and real data.

It will deal with population dynamics (intra- and interspecific competition), ecological niches and will detail the mechanisms of evolution and their genetic consequences on a population scale: natural selection (including sexual selection), influence of reproductive regimes, genetic drift. The practical sessions will enable students to master the mathematical formalization of notions seen in class and their simple computer modeling, as well as the analysis of data sets. Practical work will enable students to carry out and analyze in small groups 2 experiments lasting 1 month each (with report writing and oral presentation), in order to develop methodology and scientific reasoning.

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The EU is organized into five main themes:

Theme 1: Gene mapping and recombination. Notions of molecular biology related to gene expression, DNA repair and epigenetic processes.

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

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

Theme 4: Molecular tools for biodiversity: Barcoding, eDNA, metabarcoding. Molecular taxonomy. Limitations of hybridization. Conservation applications.

Theme 5: Extranuclear heredity. Symbiosis, parasitism and co-evolution (intra-cellular: e.g. Wolbachia). Notion of extended phenotype.

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This teaching unit will cover the elements needed to understand the way of life of the major groups of unicellular organisms at the basis of ecosystem functioning (viruses, bacteria, archaea and unicellular eukaryotes....). The course covers the biological organization of each type of organism, its modes of reproduction and diversity, leading to notions of ecology. We will look at the role of these microorganisms in the functioning and dynamics of ecosystems, considering the interactions that these organisms maintain with other living beings (the notion of "symbiosis" in all its variations).

Practical work will :

 - implementation of techniques for bacterial enumeration (CFU), identification of a particular strain from an environmental sample

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

 - demonstrating the specificity of interactions between bacteria and bacteriophages

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The main objective is to learn the basics of comparative anatomy of chordates, so as to be able to compare and classify them, before tracing the key stages in their evolutionary history. Teaching is integrative in the sense that it draws on both present-day organisms and the fossil record, so as to document the evolutionary history of the clade in its entirety and in all its aspects. Anatomical, biomechanical, phylogenetic and ecomorphological approaches will be addressed in lectures to illustrate the diversity and major characteristics of chordates. Practical work (and practical sessions) will illustrate the evolution of the diversity of integuments, skeleton, musculature, digestive and respiratory systems over long time scales.

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

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

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

These studies are supplemented by a tutored project during the semester, during which students analyze a research article recently published in the scientific literature and transcribe it into an oral presentation (conference) in English.

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

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

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

Learn all the elements needed to carry out the required laboratory protocol in order to obtain results and prepare a report.

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This EU is the logical continuation of the S4 EU (Basics of physiology and immunology) and aims to deepen knowledge of fundamental, applied and clinical immunology. We will also cover "unconventional" immunology and develop innovative immunotherapy strategies. The course will cover all aspects of modern immunology, with a strong emphasis on clinical aspects.

 Key words

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

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The aim of this course is to provide an integrated approach to the functioning of the nervous system, drawing on several neuroscience disciplines (Neurodevelopment, Functional Neuroanatomy, Neuroimaging, Cognitive Neuroscience) and focusing on complex brain functions.

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This course focuses on the morpho-functional study of cells in the nervous system (neurons, glial cells), mainly by describing the mechanisms involved in neuronal excitability (generation and propagation of action potentials) and neurotransmission (mechanisms of neurotransmitter release and synthesis, and the structure and function of neurotransmitter receptors). The concepts of synaptic plasticity are also developed.

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

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