M2 Fundamental Microbiology

Ombeline Rossier (UPSay, I2BC), Philippe Bouloc (CNRS, I2BC) and invited speakers.

Students will be evaluated on the synthetic biology project they will develop (10-15 min oral + written report). The project will be evaluated on its originality, coherence/relevance, feasibility and state of the art in the scientific context chosen bu the students.

This teaching unit aims to highlight recent advances in the field of synthetic microbiology, including cellular innovations. Through examples of fundamental and applied projects, the conferences will illustrate how and why synthetic biology approaches can contribute to the acquisition of basic knowledge in microbiology and to the rationalization of the design of microbial strains with increased efficacy and/or safety properties. Conferences on history and ethics surrounding this field will address the question of the positioning of synthetic biology in society and in the evolution of Research.

M1 level in Molecular biology.

Novembre.

ORSAY - GIF-SUR-YVETTE

Fabrice Confalonieri (PU UPSay), Stéphanie Bury-Moné (PU UPSay), and invited speakers according to the selected research topics.

Conferences by specialists. Round table with students.

This teaching unit aims to highlight recent advances in functional genomics, including big Data in Biology. The
speakers, specialists in this field of research, will present the most recent scientific data relating to comparative
genomics, metagenomics, (meta)transcriptomics, metabolomics, proteomics, the analysis of interactomes and
applications in medicine. Another objective of this teaching unit is to connect scientific questions asked and the
best method(s) to use to reach the goals. Round tables, between students and researchers, will be organized to
discuss the impact of the knowledge acquired through global approaches on new emerging concepts related to the
gene and to pervasive transcription. Students will also present their own review of a theme they will choose during
a one-day mini-symposium.

Concepts in Genetics and Genomics.

Octobre.

ORSAY - GIF-SUR-YVETTE

Day 1 -Presentation of the softwares RStudio and R -R programming (Part 1) -Practical training -Biological datasets to be use in the project Day 2 -Self-assessment test -R programming (Part 2) -Initiation to clustering algorithms -Challenges of the project -First R script to solve the project Day 3 -Self-assessment test -R programming (Partie 3) -Change R script in functions Day 4 -Student personal work Day 5 -Project feedback from the teacher -Final exam (with computers and notes) -To go further ?

Session 1 session 2 : Project 50%, Final exam 50%.

During this class, the students will learn how to use the R software, to analyse a biological dataset arising from high throughput experimental methodologies (transcriptomics). Teaching days will be divided into activities relying on:
-Formal lectures
-Practical training
-Live programming
-Pair programming
Self-assessment tests will be proposed to students each day, and programming skills will be applied in a project, evaluated at the end of the week. This project consists of identifying, without any a priori, groups of co-expressed genes. They will be represented graphically with heatmaps.

Novembre.

ORSAY - GIF-SUR-YVETTE

Florence Garnier (MC UVSQ), Fabienne Malagnac (Pr UPSay), invited speakers.

Session 1 et session 2 : F EE (written examination).

This teaching unit highlights different types of possible microbial interactions with other organisms. The relationships of mutualism and parasitism will be exposed through different examples involving bacteria, fungi, micro-algae or protists hosted by plants, animals or even other micro-organisms. The context of interaction between individuals of the same species will be addressed by presenting the molecular mechanisms of microbial communication (quorum-sensing). The modalities of biofilm formation will also be presented.

Microbiology, Biochemistry, Molecular biology.

Décembre.

VERSAILLES

Lecturers from Paris-Saclay University and invited lecturers.

Courses and conferences by lecturers specialized in the field, as well as preparation of “mini conferences” by the students themselves. Students will be evaluated on the presentations they have developed (Oral Exam) as well as on a written test (Written Exam) on one or more topics covered during the conferences. Session 1 and session 2: Final mark 0,5 x OE + 0,5 x WE.

This teaching unit aims to update students' knowledge on the latest advances in microbial cell biology. This teaching unit will cover cytoskeleton, membrane dynamics, cell cycle, stress response, polarity, differentiation, aging and programmed death of unicellular cells. Other themes are likely to be addressed, depending on current events, some of which are chosen and presented by the students themselves.

Molecular biology, Cell biology, Membrane biochemistry, Cell imaging.

Octobre.

ORSAY - GIF-SUR-YVETTE

Olga Soutourina (PU UPSay), Stéphanie Bury-Moné (PU UPSay) and people from the research institutes hosting the practical course.

Oral examination (x 0.34), report (0.33) and written examination (0.33). Session 1 0.33 EE [R if mark> 10] + 0.34 EO [R if mark > 10] + 0.33 CCTP [R if mark > 10] (CCTP report) Session 2 0.33 EE + 0.34 EO + 0.33 CCTP [R if mark > 10] means that only the examinations (CR, EO or EE) for which the student did not obtain the average in the first session are repeated in the second session.

This teaching unit aims to familiarize students with the most modern techniques to address a scientific issue in Microbiology. The training is designed to provide students with good technical and scientific expertise in the development of protocols and analysis of the results so as to best prepare them for their integration into the S4 semester. This training will be provided by the staff of one or more research teams from the Paris-Saclay Research Institute hosting the practical course. The backing of this teaching unit to laboratories and themes of Paris-Saclay Research Institutes will allow students to learn the latest techniques and to interact with researchers. The duration of this course will be 3 weeks in a Research Institute of Paris-Saclay.

Molecular Biology, Biochemistry, Cell Biology and General Microbiology.

Septembre.

ORSAY - GIF-SUR-YVETTE - JOUY-EN-JOSAS

T. Bouchez (Consulting Professor APT), Bize (Research Fellow, INRAe), C. Duquennoi (Research Fellow, INRAe), A. Filali (Research Fellow, INRAe), A. Goubet (Research Fellow, INRAe), L. Mazéas (Resaerch Fellow, INRAe), C. Midoux (Bioinformatics scientist, INRAe).

Session 1 Session 2 Oral examination.

Learning objectives : To give students an integrated view of bioprocesses (wastewater treatment plant, waste methanizer…) applied into the depollution taking into account the scientific concepts, economic and environmental challenges.
Skills referred : In-depth of knowledge of microbial communities applied to bioprocesses in waste treatment;
Understanding of principles and challenges of biological treatments applied to solid (anaerobic digestion, composting…) and liquid (wastewaster treatment plants).
Content of teaching unit : Introduction of the teaching unit: context of waste treatment;
Biological treatment of effluents: context and challenges;
Anaerobic digestion;
Towards environmental biorefineries;
The waste of the Big Bang of our day;
Ecology of communities in the water treatment plant: protists, floc structure and bioindicator;
Exploitation of microbial functions for the depollution and recovery of wastewater;
Sizing concept and modeling of biological treatment processes;
Meta-omics methods and theirs application for bioprocesses: principles and application;
Understanding and predicting the metabolic activities of microbial communities: thermodynamic approaches;
Deciphering the operation of purification microbial communities: coupling of molecular microbiology and isotope biogeochemistry.
Seminars on the activities carried out at the IRSTEA (National Institute for Research in Science and Technology for the Environment and Agriculture).

Novembre.

Responsables : Alice Lebreton (CR INRA, ENS), Lionel Navarro (CR CNRS, ENS), Olivier Espéli (DR CNRS, Collège de France), Guy Tran Van Nhieu (DR INSERM, Collège de France) Equipe pédagogique : Alice Lebreton (CR INRA, ENS), Lionel Navarro (CR CNRS, ENS), Olivier Espéli (DR CNRS, Collège de France), Guy Tran Van Nhieu (DR INSERM, Collège de France), invited lecturers.

Organization: This one-week course takes place during the first semester. It is divided in four days of lectures and one day of article presentations and lab visits. Lectures are given in English. Slides in .pdf format of each lecture are provided on Intranet. Evaluation relies on the oral presentation, quality of article analysis, answers to specific questions, and on the student's active participation (questions during lectures and presentations). Session 1 & session 2 : F EO Oral examination.

Aims – Introduction to microbial systems and their diversity
Context: The development of diverse and recent approaches (genome wide studies, single cell imaging, biophysics, modelling) has revealed key aspects of microbial biology and ecology, which will be illustrated throughout this course. The program varies every year.
Example of themes: Bacterial cell cycle and development, Microbial systems and communities, Bacterial pathogens and diversion of host innate defenses, Biophysical approaches to bacterial virulence, Bacterial chromatin dynamics, Microbiomes, Environmental microbes & phages, Regulating RNA & with RNA in bacteria, Infectious bacteria

Keywords: Bacteria, modelling, bacterial networks and communities, microbiota, adjustment to environmental cues, infection, host-pathogen interactions, virulence, metagenomics, phages, RNA-mediated regulation, immunity.

Basic knowledge in molecular and cellular biology (gene regulation, organization of prokaryotic and eukaryotic cells, signalling, etc.).

Novembre.

PARIS

Programme Semaine 1 Introduction aux statistiques et à R, description d’une variable Semaine 2 Intervalles de confiance, association entre variables Semaine 3 Tests statistiques et pratique des tests Semaine 4 Régression linéaire simple et multiple, régression logistique Semaine 5 Données de survie (censurées), méthodes exploratoires multidimensionnelles Durée : 2 à 4 heures / semaine pendant 5 semaines Examen final : examen surveillé sur ordinateur.

Le M2 de Microbiologie fondamentale propose aux étudiants de pouvoir valider une formation bioinformatique initiant à la statistique à l’aide du logiciel libre R. Les étudiants peuvent suivre le MOOC gratuitement (https://mooc-francophone.com/cours/mooc-introduction-statistique-r/) lors de la session de septembre-octobre. Un examen organisé par l’équipe pédagogique du M2 permettra de valider cette formation. Cette UE est proposée en option supplémentaire c’est-à-dire que la note ne rentre pas dans le calcul de la moyenne du M2, mais apparaît dans le supplément au diplôme, donnant la possibilité aux étudiants de valoriser officiellement le suivi de cette formation, et donc une compétence en bioinformatique.

Septembre - Octobre - Novembre.

ORSAY - GIF-SUR-YVETTE

Christophe Sola, Olga Soutourina, Alessia Zamborlini, Florence Doucet-Populaire, Isabelle Turbica, Veronique Esteve-Daix (Sanofi), Michel Huc, Sophie Lefevre, Mathieu Picardeau, Richard Dailly.

Academic lectures given by experts, conferences given by private-sectors experts, Seminars led by students. Session 1 : F 0.7 EE+0.3 OO - Session 2 : F 1 EE; one third of the final mark is obtained through an oral presentation in English on an analysis of a paper in the field of CRISPR sciences, run in groups of 2 students.

Giving a broad professional and scientific culture of current R&D issues into the biomedical field. Practical applications of current transversal research carried out in microbiology and biotechnologies will be approached, particularly targeting public health research (bacterial diversity at the genome level, CRISPR-Cas systems and their applications, drug-resistance, food-borne and emerging pathogens, biosecurity, biosafety, water microbiology) including for diagnostics & pharmaceutical industries (process and products innovation, methods of analysis, new outlets for biotechnologies, quality, ethical and legal aspects); new strategies for the fight against infectious diseases and new problems in a global and one-health perspective (vaccines, biotechnology-derived medicines). All issues are targeted with an integrative perspective.

M1 in microbiology or other Health Sciences.

Any Medical, Pharmaceutical or Industrial microbiology articles and books.

Janvier - Février.

Sandra Helinck (MCF APT), S. Layec, S. Landaud (MCF APT), Hervé Blottiere (DR, INRA), F. Fonseca (DR, INRA), Eric Spinnler (PR AgroParisTech).

Technico-economic presentation of the food sector- Intellectual and industrial property - Fundamental knowledge on microbial ecology - Gut, microbiote and dysbiosis - Microbiote/host relationship- fonctional Interactomic Effect of Technology on the sequence of species development in cheese manufacturing with a special care for soft cheeses. White and red wine technology- Microbial processes in wine – Special vinifications- Taints and troubleshooting in wine making. Fermentations of cured meat products. Microbiology in brewery - Food alterations. Flavour biosynthesis by micro-organisms – Starter production and conservation. Visit of a cheese factory : Graindorge cheese (Livarot, Calvados) Session1 session 2 EO (oral examination).

Key-words: Medical microbiology, Vaccine and Drug Industry, Diagnostics Industry, Microbiology and Public Health, Agroindustrial Industry.

Novembre.

Lecturers: Guy Tran Van Nhieu (LBPA ENS Paris-Saclay), Jacqueline Cherfils (LBPA ENS Paris-Saclay), Gérald Peyroche (ENS Paris Saclay), Frédéric Barras (Institut Pasteur Paris), Pierre Genevaux (Toulouse), Olivera Francetic (Institut Pasteur Paris), Françoise Jacob-Dubuisson (Institut Pasteur Lilles), Han Remaut (Bruxelles), Remi Fronzes (Bordeaux), Anastassios Economou (KU Louvain), Pierre-Jean Corringer (Institut Pasteur Paris), Marc Fontecave ( CdF), Lars Malmström (ETH Zürich).

This module, lasting 32 hours over a week, will alternate morning classes taught in English, with a practical internship in a research laboratory in the afternoon. The audience will be limited to 16 students. The practical training will be done in subgroups in the laboratories of the LBPA ENS Paris-Saclay, other laboratories of the University Paris-Saclay or ENS Ulm. A half-day will be devoted to an oral (project synthesis, article analysis, ..) where students will be evaluated.oral presentation (2/3 of the final grade), practical(1/3 of the final grade).

Through the progress of structure-function studies based on the resolution of crystalline structures, various electron microscopy techniques, nuclear magnetic resonance, combined with the modeling and reconstruction of complex molecular systems, it has become possible to elucidate Atomic level the functioning of multiprotein assemblages at the heart of processes and understand them in their biological context. An important challenge for tomorrow's research is now to master these data and integrate them in order to identify the molecular mechanisms at the origin of biological functions and diseases.
The aim of the course is to introduce students to a range of multi-scale molecular approaches and their mechanistic integration. The course will present students with models of studies illustrating how this mechanistic vision contributes to major advances in the understanding of complex biological and physiopathological processes. Fundamental processes will be discussed, such as protein secretion, cell motility, or stress adaptation, in relation to pathologies such as infections, cancers or neurodegenerative diseases.

Basics levels in biochemistry, molecular biology and microbiology.

The articles will be given to the trinomial students at the beginning of the week.

Novembre.

GIF-SUR-YVETTE

Stéphanie Bury-Moné (PU UPSay) & Olga Soutourina (PU UPSay).

Session 1 & Session 2 : F 0.5 x report + 0.5 x EO.

The student will carry out an investigation through bibliographic research and interaction with the host team on the research subject that he/she will conduct during his/her M2 internship. This preliminary work will aim to present the scientific context and the issues associated with its research subject as well as the methods that will be implemented to answer the question (s) asked.

General Microbiology, Molecular and Cell Biology, Genetics, Biochemistry.

Scientific articles on the research subject.

Octobre - Novembre - Décembre.

ORSAY - GIF-SUR-YVETTE

Fabrice Confalonieri (PU UPSay), Cécile Fairhead (PU UPSay), and invited speakers according to the selected research topics.

Conferences by specialists in the field. Students will present a bibliographical analysis on one of the themes addressed by the speakers.

This teaching unit consists of scientific lectures/conferences by specialists in the field, about the mechanisms
involved in the stability and evolution of genomes, and the methods to study these topics including : the "3Rs"
(Replication, Recombination and Repair of DNA), the chromosome/nucleoid structure into macro- and microdomains,
programmed mitotic rearrangements and meiotic recombination events, experimental evolution, genetic drift,
selection, speciation, comparison between Neandertal and Homo sapiens sapiens genome...

Basic concepts in Genetics, Genomics and Evolution. Basic knowledge about gene structure and genome organisation in prokaryotes and eukaryotes.

Octobre.

ORSAY - GIF-SUR-YVETTE

Cécile Lagaudrière-Gesbert, Delphine Sitterlin.

L’UE se déroulera sur une semaine. Les articles scientifiques à analyser et discuter seront transmis avant le début de l’UE. Chaque demi-journée sera dédiée à un thème et comportera une conférence, suivie d’une présentation en binôme ou trinôme. Les étudiants seront évalués sur cette présentation et la discussion qui en découlera.

L’objectif de cette unité d’enseignement est de fournir une connaissance détaillée des mécanismes moléculaires et cellulaires qui régissent les cycles infectieux de virus infectant les mammifères. Un cycle de conférences dispensées par des chercheurs spécialistes du domaine portera sur les interactions virus-hôtes :
-Structure et Fonctionnement des glycoprotéines de fusion virales
-Mécanismes d’entrée des virus dans les cellules cibles
-Structure et assemblage des virus
-Détournement de la machinerie cellulaire au profit de l’expression et de la réplication des génomes viraux : Structure-fonction des polymérases virales (exemple : polymérase des virus influenza) ; Détournement des mécanismes de traduction par les virus
-virus et immunité : Mécanismes d’échappement à la réponse Interféron
-propagation des virus au sein de l’hôte : mécanismes de franchissement des barrières naturelles
Une lecture critique d’articles de recherche sera demandée aux participants. Les exposés conduiront à des discussions sur des thématiques de recherche actuelles. Ces séances seront animées par les conférenciers invités, chercheurs en virologie dans le périmètre de Paris-Saclay et de l’Ile de France.

Les enseignements généraux suivis en première année de master de biologie sont suffisants pour suivre cette formation. Néanmoins, de bonnes connaissances de bases en biologie moléculaire et biochimie structurale sont un atout.

Novembre.

GIF-SUR-YVETTE

Report and oral presentation evaluation - Session 1 and Session 2 : F 0.4 x report + 0.6 x EO.

The laboratory internship corresponds to a qualifying training through a 6-month research activity in a field related to Microbiology. It allows the student to be trained in experimental techniques but also in project writing and oral scientific communication. The M2 supervisors identify internship proposals with all the support laboratories attached in particular to the Paris-Saclay research institutes, in other French Research institutes, or abroad. At the end of the lab training, the student writes a thesis describing the research activities carried out and the results obtained during the internship. The report is accompanied by an oral presentation to the M2 Scientific and Pedagogical Committee, during which the student presents the key elements of his/her report, the work done and the reflection carried out during his internship..

General Microbiology, Molecular and Cell Biology, Genetics, Biochemistry.

Janvier - Février - Mars - Avril - Mai - Juin - Juillet.