M1 Biologie Agrosciences Sciences du végétal-Plant Sciences

- Génétique des populations (15h) : principales notions de génétique des populations ; influence des régimes de reproduction sur la diversité génétique ; effet de la sélection et de la dérive sur l’évolution des populations ; balance entre mutation et sélection et cryptopolymorphisme ; origine de la biodiversité spécifique, processus de spéciation.

- Structure et évolution du génome eucaryote (4h30) : composants majeurs du génome, éléments transposables et diversité structurale et fonctionnelle, duplication de génome et innovation pour l’adaptation des espèces.

- Epigénétique (5h) : organisation chromatinienne (euchromatine, hétérochromatine) ; expression des gènes (modification des histones, méthylation de l’ADN) ; épissage alternatif.

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- Population genetics (15 hrs): main concepts of population genetics; influence of reproductive regimes on genetic diversity; effect of selection and drift on population evolution; balance between mutation and selection and cryptopolymorphism; origin of specific biodiversity, speciation processes.

- Structure and evolution of the eukaryotic genome (4.5 hrs): major components of the genome, transposable elements and structural and functional diversity, genome duplication and innovation for species adaptation.

- Epigenetics (5 hrs): chromatin organization (euchromatin, heterochromatin); gene expression (histone modification, DNA methylation); alternative splicing.

Ce module a pour but de présenter la notion de biodiversité dans son ensemble avec une emphase particulière sur son aspect génétique et génomique, en donnant une place importante aux bases de la génétique des populations et la compréhension de la dynamique d'évolution génétique d'une population. Il insiste aussi sur les principaux mécanismes impliqués dans l’évolution structurale des génomes et dans la dynamique de régulation de leur expression, en intégrant les mécanismes épigénétiques à l’origine de la diversité fonctionnelle.

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This module aims to present the concept of biodiversity, with a particular focus on genetic and genomic aspects, giving significant attention to the fundamentals of population genetics and understanding the dynamics of genetic evolution in a population. It also highlights the main mechanisms involved in the structural evolution of genomes and in the dynamics of their expression regulation, and includes the epigenetic mechanisms that generate functional diversity.

- Cours magistraux pour définir les concepts nouveaux.

- Exercices de mobilisation des connaissances pendant les cours ; TD de réflexion, associés aux CM, sur les concepts vus en cours.

- Atelier bibliographique avec présentation et discussion en classe, pour illustrer par des exemples les notions et concepts vus en CM.

- Projet tutoré (2h30) autour de l’analyse d’un article scientifique, intégrant les connaissances acquises durant le module, en utilisant le mind mapping pour structurer sa pensée et son discours en vue d’une présentation orale évaluée.

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- Lectures to define new concepts.

- Exercises to mobilize knowledge during lectures; tutorials, associated with lectures, on the concepts covered during lectures.

- Bibliographic study with presentation and discussion, to illustrate the notions and concepts covered in lectures with examples.

- Tutored project (2.5 hrs) based on the analysis of a scientific article, integrating the knowledge acquired during the course, using mind mapping to structure thoughts and discourse (evaluated during an oral presentation).

- Savoir résoudre un exercice de génétique des populations

- Expliquer les bases épigénétiques de la régulation de l’expression des gènes

- Décrire les processus de création de diversité des génomes eucaryotes

- Présenter de manière synthétique une étude scientifique et identifier les principaux résultats et conclusions à retenir en utilisant une carte heuristique

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- Solve a population genetics exercise

- Explain the epigenetic basis of gene expression regulation

- Describe the processes involved in the creation of diversity in eukaryotic genomes

- Present a scientific study in summary form and identify the main results and conclusions to be retained using a mind map

• Henry JP & Gouyon PH, Précis de génétique des populations, Ed Dunod - Rossignol JL et al, Génétique. Gènes et génomes, Ed Dunod.

Techniques de la présentation orale en sciences, rédaction d'abstracts, décrire des graphiques, des expériences, simulation d’une conférence scientifique avec interaction, introduction à la certification en anglais
Un groupe (15-20 étudiants de bon niveau peuvent participer à un programme de communication interculturel. Il s’agit de 8 semaines de visioconférences avec des étudiants étrangers (voir www. soliya.net), suivi par un rapport écrit et une présentation orale.

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Oral presentation techniques in science, techniques to write scientific abstracts and to describe graphs and experiments, simulation of an interactive scientific conference, introduction to certification in English
A group of 15-20 high-level students can participate in an intercultural communication program. This consists of eight weeks of videoconferences with foreign students (see www.soliya.net), followed by a written report and an oral presentation.

Début septembre :Test de niveau 

Septembre-Octobre-novembre : plusieurs séances de TD

Janvier : certification.

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Early September: test to check the level
September-October-November: several tutorial sessions
January: certification.

• Savoir présenter et participer à une conférence scientifique, appliquer les règles d’une communication écrite, obtenir le niveau B2 minimum lors de la certification en anglais
• Production orale et écrite, interaction à l'orale, compréhension de l'orale et de l'écrit
  Compétences complémentaires :
• savoir préparer et parler avec une prononciation adéquate (notamment des termes scientifiques)
  Savoir interagir avec le public de manière formelle lors de la séance de questions/réponses d’une conférence scientifique

-Savoir présenter avec un langage corporel approprié.

Sont abordées les questions suivantes :

• Le concept de méthode scientifique à travers les âges.
• Créer de la vie : défi technique ou défi théorique ?
• Qu'y a-t-il derrière un concept : histoire de la notion de programme génétique.
• Histoire des réceptions critiques du darwinisme.
• Doute nécessaire, doute instrumentalisé : le scientifique face à l'inconnu.
• Qu'est-ce qu'une imposture scientifique ?
• Science et société : nouvelles formes d'expertise, panels citoyens, débats public.
• Regards de philosophes sur l'Animal.

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The following questions are addressed:

• The concept of scientific method through the ages.
• Creating life: a technical challenge or a theoretical challenge?
• What lies behind a concept: history of the notion of genetic programs.
• History of critical reactions to Darwinism.
• Necessary doubt, instrumentalized doubt: scientists faced with the unknown.
• What is scientific fraud?
• Science and society: new forms of expertise, citizen panels, public debates.
• Philosophers' thoughts on animals.

Objectifs: L'histoire et la philosophie des sciences sont un complément nécessaire à la formation de l'esprit scientifique.

L'objectif de cet enseignement est de proposer une introduction à ces domaines, par le biais d'études de cas choisis dans les sciences du vivant.

Il s'agit de développer une réflexion critique et autonome sur les méthodes et les objets de la science en général et de la biologie en particulier.

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Objectives: The history and philosophy of science are a necessary complement to the development of scientific skills.

The aim of this course is to provide an introduction to these fields through case studies selected from the life sciences.

The goal is to develop critical and independent thinking about the methods and subjects of science in general and biology in particular.

Conférences, études de textes et documents audiovisuels,  débats, présentations orales.

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Lectures, text and audiovisual document studies,  debates, oral presentations.

• Développer un recul critique sur les questions scientifiques
• Maîtriser l'originalité de la démarche scientifique
• Acquérir une vision large des questions éthiques 
• Mettre en perspective les débats scientifiques contemporains au regard de l'histoire des sciences. 
• Préparer un exposé oral par de la bibliographie pertinente

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• Develop a critical perspective on scientific issues.
• Master the originality of the scientific approach.
• Develop a broad view of ethical issues.
• Put contemporary scientific debates into perspective in relation to the history of science.
• Prepare an oral presentation using relevant bibliography.

Bases de biologie moléculaire

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Fundamentals in molecular biology

Etude d'une accession (recherche dans les bases de données bibliographique et biologiques, analyses bioinformatiques) 

TP sur ordinateur et techniques de base en biologie moléculaire

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Study of an accession (searching bibliographic and biological databases, bioinformatic analyses)

Practical work on computers and basic techniques in molecular biology

Illustrer les principales méthodes permettant l'étude d'un gène ou une protéine (méthodes expérimental et outils in silico). Définir une question biologique pertinente à partir des données existantes sur un sujet scientifique.  Proposer un plan d'expérience. Etre en capacité de construire une requête sur des outils IA pour produire un résumé et d'être en capacité d'identifier les erreurs et les corriger. Être capable de produire une figure scientifique légendée et expliquée et de la présenter à l'oral.

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Illustrate the main methods used to study a gene or protein (experimental methods and in silico tools). Define a relevant biological question based on existing data on a scientific topic. Propose an experimental plan. Be able to construct a query on AI tools to produce a summary and be able to identify and correct errors. Be able to produce a scientific figure with captions and explanations and present it orally.

Projet tuteuré (chaque étudiant.e a pour mission d'étudier un gène ou une protéine, proposé par un.e chercheur.e). Il.elle réalise un état de l'art, effectue des analyses complémentaires (in silico) puis identifie une question biologique pertinente.

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Supervised project (each student studies a gene or protein suggested by a researcher). They review the current state of the art, perform additional analyses (in silico), and then identify a relevant biological question.

Effectuer une synthèse de données scientifiques; rechercher des sources fiables; présenter des résultats scientifiques, communiquer à l'oral; maîtriser les techniques de base de laboratoire de biologie et connaître les règles de sécurité

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Perform a synthesis of scientific data; search for reliable sources; present scientific results, communicate orally; master basic biology laboratory techniques and know safety rules

Fundamentals of physiology and metabolism at the bachelor's degree level

This unit begins with an introduction to metabolic diversity across prokaryotes and eukaryotes, establishing a foundation for understanding both universal features and key divergences. The central theme of the module is the study of metabolic responses and adaptations to environmental stress, providing a framework for a comparative approach across different biological kingdoms. The programme continues with an exploration of core metabolism, including carbon fixation, respiration, and energy production. These fundamental processes are examined within the context of their role in maintaining homeostasis and physiological performance under changing conditions. A dedicated strand focuses on specialised metabolic pathways, with particular emphasis on responses to oxidative, water, and nutrient stress. Illustrative case studies of metabolic adaptations in extremophilic bacteria, plants, and animals are used to highlight the diversity of evolutionary strategies and to explore the principle of inter-kingdom complementarity. Finally, the module concludes with an overview of modern approaches in metabolomics and integrative biology, which enable the analysis of metabolic and physiological responses to stress across multiple scales, from the cell to the whole organism.

The intended learning outcomes of this module are to achieve a comprehensive understanding of the major pathways of core metabolism (including carbon and nitrogen assimilation, respiration, energy, ...) and to develop the ability to identify and compare specialised metabolic processes that underpin physiological responses to environmental stresses. Students will also learn to relate these metabolic mechanisms to evolutionary adaptations across biological kingdoms such as prokaryotes, plants, and animals, and to evaluate evidence of metabolic complementarity between them. Additionally, the module aims to cultivate advanced competencies in the critical analysis of scientific literature and in the effective communication of research findings through the preparation and presentation of a scientific poster.

6 Lectures (CM): 9 hours
1 Tools session: 1.5 hours
3 Poster Tutorials (TD): 4.5 hours
The unit employs interactive lectures emphasising cross-kingdom comparisons. Teaching is informed by a multidisciplinary approach, integrating biochemistry, physiology, and evolutionary biology and metabolisms. A significant component involves collaborative work in small groups centred on the research and design of scientific posters.

- Demonstrate knowledge and understanding of key definitions and fundamental concepts.
- Articulate coherent reasoning concerning core metabolic pathways and metabolic adaptations to environmental stress across different biological kingdoms.
- Conduct a critical analysis of a grade-A scientific article.
- Structure and communicate scientific findings effectively, both graphically (poster) and orally (presentation).
- Demonstrate scientific rigour, relevance, and critical thinking in the interpretation and presentation of the research.

Les conférenciers sont des professionnels du monde académique ou privé bénéficiant d’une reconnaissance dans leur discipline. Les conférences se rapporteront aux thématiques suivantes : Biodiversité, Alimentation et agriculture, Société, Environnement

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The speakers are professionals from both academic and private sectors with a recognized expertise in their respective fields. The lectures will cover the following topics: Biodiversity, Food and agriculture, Society, Environment

Cette UE vise à améliorer la culture générale scientifique des étudiants dans le domaine des sciences du vivant et de ses interactions avec la biosphère et les sociétés. Elle permet aux étudiants de s'initier à des problématiques sociétales en lien avec les thématiques de la graduate school BIOSPHERA: Biodiversité, Alimentation et agriculture, Société, Environnement.

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This course aims to improve students' general scientific knowledge in the field of life sciences and its interactions with the biosphere and societies. It introduces students to societal issues related to the themes of the BIOSPHERA graduate school (Biodiversity, Food and Agriculture, Society, Environment).

Conférences en présentiel ou en visioconférence

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On-site or videoconference lectures

• Être capable d’interagir avec tous types de professionnels dans le domaine de l’environnement, du climat, de la biodiversité, de l’alimentation et de leurs interactions avec les sociétés.
• Posséder une vision large des questions environnementales, s’appuyant sur des connaissances diversifiées (scientifiques, juridiques, économiques, etc) et avoir, de ce fait, un recul par rapport à sa discipline d’origine.
• Compétences complémentaires: Capacité à synthétiser les principaux éléments d’un discours

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• Be able to interact with all types of professionals in the fields of the environment, climate, biodiversity, food, and their interactions with societies.
• Possess a broad view of environmental issues, drawing on diverse knowledge (scientific, legal, economic, etc.) 
• Additional skills: Ability to summarize the main points of a speech.

L’accent est mis sur les tests statistiques paramétriques.
Contenu : Cours + exercices sur Excel et R (Rcmdr).

L’objectif est d’apporter aux étudiants quelques notions de statistiques non développées en licence, tout en restant dans les limites de ce qui peut être raisonnablement acquis dans le temps d’un module court. L’accent est mis sur les tests statistiques paramétriques.

Tout l’enseignement, cours et travaux pratiques (en salles informatique) est obligatoire et présentiel.

Manipulation de jeux de données, définition de questions statistiques et identification de la méthode statistique à mettre en œuvre pour y répondre, autonomie en analyse de données courante (description de données, comparaison de distributions, de moyennes, corrélation et régression) grâce à un logiciel simple (Excel, R via l’interface Rcmdr).

During this course, students will be given a data set to analyse in depth. The teaching is based on active pedagogy, accompanied by a scientific tutor who will have his or her own dataset to be analysed.

During this course, students will learn to :
• Exhaustively search and synthesise the information available in public databases
(bibliographic, genomic, transcriptomic, proteomic data, etc.)
• The use of certain software to analyse these data
• Identify a relevant biological question from their synthesis
• Design and present a mini research project to answer this biological question and to deepen
the knowledge about it.

Aucun

The programme first introduces the major families of alternative proteins (plant-based, insect-derived, microbial), their functional properties, and their prospects for use in food systems. It then addresses the biotechnological approaches involved, ranging from conventional techniques such as mutagenesis, transgenesis and cisgenesis, to new genome-editing technologies, as well as the contributions of protein engineering, synthetic biology, and systems biology. Cross-cutting themes, including protein separation, industrial transformation processes, and metabolic pathway engineering, are also explored. Ethical, societal, and regulatory aspects of applying biotechnology to food production are considered throughout. The course is complemented by a research and development centre visit, allowing students to directly link theoretical knowledge with industrial applications.

The unit is structured around 14h of lectures, 16h of tutorials, and 6h dedicated to a supervised project, in addition to the R&D centre visit. Lectures provide the conceptual foundations and highlight recent advances in the field, while tutorials encourage active learning through case studies, critical discussions, and problem-solving exercises. The supervised project allows students to work independently on an applied problem, thereby integrating theoretical knowledge with creativity and analytical skills. Assessment in the first session consists of coursework (written dossier, 30%) and an oral examination (70%), while the second session consists of a final written examination (100%). This structure supports progressive, interactive learning and fosters analytical, critical, and applied competences required to address the challenges of protein biotechnology.

Assessment in this unit is designed to evaluate a combination of scientific knowledge, analytical ability, and applied problem-solving skills. The written report assesses students’ capacity to synthesise scientific literature, critically appraise biotechnological approaches, and contextualise them within ethical and regulatory frameworks. The oral examination evaluates students’ ability to communicate complex scientific concepts clearly, defend arguments, and demonstrate integrative understanding across molecular, physiological, and technological dimensions. The written examination in the second session tests comprehensive knowledge of alternative protein sources, mastery of genetic and protein engineering techniques, and the ability to apply theoretical concepts to novel or emerging biotechnological challenges.

Mackelprang, R., & Lemaux, P. G. (2020). Genetic engineering and editing of plants: an analysis of new and persisting questions. Annual Review of Plant Biology, 71, 659-687.
Małecki, J., Muszyński, S., & Sołowiej, B. G. (2021). Proteins in food systems—Bionanomaterials, conventional and unconventional sources, functional properties, and development opportunities. Polymers, 13(15), 2506.
Hadi, J., & Brightwell, G. (2021). Safety of alternative proteins: Technological, environmental and regulatory aspects of cultured meat, plant-based meat, insect protein and single-cell protein. Foods, 10(6), 1226.

Niveau d’une Licence générale en Sciences du vivant en bio-statistiques, physiologie, biologie moléculaire, biochimie. Connaissances des principes des approches haut débit de type « omiques ».

This course consists mainly in a practical approach as well as intensive scientific reasoning based on a theme close to a research question. In recent years, the theme chosen has been the following: What is the impact of a beneficial bacterium of the plant responses to biotic and abiotic stresses? Other research questions may potentially replace the current theme, but the idea is to maintain a set of integrative questions in the field of plant response to biotic and/or abiotic stresses. In parallel, the students are implementing a complete approach to a Koch postulate (diagnosis of the pathogen responsible for symptoms observed on plants).

Techniques and methodologies used: DNA extraction, PCR and quantitative PCR, different methods of inoculation of pathogens on plants and qualitative and quantitative analysis of symptoms, Koch's postulate, manipulation of different bioinformatics tools (blastn, AgriGO, G.Profiler, MEME, STRING, KEGG,...).

Interactive tutorials, generally in the form of round tables, will allow students to step back from the experimental work carried out and to broaden the scope of their experimental strategies in response to a biological question. They allow the students to refresh the basic principles of numerous techniques by integrating them into a research approach (analysis of mutants, transformation techniques for higher plants and limitations, regulation of gene expression, signalling, microscopy techniques, use of gene expression databases).

To provide students with a technical base and scientific reasoning enabling them to approach future laboratory or company internships with more confidence, thanks to the conduct of a mini research project involving various experimental approaches (plant pathology, molecular physiology, cytology, analysis of transgenic plants, analysis of transcriptomic data). These approaches are based on the plant Arabidopsis thaliana, under development or faced with biotic (plant pathogenic microorganisms) or abiotic (salt) stresses.

mainly practical courses but also some tutorial (transcriptomic analyses), and rount tablebetween students and teachers.

- Exploit online public databases as well as bioinformatics tool platforms (reinforcement)
- Design and implement a scientific approach to answer a biological question(s)
- Know the main approaches and techniques used for the functional characterisation of a gene in a model plant species
- Implement the basic approaches in phytopathology.

Good knowledge of the basics of plant physiology and metabolism.

The module involves interactive discussions, exercises (including some that involve the preparation of written reports), and work undertaken by students in small groups towards the preparation of oral presentations on a given topic.

Students will acquire theoretical and practical knowledge aimed at furthering their understanding of the flexibility of plant function in a changing and potentially stressful environment. Group-centered bibliographic research projects are focused on key players in metabolic responses to external factors, and involve the preparation of a report in the form of a structured and logical oral presentation. Supervised exercises aim at the acquisition of a more in-depth knowledge of plant biochemistry and molecular biology.

Tutorials, exercises, supervised projects

Basic knowledge of the biology of microorganisms (fungi, bacteria, viruses) and plants, as well as molecular biology and genetics, at Bachelor's level in life sciences.

Plants interact with microorganisms in their environment and must continuously adapt to them. These microorganisms can exert either negative (pathogenic) or beneficial (symbiotic) effects on plants, both in natural ecosystems and agroecosystems. This issue is particularly relevant today, as agricultural practices must ensure productivity while preserving the environment. 
The teaching unit includes 9 hours of lectures on plant–pathogen interactions (fungi, bacteria, viruses), 3 h on plant–symbiotic microorganism interactions, and 1.5 h on the plant microbiota and its interactions within the rhizosphere. Students are introduced to epidemiology (3 h of lectures), plant immunity (6 h), and methods for plant protection (3 h).
The course is complemented by a 1.5-h seminar involving the analysis of scientific articles on symbiosis, and 9 h of practical work during which students apply techniques and concepts from plant pathology to assess the susceptibility/resistance of two plant genotypes (wild type and mutant) to various pathogens, and discuss the role of the altered function in plant immunity.
Throughout the course unit, students work in teams on a plant pathology topic, culminating in an oral presentation based on a scientific poster.

Acquire the knowledge and methodologies necessary to understand the dynamics of plant–microorganism interactions, pathogenic or symbiotic, in relation to environmental factors; understand the molecular and cellular mechanisms involved in these interactions; be aware of the societal and ecological implications of such interactions; and consider both traditional and innovative control strategies aimed at improving the quality and yield of agricultural production.

The teaching unit is structured around lectures, tutorials focused on article analysis, and three practical sessions, all centered on a common theme. On the first day, students are assigned a presentation topic and grouped into pairs or trios to conduct a bibliographic review on a specific interaction—either parasitic or beneficial. At the end of the course, each group delivers an oral presentation supported by a scientific poster. Students are also assessed by a 2-hour written exam.

- Master the main infectious processes of pathogenic micro-organisms and their specific features, in relation to the various parasitism strategies. 
- Master the main plant immune mechanisms (microorganism perception mechanisms, signalling and defence). 
- Understand the epidemiological factors explaining the appearance and spread of a disease on different spatio-temporal scales. 
- Be able to describe crop protection control methods. 
- Be able to describe the diversity of symbiotic interactions in plants, the molecular dialogue between microbiota and host plant and discuss the ecological and societal importance of symbiotic interactions.
- Be able to name the niches of the plant microbiota and describe the process of establishment of the plant microbiota. 
- Know how to implement the main plant pathology techniques. 
Complementary skills:
- Be able to analyse a scientific article and produce a summary on a scientific subject.
- Know how to search for information in scientific literature.
- Be able to communicate a scientific message in English, either orally or via a scientific communication medium.

• Phytopathologie, Philippe Lepoivre, 2003, De Boeck Supérieur
• Plant Pathology, Agrios, 5th ed, 2005, Academic Press
• Symbiose, Marc-André Selosse, 2000, Vuibert - Hungry Planet: Stories of Plant Diseases, Gail L. Schumann and Cleora J. D’Arcy, 2017.

The application of genomics and bioinformatics tools to the study of the genome of cultivated plants will be presented. The specific features of genome structure, such as duplications, transposable elements and multi-genomes, as well as the genome diversity of cultivated plants, including heterozygosity, will be discussed in relation to the evolution of crops and specific agronomic traits. The specificities of organelle genomes will also be presented and discussed. The available genetic and genomic resources will be presented in light of their potential applications. The section on teaching bioinformatics through practical exercises will expand on the concepts of comparative genomics, protein motif research, and structure-function relationships. It will also introduce gene regulatory networks and protein-protein interaction networks, demonstrating how to construct and analyse them for functional annotation.
This course provides an overview of the principles of long-read sequencing and its advantages for generating high-quality de novo assemblies, including those of entire genomes from telomere to telomere (T2T). Students will explore methods for evaluating the quality of genome assemblies and discuss their key applications in genomics research. The course will introduce pangenomes and pangenomics, emphasising their role in representing genetic diversity beyond single reference genomes.

Understand the basic elements and specificities of genomics as applied to cultivated plants. Use the different bioinformatics databases and their characteristics to perform an appropriate search by selecting specific parameters. Understand the specificities of genome evolution in cultivated plants, as well as the natural and artificial processes involved in creating genetic diversity. 
Explain the principles of long-read sequencing and evaluate its advantages for de novo assembly up to T2T genomes. Describe the concepts of pangenomes and pangenomics.

- Lectures to introduce and define new concepts. 
- The course involves mainly practical work using bioanalysis tools to introduce bioinformatics, as well as supervised work for the assessed bioinformatics project.
- Supervised bibliographic work to analyse articles for an assessed oral presentation.

- Explain the importance of high-throughput sequencing and bioinformatics in plant genome analysis, outlining the advantages and limitations of next-generation sequencing techniques.
- Describe the main mechanisms of plant genome evolution, such as polyploidy, interspecific hybridization, transposition and structural rearrangements.
- Explain the molecular mechanisms involved in creating useful diversity for improving crops.
- Know how to use public databases and bioinformatics tool platforms.
- Present a scientific study and summarise the main results and conclusions; know how to communicate a scientific message.

- Economie de marché et libéralisme 
- Circuit économique et intervention publique 
- Economie de l’innovation et croissance économique 
- Recherche, Innovation et Concurrence interfirmes

- Maîtriser les concept clés de l’analyse économique (croissance économique, concurrence, libéralisme, intervention publique)
- Comprendre le lien entre innovation, croissance et profit.
- Appréhender la recherche, l’information et la connaissance comme des éléments essentiels de la compétitivité de l’entreprise.

Cours magistraux, lecture et analyse d'articles scientifiques et de la presse économique, documentaires audiovisuels, travail en petits groupes

- Etre capable d’appréhender et de décrire l’environnement économique de l’entreprise
- Comprendre les contraintes et le fonctionnement de l’entreprise pour mieux s’y insérer
- Maîtriser les enjeux de l’innovation dans la compétitivité de l’entreprise

La biologie des systèmes vise à comprendre comment les fonctions biologiques émergent des interactions entre les multiples composantes des systèmes vivants, en modélisant la dynamique de ces interactions et processus. Trois thèmes principaux seront abordés : le rythme circadien, le microbiote et le stress abiotique.

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Systems biology aims to understand how biological functions emerge from interactions between the multiple components of living systems by modelling the (dynamics of) interactions and processes. Three main topics will be discuss: circadian rythm, microbiote and abiotic stress.

Un système biologique est un ensemble d'éléments interagissant qui forment une unité biologique fonctionnelle. Un système peut être appréhendé à différents niveaux : écosystème, organisme, organe, tissu, cellule, organite, voie métabolique, processus physiologique, réseau de gènes ou de protéines, etc. L'objectif de cet enseignement est de comprendre l'organisation et le fonctionnement des organismes complexes, de structurer et d'intégrer des informations multi-échelles et multidisciplinaires (biologie intégrative), de révéler des propriétés émergentes qui resteraient insoupçonnées par l'étude séparée des différents éléments, et de permettre de prédire le comportement d'un organisme dans des conditions inédites. 

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A  biological system is a set of interacting elements that form a functional biological unit. A system can be understood at different levels: ecosystem, organism, organ, tissue, cell, organelle, metabolic pathway, physiological process, gene or protein network, etc. The aim of this teaching is: to understand the organization and functioning of complex organisms, structuring and integrating multi-scale and multidisciplinary information (integrative biology). To reveal "emergent properties" that would not have been identified by studying the different elements separately. To  be able to predict the behavior of an organism under unexplored conditions.

3 thèmes biologiques (rythmes biologiques, microbiome et stress oxydatif) avec chacun 6 heures de cours, atelier bibliographique (TD: 6h+oraux: 4h), séminaires de recherche (4h). Les étudiants devront aussi rédiger un petit projet de recherche autour d'un des thèmes de l'UE.

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Three biological themes (biological rhythms, microbiome, and oxidative stress), each with 6 hours of lectures, a literature review workshop (6 hours of tutorials + 4 hours of oral presentations), and research seminars (4 hours). Students will also be required to write a short research project on one of the course themes.

appréhender les processus biologiques de façon systémique. Comprendre les différentes démarches de modélisation.Travailler en groupe- proposer et rédiger un projet de recherche 

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To understand biological processes in a systemic way. To understand the different modeling approaches. To work in a group – to propose and write a research project.

System biology I. Integrative approaches are key steps in the thorough exploitation of omics data and their translation into knowledge. In this module, students will have courses on the architecture and the machinery of the cell, and on the genome and epigenome organization. They will learn how to combine predictive and experimental approaches to decode the genomic information through the structural and functional annotation of genomes. The integration and the querying of heterogeneous data imply to perfectly know their origin in order to take into consideration their quality, relevance and confidence levels. The understanding of this approach is the basis of holistic analyses for systems biology. 
System Biology II. Global analyses (omics) currently generate large datasets that do not capture the complexity of living systems. Systems Biology is an approach where omics data are integrated and exploited (compared) through mathematical models of biological systems or sub-systems. The complexity of biological systems and the diversity of issues to be considered require the use of different types of modelling.

System Biology I. Students will see different methods to produce transcriptome, ORFeome, proteome and interactome resources and how to integrate them in modeling approaches to have new insights on cellular processes. 

Systeme Biology II. Students will explore a number of mathematical approaches to tackle biological issues through the integration of "omics" data. The mathematical approaches include the methods known as constraint-based modeling, i.e. flux balance analysis, resource balance analysis, but also tools specific to the analysis of dynamic systems and Boolean systems.

Lectures and practical tutorials will be intermixed during this 25h-course.

On completion of the course, students will be able to:

• Have a good understanding of the challenges posed by integration of omics data. They should be able to understand and summarize a scientific paper in the field. 
• Understand and explain the challenges of using constraint-based modeling approaches to describe cellular behaviors
• Summarize and present a scientific paper in the field.

Basic concepts of formal genetics and molecular biology

Main topics : population genetics (linkage disequilibrium, population evolution, population structure); mechanisms of genome evolution; introduction to quantitative genetics and methods to study complex traits (including QTL mapping and GWAS); genetic basis of crop domestication; genetic resources and their importance in plant breeding

Skills: DNA extraction and genotyping using SSR markers; perform a QTL detection approach

Knowledge: Understanding the mechanisms of genome evolution; consolidating the fundamentals of population genetics and quantitative genetics; understanding the genetic determinism of quantitative traits and the methods used in plant breeding to improve these traits

Lectures to introduce and define new concepts; practical work and tutorials to perform genotyping, to study the segregation of a population and to detect QTL; visit of a research lab (GQE-Le Moulon)

Master the key concepts and approeches presented during lectures, practical work and tutorials (the mechanisms of genome evolution; the fundamentals of population genetics and quantitative genetics; the genetic determinism of quantitative traits and the methods used in plant breeding to improve these traits)

Bases de physiologie et de métabolisme chez les plantes niveau licence sciences de la vie

Cette UE est structurée en trois parties :
1. Introduction à la nutrition azotée et carbonée
Présentation des bases de la nutrition minérale des plantes et des enjeux actuels en agronomie, notamment la réduction des pollutions des sols, l’optimisation de la fertilisation et l’adaptation de la nutrition des espèces cultivées aux changements climatiques.
2. Travaux pratiques en laboratoire
Mise en œuvre des principales techniques de physiologie végétale permettant de quantifier la nutrition azotée et carbonée. Ces séances visent à familiariser les étudiants avec les méthodes d’analyse utilisées en recherche et en agronomie expérimentale.
3. Travaux pratiques au champ 
Mesure des teneurs en azote dans des plantes cultivées en conditions réelles. L’objectif est de montrer comment ces données permettent d’améliorer la gestion des engrais et la durabilité des systèmes de production.

Caractériser la physiologie de la nutrition minérale et carbonée à l’échelle de la plante entière et de la parcelle.

CM : 
 Nutrition minérale (azote, phosphore, absorption, assimilation, remobilisation) ; Photosynthèse et bilan de carbone ; Plantes modèles (Arabidopsis, Medicago, Brachypodium) et plantes cultivées (Colza, Maïs, Blé …) ; Cycle de l’azote, carbone et eau à l’échelle de la parcelle, étude des sols ; Relation entre la fertilisation et le rendement (qualité des graines, biomasse)
 TD : Quantification des glycomolécules par spectroscopie de masse, méthode des bilans en agriculture, visite de la Digiferme d’Arvalis. 
 TP au champ : mesures non destructives NDVI sur le site d’Arvalis de Villiers le Bâcle, prélèvements en champ des échantillons, mesures de poids frais et secs.
 TP au labo : Phénotypage d’Arabidopsis sauvages et mutantes affectés dans le transport des sucres pour les métabolismes azotés et carbonés (Dosage enzymatique des sucres solubles et des acides aminés, coloration lugol pour la détection d’amidon)

Comprendre et maitriser les connaissances et les outils permettant d’analyser le fonctionnement d’une plante entière. Avoir conscience des grands enjeux agronomiques en lien avec la nutrition des plantes et de la gestion des itinéraires culturaux dans un souci de production durable. Suivre rigoureusement un protocole expérimental. Présenter et analyser des résultats expérimentaux.

Botanique : Biologie et physiologie végétales de Sylvie Meyer, Catherine Reeb, Robin Bosdeveix, Edition Maloine.
Biologie végétale : Nutrition et métabolisme de Jean-François Morot-Gaudry, François Moreau, Roger Prat, Christophe Maurel, Hervé Sentenac, Edition Dunod.

Bon niveau en biologie moléculaire et biologie cellulaire d’une Licence générale en Sciences du vivant

1rst week: courses, tutorials and seminars on genome editing, RNA interference (and other RNA-based technologies) and synthetic biology. Several seminars will be given by reseachers, platform engineers and professionals from private companies, specialized in one of these fields.
During this practical course, students will first analyse different Arabidopsis lines, that are silenced -or not- for a reporter transgene. For that, they will carry on several experiments, that are commonly used to estimate the efficiency of a RNAi approach and/or to analyse small RNAs (RT-qPCR, DNA methylation analysis, dedicated northern for small RNAs, tissue and subcellular localisation of proteins using fluorescence microscopy, …).

The objective of this teaching will be to explore the methodologies of genome engineering, RNA interference and synthetic biology and to understand their underlying fundamental biological mechanisms. Challenges in medicine and agronomy and ethical/legal issues will be discussed.

At the end of the course, students will be able to:

• Design an adequate strategy of RNAi or genome editing, using CRISPR-Cas or other technologies;
• Understand the design of regulatory circuits or metabolic pathway in synthetic biology;
• Be aware of the recent fields of applications and ethical issues of these biotechnologies.
• Gain autonomy in basic molecular and cellular biology technics used to validate the efficiency of a RNAi constructs and/or to analyse small non coding RNAs.
• Organize themselves (or by two) to perform several experiments in parallel, like in labs
• Collaborate inside a working team
• Analyse, criticize and present their experimental results (oral and written report)
• Integrate results obtained by different scales of analysis (from DNA to the plant level) to answer a complex biological question.

• Biotechnologies. Les promesses du vivant, 2015, Vanessa Proux, Collectif, Fyp

-Stable RNA interference rules for silencing, Fellmann and Lowe, 2014, Nature Cell Biology, vol 16 - https://www.cell.com/nucleus-CRISPR - Synthetic biology: Recent progress, b.

Le programme est structuré autour de trois grands axes thématiques :

1. Biologie et technologie des semences : bases physiologiques et biochimiques du développement des semences ; mécanismes de régulation de la dormance, de la germination et de la longévité ; pathologies des semences ; progrès des biotechnologies appliquées aux semences, notamment l’amélioration des semences, les traitements (enrobage, granulation, etc.), la lutte biologique, la biostimulation et les nouvelles biosolutions.

2. Qualité des semences et chaîne de valeur : organisation des systèmes de production de semences ; procédés de préparation, de conditionnement et de conservation ; mise en œuvre des protocoles de contrôle qualité ; normes internationales pour les essais et la certification des semences ; et contributions des principaux acteurs institutionnels tels que le GEVES, le SEMAE, le FNAMS, l’INRAE ​​et les entreprises privées.

3. Économie, réglementation et innovation dans le secteur semencier : marchés mondiaux et français des semences ; enregistrement des variétés et protection de la propriété intellectuelle ; stratégies de commercialisation spécifiques à la filière semencière ; et analyse du rôle stratégique des semences dans les transitions agricoles (agroécologie, conservation de la biodiversité et sécurité alimentaire mondiale).

Ce module d'enseignement vise à offrir aux étudiants une compréhension globale et intégrée du secteur semencier, depuis la biologie fondamentale du développement des semences jusqu'à l'organisation et le fonctionnement des filières semencières nationales et internationales. Les semences ne sont pas seulement les organes reproducteurs des angiospermes ; elles constituent également un pilier de l'agriculture mondiale, garantissant la sécurité alimentaire, la compétitivité agricole et la transition écologique. La France occupe une position de leader mondial dans la production et l'exportation de semences, notamment grâce à des conditions pédoclimatiques favorables et à l'expertise reconnue de sa filière semencière. Dans ce contexte, ce module a pour objectif de former les futurs professionnels à : (i) maîtriser les processus physiologiques, biochimiques et biotechnologiques qui sous-tendent la qualité des semences ; (ii) comprendre les dimensions organisationnelles, économiques et réglementaires du secteur semencier ; et (iii) évaluer de manière critique comment les connaissances scientifiques et l'innovation contribuent à la performance agricole, à la durabilité et au commerce mondial des semences.

Ce module comprend 36 heures d'enseignement dispensées selon une approche pédagogique mixte. Les étudiants bénéficieront de 12 heures de cours magistraux pour acquérir les bases théoriques, de 14 heures de travaux dirigés consacrés à des études de cas et à l'analyse critique de recherches de pointe, et de 10 heures de projets de groupe encadrés visant à développer le travail d'équipe, la synthèse et la résolution de problèmes appliqués. L'approche pédagogique associe apports académiques et expertise professionnelle, notamment à travers des séminaires et des conférences animées par des représentants d'instituts de recherche et des acteurs industriels. Cette double approche garantit un lien étroit entre les avancées scientifiques, les cadres réglementaires et les pratiques industrielles.

À la fin de cette unité, les étudiants devront démontrer :

- Des compétences scientifiques avancées : maîtrise de la biologie, de la physiologie et de la biotechnologie des semences, avec la capacité d’analyser et d’interpréter les mécanismes influençant la qualité et la performance des semences.

- Des compétences professionnelles appliquées : compréhension des systèmes d’assurance qualité, des cadres réglementaires et des structures économiques régissant le secteur semencier, aux niveaux national et international.

- Des compétences critiques et stratégiques : capacité d’évaluer la contribution de l’innovation semencière à la productivité agricole, à la durabilité environnementale et à la résilience socio-économique.

- Des compétences transversales : capacité à travailler en équipe, à communiquer scientifiquement (à l’écrit et à l’oral) et à prendre des décisions fondées sur des données probantes dans un contexte professionnel.

Http://www.gnis.fr/ http://www.seedbiology.de/ http://seedscisoc.org/ http://www.worldseed.org/.

Basic concepts of of formal genetics and molecular biology and of plant structure

The aim of this course is to understand and master key concepts in plant developmental biology at the molecular, cellular and whole-organism levels. The topics covered, whether in model or cultivated species, will concern the major stages of plant life and morphogenesis, responses to environmental change, natural diversity and variation, and certain aspects of Evo-Devo. This knowledge can be re-used to explore new themes in future courses, whether or not they specialize in the study of development.

At the end of the course, students will be able to:
- To understand in a theoretical and practical way the development of plants and their adaptations as the main stages of angiosperms development and their molecular and cellular determinism
- To know the major regulators of developmental transitions and their signaling pathways, whether endogenous (hormones, peptide signals, etc...) or exogenous (light and photoperiod) and their possible interactions. 
- To be able to formulate hypotheses and to set up an experimental approach to answer them
- To gain autonomy in learning recent methods of plant cellular and molecular analysis used in development biology (genetic forward, gene targeting and genome editing, protein-protein and protein-DNA interaction studies, analysis of the temporal expression of a gene, etc.)

The UE will include a proportion of traditional teaching (lectures/TD/TP), sessions centered on debate and the formulation of questions, and a series of presentations during which students will be asked to present and discuss analysis techniques. The UE is divided into 3 pedagogical and thematic blocks:
- What is a plant cell and plant development?
- How to study plant development?
- How developmental knowledge can be useful?

The assessment will focus on the ability to integrate theoretical information, data analysis and bibliographic references presented in the form of presentations and written reports.

Training in the experimental approach – designing and implementing a biological experiment independently

Lecture: Experimental procedures, characteristics of a scientific experiment
Tutorial: Designing an experiment to validate results from an omics approach
Practical: Implementing the experiment

Working in a team,
designing and conducting a relevant experiment to answer a given biological question,
critically analyzing a methodology and data

Basic knowledge in microbial taxonomy, in biostatistics and in the use of R language

Knowledge and implementation of molecular and bioinformatic tools for the analysis of microbial ecosystems using metagenetic approaches (e.g. 16S gene amplicon sequencing; or other markers depending on the microbial ecosystem studied). Knowledge of the principles of descriptive and functional microbial ecology. The course will aim to compare several samples taken either from a food microbial ecosystem, from environmental microbiota or plant, human or animal digestive microbiota, or from biotechnological digesters used to treat bio-waste. Descriptive and functional knowledge of these ecosystems will be presented in lectures, and the acquisition of the skills necessary for data processing will be addressed in tutorials and practicals. Emphasis will be placed on the critical study of the different stages of analysis using bioinformatics tools that are easy for microbiologists to use and implemented on a Galaxy interface or R biostatistics packages specific to molecular ecology studies (e.g. Phyloseq package).

Face-to-face (lectures; tutorials; practicals). Skills will be acquired during tutorials using test data sets, then put into practice on unknown data sets (see Practical Course), the analysis of which will form part of the assessment. Opening an account on the Migale bioinformatics platform in Jouy-en-Josas.

At the end of the unit the students will have complete independence and autonomy to compute and analyse 16S- amplicon sequencing metagenomic data from various microbial ecosystems.

Stage en laboratoire ou en entreprise, en France ou à l’étranger.

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Internship in a laboratory or in a private company, in France or abroad.

Contribuer à un projet de recherche en s'intégrant dans une équipe tout en faisant preuve d'autonomie et d'initiative ; mettre en œuvre une démarche scientifique pour répondre à une problématique donnée ; recueillir, analyser et synthétiser les informations de la bibliographie ; analyser et présenter à l'oral et à l'écrit des résultats expérimentaux.

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Contribute to a research project by working as part of a team while demonstrating autonomy and initiative; implement a scientific approach to address a given issue; collect, analyze, and synthesize information from the bibliography; analyze and present experimental results both in oral and written form.

Stage en laboratoire ou en entreprise, en France ou à l’étranger.
1 tuteur par étudiant (suivi recherche de stage et pendant le stage).

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Internship in a laboratory or in a private company, in France or abroad.
One tutor per student (support during the internship search and during the internship).