Main teaching language :English

Objectives:
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.

Content:
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).

Number of European credits : 4 ECTS

Skills to be acquired: 
– 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.
Complementary skills:
– Present a scientific study: explain the approach and summarize the main results and conclusions to be retained; know how to communicate a scientific message.

Coordinators:
Marie Dufresne (marie.dufresne@universite-paris-saclay.fr)
Axel de Zélicourt  (axel.de-julien-de-zelicourt@universite-paris-saclay.fr)

Enseignement en français

Description du contenu de l’enseignement: L’UE a été créée afin de permettre à tout étudiant en Sciences d’appréhender le monde économique et le monde de l’entreprise : après une série de conférences d’Economie générale, le monde de l’entreprise est présenté à travers les grandes fonctions de l’entreprise, de la multinationale à la start-up. Ces enseignements s’appuient sur des enseignants ayant une expérience de création d’entreprise et des professionnels.

 Objectifs :

– 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.

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

Nombre de crédits européens: 4 ECTS

Compétences à acquérir:
– 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

Responsable: Fabrice Lequeux, MCF Université Paris-Saclay (fabrice.lequeux@universite-paris-saclay.fr)

Integrative Plant Physiology (Paris-Saclay)
Optional course unit D, option 1

Prerequisites (strongly recommended): Good knowledge of the basics of plant physiology and metabolism.

Objectives: 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.

Content: 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.

Number of European credits: 4 ECTS

Skills to be acquired:
– Understand key aspects of plants’ response to the environment
– Be able to integrate information presented under the various topics covered in the lectures
– Develop skills and critical analysis of laboratory practices in the context of a functional genomics
study
– Develop teamwork skills to prepare presentations
– Be able to carry out a literature review and structure the information so as to present it in the form of a critical and clearly illustrated oral presentation.

Coordinators:
Graham Noctor: graham.noctor@universite-paris-saclay.fr
Hélène Vanacker: helene.vanacker@universite-paris-saclay.fr

Teaching language: English

Proteins & Biotechnologies (Paris-Saclay)
Optional course unit D, option 2

The program 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.

Number of European credits:4 ECTS

Skills to be acquired : 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.

Coordinators:
Loïc Rajjou: loic.rajjou@agroparistech.fr
Julia Zinsmeister:  julia.zinsmeister@agroparistech.fr

Main teaching language: English

Physiologie des Systèmes (Paris Cité)
Optional course unit E, option 1

Enseignement: français/ anglais

Type d’UE/ECUE UE à choix : parcours PAPH et SV
Responsable de l’UE/ECUE : A. Diet/ G. Gangarossa
Nombre d’ECTS : 3

Objectifs:
Analyser et intégrer les différents niveaux d’informations d’un organisme pour appréhender de façon globale et modéliser son fonctionnement en interaction avec l’environnement.

Compétences visées: Intégrer et synthétiser des informations, argumenter pour défendre une hypothèse.

Contenu de l’UE/ECUE : L’UE sera axée sur les communications/coopérations entre différents organes / systèmes pour une fonction biologique. L’accent sera mis sur l’intégration des données permettant de modéliser ces processus complexes. Les exemples seront issus des règnes animal et végétal : stratégies métaboliques en lien avec le développement et l’adaptation, interactions avec le microbiote, rythmes biologiques par exemple.

Plant-microbe interactions (Paris-Saclay)
Optional course unit E, option 2

Main teaching language : English

Objectives:
• Acquire the knowledge and the methods needed to understand the dynamics of plant-microorganism interactions, whether pathogenic or symbiotic, in relation to environmental factors.
• Understand the molecular and cellular mechanisms involved in these interactions.
• Know the societal and ecological stakes of these interactions.
• Consider traditional and innovative control methods for improving the quality and the yield of agricultural production.

Number of ECTS credits : 4 ECTS

Skills to be acquired :
– Master the main infection processes of pathogenic microorganisms and their specific features, in relation to the different parasitic strategies.
– Master the main immune mechanisms of plants (mechanisms of microorganism perception, signaling and defence).
– Understand the epidemiological factors explaining the emergence and the spread of a disease at different spatial and temporal scales.
– Be able to describe the control methods used in crop protection.
– Be able to describe the diversity of symbiotic interactions in plants and the molecular dialogue between the microbiota and the host plant, and to discuss the ecological and societal importance of symbiotic interactions.
– Be able to name the niches of the plant microbiota and to describe how the plant microbiota becomes established.
– Be able to implement the main plant pathology techniques.

Coordinator:
Marie Garmier : marie.garmier@universite-paris-saclay.fr

Genome engineering and RNA interference (Paris Cité)
Optional course unit G, option 1

Main teaching langage: English

Objectives:
The objective of this course 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, as well as ethical/legal issues, will be discussed.

Content:
1rst week: lectures (8h), tutorials (7h) on genome editing, RNA interference (and other RNA-based technologies) and synthetic biology. Several seminars (one hour each) could be given by researchers, platform engineers and professionals from private companies, specialized in one of these fields.
2nd week: a 5-day practical course (21h) focused on RNA interference mechanisms and applications in plants. During this practical course, students will 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 to analyse small RNAs: RT-qPCR, DNA methylation analysis, dedicated northern for small RNAs, tissue and subcellular localisation of proteins using fluorescence microscopy, …
The course will include a 1h30-seminar involving the analysis of scientific articles on symbiosis, and 9h 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.

Number of European credits : 4 ECTS

Skills to be acquired:
– 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

Coordinators :
Christine Lelandais : christine.lelandais@u-pariscite.fr
Céline Sorin : celine.sorin@u-pariscite.fr

Physiologie de la nutrition et agronomie (Paris-Saclay)
UE à choix G, option 2

Langue principale d’enseignement : Français

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

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

Contenu :
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.

Nombre de crédits européens : 4 ECTS

Compétences à acquérir : 
• 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

Coordinatrices :
Sophie Filleur : sophie.filleur@u-pariscite.fr
Rozenn LE HIR: rozenn.le-hir@inrae.fr