Duration
40h Th, 20h Pr, 20h AUTR
Number of credits
| Master in bio-informatics and modelling (120 ECTS) | 5 crédits | |||
| Master in biochemistry and molecular and cell biology (120 ECTS) | 5 crédits |
Lecturer
Frédéric Bouché, Franck Dequiedt, Marc Hanikenne, N..., Claire Périlleux, Sébastien Rigali
Coordinator
Language(s) of instruction
French language
Organisation and examination
Teaching in the first semester, review in January
Schedule
Units courses prerequisite and corequisite
Prerequisite or corequisite units are presented within each program
Learning unit contents
This module will address the diversity of physiological and developmental responses to perceived abiotic environmental cues/stress in different groups of organisms. Different types of stress (nutrient deficiency/excess, light/UV, temperature, toxins, etc.) or other environmental signals will be discussed to illustrate the molecular mechanisms involved in their perception, signal transduction, and short- and long-term physiological and developmental responses.
It is closely linked to the "Development, from cell to organism" module, where signal perception/transport systems (receptors) will be more specifically described. To avoid excessive redundancy with this complementary module, particular attention will be paid here to the mechanisms involved in modifying gene expression (transcription factors, regulatory networks, epigenetics, transcriptomics) in response to environmental signals.
Learning outcomes of the learning unit
At the end of theoretical instruction in the "Responses to the environment" module, students will be able to:
- Understand the mechanisms by which different stressors are perceived, and the transduction pathways that enable an appropriate developmental response in different groups of organisms (bacteria, plants, model animals;
- Detail a few selected examples for each type of organism and/or signal;
- Describe the different mechanisms controlling gene expression;
- Know how to determine the most appropriate methodological/informatics approaches to consider, depending on the biological question.
- Understand and explain how datasets for transcriptomic analyses are generated;
- Analyze and interpret a dataset from a transcription regulation study (e.g. RT-qPCR, RNA-seq, ChIP-seq, Regulon prediction);
- Use computational tools to identify/predict regulons/signaling cascades;
- Use computational tools to identify/predict transcription factor binding sites.
Prerequisite knowledge and skills
This module will build on the concepts previously covered in the following courses:
- Plant Physiology (BIOL0217-1) ;
- Introduction to Microbiology (MICRO719-1)
- Bacteriology (MICR0721-1)
- Molecular gene biology I (GENE9002-1) and II (GENE9003-1)
- Knowledge of concepts and notions covered in the "Development from cell to organism" module.
- Knowledge of concepts and notions covered in the "Toolbox: Nucleic acid analysis" module.
- Basic knowledge of R software.
Planned learning activities and teaching methods
Theoretical courses, covering the diversity of responses to environmental signals in different groups of organisms.
Practical courses, using different methods (bioinformatic, RT-qPCR) to characterize and interprete the response to selected environmental signals/stresses.
Mode of delivery (face to face, distance learning, hybrid learning)
Blended learning
Additional information:
Theoretical courses will be given in the mornings.
The afternoons, dedicated to practical/guided work, will take place in the classroom and/or on home-working.
Recommended or required readings
Course slideshows will be added to the module's dedicated eCampus space.
Exam(s) in session
Any session
- In-person
written exam ( open-ended questions )
Written work / report
Additional information:
In line with the module's objectives and the theoretical and practical skills to be acquired, assessment will take a hybrid form:
1) For the "Microbiology" and "Plant Biology" sections, the evaluation will consist of written reports associated with the practical sessions. These reports will consist of the application of the methodologies covered in the practical work to a biological question, which must be contextualized using the concepts covered in the theoretical course. More detailed instructions will be provided at the start of the module's practical sessions.
2) For the "Animal Biology/Epigenetics" section, the evaluation will take the form of open-ended questions requiring knowledge of the theory course content.
The reports will count for 80% of the final grade (40% each) and the theory exam for 20%. The reports are individual work and must be handed in no later than 7 days before the end of the January session (e.g. deadline: 20/01 at 23:59 if session ends on 27/01). For reasons of fairness, 2 points out of 20 will be deducted for each day the report is late.
Work placement(s)
Each of the course co-teachers will propose one or more internships for the "SSTG0065-A-a" course (laboratory internship).
Organisational remarks and main changes to the course
For practical work, students are required to bring a computer (or tablet) with R installed and working.
Practical work and/or tutorials are compulsory, as they are essential for producing the reports on which part of this module will be assessed. In the event of absence, even if justified, students are required to get back to the content of these sessions. The report must be completed even in the event of absence.
Contacts
The supervisors are available to answer your questions: either during the lectures/practical sessions given as part of this theme week, or by e-mail (during office hours and no later than 3 days before the exam or report submission).
Module coordinator and microbiology module:
Sébastien RIGALI (srigali@uliege.be)
Co-teachers:
Partim Biol. animale: Franck Dequiedt (fdequiedt@uliege.be)
Partim Biol. Végétale-Réponses métaboliques: Claire Périlleux (cperilleux@uliege.be)
Partim Biol. végétale-Nutrition minérale: Marc Hanikenne (marc.hanikenne@uliege.be)
Partim Biol. Végétale-Effets de la température: Frédéric Bouché (fbouche@uliege.be)
Questions related to practical courses should be addressed to Sébastien Rigali for the partim. Microbiologie and to Frédéric Bouché for the Partim. Plant Biology.