3 ECTS credits
90 h study time
Offer 1 with catalog number 4016090FNR for all students in the 1st semester at a (F) Master - specialised level.
The course Quantitative Cell Biology will consist of three equal parts, dealing with (1) a theoretical knowledge of the main cell biological aspects, (2) the main techniques to study cell biology, and (3) mathematical modelling of complex cell biological systems
1) Introduction to Cell Biology (Prof. Dr. Jo Van Ginderachter)
This part aims to introduce the students to the main basic principles of Cell Biology. The focus lies on the theoretical knowledge of these fundamental cell biology principles. The recommended handbook is Molecular Biology of the Cell (Alberts et al, Garland Science) and this book is used as a source of figures and theoretical content for this part of the course.
Following aspects of cell biology will be discussed:
- Universal features of eukaryotic cells (selection of Chapter 1, Alberts et al).
- The plasma membrane (selection of Chapter 10, Alberts et al)
- The cytoskeleton (selection of Chapter 16, Alberts et al)
- Compartimentalization of the cell: The nucleus (selection of Chapter 12, Alberts et al)
The endoplasmic reticulum (selection of Chapter 12, Alberts et al)
The Golgi apparatus (selection of Chapter 13, Alberts et al)
The mitochondrion (selection of Chapter 14, Alberts et al)
2) Important cell biology techniques and their applications (Dr Kiavash Movahedi).
This part aims to introduce the students to 3 main cell biology techniques, which are amply used in research (both in academia as in industry). The focus lies on both the theoretical knowledge of these fundamental cell biology techniques and an understanding of their applications.
Following techniques will be discussed:
- Manipulating DNA and proteins. This chapter includes: techniques for the fractionation of cell components, techniques for the isolation of proteins, techniques to isolate genes (PCR, reverse transcription, gene cloning, plasmid expression vectors, construction of transgenic mice)
- Light microscopy. This chapter includes: light as electromagnetic waves, light refraction, basis of a compound microscope, introduction to bright-field microscopy, introduction to dark-field microscopy, introduction to fluorescence microscopy (basics of fluorescence, filter sets, photodetectors), using fluorescence to visualize cells or cellular structures (functional dyes, immunofluorescence, fluorescent proteins, FRAP, FLIP, FRET), introduction to laser scanning confocal microscopy, introduction to two-photon microscopy.
- Flow cytometry and cell sorting. This chapter includes: the flow cytometric set-up, electrostatic cell sorting, compensation
3) Mathematical modelling of complex cell biology systems (Enzyme kinetics and biochemical reaction networks) (Prof Dr Sophie De Buyl)
This part aims to introduce the students to mathematical modelling of exemplary biological problems. The focus lies on applicability, rather than theoretical knowledge.
Following aspects will be discussed:
- Modelling chemical reaction networks (law of mass action, numerical simulations, separation of time scles and model reduction
- Modelling biochemical reactions (enzyme kinetics)
- Modelling gene regulatory networks (modelling gene expression)
4) The practical session will consist of: 1) performing a flow cytometry experiment (1 day experiment) and will be held in the research lab (Cellular and Molecular Immunology lab).
2) exercise session on mathematical modelling
Contact: jo.van.ginderachter@vub.be, kiavash.movahedi@vub.be, Sophie.de.Buyl@vub.be
The powerpoint presentations, shown during the lectures, and a list of exercises are available on "Canvas".
The recommended handbook is Molecular Biology of the Cell (Alberts et al, Garland Science)
This course unit has the following intended learning outcomes. At the end of the course unit, the student should be able to:
* know and understand the role of the various elements of the cell discussed in the course,
* know and understand the technical approaches used to study cells that are discussed in the course, when to use them and what are their limitations
* know and understand which type of mathematical modelling should be employed in which situation and perform the mathematical modelling.
This course contributes to the following programme outcomes of the Master of Science in Biomedical Engineering:
MA_A: KNOWLEDGE ORIENTED COMPETENCES
1. exact sciences with the specificity of their application to engineering
8. collaborate in a (multidisciplinary) team
11. think critically about and evaluate projects, systems and processes, particularly when based on incomplete, contradictory and/or redundant information
MA_B: ATTITUDE
15. the flexibility and adaptability to work in an international and/or intercultural context
MA_C: SPECIFIC BIOMEDICAL KNOWLEDGE
18. To apply acquired knowledge and skills for the design, development, implementation and evaluation of biomedical products, systems and techniques in the health care sector.
The final grade is composed based on the following categories:
Oral Exam determines 67% of the final mark.
SELF Report determines 33% of the final mark.
Within the Oral Exam category, the following assignments need to be completed:
Within the SELF Report category, the following assignments need to be completed:
This offer is part of the following study plans:
Master of Photonics Engineering: On campus traject
Master of Photonics Engineering: Online/Digital traject