BIC-31312 Systems@Work: A Toolbox of Systems Biology

Course

Credits 12.00

Teaching methodContact hours
Individual Paper12
Course coordinator(s)prof. dr. D Weijers
Lecturer(s)prof. dr. D Weijers
prof. dr. SC de Vries
prof. dr. ir. BJG Scheres
Examiner(s)prof. dr. D Weijers

Language of instruction:

Dutch and/or english

Assumed knowledge on:

MOB-30306 Control of Cellular Processes and Cell Differentiation.

Continuation courses:

MSc Theses

Contents:

The availability of the primary DNA sequences of organisms has given unprecedented insight into evolution of genomes and the realization that the building blocks of cells share many common elements. This means that traditional subdivisions between animals, plants and prokaryotes begin to disappear. Another effect is the growing need to integrate experimental details from many areas such as bioinformatics, biochemistry, cell biology, physiology and genetics to translate the DNA blue print into a working, living cell. This has given rise to a new field in biology, called systems biology. The primary goal of the Systems-Toolbox is to provide students a broad experimental overview of this new non-reductionist approach to a complex biological problem. Examples are understanding a complex phenotype or finding networks of proteins involved in a biosynthetic or signal transduction pathway.
The course is aimed to deal with a selection of the following topics:
1. bioinformatics approaches to integrate proteomics and genomics data;
2. biochemical analysis and in vivo visualization of protein interactions:
- protein interaction assays;
- isolation of protein complexes and protein identification by LC/MS/MS;
- introducing tagged proteins to visualize protein complexes;
3. isolation and characterization of cloned genes for use in various expression systems;
4. gene expression analysis:
- RT PCR;
- laser scanning confocal microscopy;
5. basics of FRET detection; relation with other methods;
6. advanced microscopic analysis of protein interactions in live plant cells.

Depending on the status of a particular project, a choice will be made from the above techniques.

The course is run in parallel with A Toolbox in Synthetic Biology (SSB-31312), both in period 5 and period 6. The two courses share common work discussions to broaden horizons and demonstrate where systems and synthetic approaches intersect. Enrollment for each course is separate at the respective secretariats.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- work with an integrated set of advanced tools to determine protein networks that perform specific tasks at the cell level;
- be involved in several experiments simultaneously, occasionally in different research groups;
- collect background information independently;
- perform research in a small group;
- document the results of their experiments properly and present them written and orally.

Activities:

- carry out experiments according to available manuals and protocols;
- perform database and neural network-based searches;
- work as a member of a team.

Examination:

The final mark will be based on theoretical insight in the project and laboratory skills shown during the work (50%), on the quality of the oral presentation (20%) and written report (30%) of the results of the work.

Literature:

Will be provided during the course.

ProgrammePhaseSpecializationPeriod
Restricted Optional for: MBTBiotechnologyMScC: Medical Biotechnology5WD, 6WD
MMLMolecular Life SciencesMSc5WD
MBFBioinformaticsMSc5WD, 6WD