BMB535: Experimental Proteomics - Characterization of cellular signaling using quantitative proteomics (5 ECTS)

STADS: 01011501

Level
Bachelor course

Teaching period
The course is offered in the spring semester.

Teacher responsible
Email: mrl@bmb.sdu.dk

Timetable
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Comment:
Kurset ligger i uge 34-35. Nærmere info følger i januar.

Prerequisites:
None

Academic preconditions:
The course BMB533 must be passed. It is required that the content of the course BMB508 is known.

Course introduction
The course aims to give students an insight into the planning, implementation and evaluation of a molecular biology experiment in which various molecular biology techniques will be combined with proteome analysis, phosphoproteomics and bioinformatics (pathway analysis). During the course, students will characterize phosphorylation-dependent signaling pathways in eukaryotic cells (e.g. stem cells or human neurons) after knock-down of essential genes (e.g. kinases) or by extracellular stimulation (e.g. cellular differentiation).

Qualifications

• Ability to independently plan studies with the methods used
• Present and pass on knowledge obtained in the course
• Critically evaluate the results obtained with the methods used in the course
• The course includes laboratory-based projects, providing personal competence in organizing the laboratory work.
• The laboratory projects will be made in teams in order to strengthen their ability to cooperate in all phases of the work.

Expected learning outcome
After the course the student is expected to be able to:

• Describe the basic principles behind tandem mass spectrometry
• Understand and interpret data generated by tandem mass spectrometry
• Describe different methods used for quantitative proteomics
• Understand the role of post-translational modifications in cellular signaling in eukaryotic cells
• Understand the principle of the characterization of phosphorylated proteins by tandem mass spectrometry, including enrichment of phosphorylated peptides
• Understand the principles of working with cell cultures and protein knock-down
• Explain and perform methods for validation of knock-down experiments, incl. Western blotting, PCR and Selected/Parallel Reaction Monitoring (SRM/PRM)
• Use the bioinformatics programs utilized in the course

Subject overview
Theory:
Introduction to proteomics and tandem mass spectrometry
Introduction to phosphorylation and characterization of cellular signaling pathways
Introduction to protein knock-down techniques, and validation of knock-down efficiency using Western blotting, PCR or SRM / PRM
Introduction to neural differentiation

Methods/Techniques:
Quantitative proteomics/phosphoproteomics (including purification and characterization of phosphorylated peptides)
Electrospray tandem mass spectrometry
Bioinformatics (incl. protein/peptide identification and quantitation and pathway analysis programs)
Western blotting
SRM/PRM
Cell culture
RNAi knock-down
(others)

Literature
There isn't any litterature for the course at the moment.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
Active participation in laboratory work. Pass/fail, internal evaluation by teacher. (01011512)

Assessment and marking:
Test in blackboard, group presentation and laboratory work. Pass/fail, internal censorship by teachers. (01011502)

The mode of a reexamination may differ from the mode of the ordinary examination.

Expected working hours
The teaching method is based on three phase model.
Intro phase: 15 hours
Skills training phase: 55 hours, hereof:
 - Tutorials: 15 hours
 - Laboratory exercises: 40 hours

Educational activities Study phase: 55 hours

Language
This course is taught in English, if international students participate. Otherwise the course is taught in Danish.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.