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 autumn semester.

Teacher responsible
Email: mrl@bmb.sdu.dk

Timetable
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Comment:
Kurset ligger i uge 34-35

Prerequisites:
None

Academic preconditions:
Students taking the course are expected to:

• Have knowledge of fundamental molecular biology terms and biochemistry processes (the content of BMB533 and BMB508 is assumed known)
• Be able to use traditional it-tools, including excel
• Active participation is expected, including an oral presentation from the students in groups
• Knowledge regarding general laboratory safety is expected

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).

The course builds on the knowledge acquired in the courses at the second year and combines elements from several courses into one molecular biology problem which is explored experimentally and related to information extracted from relevant literature.

In relation to the competence profile of the degree it is the explicit focus of the course to:

• Ability to independently plan and perform 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
The learning objectives of the course are that the student demonstrates the ability 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
The following main topics are contained in the course:

• 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)

NB: This training course is conducted according to legal safety instructions, but using experimental protocols and chemicals that are suspected to be potentially harmful to pregnant / lactating. Pregnant / nursing students should therefore contact the course coordinator in good time before course registration or as soon as possible.

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

1. Active participation in the exercises. Pass/fail, internal marking by teacher. (01011512)

Assessment and marking:

1. Test in blackboard, group presentation and laboratory work. Pass/fail, internal marking by teacher. (5 ECTS).(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

Educational form
Activities during the study phase:

• Read the compendium 
• Read a few articles
• Watch a few videos
• Preparation for laboratory work

As the course is an intense summer course, the course days will consist of element both from the intro- and training phase, whereas the study phase will take place both prior and during the course.

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

Remarks
The course has limited seats and in case of too many applications, priority is given to the timely registration by date of registration.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.