BMB535: Experimental Proteomics - Characterization of cellular signaling using quantitative proteomics
Study Board of Science
Teaching language: Danish or English depending on the teacher, but English if international students are enrolled
EKA: N200012112, N200012102
Assessment: Second examiner: None
Grading: Pass/Fail
Offered in: Odense
Offered in: Summer school (autumn)
Level: Bachelor
STADS ID (UVA): N200012101
ECTS value: 5
Date of Approval: 29-04-2019
Duration: 1 semester
Version: Approved - active
Comment
The course has limited seats and in case of too many applications, priority is given to the timely registration by date of registration.
Entry requirements
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
Participant limit
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
Content
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
- Introduction to protein knock-down techniques including validation of knock-down efficiency using Western blotting, PCR or SRM/PRM.
- Introduction to neural differentiation.
Methods/Techniques:
- Quantitative proteomics/phosphoproteomics (including purification and characterisation of phosphorylated peptides)
- Tandem mass spectrometry•Bioinformatics (incl. protein/peptide identification and quantification as well as programmes for pathway-analysis)
- Western blotting
- SRM/PRM
- Cell growing
- RNAi knock-down
- (perhaps additional methods)
NB: This exercise course is conducted according to statutory safety instructions, but uses experimental protocols and chemicals which are suspected of being potentially harmful to pregnant/breastfeeding. Pregnant/Nursing Students should therefore contact course coordinator well in advance of course registration or as soon as possible.
Literature
Examination regulations
Prerequisites for participating in the exam a)
Timing
August
Tests
Active participation in the exercises
EKA
N200012112
Assessment
Second examiner: None
Grading
Pass/Fail
Identification
Full name and SDU username
Language
Normally, the same as teaching language
Examination aids
To be announced during the course
ECTS value
0
Additional information
The prerequisite examination is a prerequisite for participation in exam element a)
Exam element a)
Timing
August
Prerequisites
| Type | Prerequisite name | Prerequisite course |
|---|---|---|
| Examination part | Prerequisites for participating in the exam a) | N200012101, BMB535: Experimental Proteomics - Characterization of cellular signaling using quantitative proteomics |
Tests
Test in itslearning, group presentation and laboratory work
EKA
N200012102
Assessment
Second examiner: None
Grading
Pass/Fail
Identification
Full name and SDU username
Language
Normally, the same as teaching language
Examination aids
To be announced during the course
ECTS value
5
Indicative number of lessons
Teaching Method
At the faculty of science, teaching is organized after the three-phase model ie. intro, training and study phase.
- Intro phase: 15 hours
- Skills training phase: 55 hours, hereof: tutorials: 15 hours and laboratory exercises: 40 hours
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.
Teacher responsible
| Name | Department | |
|---|---|---|
| Martin Røssel Larsen | mrl@bmb.sdu.dk | Biomedicinsk Massespektrometri og systembiologi |
| Pia Jensen | pjensen@bmb.sdu.dk | Institut for Biokemi og Molekylær Biologi |