6 EC
Semester 1, period 1
5234ADMI6Y
| Owner | Master Biomedical Sciences |
| Coordinator | dr. ir. M.A. Hink |
| Part of | Master Biological Sciences, Master Biomedical Sciences, track Cell Biology and Advanced Microscopy, |
Aim:
The general aim of this course is to get hands-on experience and theoretical background in performing state-of-the-art advanced (light) microscopy applied to cell biology. Due to the revolution in genetic encoded labeling (GFPs, switchable probes, FlAsH-tagging, etc) and the revolution in advanced (light) microscopy (confocal, super-resolution, FRET, dynamics etc) it is now possible to image and quantify the dynamics of molecular processes inside cells with unprecedented resolution, speed and accuracy. Because the application of advanced microscopy is essential for modern research in (clinical) cell biology, this course provides training in the diverse modes of advanced microscopy. The microscope setups on which the training is provided, are part of the van Leeuwenhoek Centre for Advanced Microscopy (LCAM) in Amsterdam, in which the research groups of Molecular Cytology (Swammerdam Institute for Life Sciences, UvA), of Cell Biology and Histology of the University Medical Center Amsterdam (UMCA) and the Cellular Biophysics Group, Dept of Cell Biology Netherlands Cancer Institute (NKI) collaborate and organize their advanced microscopy infrastructure.
Covered microscope techniques:
Handouts, (digital) papers
Handouts
ImageJ variant Fiji (http://fiji.sc/)
Microsoft Excel (or comparable) (Surfspot)
Adobe Reader
SVI Huygens image processing package
Participants should bring their laptop for tutorials & computer practicals and pre-install all software packages mentioned above
Course setup:
For each day one microscopy technique is highlighted by giving the basic theoretical background including tutorials (morning) and hands on experience at the microscope (afternoon). The course starts with a theoretical introduction in optical spectroscopy (fluorescence, absorption, anisotropy), microscope optics, fluorescent probes, image processing & data statistics. Participants will learn the basic principles behind the technique, their applications and limitations. During the tutorial, linked to the lecture, the participants will answer theoretical questions to strengthen their knowledge of the technique. An important part of the tutorial is to analyse, calculate and draw conclusions from experimental data. The participants will be instructed how to analyse microscopy data. The participants will handle the software program ImageJ and perform data statistics. These theoretical courses are accompanied by hands-on practicals on advanced microscopy. The participants will together with the instructor prepare samples and handle the microscope. Measurements will be optimized for the technique discussed and the data will be analysed. Participants will answer questions from the practical reader to strengthen their knowledge and learn important aspects related to cellular microscopy experiments in practice.
After three weeks there will be a written exam. In the final week the participants will work in small groups joining a mini-research project, focusing on a specific technique and topic of choice. Dependent of the chosen subject the participants will together with their advisor design and setup experiments (possibly with cell culture, transfections, sample preparations). After measuring the samples at the microscope the participants will analyse their results and present the outcome and recommendations at the final day.
Activity | Number of hours |
Hoorcollege | 32 |
Laptopcollege | 30 |
Practicum | 32 |
Presentatie | 4 |
Tentamen | 3 |
Zelfstudie | 67 |
Requirements of the programme concerning attendance (OER-B):
Additional requirements for this course:
Absence from practicals needs to be discussed to the course coordinator.
| Item and weight | Details |
|
Final grade | |
|
1 (100%) Tentamen |
The written exam after 3 weeks will test all theoretical and practical skills (from lectures, tutorials and practicals) obtained during the first three weeks of the course. The exam will contain 10-12 open questions including subquestions. An example exam is available at Blackboard. This written exam determines for 75% the final course grade.
The mini-research project will be graded by the daily supervisor on basis of active participation and skills shown. In addition all course lecturers, instructors and advisors will grade the project presentation at the the final day. Thisassignment determines for 25% the final course grade.
Contact the course coordinator to make an appointment for inspection.
In the last week students will work in groups of 2 or 3 participants to do a mini-research project. Dependent of the chosen subject the participants will together with their advisor design and setup experiments (possibly incl. cell culture, transfections, sample preparations). After measuring the samples at the microscope the participants will analyse their images and present the results and recommendations at the final day.
The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl
| Weeknummer | Onderwerpen | Studiestof |
| 1 Theoretical courses, tutorials and practicals | Microscopy techniques | Lectures, Tutorials, Practicals via handouts |
| 2 Theoretical courses, tutorials, practicals & selfstudy | Microscopy techniques | Lectures, Tutorials, Practicals via handouts |
| 3 Theoretical courses, tutorials, practicals & selfstudy | Microscopy techniques | Lectures, Tutorials, Practicals via handouts |
| 4 Exam, project week & presentation | Mini-Research Project | Practical work to be discussed in final presentation |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 |
Non-BMS-CBAM students should contact the coordinator for the selection procedure, since only a limited number of participants can join the course.
Location: Universiteit van Amsterdam, Science Park Amsterdam (FNWI), UMCA hospital & NKI.
Maximum: 30
Blackboard/Canvas: Course overview and materials (lecture slides, tutorials, results & test exam)
Language: English
Prior Knowledge: Cell biology (like BMS course Molecular Biology of the Cell)