3 ECTS credits
79 h study time
Offer 1 with catalog number 4024249ENR for all students in the 2nd semester at a (E) Master - advanced level.
Lecture part (HOC)
The course will introduce students to the application of electron microscopy to investigating the structure of biological materials and molecules. Toward the end of the lectures, the students will have a theoretical understanding of the different types – Scanning and Transmission - of electron microscopes, methods of sample preparation, sample imaging, and image analysis techniques.
The course will begin with introducing electrons and imaging principles using electrons. Next, general concepts behind the construction of an electron microscope will be explained, and constraints on sample properties will be highlighted. Further, the Scanning Electron microscopes will be described and their applications to imaging of the surfaces of nanostructures with a particular focus on biological objects will be demonstrated. Methods of elemental analysis will also be discussed in this section.
The remainder of the course will focus on high-resolution transmission electron microscopy. The methods of sample preparation for cryo and negative stain TEM will be described including new methods of cryo-EM sample preparation and FIB milling techniques used for preparation of lamellas for cryo-tomography.
The next 3 lectures will be dedicated to a detailed understanding of image formation and image processing techniques. The principle of phase contrast will be introduced followed by the explanation of image averaging and classification techniques. After this, principles of 3D reconstruction from 2D projections will be explained and practical implementation of the iterative algorithms for 3D reconstructions and 3D classifications will be explained. The descriptions of algorithms will be supplemented by numerous examples of the high-resolution reconstruction of biological macromolecules. Finally, the principles of cryo-tomography and sub-tomogram averaging will be explained and recent progress with cryo-EM will be demonstrated on recently published examples.
Practical Part (WPO)
During the practicals, the students will acquire practical skills in the preparation of samples for negative stains and cryo-TEM imaging. Next, they will learn how to manipulate an electron microscope, acquire images with various magnifications, and optimize contrast using defocusing. They will see the functioning of a high-end fully automated electron microscope in an extended demo where sample loading, collection of grid atlases, and the selection of imaging areas will be shown together with automated image collection. The remaining part of the practical work will be dedicated to image processing. During this part, the students will learn how to handle raw cryo-EM micrographs of single particle cryo-EM datasets and how to obtain a high-resolution 3D reconstruction of a protein from the raw images. They will develop skills in image processing using software and will understand in practice how drift correction and defocus estimation are performed. They will learn how to do 2D classification and how to select the right 2D classes for further processing. Later on they will obtain initial 3D models and refine them to high resolution using the state-of-the-art software CryoSPARC. Finally, the quality of the obtained map will be assessed, and 3D protein models built into the maps. Subgroup reports will be written describing the results obtained by the students and will contain critical assessment of the individual steps and the obtained results.
n.a.
The final grade is composed based on the following categories:
Oral Exam determines 80% of the final mark.
Other Exam determines 20% of the final mark.
Within the Oral Exam category, the following assignments need to be completed:
Within the Other Exam category, the following assignments need to be completed:
Examination of the HOC part occurs in an individual oral exam with 60 minutes of preparation time. In the WPO there will be a general evaluation of each student (attitude, ability to work with instruments and computer skills) and the reports will be evaluated. Presentations will be given where questions will be asked to individual students and where differentiation in grades will be possible.
This offer is part of the following study plans:
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Medical Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Agrobiotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Cell and Gene Biotechnology: Synthetic Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Food Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Sustainable Chemical Biotechnology (only offered in Dutch)
Master of Bioengineering Sciences: Chemistry and Bioprocess Technology: Micro- and Nanobiotechnology (only offered in Dutch)