C9940 3-Dimensional Transmission Electron Microscopy (3DEM)

Faculty of Science
Spring 2017
Extent and Intensity
2/0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
Mgr. Jiří Nováček, Ph.D. (lecturer)
Dr. rer. nat. Jürgen Plitzko (lecturer)
Dr. Tanvir Shaikh (lecturer)
Guaranteed by
prof. RNDr. Vladimír Sklenář, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Timetable
Mon 20. 2. to Mon 22. 5. Mon 14:00–15:50 E35/211
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
Transmission electron microscopy (TEM) in its various flavours is nowadays an established characterization tool for structures in life as well as in material science. Especially in todays ‘nano-world’ it is, by and large the only technique for an in-depth visual investigations at the nanometer scale and even in the sub-nanometer regime. The study of complex materials and hybrid compounds, and their interfaces and defects by TEM was and is a major focus in material science. Moreover, three-dimensional (3D) electron microscopy (3DEM) has a particularly important role in the repertoire of techniques strcutural biologists use for probing the structure and functions of molecules and macromolecular complexes in their functional cellular context. 3DEM in life sciences comprises three major branches: cryo-electron crystallography, cryo-electron microscopy of purified single particles (where ‘particles’ stand for proteins and macromolecular complexes) and cryo-electron tomography (the three dimensional investigation of any non periodic - ‘pleiomorphic’ - object). This course will explain the basics of transmission electron microscopy, electron tomography and single particle cryo-EM. It will include the experimental setups and instrumental prerequisites for 3D work, and their actual implementation. Specimen preparation methods suited for biological applications will be described and explained in detail. Since all tomographic methods are based on different reconstruction algorithms, and elaborate image processing and visualization routines, they will be included in this tutorial as well. At the end of the course students should understand the principles of structural analysis by TEM and its application in chemistry, biochemistry, structural biology, biophysics and materials science.
Syllabus
  • 1. Introduction: TEM history and contemporary trends - applications of TEM to structural studies. 2. Introduction to electron optics, image formation, diffraction and automation. 3. Specimen preparation, negative stain, thin-film vitrification, high-pressure freezing, cryo-sectioning and modern micromachining methods. 4. Radiation effects; Introduction to image analysis; Sources of noise. 5. Principle and background of Fourier analysis, contrast transfer function (CTF), convolution and cross-correlation. 6. Electron tomography. 7. Principles of image analysis and 3D reconstruction methods 8. Single Particle analysis and image processing 9. 3D Visualization methods 10. Hybrid Methods: Combining X-ray crystallography and cryo-EM, combining light-microscopy and cryo-EM
Teaching methods
Lectures, seminars and tutorials
Assessment methods
Oral examination
Language of instruction
English
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.
  • Enrolment Statistics (Spring 2017, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2017/C9940