课程大纲
COURSE SYLLABUS
1.
课程代码/名称
Course
Code/Title
电子显微学在生物学中的应用/The Application of Electron Microscope In Biology
2.
课程性质
Compulsory/El
ective
Elective
3.
课程学分/学时
Course
Credit/Hours
3/48
4.
授课语言
Teaching
Language
Bilingual (English and Chinese)
5.
授课教师
Instructor(s)
刘忠民 （Zhongmin Liu）
6.
是否面向本科
生开放
Open to
undergraduate
s
or not
not
7.
先修要求
Pre-requisites
（如面向本科生开放，请注明区分内容。
If the course is open to undergraduates, please
indicate the difference.）
Cell Biology, Biochemistry
8.
教学目标
Course Objectives
（如面向本科生开放，请注明区分内容。 If the course is open to undergraduates,
please indicate the
difference.）
冷冻电子显微学是现今结构生物学领域中发展最快、应用最广的前沿交叉学科。本课程的目标是
为生物学各专业的学生传授电子显微学的基本原理和实验方法。通过课程的理论和实验紧密结合的学
习方式，让学生能够基本理解冷冻电子显微学的研究对象、研究方法和研究思路，并最终学会了解应
用电子显微学来解析生物大分子的三维结构，解决生物医学中的问题。
As one of the fastest growing frontier discipline, cryo-Electron Microscope （cryo-EM） has been emerg
ing
as the most powerful tool in determining the high resolution structures of bio-macromolecules. Our aim is to
teach the basic principles and methods in cryo-Electron Microscope, especially Single Particle Analysis
. With
this course, we will present the basic knowledge of the Single Particle Analysis, the principle of
negative
staining Electron Microscope and cryo-EM sample preparation, to teach students to apply the knowledges
and skills to solve biomolecular structures and biomedical problems.
9.
教学方法
Teaching Methods
（如面向本科生开放，请注明区分内容。 If th
e course is open to undergraduates, please indicate the
difference.）
通过本课程的学习，学生可以
1
、
了解电子显微学的发展史；
2、 初步掌握生物大分子冷冻电镜的原理以及冷冻电镜样本的制备过程；
3、 初步掌握解决生物样本冷冻电镜应用中的常见问题；
4、 了解单颗粒冷冻电子显微学的基本原理和应用。
At the end of the course, students should be able to
1. Understand the history of electron microscope development;
2. Grasp the knowledge of cryo-EM and cryo-EM sample preparation;
3. Fix common problems in biological EM;
4. Preliminarily understand the principle of Single Particle Analysis.
10.
教学内容
Course Contents
（如面向本科生开放，请注明区分内容。 If the course is open to undergraduates, please indicate the
difference.）
Section 1
Introduction (4 hrs)
The historical background of the development of electron microscopy
Hardware breakthrough
The development of EM sample preparation
Algorithm in processing EM images
Classification of EM
The future of TEM in biology
Section 2
Basic anatomy of the TEM (3 hrs)
Electron gun
Column
Condenser
Vacuum
Camera
Section 3
Fourier transforms and reciprocal space for the beginner (2hrs)
Section 4
Image Formation (2hrs)
Section 5
Fundamental challenges in biological EM (6 hs)
Preservation of the native structure of biological sample
Radiation damage
Beam induced motions of EM samples
Low contrast
Heterogeneity of biological samples
Low dose cryo-EM mode
Fast camera
Signalling in EM images
Student Presentation I: tackling the problems in biological EM (2 hs)
Section 6
Sample preparation for TEM (4 hs)
Sample preparation pathways
Grid preparation
Negative staining EM sample preparation
Cryo-EM sample preparation
Cryo-negative-staining
Substrates for cryo-EM
Section 7
How to operate a TEM in checking biological sample (2 hs)
Basic operations of TEM
Basic microscope alignment
Negative staining EM
Cryo-EM low dose mode setup
Section 8
Single-particle analysis (10 hs)
Basic principle of single particle analysis
Workflow of a typical structure determination
Limitations of single-particle analysis
Biological sample preparation for single-particle analysis
Grid screening and evaluation
Common troubles in vitrifying single-particle samples
Application examples of single-particle analysis
Application of Alphafold in single-particle analysis
Student Presentation II: Single particle cryo-EM applications in Biology (2 hs)
Section 9
Introduction of cryo-Electron tomography (4 hs)
Correlative light electron microscopy
Basic principle of cryo-Electron tomography
Brief introduction of sub-tomography
Applications of cryo-ET in cell biology
Challenges in cryo-electron tomography
Brief introduction of electron crystallography (1 hs)
Brief introduction of electron crystallography
Application examples of electron crystallography
Section 10
Labelling technology in biological EM (2 hs)
In situ labelling
Labelling in single particle analysis
Section 11
Application of EM in studying Covid-19 virus (2 hs)
EM in virus
Application of single particle analysis in studying Covid-19
Application of Cryo-electron tomography in studying Covid-19
Application of sub-tomography in studying Covid-19
Section12
Model building, refinement and validation(2 hs)
11.
课程考核
Course Assessment
（
○
1 考核形式 Form of examination；
○
2 .分数构成 grading policy；
○
3 如面向本科生开放，请注明区分内容。
If the course is open to undergraduates, please indicate the difference.）
Assignments and quiz 35%
Discussion and presentation 45%
Attendance 20%
12.
教材及其它参考资料
Textbook and Supplementary Readings
Books:
《Three-Dimensional Electron Microscopy of Macromolecular Assemblies》by Joachim Frank
《
Diffraction Physics
》
Third Revised Edition by John M.Cowley
《电子衍射物理教程》 by 王蓉
《电子晶体学与图像处理》by 李方华
《薄晶体电子显微学》by P. Hirsch
《生命科学中的电子显微镜技术》by 丁明孝等主编
Video：
冷冻电子显微镜（Cryo-EM）入门 by 加州理工学院 Grant J.Jensen
链接：https://www.coursera.org/learn/cryo-em
MRC Lectures:
ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/EM-course
Advances in Cryo-EM related book
Cryo-EM Part A-C & Recent advances in cryo-EM (Methods in Enzymology)
http://www.sciencedirect.com/science/bookseries/00766879/481
http://www.sciencedirect.com/science/bookseries/00766879/482
http://www.sciencedirect.com/science/bookseries/00766879/483
http://www.sciencedirect.com/science/bookseries/00766879/579
