WORKSHOPS & COURSES
The Winter-Spring 2023 EM Course
About the course
Electron microscopy in combination with image analysis is increasingly powerful in producing 3D structures of individual molecules and large macromolecular complexes that are unapproachable by other methods. This course is focused on the concepts and theories behind electron microscopy. In the first class, we will poll the students on how to customize this course to ensure we cover the key questions they may have. Each week SEMC staff lead discussions on the practice of solving molecular structures by electron microscopy.
Course Schedule
Classes in SEMC or NYSBC seminar rooms (Winter course: Mondays 4-5pm and Wednesdays 4-5pm | Practicals may start earlier to continue later | Short course weeks: 9:00am-11am)
EM fundamentals section
| Jan 9 | Lecture | Intro & redefining the course | Ed Eng (NYSBC) [pdf] |
| Jan 11 | Recitation | Basic anatomy of the electron microscope | Ed Eng (NYSBC) [pdf] |
| Jan 16 | no class | Martin Luther King Jr Holiday | |
| Jan 18 | Practical: | TEM introduction: autoloaders | 3-4pm sec A 4-5pm sec B[worksheet] |
| Jan 23 | Lecture | New cryoEM hardware and supporting a facility | Michael Alink (NYSBC)[pdf] |
| Jan 25 | Lecture |
Sample prep vitrification – overview, grids and support films, tips and tricks when going into cryoEM, RT vs cryo
|
Ed Eng (NYSBC) [pdf] |
| Jan 30 | Practical: | chameleon demo | 3-4pm sec A 4-5pm sec B[worksheet] |
| Feb 1 | Recitation | Roundtable (on various topics) | Ed Eng (NYSBC) [pdf] |
Single Particle Analysis
| Feb 6 | Lecture | Introduction to SPA & cryoEM history |
Joachim Frank (Columbia University, Note: Zoom lecture) [pdf]
|
| Feb 8 | Recitation | Image formation and data collection considerations | Ed Eng (NYSBC) [pdf] |
| Feb 13 | Lecture | Data Processing (more on theory and algorithms) |
Amedee des Georges (CUNY/ASRC) [pdf]
|
| Feb 15 | Recitation | Validation methods | Ed Eng (NYSBC) [pdf] |
| Feb 20 | no class | President’s Day Holiday | |
| Feb 22 | Recitation | Roundtable (on various topics) |
Zephan Melville & Mahira Aragon (NYSBC)
|
EM challenges and new frontiers
| Feb 27 | Practical | cryoSPARC | locally lead |
| Mar 1 | Recitation | Journal Club | cryoSPARC – 3D variability |
| Mar 6 | Practical | cryoEDU workshop | guest lecture by https://cryoedu.org [pdf] |
| Mar 8 | Practical | TOPAZ workshop | led by Alex Noble, SEMC/NYSBC [outline pdf][slides pdf] |
| Mar 13 | Recitation | Journal Club | Time resolved EM |
| Mar 15 | Recitation | Journal Club | Preferred orientation |
| Mar 20 | Practical: | Coot workshop – Fitting atomic models (part 1 of 2) | led by Christina Zimanyi, SEMC/NYSBC [outline pdf] |
| Mar 22 | Practical: | Coot workshop – Fitting atomic models (part 2 of 2) | led by Christina Zimanyi, SEMC/NYSBC |
| Mar 27 | Recitation | Journal Club | Live cell imaging |
| Mar 29 | Recitation | Journal Club | Time resolved EM (part 2) |
| Apr 3 | Recitation | Journal Club | HIV trimer controversy |
| Apr 5 | Recitation | Wrap up | 4x15min sections (1: kitchen sink, 2:) |
Tomography section
April 10-14 : Short course Keynote – Intro to Tomography
See the tomography short course here. Students that attend the full course will be allowed to participate in the morning lectures.
Previous courses:
Lecture slides from the 2016 course may be found here, 2017 course may be found here, 2018 course may be found here, 2019 course may be found here, the 2020 course may be found here and 2021 course may be found here.
The lecture slides are provided for educational purposes only. All rights are reserved by their original authors. Please contact them if you would like to use or repost their content.
Recitations:
Practicals/Journal club in the SEMC conference room (starts @3:30pm)
Course instructors:
Edward Eng (NYSBC, Manager): Course leader
Mahira Aragon (NYSBC): Teaching assistant
Zephan Melville (NYSBC): Teaching assistant
Grading:
For researchers taking the course for credit, the final score will be tabulated as follows:
- Recitation 40%
- Practical Worksheet 10% x 4
- Attendance 20%
Suggested class structure (1.5 hr class)
- The course will be offered by the New York Structural Biology Center . Classes will be held Mondays and Wednesdays 4-5pm. Times may be subject to change.
Note: If you are taking the course for credit make sure to sign up through your institution’s registrar as well.
- CUNY GC course BICM88900, class number 58654 – Special Topics in Biochemistry – 3 credits
- Columbia BCHM G6400 – Cryo-Electron Microscopy – 4 credits