NYSBC - New York Structural Biology Center

The Winter-Spring 2018 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 and will be taught in a reverse classroom format based on Grant Jensen’s online course (Getting Started in Cryo-EM [https://cryo-em-course.caltech.edu/] from Caltech). Students will be responsible for watching these online lectures prior to class. Each week guest lecturers and SEMC staff lead discussions on the practice of solving molecular structures by electron microscopy.

The course will be held at the New York Structural Biology Center at 89 Convent Ave (133rd St).

To register for the course go to: https://www.surveymonkey.com/r/WinterCourse18 .

Course Syllabus:

Classes in A-11 seminar room (Mondays 3:30-5pm and select Wednesdays 3:30-5pm)

EM fundamentals section (month of January)

  • Jan 8 : Introduction & SEMC tour [SEMC staff, NYSBC]
  • Jan 10 : Challenges in biological EM & Sample Prep [Ashleigh Raczkowski/Kelsey Jordan & Ed Eng, NYSBC]
  • Jan 15 : No class - Martin Luther King
  • Jan 17 : Basic anatomy of the electron microscope [Laura Kim & Ed Eng, NYSBC]
  • Jan 22 : Fourier transforms, Image Formation [Yong Zi/Micah Rapp & Anchi Cheng, COLU/NYSBC]
  • Tomography section

  • Jan 29 : Tomography (part I: Intro and overview of ET) [Wei Dai, Rutgers]
  • Feb 5 : Tomography (part II: FIB-SEM) [Bill Rice, NYSBC]
  • Feb 12 : Tomography (part III: Cryo-Applications & Sub-tomogram averaging) [Alex Noble, NYSBC]
  • Feb 19 : No class - President's Day
  • Single particle section

  • Feb 26 : Single-particle analysis (part I: Intro and overview of SPA) [Joachim Frank, COLU]
  • Mar 5 : Single-particle analysis (part II: Sample preparation and data collection for SPA) [Israel Fernandez, COLU]
  • Mar 12 : Single-particle analysis (part III: Data Analysis and reconstruction workflow) [Reza Khayat, Amedee des Georges CUNY, ASRC]
  • Mar 19 : Single-particle analysis (part IV: Reconstruction workflow (cont), and Interpretation and Limitations) [Rich Hite, MSKCC]
  • EM crystallography section

  • Mar 26 : 2D crystallography (part I: Intro and overview of 2DX) [Iban Ubarretxena, MSSM]
  • Apr 2 : 2D crystallography (part II: Helical) [Hernando Sosa, AECOM]
  • Apr 4 : MicroED [Bill Rice, NYSBC]
  • EM challenges and new frontiers

  • Apr 9 : Validation methods [Tom Walz, RU]
  • Apr 16 : EMDataBank: Structure Data Archiving, Validation Challenges [Cathy Lawson, Rutgers]
  • Apr 23 : Moderate Resolution Fitting [SEMC staff, NYSBC]
  • Apr 30 : Fitting Atomic Models [Oli Clarke, COLU]
  • May 2 : Conclusion & open discussion (short class) [SEMC staff, NYSBC]

  • Lecture slides from the 2016 course may be found here and 2017 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.

    Practicals/Journal club in the SEMC conference room (usually starts @3:30pm)

  • Jan 24 : Fourier transforms and reciprocal space, and Image Formation
  • Jan 31 : Tomography
  • Feb 7 : Tomography
  • Feb 14 : Tomography
  • Feb 21 : [Journal Club]
  • Feb 28 : Single particle
  • Mar 7 : Single particle
  • Mar 14 : Single particle
  • Mar 21 : [Journal Club]
  • Mar 28 : EM crystallography
  • Apr 11 : EM crystallography
  • Apr 18 : [Journal Club]
  • Apr 25 : EM challenges
  • Click here for a detailed syllabus



    Class structure (1.5 hr class)

    30 min Introduction by guest lecturer on applying the class topic to scientific questions with focus on the nuts & bolts of the technique. Examples may be from their own research or a recent paper.

    15 min Coffee break/informal conversation

    45 min Open ended discussion covering concept check questions on the topic



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