The Winter-Spring 2016 EM Course is concluded.

Detailed Syllabus:

Jan 11 : Introduction & SEMC tour

Welcome to the Simons Electron Microscopy Center and explanation of the course. A tour of NYSBC and SEMC will be given.

The trailer for the Jensen lab lectures will be played along with details on how to watch them.

Getting Started in Cryo-EM with Professor Grant Jensen
Time: 2:52
Link: https://youtu.be/gDgFbAqdM_c

Welcome to Cryo-EM
Time: 7:36
Link: https://youtu.be/q17nGZPCeoA

Jan 18 : No class - Martin Luther King Holiday

Jan 25 : Basic anatomy of the electron microscope

To prepare watch Jensen lectures part 1 before class.

Online video lectures

Introduction: Why Electrons?
Time: 8:39
Link: https://youtu.be/GBU1eA1PqeQ

Part 1: Basic Anatomy of the EM
Time: 0:43
Link: https://youtu.be/GBU1eA1PqeQ

Part 1: Electron Guns
Time: 19:00
Link: https://youtu.be/C6DSFK7zJo0

Part 1: EM Lenses
Time: 32:15
Link: https://youtu.be/SKjxp-al_UI

Part 1: The Column
Time: 26:09
Link: https://youtu.be/hc2s4uSbpyI

Part 1: Sample Chamber
Time: 14:05
Link: https://youtu.be/EaXbk9OQDHw

Part 1: Energy Filters
Time: 7:06
Link: https://youtu.be/UzKNE8ZZBxw

Part 1: Detectors
Time: 11:56
Link: https://youtu.be/-0bjbWgxH2k

Part 1: Vacuum Systems
Time: 9:50
Link: https://youtu.be/LUlM0kl6Lp0

Part 1: Summary and Safety
Time: 5:13
Link: https://youtu.be/2rC8nFMRW4I

Feb 1 : Fourier transforms and Image Formation

To prepare watch Jensen lectures part 2 & 3 before class

Online video lectures

Part 2: Fourier Transforms for Beginners
Time: 0:54
Link: https://youtu.be/-EAQm8wgLbc

Part 2: 1-D Sine Waves and Their Sums
Time: 32:55
Link: https://youtu.be/OESy_ltOCvI

Part 2: 1-D Reciprocal Space
Time: 20:07
Link: https://youtu.be/IUaqeoMK5y4

Part 2: 2-D Waves and Images
Time: 19:16
Link: https://youtu.be/nyk75ufbP74

Part 2: 2-D Transforms and Filters
Time: 32:56
Link: https://youtu.be/fEyLh9HqsWU

Part 2: 3-D Waves and Transforms
Time: 13:17
Link: https://youtu.be/INtehLmqfmA

Part 2: Convolution and Cross-Correlation
Time: 15:06
Link: https://youtu.be/MQm6ZP1F6ms

Part 3: Image Formation
Time: 0:49
Link: https://youtu.be/HTJsYTGAhYg

Part 3: Amplitude and Phase Contrast
Time: 30:14
Link: https://youtu.be/jhniWbY2Jhc

Part 3: Wave Propagation and Phase Shifts
Time: 30:06
Link: https://youtu.be/YXIvVCoHbp4

Part 3: The Contrast Transfer Function
Time: 33:49
Link: https://youtu.be/mPynoF2j6zc

Part 3: Defocus and Its Effects
Time: 21:29
Link: https://youtu.be/izLp5vpoFyQ

Part 3: Envelopes
Time: 16:21
Link: https://youtu.be/joNEW0Nb2no

Part 3: CTF Correction
Time: 31:45
Link: https://youtu.be/GYDLhg49UQA

Feb 8 : Challenges in biological EM & Sample Prep

To prepare watch Jensen lectures part 4 before class

Online video lectures

Part 4: Fundamental Challenges in Biological TEM
Time: 3:05
Link: https://youtu.be/jYhp4aLZEb4

Part 4: Sample Prep: Room Temperature Methods
Time: 20:27
Link: https://youtu.be/aXj9rCr2Imk

Part 4: Sample Prep: Methods Involving Freezing
Time: 27:47
Link: https://youtu.be/7HHdFBA-fDs

Part 4: Sample Prep: Grids
Time: 11:08
Link: https://youtu.be/uHbyk2_tZn4

Part 4: 3-D Reconstruction
Time: 11:18
Link: https://youtu.be/_Ngybc0Rjo0

Part 4: Dose Limitations
Time: 22:06
Link: https://youtu.be/4BEXfZo-zDs

Feb 15 : No class - President's Day

Feb 22 : Tomography (part I)

Part 5: Tomography
Time: 23:20
Link: https://youtu.be/tOnijBqdJ1E

Part 5: Tomography Data Collection and Reconstruction
Time: 40:56
Link: https://youtu.be/WHiVBQy2i-w

Feb 29 : Tomography (part II)

Part 5: Tomography Identifying Objects of Interest
Time: 24:31
Link: https://youtu.be/pZr4fagyp84

Part 5: Tomography Limitations
Time: 29:48
Link: https://youtu.be/PHbqQKqJWbc

Part 5: Tomography Parameters and Handedness
Time: 12:03
Link: https://youtu.be/96bWLdetKMs

Mar 7 : Single-particle analysis (part I)

To prepare watch Jensen lectures part 6 before class.

Online video lectures

Part 6: Single Particle Analysis
Time: 21:59
Link: https://youtu.be/IwR3MmnIpJI

Part 6: SPA Sample Prep
Time: 22:50
Link: https://youtu.be/poJGBbRR64Y

Mar 14 : Single-particle analysis (part II)

Part 6: SPA Data Collection
Time: 21:03
Link: https://youtu.be/UEsC8Il6nCQ

Part 6: SPA Reconstruction Basic Workflow
Time: 31:53
Link: https://youtu.be/7Zt5Tu75gXk

Mar 21 : Single-particle analysis (part III)

Part 6: SPA Reconstruction Additional Topics
Time: 44:28
Link: https://youtu.be/djQ8JCvHs5k

Part 6: SPA Interpretation and Limitations
Time: 26:26
Link: https://youtu.be/yvXhdbaS_kU

Mar 28 : EMDataBank: Structure Data Archiving, Validation Challenges

Lecture and discussion on the EMDataBank.

Apr 4 : 2D crystallography (part I)

To prepare watch Jensen lectures part 7 before class.

Online video lectures

Part 7: 2D Crystallography Intro and Sample Prep
Time: 6:25
Link: https://youtu.be/Qn7aP-fRT5I

Part 7: FT of a 2D Crystal
Time: 24:32
Link: https://youtu.be/EZ08dXR4JaU

Part 7: 2D Crystallography Data Collection and Reconstruction
Time: 17:01
Link: https://youtu.be/ViDGSwMOjLQ

Apr 11 : 2D crystallography (part II)

To prepare watch Jensen lectures part 7 before class. Class will have an additional lecture on helical tubes.

Online video lectures

(repeat) Part 7: 2D Crystallography Data Collection and Reconstruction
Time: 17:01
Link: https://youtu.be/ViDGSwMOjLQ

Part 7: Helical Tubes
Time: 3:57
Link: https://youtu.be/GKcvGoD3jfg

Part 7: Farewell
Time: 2:58
Link: https://youtu.be/IyDanBwRcs8

Apr 18 : Validation methods

Lecture and discussion on Structure Validation.

Apr 25 : Fitting Atomic Models

Lecture and discussion on Fitting Atomic Models into EM maps.

Apr 26 : Forum Presentation - Multiscale Biomolecular Modeling in 4-D

Seminar connecting with the Apr 25 class.

As observed in computer simulations or in multi-scale structures, the behavior of "biological machines" that emerges on temporal and spatial scales in not only more than the sum of the parts, but quite different and unexpected. Examaples include: (1) A novel "fast mutual information" analytics, which can transform time domain data into spatial images through a hand-shaking between fast and slow degrees of freedom. The statistical data mining takes advantage of the detailed time series of computer simulations and it yields spatial heat maps that can be visualized on molecular structures or in the form of interaction networks. (2) The hierarchical structures revealed by electron microscopy or tomography imaging of molecular systems. Fitting and segmentation in the spatial anda temporal domain reveal the complex arrangement of the molecular building blocks of living organisms. (3) Computer graphics. There is currently a paradigm shift under way towards the use of more realistic global illumination models. We adapted the "screen-space ambient occlusion" approach that originated in the video game industry to our open-source multi-scale modeling program, Sculptor. Our approach has been uniquely customized with shading that is tuned for pockets and cavities of a user-defined size, making it useful for visualizing molecular features at multiple spatial scales of interest. The three examples demonstrate that it is often useful to employ a "systems" perspective in computational modeling of 4-D biological structures whenever complex phenomena arise that cannot be predicted from isolated degrees of freedom.

[pdf]<

Apr 26 : Workshop - Multi-Scale Fitting and 4-D Modeling Workshop

Workshop by Willy Wriggers, Julio Kovacs, and Manuel Wahle connecting with the Apr 25 Class.

A hands-on workshop on three multi-scale visualization and modeling packages will be held on Tuesday, April 26 by Willy Wriggers, Julio Kovacs, and Manual Wahle. Situs (http://situs.biomachina.org) is a script-based program package for the 3-D fitting of atomic resolution structures into low-resolution density maps, e.g., from electron microscopy, tomography, or small angle x-ray scattering. TimeScapes bridges between fast and slow time scales and generates 3-D spatial heat map images from a statistical analysis of 1-D time series (or equivalent independent variable) data. Sculptor is a multi-scale molecular graphics package that serves both as a frontend for Situs algorithms and as a standalone 3-D visualization program. The three packages are freely available at the Wriggers lab website and are also supported by the SBGrid consortium (sbgrid.org) in the upcoming release.

[Situs_pdf]
[TimeScapes_pdf]
[Sculptor_pdf]

May 2 : Conclusion & open discussion (short class)

Reading list

Basic anatomy of the electron microscope

Climb of Cryo-EM

Fourier transforms and reciprocal space

Hoffman Introduction to Fourier Theory

Shatkay Fourier Theory Intro

Image Formation

Quantitative characterization of electron detectors for transmission electron microscopy

Comparison of optimal performance at 300 keV of three direct electron detectors for use in low dose electron microscopy

Fundamental challenges in biological EM

Beam-induced motion of vitrified specimen on holey carbon film.

Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.

Tomography

Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography

Structural Analysis of the Roles of Influenza A Virus Membrane-Associated Proteins in Assembly and Morphology.

Single-particle analysis

2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome

2.2 Å resolution cryo-EM structure of ß-galactosidase in complex with a cell-permeant inhibitor.

2D cystallography

Membrane protein structure determination by electron crystallography.

Membrane protein structure determination by electron crystallography.

High-throughput methods for electron crystallography.

Validation methods & Fitting Atomic Models

Validation Methods, TPPP

MDFF Paper, Trabuco, et al. 2008

Review of various flexible fitting methods, Ahmed, et al. JSB, 2012

Appion

Appion webpage