Program
Electron Crystallography Workshop
at UC Davis, August 7-11, 2006
Organization:
Rena Hill (RMHill@ucdavis.edu)
Scientific Organization:
Ben Hankamer (B.Hankamer@imb.uq.edu.au)
Henning Stahlberg (HStahlberg@ucdavis.edu)
Web Site:
Emergency Phone Numbers:
Henning Stahlberg: +1 (530) 574 0835 (mobile)
Rena Hill: +1 (530) 400 0230 (mobile)
Lodging:
UCD Conference Housing, Tercero Area
Seminars:
1022 Life Sciences, University of California, Davis, CA 95616
Practicals:
WetLab: 15 Briggs Hall, UC Davis (Phone: (530) 754 8285)
TEM: 29 Briggs Hall, UC Davis (Phone: (530) 754 8338)
Computing: 2060 Science Lecture Building, Computer Room, UC Davis
Sponsors:
Program
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Sunday, August 6, 2006 |
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Afternoon |
Arrival Registration 4:00 pm – 6:00 pm Foyer of UCD Conference Housing, Tercero |
Rena Hill Ben Hankamer Henning Stahlberg Hui-Ting Chou Po-Lin Chiu Ludovic Renault |
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7:00 pm |
Dinner Buffet. Putah Creek Lodge (at the bottom of the map below) |
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Monday, August 7, 2006 |
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8:00 am |
Breakfast. |
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9:00 am |
Welcome 1022 Life Sciences |
Ben Hankamer Rena Hill Henning Stahlberg |
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9:30 am |
Detergents and their properties - Main detergent types: Ionic, non-ionic etc. - Common classes of non-ionic detergents (malt, gluc. etc) - CMC, Micelle size, hydrophobic lipophobic balance. - Important properties of detergents for membrane protein purification and stabilization. - Detergent exchange - Important properties of detergents for membrane protein crystallization - Alternative amphiphiles - Specialized properties: temperature dependent phase separation and hydrophobicity - Statistics: Best detergents - Detergent suppliers – and purity |
Ben Hankamer |
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10:20 am |
Coffee Break |
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10:45 am |
Lipids and their properties - Definition of a lipid – briefly describe biophysical properties - How do lipids differ from detergents? - Main types of lipids - Important properties of lipids for 2D crystallization. (Saturation, liquid crystal:crystalline phase transition). - Statistics: Best lipids for crystallization. - Choosing lipids for crystallization |
Daniel Levy |
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12:00 pm |
Lunch. |
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1:00 pm |
Detergents: Purifying, solubilizing and crystallizing membrane proteins - 2D and 3D crystal types - Native 2D crystals - Dilution - Dialysis - Biobeads - Monolayers - Factors affecting crystallization - Towards systematic 2D crystallization screens |
Ben Hankamer |
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2:00 pm |
Practical: 2D crystallization - Monolayer Trial (Daniel Levy, Amy Anderson) - Dialysis Trial (Tom Walz, Po-Lin Chiu) - Biobead Trial (Ben Hankamer, Rena Hill, Ludovic Renault) |
Practical: Image Processing - Installation of MRC, 2dx, possibly IPLT on the private portable computers - Introduction to the image processing in small sub-groups |
Ben Hankamer Daniel Levy Stahlberg Lab Tom Walz |
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5:30 pm |
Dinner, Tercero Dining Area. |
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6:30 pm |
Student Posters and Coffee, in 1022 LSA |
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7:30 pm |
Round table discussion: Improved approaches to 2D crystal production |
Tom Walz Ben Hankamer |
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9:00 pm |
Open hour. |
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Tuesday, August 8, 2006 |
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8:00 am |
Breakfast. |
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9:00 am |
TEM: Instrumentation - Vacuum, Gun (FEG/Thermal, Acc. Voltage), Stage (LN2, Helium), Low-Dose, Spot Scanning, Detection (Film/CCD) |
Ken Downing |
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9:45 am |
Sample Preparation - Methods for enriching crystals from a mixture of crystals and vesicles. - Harvesting crystals: preventing damage to crystals during transfer (monolayer, bilayers). - Benefits of glucose, trehalose etc. - Back injection, Carbon sandwich and other techniques |
Nobuhiko Gyobo |
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10:30 am |
Coffee Break |
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10:45 am |
Data collection: Imaging - Alignment (Coherence, Beam tilt, stability) - Data collection (Defocus, Astigmatism) - Dose limitation and dose measurement |
Dieter Typke |
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11:20 pm |
Data collection: Diffraction - Principle, Alignment, Operation mode (Exp. Time, etc.), Film/CCD |
Janet Vonck |
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12:00 pm |
Lunch. |
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1:00 pm |
TEM development at FEI |
Wim Busing |
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1:30 pm |
TEM development at JEOL |
Barbara Armbruster |
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2:00 pm |
CCD camera development at TVIPS |
Mathias Stumpf |
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2:30 pm |
Sample holders and other developments at GATAN |
Bob Morrison |
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3:00 pm |
Practical: Sample Preparation / CryoEM data collection - RT & Cryo: Neg. stain (Hui-Ting Chou) - Cryo: Back injection (Nobuhiko Gyobo) - Cryo: Sandwich (Nobuhiko Gyobo) - Cryo-EM imaging (Dieter Typke, Nobuhiko Gyobo, James Evans) - e-Diffraction (Janet Vonck, Ludovic Renault) |
Practical: Image Processing - Installation of MRC, 2dx, possibly IPLT on the private portable computers - Introduction to the image processing in small sub-groups |
Janet Vonck Nobuhiko Gyobo Dieter Typke Bryant Gipson Ansgar Philippsen Andreas Schenk |
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5:30 pm |
Dinner, Tercero Dining Area |
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6:30 pm |
Student Posters and Coffee, in 1022 LSA |
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7:30 pm |
Deceleration CCD |
Ken Downing |
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8:00 pm |
Phase Plate Technology |
Bob Glaeser |
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8:30 pm |
Experiences with a Cs corrected and energy filtered TEM |
James Evans |
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9:00 pm |
Dynamic Transmission Electron Microscopy (DTEM) |
Nigel Browning |
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9:30 pm |
Open Hour |
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Wednesday, August 9, 2006 |
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8:00 am |
Breakfast. |
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9:00 am |
Overview of algorithms for 2D crystal image processing - Fourier-space solutions (filtering, unbending) - Real-space solutions |
Henning Stahlberg |
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9:30 am |
Fourier Theory - Real space / Fourier space - FFT, Correlation, Convolution, Autocorrelation - Lattice lines |
Bob Glaeser |
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10:00 am |
Symmetry - Point groups - Unit cells and lattices - Symmetry operations - Space groups, plane groups, crystallographic notation |
Michael Landsberg |
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10:30 am |
Coffee Break |
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10:45 am |
MTF - Determination of the MTF of CCD - Scanner vs. Film |
Dieter Typke |
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11:15 am |
Image Processing in 2D: MRC software for real-space images - Format - Documentation - Work-flow - Programs |
Anchi Cheng |
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12:00 pm |
Lunch. |
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1:00 pm |
Practical: Sample Preparation / CryoEM data collection - RT & Cryo: Neg. stain (Hui-Ting Chou) - Cryo: Back injection (Nobuhiko Gyobo) - Cryo: Sandwich (Nobuhiko Gyobo) - Cryo-EM imaging (Dieter Typke, Nobuhiko Gyobo, James Evans) - e-Diffraction (Janet Vonck, Hui-Ting Chou) |
Practical: Image Processing - Introduction to the image processing in small sub-groups |
Janet Vonck Nobuhiko Gyobo Dieter Typke Bryant Gipson Ansgar Philippsen Andreas Schenk |
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4:10 pm |
Automation of TEM data collection - Leginon |
Clint Potter |
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4:50 pm |
Beam-induced movement of samples - SpotScanning - Beam-induced drum-head movement vs. charging |
Bob Glaeser |
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5:30 pm |
Dinner, Tercero Dining Area |
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6:45 pm |
Scanning Transmission Electron Microscopy - Comparison of STEM vs. TEM - How is STEM implemented - Aberration corrected STEM - What are the applications and implications to biological samples - High-resolution results. |
Nigel Browning |
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7:30 pm |
High resolution membrane protein structure |
Tom Walz |
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8:15 pm |
Tubulin |
Ken Downing |
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9:00 pm |
Open hour |
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Thursday, August 10, 2006 |
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8:00 am |
Breakfast. |
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9:00 am |
Tilt geometry |
Henning Stahlberg |
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9:30 am |
2dx: Image processing of 2D crystal images using 2dx_image |
Bryant Gipson |
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10:15 am |
Coffee Break |
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10:30 am |
Image Processing: MRC software for e-diffraction evaluation - Algorithm - Programs |
Janet Vonck |
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11:15 am |
IPLT architecture |
Ansgar Philippsen |
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12:00 pm |
Lunch. |
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1:00 pm |
IPLT: Image processing of e-diff pattern |
Ansgar Philippsen |
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1:45 pm |
Practical: Image processing of non-tilted 2D crystal data - MRC: Processing of 2D crystal images (Janet Vonck, Anchi Cheng) - 2dx: Processing of non-tilted and tilted images (Bryant Gipson, Henning Stahlberg) - IPLT: Processing of e-diff pattern (Ansgar Philippsen, Andreas Schenk) |
Practical: Image processing trouble shooting session - Targeted problem sessions in small groups with requested teachers
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Bryant Gipson Ansgar Philippsen Andreas Schenk Henning Stahlberg Janet Vonck |
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5:30 pm |
Dinner, Tercero Dining Area |
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6:45 pm |
Quality Assessment |
Anchi Cheng |
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7:30 pm |
A Maximum Likelihood approach to 2D crystals |
Xiangyan Zeng |
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8:15 pm |
Advantages of higher (icosahedral) symmetries |
Holland Cheng |
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9:00 pm |
Open hour |
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Friday, August 11, 2006 |
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8:00 am |
Breakfast. |
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9:00 am |
Tilted Transfer Function (TTF): SpotSplitting and Fourier spot deconvolution |
Henning Stahlberg |
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9:30 am |
A new method for Tilted Transfer Function correction |
Ansgar Philippsen |
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10:00 am |
Coffee Break |
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10:10 am |
Merging with the MRC software (2D) - Phase origin, Defocus, Beam-tilt - ORIGTILT - MAKETRAN |
Henning Stahlberg |
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10:35 am |
Merging with the MRC software (3D) - Tilt geometry refinement - ORIGTILT - Lattice lines |
Anchi Cheng |
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11:00 am |
3D reconstruction - Lattice line interpolation, 3D volume generation, NCS - 3D Visualization with O / Dino |
Andreas Schenk |
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11:30 am |
Molecular Replacement and Structure Refinement |
Piotr Sliz |
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12:00 pm |
Lunch. |
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1:15 pm |
Calculation of the variance of a 3D map by the bootstrap method |
Anchi Cheng |
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2:00 pm |
Practical: Image processing of tilted 2D crystal data - MRC: Processing of 2D crystal images (Janet Vonck, Anchi Cheng) - 2dx: Processing of non-tilted and tilted images (Bryant Gipson, Henning Stahlberg) - IPLT: Processing of e-diff pattern (Ansgar Philippsen, Andreas Schenk) |
Practical: Image processing trouble shooting session - Targeted problem sessions in small groups with requested teachers
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Bryant Gipson Ansgar Philippsen Andreas Schenk Henning Stahlberg Janet Vonck |
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5:00 pm |
Data Deposition: PDB, EBI |
Ben Hankamer |
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5:30 pm |
Closing Remarks |
Ben Hankamer Henning Stahlberg |
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6:00 pm |
Free Time |
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7:00 pm |
Dinner:
Bistro 33 226 F Street Davis, CA 95616 Tel: (530) 756 4556
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Saturday, August 12, 2006 |
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8:00 am |
Breakfast. |
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9:00 am |
Departure |
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Speakers
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Barbara Armbruster Assist. TEM Product Manager, Biology JEOL USA, Inc. 5653 Stoneridge Dr., Suite 110 Pleasanton, CA 94588 +1-925-737 1748
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Nigel Browning Lawrence Livermore National Laboratories Chemistry and Materials Science Livermore, CA 94550 +1-530-754 5358
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Wim Busing Life Sciences Product Manager TEM FEI Company Bldg. Aae-III-075, Achtsewg Noord 5 P.O. Box 80066 5600 KA Eindhoven The Netherlands +31 40 23 56115
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Anchi Cheng Department of Cell Biology Scripps Research Institute 10550 North Torrey Pines Road La Jolla, CA 92037 +1-858-784 9535
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Holland Cheng Molec. & Cell. Biology UC Davis, Davis, CA 95616 +1-530-752 5659
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Ken Downing Lawrence Berkeley National Laboratory Life Sciences Division One Cyclotron Road Mail Stop 941 (Donner) Berkeley, CA 94720
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James Evans Molec. & Cell. Biology UC Davis, Davis, CA 95616 +1-530-754 8285
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Nobuhiko Gyobu Japan Biological Information Res. Center (JBIRC) Japan Biological Information Consortium (JBIC) Aomi 2-41-6, Koto-ku Tokyo 135-0064, Japan +81-3-3599 8092
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Bryant Gipson Molec. & Cell. Biology UC Davis, Davis, CA 95616 +1-530-754 8285
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Robert M. Glaeser Department of Molecular and Cellular Biology University of California at Berkeley 229 Stanley Hall #3206 Berkeley, CA 94720-3206 +1-510-642 2905
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Ben Hankamer Institute for Molecular Bioscience University of Queensland St. Lucia Campus Brisbane QLD 4072 Australia +61-7-3346 2012
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Daniel Levy Institut Curie UMR CNRS 168 11 rue P.M.Curie F-75005 Paris France +33-1 42 34 67 81
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Robert Morrison Product Manager, TEM Holders Worldwide Gatan UK 25 Nuffield Way Abingdon Oxon OX14 IRL, UK +44-1865-253630
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Ansgar Philippsen Biozentrum Klingelbergstr. 72 CH-4065 Basel Switzerland +41-61-267 2254
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Clint Potter CB 129 10550 North Torrey Pines Rd. La Jolla, CA 92037 +1-(858) 784-9050
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Andreas Schenk Biozentrum Klingelbergstr. 72 CH-4065 Basel Switzerland +41-61-267 2254
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Piotr Sliz Harvard Medical School Center for Molecular and Cellular Dynamics 250 Longwood Ave., Rm. SGM-130 Boston, MA 02115 +1-617-620 3019
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Henning Stahlberg Molec. & Cell. Biology Briggs Hall 5 UC Davis, Davis, CA 95616 +1-530-752 8282
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Matthias Stumpf Tietz Video & Image Processing Systems (TVIPS) Eremitenweg 1 D-82131 Gauting Germany +49-89-850 6567
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Dieter Typke Lawrence Berkeley National Laboratory Life Sciences Division One Cyclotron Road Mail Stop 941 (Donner) Berkeley, CA 94720 +1-510-495 2840
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Janet Vonck Dept. of Structural Biology MPI for Biophysics Max-von-Laue Str. 3 D-60528 Frankfurt am Main Germany +49-69-6303-3004 Janet.Vonck@mpibp-frankfurt.mpg.de
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Tom Walz Department of Cell Biology Harvard Medical School 240 Longwood Avenue Boston, MA 02115 +1-617-432 4090
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Xiangyan Zeng Molec. & Cell. Biology Briggs Hall 15 UC Davis, Davis, CA 95616 +1-530-754 8285
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Workshop Participants
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Priyanka Abeyrathne Dept. of Molecular & Cell. Biology University of Guelph Guelph, Ontario Canada N1G 2W1
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Jason Bell Kowalczykowski Lab Molecular & Cell. Biol. UC Davis Davis, CA 95616 +1-(530) 754 9704
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Wei-hau Chang Institute of Chemistry Academia Sinica No 128 Sec 2 Academia Road, Nangang 115, Taipei, Taiwan |
Roseann Csencsits MS 1-116 Lawrence Berkeley Laboratory 1 Cyclotron Road Berkeley, CA 94720
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Sarah Louise Greig School of Biological Sciences The University of Auckland Private Bag 92019 Auckland New Zealand
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Richard Hite Harvard Medical School Department of Cell Biology 240 Longwood Ave Seeley G Mudd Room 526 Boston MA 02115
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Ailong Ke Department of Molecular Biology and Genetics Cornell University 251 Biotechnology Building Ithaca, NY, 14853
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Debbie Kelly Dept. of Cell Biology Harvard Medical School 240 Longwood Avenue SGM 529 Boston, MA 02115
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Alison Nisbet Killilea LBNL 1 Cyclotron Road MS 1-116 Berkeley, CA 94720
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Cezar Khursigara 50 South Drive National Institutes of Health Bldg. 50, Rm. 4306 Bethesda, MD. 20892
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Michael Landsberg Institute for Molecular Bioscience Queensland Biosciences Precinct Services Rd The University of Queensland St Lucia, QLD, 4072, AUSTRALIA
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Julie Norville 604b Ashdown House 305 Memorial Drive Cambridge, MA 02139
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Brad Pessavento Lawrence Livermore National Laboratory PO Box 808, L-448 Livermore, CA 94551
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Andrew John Pomfret Skirball Institute Lab 3-13, NYU School of Medicine, 540 1st Avenue, New York, NY 10016
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Stefan Raunser Department of Cell Biology Harvard Medical School Building Seeley Mudd 529 240 Longwood Avenue Boston, MA 02115
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Andreas Sonnen The Division of Structural Biology The Wellcome Trust Centre for Human Genetics Roosevelt Drive Headington Oxford OX3 7BN
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Svetomir Borissov Tzokov Department of Molecular Biology and Biotechnology The University of Sheffield Firth Court, Western Bank Sheffield S10 2TN United Kingdom
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Hector Viadiu Seeley Mudd Bldg. 526 Dept. Cell Biology Harvard Medical School 240 Longwood Ave. Boston, MA 02115
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Chao Wang 12-13 Parks Road Oxford OX1 3PH
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Huaibin Wang NYU School of Medicine MSB 3 329, 550 1st Ave New York, NY 10016
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Other Participants
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Amy Anderson Stahlberg Lab Molec. & Cell. Biology UC Davis, Davis, CA 95616
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Po-Lin Chiu Stahlberg Lab Molec. & Cell. Biology UC Davis, Davis, CA 95616
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Hui-Ting Chou Stahlberg Lab Molec. & Cell. Biology UC Davis, Davis, CA 95616
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Rena Hill Stahlberg Lab Molec. & Cell. Biology UC Davis, Davis, CA 95616
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Richard Humphrey Tietz Video & Image Processing Systems (TVIPS) 79 Scimitar View NW Calgary, Alberta Canada T3L 2B4 tel: 403-613-7064
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Ludovic Renault Stahlberg Lab Molec. & Cell. Biology UC Davis, Davis, CA 95616
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Matthew Rolnick Stahlberg Lab Molec. & Cell. Biology UC Davis, Davis, CA 95616
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Peter Sparlinek Tietz Video & Image Processing Systems (TVIPS) Eremitenweg 1 D-82131 Gauting Germany +49-89-850 6567
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