| 2nd EMBO Practical Course and |
| 3rdCourse on Single
Particle Cryo Electron Microscopy and 3D Image Processing of Macromolecular Assemblies and Cellular Tomography
(CEM3DIP2020), 19 - 30 January 2020, Kolkata - Timetable. |
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09:30 to 10:30 |
11:30 - 12.30 |
12:30
to 13:30 |
13:30
- 18:00 |
18:00
- 19:00 |
19:00
to 20:00 |
20:00
to 21:00 |
| 19/01/2020
Sunday |
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13:00 - 14:00 Lunch |
14:00:
Inauguration by Prof. Sourav Pal, Director, IISER Kolkata |
16:00 - 16:30:
Coffee Break |
17:30 - 20:00 Participants
and Speakers Mixer, Round table discussion, networking through one to one
meeting, flash introduction. (P. Datta, J.
Sengupta, S. Polley and M. Dutta) |
Dinner |
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14:30: Overview
of Course and introduce all people (R. Natesh, P. Datta and S. Polley) |
16:30 - 17:30
GL1: Deep undestanding of protein function using
structural cryo electron microscopy - Elena
Orlova |
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| 15:00 -
16:00 L1: KEYNOTE
LECTURE 1: Single-Particle methods in electron
microscopy. Past, Present and future - Joachim
Frank |
| 20/01/2020 Monday |
10:30 - 11:30 L2 : EM sample, specimen
preparation methods.- Ramanathan
Natesh |
L3: Principles of TEM image
formation, Particle detection from TEM images and noise handling - Rajendra K Agarwal |
Lunch |
Practical 1: CryoEM specimen
preparation (Vitrobot) -Hands on data collection and platform tour - (Jayati/Natesh/Smarajit/Moumita/Manidipa/Partha) |
L4: Basic concepts of fourier
Transform in TEM image analysis - Elena Orlova |
Dinner |
| 21/01/2020 Tuesday |
09:00
- 10:00, L5: Contrast transfer function, Point spread
function and its effect on image acquisation and concepts of convolution - Elena Orlova |
10:00 - 11:00 GL2: "Functional Complexes of
the mammalian ribosome as revealed by cryo-EM" - Rajendra K Agarwal |
Lunch |
11:15
- 12:30 GL3: "Time-Resolved Cryo-electron
Microscopy" - Joachim Frank |
13:30 - 18:00 Practical 2: CryoEM
specimen preparation (Vitrobot) -Hands on data collection and platform tour -
(Jayati/Natesh/Smarajit/Moumita/Manidipa/Partha) |
18:00 - 19:00
Participants Poster session 1 (P1 to P10) |
Dinner |
| 22/01/2020
Wednesday |
10:30 - 11:30
L6: Movie processing, image selection and initial model
genration - Jose Maria Carazo |
L7: Methods of single particle 3D
orientation determination - Partha P Datta |
Lunch |
Practical 3: EMAN v2.1. Defocus
determination, particle picking, 2D classification, Image processing and 3D
reconstruction - Steven
Ludtke/Jayati/Monidipa/Natesh |
GL4: "In situ structure determination of viral proteins by cryo
-electron tomography" - Moumita Dutta |
Participant Poster Session 2 (P11 to P20) |
Dinner |
| 23/01/2020 Thursday |
L8:
Multivariate Statistical Analysis and Classification of
single particles - Montserrat Samso |
L9: Classifications and Refinement,
Dealing with Heterogeneity and Resolution - Smarajit
Polley |
Lunch |
Practical 4: Relion, Session 1. Somnath/Nayanika
Sengupta |
GL5: "High-resolution
single-particle cryo-EM" - Dmitry Lyumkis |
Participant Poster Session 3 (P21 to P30) |
Dinner |
| 24/01/2020 Friday |
L10: Single-particle 3D
reconstruction, post-processing, and evaluation of anisotropy and resolution
- Dmitry Lyumkis |
L11: Point Group Symmetries. Manidipa
Banerjee |
Lunch |
Practical 5: Relion,
Session 2. Somnath/Nayanika Sengupta |
GL6: "Local and Local Directional Resolution: Its impact in map
validation, map sharpening and beyond" - Jose
Maria Carazo |
Participant Poster Session 4 (P31 to P39) |
Dinner |
| 25/01/2020 Saturday |
L12: Helical Reconstruction - Arjen Jakobi |
L13: Micro ED - 3D electron
Crystallography - Brent L. Nannenga |
Lunch |
Practical 6: Scipion 1 - On the fly
data preprocessing, 2D classifiation using deep learning and intial volime
generation - Carlos Oscar Sorzano and Jose Maria Carazo |
18:00
- 18:45 GL7: "The many layers of Allosterism of the
Ryanodine Receptor" - Montserrat Samso |
18:45 - 19:30 GL8: "Structural
Basis for the filament formation of selective autophagy receptors" - Arjen Jakobi |
Dinner |
| 26/01/2020 Sunday |
L14: Validation of 3D EM
reconstructions - Jose Maria Carazo |
L15:
Partciicipating Industry Thermofisher Scientific,
Invited Lecture: Microscopes for cryo-EM data Collection |
Lunch |
Practical 7: Scipion
2 - 3D reconstruction - Carlos Oscar Sorzano and
Jose Maria Carazo |
18:00 - 18:45
GL9: "MicroED method development and
application" - Brent L. Nannega |
18:45 - 19:30 GL10: "Capturing
and imaging membrane fusion using electron cryo-tomography" - Kelly Lee 19:30 -20:00:
Participants Oral Presentation 1 (ST1 to ST3) |
Dinner |
| 27/01/2020 Monday |
09:30 - 17:30: GROUP EXCURSION - HISTORIC AND MODERN PLACES OF KOLKATA
AND DINNER-CUM RIVER CRUISE |
18:30 - 20:30 - Course Dinner |
| 28/01/2020 Tuesday |
L16: Reconstruction principles and
applications of Cryo Tomography. Cellular Tomography and Subtomogram averaging - Grant Jensen |
L17: Cryo-FIB Milling of cells for
electron Tomography - Elizabeth Wright |
Lunch |
Practical
8: Tomographic reconstruction practicals
(IMOD& PEET) - V.M. Prasad/K. Lee/G.
Jensen/E. Wright/M. Dutta |
GL11: Keynote Lecture 2 :
"Progress and potential of electron cryotomography" - Grant Jensen |
Participants
Oral Presentation 2 (ST4 to ST9) |
Dinner |
| 29/01/2020 Wednesday |
L18: Participating Industry Invited
Lecture: High pressure freezing, freeze ubstitution and/ or cryo-sectioning
of frozen hydrated samples and detectors for cryoEM Data Collection - Leica/JOEL |
L19: Interpretation of maps,
fitting / docking of atomic structures Rangana Warshamanage |
Lunch |
Practical 9: Interpretation of
maps, fitting of atomic structures (Coot/Chimera) and refinement (refmac) - Rangana Warshamanage |
18:00
L20a: "Closing the gaps: Improving direct electron
detection and beyond" - Dr. Sahil Gulati -
AMETEK-GATAN 18:30 L20b: "Participating Industry
Invited Lecture" |
GL12: "Studies of virus
assembly using electron cryo-tmography" - Elizabeth
Wright |
Dinner |
| 30/01/2020 Thursday |
L21: Flexible fitting into cryo-EM
maps and applications - Florence Tama |
L22: Validation, Assessment, Data deposition: EMDB, EMPIAR and PDB:
trends, developments, opportunities and challenges - Osman Salih |
Lunch |
Practical 10: Flexible fitting
(MDFit and Ensemble fittings) - F. Tama/O.
Miyashita/J. Sengupta |
Questions,
Suggestions, Summary, feedback, Certificate distribution. |
Dinner |
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| Interactions
with the speakers can be done during Dinner time. |
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All days
Breakfast will be served at 07:30 and Tea will be served at venues at
10:45and at 15:00 |
| Abbreviations: L - Lecture, GL - Guest
Lecture, Pxx - Poster
(xx) Number,STxx - Selected
Participants Talks (xx) Number |
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