BioMaPS/DIMACS/MBBC/PMMB Short Course: Transcriptional Regulation from
Molecules to Systems and Beyond

June 21 - 25, 2004
DIMACS Center, CoRE Building, Rutgers University

Organizers:

Wilma Olson, Rutgers University, olson@rutchem.rutgers.edu

Anirvan Sengupta, Rutgers University, anirvan@physics.rutgers.edu

Workshop Program:

Monday, June 21, 2004

 8:15 - 9:15   Registration - 1st Floor Lobby, CoRE Building
               Breakfast - DIMACS Lounge, Room 401

 9:15 - 9:30   Welcome and Opening Remarks
               Brenda Latka, DIMACS Associate Director
 
 9:30 - 11:00  Introduction to Bacterial Transcription I
               Richard Ebright, Rutgers University	

11:00 - 11:20  Break

11:20 - 12:50  Introduction to Bacterial Transcription II
               Richard Ebright, Rutgers University	

12:50 -  2:00  Lunch

 2:00 -  3:00  X-ray Crystallographic Insights into Bacterial Transcription:  
               A Detailed View of the Flagellar Sigma/Anti-Sigma Complex
               Margareta Sorenson, (Seth Darst Group), Rockefeller University	

 3:00 -  3:40  Modeling Transcription Complexes Using FRET
               Jennifer Knight,(Ronald Levy Group), Rutgers University

 3:40 -  4:00  Break

 4:00 -  4:20  Molecular Simulations in Structural Biology, Macro-Molecular Assemblies
               Ronald Levy, Rutgers University

 4:20 -  5:00  Allosteric Regulation of the lac Repressor
               Emilio Gallicchio, Rutgers University	

 5:15 	       Reception -  4th Floor, CoRE Building

 6:00	       Dinner -  4th Floor, CoRE Building

Tuesday, June 22, 2004
 
 9:00 -  9:30  Registration and Breakfast - 4th Floor, CoRE Building
               
 9:30 - 11:00  Introduction to Eukaryotic Transcription
               Danny Reinberg, UMDNJ	

11:00 - 11:20  Break

11:20 - 12:20  Crystallographic Studies of Protein-Protein Interactions in 
               Transcription Regulation: CAP-RNAP and trpR
               Cathy Lawson, Rutgers University	

12:20 -  1:40  Lunch
	
 1:40 -  2:40  Enhancers and Insulators: Mechanism of Action Over a Distance
               Vasily Studitsky, UMDNJ	

 2:40 -  3:40  Sequence-Dependent Kinetic Model for Transcription 
               Elongation by RNA Polymerase
               Lu Bai, (Michelle Wang group), Cornell University	

 3:40 -  4:00  Break

 4:00 -  5:00  Single-Molecule Studies of Bacterial Transcription
               Terence Strick, Cold Spring Harbor Laboratory	

Wednesday, June 23, 2004

 9:00 -  9:30  Registration and Breakfast - 4th Floor, CoRE Building

 9:30 - 10:30  Kinetic Studies of Transcription Initiation in T7 RNA Polymerase
               Smita Patel, UMDNJ	

10:30 - 10:50  Break
	
10:50 - 11:40  Kinetic Studies of Transcription Initiation by E. coli RNA 
               Polymerase: Evidence for Conformational Changes in 
               Open Complex Formation
               Ruth Saecker, University of Wisconsin	

11:40 - 12:30  Role of Upstream DNA Sequences in Transcription Initiation 
               at the Lambda PR Promoter
               Caroline Davis, (Tom Record Group), University of Wisconsin

12:30 -  2:00  Lunch	

 2:00 -  3:00  On the Role of DNA Elasticity in Transcription Regulation
               David Swigon, Rutgers University	

 3:00 -  3:45  Microscale and Macroscale Mobility of the RNAP Transcription Complex
               Vitaly Epshtein, NYU Medical Center
 
 3:45 -  4:05  Break

 4:05 -  4:50  The Double Ratchet Mechanism of Transcriptional Elongation
               Andrei Ruckenstein, Rutgers University

Thursday, June 24, 2004

 9:00 -  9:30  Registration and Breakfast - 4th Floor, CoRE Building

 9:30 - 11:00  Regulation of Bacterial Transcription
               Richard Ebright, Rutgers University	

11:00 - 12:45  Break - Poster Session

12:45 -  2:00  Lunch	

 2:00 -  3:15  Computational Detection of Cis-Regulatory 
               Modules in the Drosophila Genome
               Saurabh Sinha, Rockefeller University	

 3:15 -  3:35  Break

 3:35 -  4:35  Predictive Learning of Combinatorial Transcriptional Regulation
               Michael Beer, Princeton University	

 4:35 -  5:35  Transcriptional Regulation during Bacteriophage Development
               Konstantin Severinov, Rutgers University

Friday, June 25, 2004

 9:00 -  9:30  Registration and Breakfast - 4th Floor, CoRE Building

 9:30 - 10:30  Noise in Gene Expression and Switching
               Anirvan Sengupta, Rutgers University	

10:30 - 11:45  Transcriptional Control and Pattern Formation in the 
               Drosophila Segmentation Gene Network
               Carlos Alonso and Johannes Jaeger, (John Reinitz Group)
               SUNY at Stony Brook	

11:45 - 12:00  Epilogue
               Wilma Olson and Anirvan Sengupta	

12:00 -  1:15  Lunch	

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