CIRC Symposium Series
October 17, 2014
11:30 AM - 01:00 PM
URMC 2-6408 (K-207 Auditorium)
Quantitative Imaging Opportunities at the University of Rochester: Some Recent Developments and Examples
Ronald Wood, Ph.D.
Departments of Obstetrics and Gynecology, Urology, Neurobiology and Anatomy
The University of Rochester has a site license agreement for the Amira software suite that provides 3D imaging and analysis capabilities for confocal/multiphoton, microCT, histology sections, MRI and high resolution ultrasound instrumentation. This suite has proven to be valuable to multiple programs at URMC. Recently we have generated vascular data sets too large for desktop workstations, and we have begun work with the Center for Integrated Research Computing. The CIRC Bluehive and the VISTA Collaboratory will enable us to undertake quantitative analysis of cascading vascular networks, beginning with mouse size imaging volumes at 17.5 micron voxel resolution. The same solutions will be applicable to large confocal and multiphoton data sets.
On-Going Research Talk: Stacking in RNA: NMR Spectra of Four RNA Tetramers Provide Rigorous Benchmarks of Molecular Dynamics Predictions
Department of Chemistry
Molecular dynamics (MD) simulations for RNAs r(AAAA), r(CAAU), r(GACC), and r(UUUU) are benchmarked against 1H-1H NOESY distances and 3J scalar couplings to test effects of RNA torsion parameterizations. The force fields AMBER ff99, parmbsc0, parm99Chi_Yil, ff10, and parmTor all predict experimentally unobserved stacks, intercalations, and incorrect chi, epsilon, and sugar pucker populations. Results from 540 microseconds of MD show that more accurate force field parametrizations by quantum mechanics improve predictions, but further improvements are necessary to provide reasonable agreement with NMR. ParmTor and ff10 should be used in concert for any future RNA MD studies, and their predictions compared with any experimental data and as high a level of quantum mechanical confirmation as possible to eliminate as many force field artifacts as possible. NMR data and the scoring method presented here provide a rigorous benchmark for future changes in force fields and MD methods.