Visualization of Biological Complexity Resource

Visualization of Biological Complexity Resource

Research Emphasis

The resource develops methods for the three-dimensional (3-D) visualization of biological systems over a wide range of scales, from macromolecular assemblies to cells, using electron microscopy and advanced computational methods. Driven by research projects studying the mitochondrion, kinetochore, calcium release channel, and ribosome, the following three areas of technology and research development are pursued.

Cryoelectron tomography: This center is working to improve tomographic resolution for identification of macromolecular complexes in cells and to extend cryotomographic applications to cells within tissue. Improved imaging during tilt-series collection is achieved by means of electron microscope automation, energy filtering, and advanced phase-contrast techniques. Computational methods are being developed to enhance reconstruction fidelity and to aid in visualization and extraction of macromolecular and organellar motifs. Study of 3-D subcellular structure in frozen-hydrated tissue is facilitated by developments in cryoultramicrotomy and cryofocused ion-beam milling, which are carried out in collaboration with Rensselaer Polytechnic Institute (see below) and Dr. Eric Lifshin, Metrology and Characterization Center, Albany NanoTech, University at Albany.

Time-resolved cryoelectron microscopy: Time-resolved imaging of macromolecular interactions, using single-particle reconstruction methodology, enables the understanding of physiologic function from 3-D snapshots of a dynamic system. The goal is to develop methods to initiate reactions involving macromolecules, trap them in intermediate states, and visualize them using cryoelectron microscopy. This work is aided by collaboration with scientists at Rensselaer Polytechnic Institute: Dr. Omkaram Nalamasu and J. Jay McMahon (Center for Integrated Electronics), Dr. Toh-Ming Lu (Department of Applied Physics), and Dr. Pulickel Ajayan (Department of Materials Science and Engineering). The center also collaborates with Dr. Howard White of the Eastern Virginia Medical School in the development of a computer-controlled time-resolved plunge-freezing machine.

Classification of heterogeneous data in single-particle reconstruction: The reconstruction of macromolecular complexes from thousands of low-dose images that show the molecule in different views makes the tacit assumption that the molecule exists in the specimen in the same conformation or binding state. In practice, this assumption is often not fulfilled. In those cases, the reconstruction is blurred and fails to reflect the true structure of any of the conformers. This center is systematically exploring methods capable of sorting heterogeneous molecule populations, so that subpopulations can be found and separately reconstructed. This work is being done in collaboration with Dr. Jose-Maria Carazo of Universidad Autonoma de Madrid, Dr. Gabor Herman of the City University of New York, Dr. Harry Zuzan of McGill University, and Dr. Pawel Penczek of the University of Texas, Houston.

Resource Capabilities

Instruments

The resource has two unique electron microscopes. The AEI EM7 MkII high-voltage electron microscope (HVEM, 100-1,200 KeV) can be used for electron tomography on specimens thicker than 1 µm. The JEOL JEM-4000FX intermediate-voltage electron microscope (IVEM, 100-400 KeV) is equipped with a Gatan GIF 2002 energy filter and is configured for low-dose, automated cryoelectron tomography. It is equipped for single- and double-tilt cryoelectron tomography and has full analytical capability with scanning transmission electron microscope, electron energy loss spectroscopy, and energy-dispersive X-ray spectroscopy. The resource also has shared use of an FEI Tecnai F-20 200 KeV field-emission cryoelectron microscope. A wide range of cryospecimen preparation equipment is provided, including an FEI Vitrobot, a Bal-Tec high-pressure freezer, and two Leica cryoultramicrotomes. The resource has shared access to a cryoequipped FEI Strata dual-beam focused ion beam at nearby Albany NanoTech.

Software, Computing

SPIDER, and the associated graphics user interfaces WEB and JWEB, are used for all image processing in single-particle and tomographic reconstruction. Procedures are carried out using the SPIDER Reconstruction Engine, which contains a user-friendly graphic interface and makes use of a project database. This flexible system aids beginners while providing a convenient means for advanced users to modify algorithms encoded in batch files. 3-D visualization is done using a variety of commercial products, such as Iris Explorer, Amira, O, and Insight as well as our own Sterecon, a system used to draw contours of stereoscopically represented reconstructions. Computing hardware includes five multiprocessor Linux workstations. One of these is dedicated to high-end graphics applications, and another, with 3 terabytes of redundant array of independent disk (RAID) storage, is dedicated to high-speed processing. A Power Mac G5 quad-core graphics workstation, several Silicon Graphics workstations, and three laptop workstations are also provided. Several of these computers are located in a dedicated room that is equipped with large-screen and projection displays for collaborative work. A Linux cluster with 13 dual-core processors and 3 terabytes of RAID storage is available, either as a stand-alone cluster or, on a shared basis, integrated into a larger cluster.

Publications

1. Marko, M., Hsieh, C., Moberlychan, W., Mannella, C. A., and Frank, J., Focused ion beam milling of vitreous water: Prospects for an alternative to cryo-ultramicrotomy of frozen-hydrated biological samples. Journal of Microscopy 222:42–47, 2006.

2. Hsieh, C.-E., Leith, A., Mannella, C. A., Frank, J., and Marko, M., Towards high-resolution three-dimensional imaging of native mammalian tissue: Electron tomography of frozen-hydrated rat liver sections. Journal of Structural Biology 153:1–13, 2006.

3. Gao, H., Ayub, M. J., Levin, M. J., and Frank, J., The structure of the 80S ribosome from Trypanosoma cruzi reveals unique rRNA components. Proceedings of the National Academy of Sciences USA 98:11991–11996, 2005.

4. Rath, B. K., Hegerl, R., Leith, A., Shaikh, T. R., Wagenknecht, T., and Frank, J., Fast 3D motif search of EM density maps using a locally normalized cross-correlation function. Journal of Structural Biology 144:95–103, 2005.