Silicon Graphics Iris Workstation Research Articles

Three-dimensional imaging of the yeast actin cytoskeleton through the budding cell cycle.

The actin cytoskeleton of Saccharomyces cerevisiae is composed of a single, conventional actin isoform that is 86% identical to mammalian actins in addition to a battery of similarly conserved associated proteins. This conservation of components and their functions has led yeast geneticists and cell biologists to use the experimental power of yeast toward the study of the regulation of actin cytoskeleton assembly and the basic, housekeeping functions of the actin cytoskeleton (for a comprehensive review, see Botstein et al., 1997 ). Important to these studies has been the visualization of the actin cytoskeleton through the cell cycle and how mutations in regulators and components of the yeast cytoskeleton affect this organization. The first images of the yeast actin cytoskeleton showed that it consists of two filament-based structures: the actin cortical patch and the actin cables (Adams and Pringle, 1984 ; Kilmartin and Adams, 1984 ). The actin cortical patches show a polarized distribution that changes during the cell cycle: first they appear at the incipient bud site, suggesting a role in bud emergence; soon thereafter they are also found within the growing bud, indicating a role in bud growth; and late in the cell cycle they reorganize into two rings in the neck, where they are believed to be involved in septation and cytokinesis. By electron microscopy, the actin cortical patches have been shown to be invaginations of the plasma membrane around which actin filaments and actin-associated proteins are organized (Mulholland et al., 1994 ). Recently it has been shown that subsets of actin cortical patches can move at speeds of up to 1 μm/s (Doyle and Botstein, 1996 ; Waddle et al., 1996 ). The actin cables, which consist of bundled actin filaments, were observed to generally run along the long axis of budding cells. This organization fits well with the understanding that actin is involved in polarized cell growth, dynamic reorganization of the cell cortex, membrane trafficking at the cell cortex, and organelle segregation at cell division. Because certain aspects of the organization of the yeast actin cytoskeleton cannot be well addressed or documented by conventional two-dimensional microscopy, I have investigated the use of a DeltaVision deconvolution microscope for visualization of the yeast actin cytoskeleton in three dimensions. This instrument digitally captures focal sections in the Z plane and mathematically removes out-of-focus light by examining neighboring focal sections, from each section in a process called iterative deconvolution (Agard et al., 1989 ; Scalettar et al., 1996 ). The clarified focal sections can then be assembled to produce high-resolution three-dimensional images. I have found that this technology is extremely powerful for the study of yeast cell anatomy. With respect to the organization of the actin cytoskeleton, I have confirmed that the actin cables (like the patches) are cortical in their arrangement and can be observed to attach both at their ends and laterally to the cortical patches. In some cases, multiple cables can be seen to attach to single cortical patches. In addition, I have observed the earliest stages of bud emergence and have found that buds first emerge through a ring of cortical patches, and only after this stage do the cortical patches migrate into the bud. In my strain background (S288C), I do not observe a polarized distribution of cortical patches in the bud at any time during bud growth.

Motion control of 7-DOF arms: the configuration control approach

Graphics simulation and real-time implementation of configuration control schemes for a redundant seven-degree-of-freedom (7-DOF) Robotics Research arm are described. The arm kinematics and motion control schemes are described briefly. This is followed by a description of a graphics simulation environment for 7-DOF arm control on the Silicon Graphics IRIS Workstation. Computer simulation results are presented to demonstrate elbow control, collision avoidance, and optimal joint movement as redundancy resolution goals. The laboratory setup for experimental validation of motion control of the 7-DOF Robotics Research arm is then described. The configuration control approach is implemented on a Motorola-68020/VME-bus-based real-time controller, with elbow positioning for redundancy resolution. Experimental results demonstrate the efficacy of configuration control for real-time control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Computer processing and analysis of X-ray fibre diffraction data

The processing and analysis of fibre diffraction data is often cumbersome. Presented here is a compact interactive computer program, PROFIDA (processing of fibre diffraction data), for fast processing of fibre diffraction data from biological molecules without many of the difficulties. Interactive rotation and centring of the diffraction pattern allow four-quadrant averaging and background subtraction. Furthermore, film coordinates may be transformed into reciprocal-space coordinates for any orientation of the specimen. Specimen tilt towards the incident-beam direction may be determined and the appropriate correction made. In addition, a routine that scales and merges data sets from a film pack is available. Data analysis is supported by an integration routine that allows layer-line profiles to be examined and integrated and layer-line plots to be produced under control of the cursor. The program is written in C to run on the Silicon Graphics Iris workstation with a button-and-dial box using the Iris graphics library.

Benchmarking High-Performance Computing Systems By Means of Local-Creutz Simulations of the d = 2 Ising Model

We have benchmarked various high-performance com puter systems by means of a code that solves the Ising model in two dimensions. We use a simple and porta ble Fortran implementation of the local-Creutz algo rithm. We compare the wall-clock times needed to per form 250,000 iterations of the algorithm on a lattice of 162 spins, for the Thinking Machines Corporation CM-2, the NEC SX-2, one CRAY Y-MP 4/32 processor, the Alliant FX/2800 with a variable number of proces sors, the IBM 3090-200 VF, an IBM 6000 RISC worksta tion, and a Silicon Graphics Iris workstation.

Computer-Aided Control System Design Environment

A computer-aided engineering environment for the design, analysis, and control of mechanical systems is defined and a detailed example is given. The overall integrated environment includes commercially available systems for 3D geometric modeling and animation, multibody system dynamics, finite element analysis, and control system design. The platform for the environment is the Silicon Graphics IRIS Workstation. This environment allows students in mechanical and aeronautical engineering to rapidly develop and test control strategies for mechanical systems. Transfer functions from the multibody system model, together with mathematical models of any electrical, pneumatic, and hydraulic components, are used for control system synthesis. The controller architecture and parameters are specified in block diagram form and converted to a real-time program. This controller program, with any nonmechanical component models included, is combined with the original nonlinear mechanical system model. The dynamic response of this complete system is studied to verify the controller design for this nonlinear, more realistic system model. Once satisfied with the controller design, the student can then download the real-time controller program to a microprocessor for controlling the actual physical plant. This environment will be used in the senior elective/first year graduate course Dynamics and Control of Multibody Systems, developed by the author and offered in the Spring ’91 semester.

Distributed Interactive Graphics Applications in Computational Fluid Dynamics

Implementation of two distributed graphics pro grams used in computational fluid dynamics is discussed. Both programs are interactive in na ture. They run on a CRAY-2 supercomputer and use a Silicon Graphics Iris workstation as the front-end machine. The hardware and supporting software are from the Numerical Aerodynamic Simulation project The supercomputer does all numerically intensive work and the workstation, as the front-end machine, allows the user to perform real-time interactive transformations on the displayed data. The first program was written as a distributed program that computes particle traces for fluid flow solutions existing on the su percomputer. The second is an older post-pro cessing and plotting program modified to run in a distributed mode. Both programs have realized a large increase in speed over that obtained using a single machine. By using these pro grams, one can learn quickly about complex features of a three-dimensional flow field. Some color results are presented.

TOM: a FRODO subpackage for protein-ligand fitting with interactive energy minimization

We have implemented the docking subpackage TOM into FRODO 1 for studying protein-ligand interactions with interactive energy-minimization procedures. When using TOM, models of protein-ligand complexes are first created in a graphics display unit, followed by interactive energy-minimization treating both ligand and parts of the receptor as flexible units. The potential energy function includes Coulomb and van der Waals interactions. At present, two versions of TOM are available, running on a DEC VAX computer, an Evans and Sutherland PS300 display unit, or a Silicon Graphics IRIS workstation.

Ribbon models of macromolecules

A smooth 3D ribbon model of a protein is easily constructed by creating a set of nearly parallel B-spline curves fitted to the peptide plane. These models may be coded by residue to depict such information as secondary structure, residue type or temperature factors. The computation of the curves defining the ribbon model is explained in detail. Solid surface models of the protein backbone may be rendered, using the ribbon curve as a basis. Nucleic acid molecules may be represented as ribbon models in much the same fashion. The method is applicable to both vector and raster devices, and is illustrated with the Evans and Sutherland PS300 and the Silicon Graphics Iris workstation.