New programs: XELE—a polypeptide model-building program for a graphics workstation

A model-building program, XELE, for use in protein crystallography has been written in C under UNIX on a graphics workstation. This program makes full use of the X Window system to display the electron density distribution and to manipulate the polypeptide model, and therefore is named XELE. It utilizes a fast three-dimensional rendering package, Dorè, and is portable to other types of graphics workstations. A part of the program for the man-machine interface uses the library of X Window and X Toolkit, and therefore is highly interactive. The structure analysis program package, PROTEIN, is also implemented in an interactive mode using X Window, and has been interfaced with XELE.     

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

SUMMARY: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol., 13, 964-969, 1996) that provides methods for reconstruction, comparison, and testing of trees and models on DNA as well as protein sequences. To reduce waiting time for larger datasets the tree reconstruction part of the software has been parallelized using message passing that runs on clusters of workstations as well as parallel computers. AVAILABILITY: http://www.tree-puzzle.de. The program is written in ANSI C. TREE-PUZZLE can be run on UNIX, Windows and Mac systems, including Mac OS X. To run the parallel version of PUZZLE, a Message Passing Interface (MPI) library has to be installed on the system. Free MPI implementations are available on the Web (cf. http://www.lam-mpi.org/mpi/implementations/).     

Large Neural Network Simulations on Multiple Hardware Platforms

To efficiently simulate very large networks of interconnected neurons, particular consideration has to be given to the computer architecture being used. This article presents techniques for implementing simulators for large neural networks on a number of different computer architectures. The neuronal simulation task and the computer architectures of interest are first characterized, and the potential bottlenecks are highlighted. Then we describe the experience gained from adapting an existing simulator, SWIM, to two very different architectures–vector computers and multiprocessor workstations. This work lead to the implementation of a new simulation library, SPLIT, designed to allow efficient simulation of large networks on several architectures. Different computer architectures put different demands on the organization of both data structures and computations. Strict separation of such architecture considerations from the neuronal models and other simulation aspects makes it possible to construct both portable and extendible code.     

Load balancing on temporally heterogeneous cluster of workstations for parallel simulated annealing

Simulated annealing (SA) is a general-purpose optimization technique widely used in various combinatorial optimization problems. However, the main drawback of this technique is a long computation time required to obtain a good quality of solution. Clusters have emerged as a feasible and popular platform for parallel computing in many applications. Computing nodes on many of the clusters available today are temporally heterogeneous. In this study, multiple Markov chain (MMC) parallel simulated annealing (PSA) algorithms have been implemented on a temporally heterogeneous cluster of workstations to solve the graph partitioning problem and their performance has been analyzed in detail. Temporal heterogeneity of a cluster of workstations is harnessed by employing static and dynamic load balancing techniques to further improve efficiency and scalability of the MMC PSA algorithms.     

Field spectroradiometry for discrimination of wetland components: a case study of a tropical inland wetland in India

Remote sensing has emerged as an effective tool for mapping, monitoring and assessment of wetland ecosystems. Spectral resolution of hyperspectral imagery allows collection of extensive information on dynamics of wetland components. Development of comprehensive spectral libraries using field spectroradiometry is imperative to tap the potential of hyperspectral imagery. In this study, an attempt has been made (i) to test the efficacy of field spectroradiometry data and processing techniques for identification and discrimination of wetland components, and (ii) to develop an approach for creating an extensive library for wetland components. Canopy level spectra of 13 macrophyte species representing different life-forms and water column reflectance spectra were collected seasonally at 16 sites in Bhindawas wetland of India for the years 2014 and 2015. Field spectra were processed using spectroscopic techniques including smoothing, derivative analysis and continuum removal. Results show derivative transforms to be efficient in identification and discrimination of wetland components. Magnitude and position of red-edge peak successfully discriminated different macrophytes with maximum and minimum value for Nymphoides indica and Hydrilla verticillata respectively. Continuum removal further strengthens the attributes of spectral data for species discrimination. Algorithms developed based on derivative transforms of water column spectra allow for continuous monitoring of bio-optical parameters and trophic status of the wetland. As a result of this research, sample-sets of field spectra providing a sound base for mapping and monitoring of wetland components were compiled, leading to the development of the first spectral library for an inland freshwater wetland in the Indian subcontinent. This research output in conjunction with advanced analytical tools and algorithms shall be utilized for wetland assessment in future studies.     

A method for extracting genomic DNA suitable for medium-throughput applications from plant tissues rich in contaminants

Isolating nucleic acids from sources rich in contaminants is particularly cumbersome when treating a large number of samples. Several protocols have been published that address the problem of nucleic acid extraction and purification, but few address sample number. We describe a method for extracting DNA from recalcitrant tree species by using a commercial grinding apparatus. This alleviates the hard work of sample preparation prior to lysis and purification. Our method has been tested extensively on different fruit tree species and in projects that require the simultaneous processing of hundreds of samples. Moreover, it does not require the availability of robotic workstations.     

Macintosh sequence analysis software

The analysis of information in nucleotide and amino acid sequence data from an investigator’s own laboratory, or from the ever-growing worldwide databases, is critically dependent on well planned and written software. Although the most powerful packages previously have been confined to workstations, there has been a dramatic increase over the last few years in the sophistication of the programs available for personal computers, as the speed and power of these have increased. A wide choice of software is available for the Macintosh, including the LaserGene suite of programs from DNAStar. This review assesses the strengths and weaknesses of LaserGene and concludes that it provides a useful and comprehensive range of sequence analysis tools.     

MD display: An interactive graphics program for visualization of molecular dynamics trajectories

MD Display was developed as a means of visualizing molecular dynamic trajectories generated by Amber.¹ The program runs on Silicon Graphics workstations, and features a simple user interface, and convenient display and analysis options. The program has now been extended to accept input from several other molecular dynamics programs.     

The mammalian cardiac muscle thick filament: crossbridge arrangement

Although skeletal muscle thick filaments have been extensively studied, information on the structure of cardiac thick filaments is limited. Since cardiac muscle differs in many physiological properties from skeletal muscle it is important to elucidate the structure of the cardiac thick filament. The structure of isolated and negatively stained rabbit cardiac thick filaments has been analyzed from computed Fourier transforms and image analysis. The transforms are detailed, showing a strong set of layer lines corresponding to a 42.9 nm quasi-helical repeat. The presence of relatively strong "forbidden" meridional reflections not expected from ideal helical symmetry on the second, fourth, fifth, seventh, eighth, and tenth layer lines suggest that the crossbridge array is perturbed from ideal helical symmetry. Analysis of the phase differences for the primary reflections on the first layer line of transforms from 15 filaments showed an average difference of 170 degrees, close to the value of 180 degrees expected for an odd-stranded structure. Computer-filtered images of the isolated thick filaments unequivocally demonstrate a three-stranded arrangement of the crossbridges on the filaments and provide evidence that the crossbridge arrangement is axially perturbed from ideal helical symmetry.     

GeneView: multi-language human gene mapping library with a graphical user interface

GeneView is a newly developed human gene mapping library systemthat works on an X-Window platform. This system is designedfor researchers who routinely utilize gene mapping data in thelaboratory but are unfamiliar with computer technology. GeneViewoffers various features, including friendly user interface,fast operation and visualization facility. Genetic loci aredisplayed graphically with an idiogram. This system can be operatedin multiple languages. A current version supports Japanese andEnglish, and can be easily expanded to include other languages.A prototype of GeneView is now installed on a SPARC (Sun4) workstation.Because of the X-Window platform, GeneView should be compatiblewith various types of workstations.     

Generation of a P1 artificial chromosome library of the Southern pufferfish

We describe the generation of a P1 artificial chromosome genomic library from the Southern pufferfish, Spheroides nephelus. The arrayed library consists of approximately 30,000 clones and has an average insert size of 125-150 kb. The coverage is estimated to encompass seven to eight genome equivalents. The library has been used for isolating numerous genomic clones and for establishing contigs of several multigene families. Analysis of several of the clones from this library suggests a preponderance of CA repeat tracts relative to their abundance in humans. The library and high-density filters have been made available to the scientific public through genomics distribution companies.     

Optimal dispatching of multipriority jobs to two heterogeneous workstations

The general problem scenario of this paper is the following: Jobs of various priorities, stationed in a common storage area, are waiting to be dispatched to two non-identical workstations. Any of the waiting jobs can be accessed from the storage at any given time. Each job can be processed on either of the workstations, but once a job has been assigned it may not be preempted. By job priority it is meant that a higher priority job has disptach preference over a lower priority job. The processing time of a job on a given workstation is assumed to be random, the distribution being dependent on the job type and the configuration of the workstation. Specifically, the first problem studied considers only two classes of jobs: (1) “hot” jobs, whose processing is to be expedited and thus have the higher dispatch priority, and (2) “routine” jobs which may be assigned to an available workstation only if the workstation has been rejected by all “hot” jobs. The processing times are assumed to be exponentially distributed with means depending on the job class and workstation. We assume that, on the average, one workstation is faster than the other with regard to processing any job. The dispatching objective for each job class is to minimize its expected flowtime. It is shown that threshold dispatching policies are optimal for this problem. That is, the faster processor should be utilized whenever possible, and for each class there exists an explicit threshold such that when the number of jobs of that class in the buffer exceeds this threshold then a job of that class is dispatched to the slower processor, otherwise these jobs wait for the faster processor to become available. For the higher priority jobs, this threshold is shown to be a function only of the various processing rates of the two workstations. For the lower priority jobs, the threshold also depends on the number of higher priority jobs in the buffer. The results is extended to a system with n priority classes. Again, it is shown that when the processing times are exponentially distributed with different rates and the dispatching objective for each class is to minimize its expected flowtime, the optimal dispatching policies are of threshold type. Explicit thresholds are easily derived.     

A trace display and editing program for data from fluorescence based sequencing machines.

'Ted' (Trace editor) is a graphical editor for sequence and trace data from automated fluorescence sequencing machines. It provides facilities for viewing sequence and trace data (in top or bottom strand orientation), for editing the base sequence, for automated or manual trimming of the head (vector) and tail (uncertain data) from the sequence, for vertical and horizontal trace scaling, for keeping a history of sequence editing, and for output of the edited sequence. Ted has been used extensively in the C.elegans genome sequencing project, both as a stand-alone program and integrated into the Staden sequence assembly package, and has greatly aided in the efficiency and accuracy of sequence editing. It runs in the X windows environment on Sun workstations and is available from the authors. Ted currently supports sequence and trace data from the ABI 373A and Pharmacia A.L.F. sequencers.     

Cloning gene ura5 for the orotidylic acid pyrophosphorylase of the filamentous fungus Podospora anserina: transformation of protoplasts

From a genomic library of the filamentous fungus Podospora anserina, we have cloned a 4.9-kb fragment which complements an Escherichia coli mutant strain deficient for orotidylic acid pyrophosphorylase (pyrE gene). The recombinant plasmid pPAura5 also transforms to prototrophy a mutant strain of P. anserina carrying a mutation in the ura5 gene and lacking OMPppase activity.     

Characterization of a human chromosome 8 cosmid library constructed from flow-sorted chromosomes.

A cosmid library for human chromosome 8 has been constructed from flow-sorted chromosomes in the vector sCos-1. This library is 85% human and has been arrayed into 210 microtiter plates representing four genome equivalents. Cosmids have been isolated with 10 of 11 probes representing nine different loci from chromosome 8.     

Generation of a zebrafish P1 artificial chromosome library.

We have constructed a genomic P1 artificial chromosome library from the zebrafish. The library has been arrayed and archived in two hundred seventy-one 384-well microtiter dishes. It encompasses four to five genome equivalents with an average insert size of approximately 115 kb and is readily accessible to the scientific community. The library has been used by numerous investigators in the community and shown to be a useful reagent for chromosomal walking and positional cloning.     

Transport phenomena in solid state fermentation: Oxygen transport in static tray fermentors

A mathematical model has been developed for describing the oxygen concentration during the exponential growth of microorganisms, in a static solid substrate bed supported on a tray fermentor. The model equations comprise of one partial differential equation for mass transfer and an ordinary differential equation of growth. After nondimensionlisation, analytical solution to the model has been obtained by the method of Laplace transforms. An expression for critical thickness of bed is deduced from the model equation. The significance of the model in the design of tray fermentors is discussed. The validity of the discussion is verified by taking an illustration from the literature.     

A bacterial artificial chromosome (BAC) library of Malus floribunda 821 and contig construction for positional cloning of the apple scab resistance gene Vf.

The apple scab resistance gene Vf, originating from the wild species Malus floribunda 821, has been incorporated into a wide variety of apple cultivars through a classical breeding program. With the aim of isolating the Vf gene, a bacterial artificial chromosome (BAC) library consisting of 31 584 clones has been constructed from M. floribunda 821. From the analysis of 88 randomly selected BAC clones, the average insert size is estimated at 125 kb. If it is assumed that the genome size of M. floribunda 821 is 769 Mb/haploid, the library represents about 5x haploid genome equivalents. This provides a 99% probability of finding any specific sequence from this library. PCR-based screening of the library has been carried out using eight random genomic sequence-characterized amplified regions (SCARs), chloroplast- and mitochondria-specific SCARs, and 13 high-density Vf-linked SCAR markers. An average of five positive BAC clones per random SCAR has been obtained, whereas less than 1% of BAC clones are derived from the chloroplast or mitochondrial genomes. Most BAC clones identified with Vf-linked SCAR markers are physically linked. Three BAC contigs along the Vf region have been obtained by assembling physically linked BAC clones based on their fingerprints. The overlapping relatedness of BAC clones has been further confirmed by cytogenetic mapping using fiber fluorescence in situ hybridization (fiber-FISH). The M. floribunda 821 BAC library provides a valuable genetic resource not only for map-based cloning of the Vf gene, but also for finding many other important genes for improving the cultivated apple.