VOSTORG: a package of microcomputer programs for sequence analysis and construction of phylogenetic trees

VOSTORG is a new, versatile package of programs for the inference and presentation of phylogenetic trees, as well as an efficient tool for nucleotide (nt) and amino acid (aa) sequence analysis (sequence input, verification, alignment, construction of consensus, etc.). On appropriately equipped systems, these data can be displayed on a video monitor or printed as required. They are implemented on IBM PC/XT/AT/PS-2 or compatible computers and hardware graphic support is recommended. The package is designed to be easily handled by occasional computer users and yet it is powerful enough for experienced professionals.     

Diagnostic tools for filariasis elimination programs

The ambitious and exciting Global Programme to Eliminate Lymphatic Filariasis (GPELF) is largely based on a strategy of mass drug administration (MDA) of repeated rounds of antifilarial medications to endemic populations around the world. Diagnostic tools are important to GPELF because they affect decisions regarding where to distribute MDA, how to measure its effects, how to define targets and endpoints for stopping MDA, and how to monitor populations for possible resurgence of filariasis transmission following suspension of MDA. This article reviews available diagnostic tests for filariasis and their potential use as tools for different phases of filariasis elimination programs.     

IBM microcomputer programs that analyze DNA sequences for tRNA genes

A set of four computer programs that search DNA sequence datafiles for transfer RNA genes have been written in IBM (Microsoft)BASIC for the IBM personal computer. These programs locate andplot predicted secondary structures of tRNA genes in the cloverleafconformation. The set of programs are applicable to eukaryotictRNA genes, including those containing intervening sequences,and to prokaryotic and mitochondrial tRNA genes. In addition,two of the programs search up to 150 residues downstream oftRNA gene sequences for possible eukaryotic RNA polymerase IIItermination sites comprised of at least four consecutive T residues.Molecular biologists studying a variety of gene sequences andflanking regions can use these programs to search for the additionalpresence of tRNA genes. Furthermore, investigators studyingtRNA gene structure-to-function relationships would not needto do extensive restriction mapping to locate tRNA gene sequenceswithin their cloned DNA fragments. Received on October 29, 1985; accepted on January 28, 1986     

Spiral nerve cuff electrode for recordings of respiratory output

Sahin, Mesut, Musa A. Haxhiu, Dominique M. Durand, andIsmail A. Dreshaj. Spiral nerve cuff electrode for recordings ofrespiratory output. J. Appl. Physiol.83(1): 317-322, 1997.The feasibility of using the spiral nervecuff electrode design for recordings of respiratory output from thehypoglossal (HG) and phrenic nerves is demonstrated in anesthetized,paralyzed, and artificially ventilated cats. Raw neural discharges ofthe HG nerve were analyzed in terms of signal-to-noise ratios andfrequency spectra. The rectified and integrated moving average activity of the HG nerve had a peak value of 1.74 ± 0.21 µV and a baseline value of 0.72 ± 0.11 µV at elevated respiratory drive induced byincreases in CO₂ or oxygendeprivation when recorded with 10-mm-long cuffs. The frequency contentof the HG electroneurogram extended from several hundred hertz to 6 kHz. Spiral nerve cuff recordings without desheathing of the nerveprovided large enough signal-to-noise ratios that allowed them to beused as a measure of respiratory output and had much wider frequencybandwidths than the hook electrode preparations. A major advantage ofthe cuff electrode over the hook electrode was its mechanicalstability, which significantly improved the reproducibility of therecordings both in terms of signal amplitudes and frequency contents.

     

A comprehensive system of cosinor treatment programs written for the Apple II microcomputer

A comprehensive set of cosinor treatment programs has been written for an Apple II microcomputer. The system includes Single Cosinor, Mean (population) Cosinor and Serial Sections analyses as well as extensive graphics and file management. The package is integrated and used through a hierarchically ordered system of menus and choices. 48k memory and two disk drives are required, and both EPSON and SILENTYPE printers are supported.     

The SEQANAL and SEQTALK programs: a new method of access to high-resolution nucleotide sequence comparison and analysis programs from a remote laboratory mini- or microcomputer

A new method of access has been devised for biologists requiringthe use of computer programs offering high-resolution analysisand comparison of nucleotide sequence data. The strategy involvesthe development of a pair of computer programs, called SEQANALand SEQTALK, designed to operate in tandem. SEQANAL is a largeand complex program intended to be used to discover regionsof internal repeats and dyad symmetries within one sequence,or regions of homology, complementarity or optimal alignmentbetween two sequences. Three algorithms are supported: thoseof Staden (1977, 1978); of Korn et al. (1977); Queen and Korn(1980); and the newly-described exhaustive tree-searching algorithmof Burnett et al. (1985, 1986). The SEQTALK program is a small,portable, interactive, frontend program with which the usercan specify the instructions to control the SEQANAL program.Together, the SEQANAL and SEQTALK programs permit analyses tobe performed at a remote facility on a mainframe computer underthe complete control of a distant user equipped with minimalcomputing facilities, and without needing networking facilities. Received on May 23, 1985; accepted on August 13, 1985     

ANTHEPROT: a package for protein sequence analysis using a microcomputer

A simple microcomputer package is described to make the theoreticalanalysis of protein sequences. Several methods designed to comparetwo sequences, to model proteolytic reactions and to predictthe secondary structure, the hydro-phobic/hydrophilic regionsand the potential antigenic sites of proteins have been includedin an Apple II microcomputer software. The package comprises21 programs as well as the secondary structure database of Kabschand Sander (1983). Received on November 24, 1987; accepted on March 8, 1988     

UDP-glucuronosyltransferase: fluorometric determination and microcomputer method for bisubstrate kinetics analysis

A method for analysing UDP-glucuronosyltransferase activity in rainbow trout hepatic microsomes is described, using 1-naphthol as a substrate and fluorometric determination of glucuronide. Kinetic constants are computed with a classical plot in a weighted regression. The computer uses the least-squares method for each value of a variable which is set and incremented. To get confidence intervals, the computer generates random values around experimental data (in a confidence interval they determine), and then computes again. With each simulation, a weighted regression with classical secondary plots gives simulated kinetic parameters. From each population of simulated values, an interval containing a given percentage of the population is determined.     

Analysis for free: comparing programs for sequence analysis

Programs to import, manage and align sequences and to analyse the properties of DNA, RNA and proteins are essential for every biological laboratory. This review describes two different freeware (BioEdit and pDRAW for MS Windows) and a commercial program (Sequencher for MS Windows and Apple MacOS). Bioedit and Sequencher offer functions such as sequence alignment and editing plus reading of sequence trace files. pDRAW is a very comfortable visualisation tool with a variety of analysis functions. While Sequencher impresses with a very user-friendly interface and easy-to-use tools, BioEdit offers the largest and most customisable variety of tools. The strength of pDRAW is drawing and analysis of single sequences for priming and restriction sites and virtual cloning. It has a database function for user-specific oligonucleotides and restriction enzymes.     

Portable microcomputer software for nucleotide sequence analysis.

The most common types of nucleotide sequence data analyses and handling can be done more conveniently and inexpensively on microcomputers than on large time-sharing systems. We present a package of computer programs for the analysis of DNA and RNA sequence data which overcomes many of the limitations imposed by microcomputers, while offering most of the features of programs commonly available on large computers, including sequence numbering and translation, restriction site and homology searches with dot-matrix plots, nucleotide distribution analysis, and graphic display of data. Most of the programs were written in Standard Pascal (on an Apple II computer) to facilitate portability to other micro-, mini-, and and mainframe computers.     

GlycoBase and autoGU: tools for HPLC-based glycan analysis

Summary: The development of robust high-performance liquid chromatography(HPLC) technologies continues to improve the detailed analysisand sequencing of glycan structures released from glycoproteins.Here, we present a database (GlycoBase) and analytical tool(autoGU) to assist the interpretation and assignment of HPLC-glycanprofiles. GlycoBase is a relational database which containsthe HPLC elution positions for over 350 2-AB labelled N-glycanstructures together with predicted products of exoglycosidasedigestions. AutoGU assigns provisional structures to each integratedHPLC peak and, when used in combination with exoglycosidasedigestions, progressively assigns each structure automaticallybased on the footprint data. These tools are potentially verypromising and facilitate basic research as well as the quantitativehigh-throughput analysis of low concentrations of glycans releasedfrom glycoproteins. Availability: http://glycobase.ucd.ie Contact: matthew.campbell{at}nibrt.ie Associate Editor: Limsoon Wong Present address: Dublin-Oxford Glycobiology Laboratory, NationalInstitute for Bioprocessing Research and Training, Conway Institute,University College Dublin, Dublin, Ireland. Present address: Ludger Ltd, Culham Science Centre, Abingdon,Oxfordshire OX14 3EB., UK.     

VitaPad: visualization tools for the analysis of pathway data

MOTIVATION: Packages that support the creation of pathway diagrams are limited by their inability to be readily extended to new classes of pathway-related data. RESULTS: VitaPad is a cross-platform application that enables users to create and modify biological pathway diagrams and incorporate microarray data with them. It improves on existing software in the following areas: (i) It can create diagrams dynamically through graph layout algorithms. (ii) It is open-source and uses an open XML format to store data, allowing for easy extension or integration with other tools. (iii) It features a cutting-edge user interface with intuitive controls, high-resolution graphics and fully customizable appearance. AVAILABILITY: http://bioinformatics.med.yale.edu CONTACTS: matthew.holford@yale.edu; hongyu.zhao@yale.edu.     

Polarized-light sensitivity in rainbow trout (Oncorhynchus mykiss): characterization from multi-unit responses in the optic nerve

Integrated spike activity of axons from the optic nerve was measured in an investigation of the e-vector sensitive mechanism underlying the ability of rainbow trout (Oncorhynchus mykiss) for orientation in downwelling, linearly-polarized light. In anaesthetized, immobilized fish, one eye was exposed to incremental light flashes which were superimposed over closely controlled background conditions. Under scotopic and various photopic conditions, intensity/response curves were generated from the on-response of the optic nerve. Relative sensitivity curves were then obtained as a function of e-vector direction for the 5 kinds of receptor cells in this trout's retina: rods, ultraviolet cones (UV), short wavelength cones (S), medium wavelength cones (M), and long wavelength cones (L).Under scotopic conditions, no sensitivity to e-vector was apparent: thus, rods do not mediate polarization sensitivity. Under photopic conditions, parr weighing 8–10 g exhibited e-vector sensitivity in two orthogonal channels. A UV stimulus (380 nm) on a white background evoked a three-peaked response (0°, 90°, and 180°) to the e-vector orientations presented in 30° increments between 0° and 180°. In contrast, when the background was illuminated with appropriate short and long wavelength cut-off filters, M-and L-cones showed maximum responses only to the horizontal (90°) plane whether they were stimulated at their -absorption band or their -absorption band in the near UV. Isolated UV-cones gave maximum responses to the vertical (0° and 180°) e-vector, thus corresponding to a second channel. The blue sensitive, S-cones, did not show evidence of polarization sensitivity. As well, no evidence of the polarization sensitivity was observed under UV isolating background conditions in larger individuals, 50–78 g smolts, although the other cone mechanisms responded as in smaller individuals.     

Pharmacologic tools for assessment of adrenergic nerve activity in human hypertension

Measurement of plasma norepinephrine concentration (plasma NE) has not resolved the role of the adrenergic system in the pathogenesis or maintenance of hypertension. A better picture is gained if plasma NE measurement is combined with the assessment of sympathetic drive and reactivity by the use of specific sympathetic antagonists and agonists. In mild hypertension, the decrease in heart rate and cardiac output after beta-adrenoceptor blockade correlates with the level of plasma NE. In established hypertension, the fall in blood pressure or peripheral vascular resistance after alpha-adrenoceptor blockade is related to plasma NE levels. Similarly, changes in forearm vascular resistance induced by local alpha-adrenoceptor blockage correlates with plasma NE in hypertension. Cardiovascular responsiveness to adrenergic agonists is altered in hypertension. The response to cardiac beta-receptor stimulation decreases during the course of the disease. To the contrary, vascular responses to exogenous NE increase with the progression of the hypertensive disease. Results with total autonomic blockade indicate that in some patients with early or borderline hypertension, increased sympathetic tone is involved in the maintenance of blood pressure. In established hypertension, there is no definite indication of increased sympathetic tone, but the sympathetic nervous system may nevertheless play a prominent role in the maintenance of the blood pressure. A vascular hyperreactivity to adrenergic stimulation is characteristically associated with established hypertension. The nature of this hyperreactivity has not been fully elucidated, but it is very likely that it reflects structural vascular changes in hypertension.     

Computer tools for the analysis of schooling

Synopsis Quantification of fish school structure is difficult because of: (1) the large amount of positional data that must be recorded, (2) the fact that schools are moving, and (3) the fact that schools are threedimensional. Computer tools for addressing these problems include x,y digitizing devices interfaced to computers and interactive computer graphics systems. General computer algorithms now exist for 3-D reconstruction of schools given any two 2-D views such as photographs.Our computerized film analyzer, the Galatea system, is described in detail. This system allows for rapid, accurate input of multiple points which can be followed through each frame in a film sequence. Its software packages perform 3-D reconstructions, analyze undulatory motion, and do extensive statistical tests.     

A microcomputer program for analysis of nucleic acid hybridization data

The study of nucleic acid hybridization is facilitated by computer mediated fitting of theoretical models to experimental data. This paper describes a non-linear curve fitting program, using the `Patternsearch' algorithm, written in BASIC for the Apple II microcomputer. The advantages and disadvantages of using a microcomputer for local data processing are discussed.     

Neural conduction velocity of the human auditory nerve: bipolar recordings from the exposed intracranial portion of the eighth nerve during vestibular nerve section

We measured the conduction velocity of the intracranial portion of the auditory nerve in 3 patients undergoing vestibular nerve section to treat Ménière's disease. The conduction velocity varied from patient to patient, with an average value of 15.1 m/sec. The latency of peak III of the brain-stem auditory evoked potentials (BAEPs) increased by an average of 0.5 msec as a result of exposure of the eighth nerve, and if that increase is assumed to affect the entire length of the auditory nerve (2.6 cm) evenly, then the corrected estimate of conduction velocity would be 22.0 m/sec. Estimates of conduction velocity based on the interpeak latencies of peaks I and II of the BAEP, assuming that peak II is generated by the mid-portion of the intracranial segment of the auditory nerve, yielded similar values of conduction velocities (about 20 m/sec).