Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA.

A novel procedure for efficient computation of three-dimensional protein structures from nuclear magnetic resonance (n.m.r.) data in solution is described, which is based on using the program DIANA in combination with the supporting programs CALIBA, HABAS and GLOMSA. The first part of this paper describes the new programs DIANA. CALIBA and GLOMSA. DIANA is a new, fully vectorized implementation of the variable target function algorithm for the computation of protein structures from n.m.r. data. Its main advantages, when compared to previously available programs using the variable target function algorithm, are a significant reduction of the computation time, and a novel treatment of experimental distance constraints involving diastereotopic groups of hydrogen atoms that were not individually assigned. CALIBA converts the measured nuclear Overhauser effects into upper distance limits and thus prepares the input for the previously described program HABAS and for DIANA. GLOMSA is used for obtaining individual assignments for pairs of diastereotopic substituents by comparison of the experimental constraints with preliminary results of the structure calculations. With its general outlay, the presently used combination of the four programs is particularly user-friendly. In the second part of the paper, initial results are presented on the influence of the novel DIANA treatment of diastereotopic protons on the quality of the structures obtained, and a systematic study of the central processing unit times needed for the same protein structure calculation on a range of different, commonly available computers is described.     

Further procedures for sequence analysis by computer

A previous paper¹ described programs for sequence data handling and analysis by computer. The facilities of this basic set are extended by further easily used programs.     

Current methods of gene prediction,their strengths and weaknesses

While the genomes of many organisms have been sequenced over the last few years, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed that try to address one part of this problem, which consists of locating the genes along a genome. This paper reviews the existing approaches to predicting genes in eukaryotic genomes and underlines their intrinsic advantages and limitations. The main mathematical models and computational algorithms adopted are also briefly described and the resulting software classified according to both the method and the type of evidence used. Finally, the several difficulties and pitfalls encountered by the programs are detailed, showing that improvements are needed and that new directions must be considered.     

mRNA-FAST (mRNA-Function, Activity, STructure) computer system]

Computer system mRNA-FAST (mRNA--Function, Activity, STructure; http://wwwmgs.bionet.nsc.ru/mgs/dbases/trsig/) is described. The system has been developed to analyze nucleotide sequences of mRNA and to measure their essential properties. The system compiles the data base on translation signals including nucleotide sequences of the regulatory regions with structural and experimental information on their specific activities. It also contains programs to search for local homology between mRNA and translation signals, to search for potential signals basing on analysis of the oligonucleotide dictionaries, and to model secondary RNA structure. Possible applications of the system mRNA-FAST are discussed.     

Newborn screening for Pompe disease: an update, 2011

There is mounting evidence in support of universal newborn screening for Pompe disease. Early treatment of children with infantile Pompe disease, prior to clinical diagnosis, is clearly of benefit in prolonging survival and improving cardiac and motor function. Several testing methods applicable to newborn screening using dried blood spots have been described and several are currently being tested in pilot screening programs. Although challenges remain, particularly in identification of the best strategy for follow-up and management of later onset Pompe disease, these challenges can surely be overcome as they have been with other disorders added to the newborn screening panel. It is anticipated that the results of the several pilot programs currently ongoing or in the planning stages in the United States will provide the data necessary to recommend universal newborn screening for Pompe disease for all infants.     

Observations on programs to estimate the parameters of enzyme kinetics

This paper gives a critical account of the two major programs so far published specifically to estimate the parameters of enzyme kinetics. The dangers of submitting data to the programs without proper checks are discussed, and a screening test is described to identifty sets of data which may not be best fitted by a rectangular hyperbola.     

Computer System mRNA-FAST (mRNA Function,Activity, STructure)

Computer system mRNA-FAST (mRNA Function, Activity, STructure; http://wwwmgs.bionet.nsc.ru/mgs/dbases/trsig/) is described. The system has been developed to analyze nucleotide sequences of mRNA and to measure their essential properties. The system compiles the data base on translation signals including nucleotide sequences of the regulatory regions with structural and experimental information on their specific activities. It also contains programs to search for local homology between mRNA and translation signals, to search for potential signals basing on analysis of the oligonucleotide dictionaries, and to model secondary RNA structure. Possible applications of the system mRNA-FAST are discussed.     

Computer programs for the assembly of DNA sequences.

A collection of user-interactive computer programs is described which aid in the assembly of DNA sequences. This is achieved by searching for the positions of overlapping common nucleotide sequences within the blocks of sequence obtained as primary data. Such overlapping segments are then melded into one continuous string of nucleotides. Strategies for determining the accuracy of the sequence being analyzed and reducing the error rate resulting from the manual manipulation of sequence data are discussed. Sequences mapping from 97.3 to 100% of the Ad2 virus genome were used to demonstrate the performance of these programs.     

Computer programs for the analysis and the management of DNA sequences.

A program package is described for the management and the analysis of DNA sequence data. The programs - with the exception of a few Fortran routines - are written in the programming language APL. They are best used interactively although batch processing is possible. The package has been in constant use for about 3 years and contains programs for most of the routine problems presently found in a DNA sequencing laboratory.     

A computer-assisted cell identification system

A computer and optical microscope image processing system for the acquisition, editing and analysis of quantitative, multivariate, cell nuclear data is described. The experimental equipment and methods are discussed, the mathematics used are presented, and the additions, modifications and deletions to the TICAS 11/45 set of computer programs for the analysis of the data are outlined.     

Computer programs to assist in high resolution thermal denaturation and circular dichroism studies on nucleic acids

Computer programs are described that direct the collection, processing, and graphical display of numerical data obtained from high resolution thermal denaturation (1-3) and circular dichroism (4) studies. Besides these specific applications, the programs may also be useful, either directly or as programming models, in other types of spectrophotometric studies employing computers, programming languages, or instruments similar to those described here (see Materials and Methods).     

Statistical analysis and graphical display of multivariate data on the Macintosh

Two Macintosh programs written for multivariate data analysisand multivariate data graphical display are presented. MacMulincludes principal component analysis (PCA), correspondenceanalysis (CA) and multiple correspondence analysis (MCA), witha complete, original and unified set of numerical aids to interpretation.GraphMu is designed for drawing collections of elementary graphics(curves, maps, graphical models) thus allowing comparisons betweenvariables, individuals, and principal axes planes of multivariatemethods. Both programs are self-documented applications andmake full use of the user-oriented graphical interface of theMacintosh to simplify the process of analysing data sets. Anexample is described to show the results obtained on a smallecological data set. Received on January 24, 1989; accepted on July 17, 1989     

Some practical aspects of computer applications in a fermentor hall

The use of computers in a fermentation pilot plant is described from a practical point of view. The aim is not the application of a computer to a single special process but a general application of computers to prepare and present data for the following analysis of fermentation processes. The hardware is normally bought from computer manufacturers, but some additional installations are useful. Application software has to be developed by the biotechnologist, therefore the software structure is the most important part of the computer application. Data storage is divided into three parts: short-time memory, long-time storage, and a medium memory mainly to be used in process analyses and process control. Four types of programs are used: main schedule tasks, low-priority on-line tasks, sense-switch routine, and different off-line programs. A table of all programs is presented, the main schedule task is described in detail to demonstrate the software structure.     

Family physician anesthetists: continuing education,observations, evaluation

A method is described whereby continuing education for family practitioner anesthetists is taken to community hospitals, where patterns of practice, local problems and facilities are different from those of larger urban areas. Five Ontario communities were visited for 4½ days each, by invitation, providing the visiting clinician with an opportunity to observe the quality of anesthesia services and to measure, through a self-evaluation test, the deficiencies in applied basic and clinical knowledge thought to be necessary for modern, safe practice. These programs were well received and thought to be of real benefit to the participants. Similar programs could be provided in general medicine, cardiology, gastroenterology, pediatrics and psychiatry.     

Melding ecology,classical weed biocontrol,and plant microbial ecology can inform improved practices in controlling invasive plant species

Early research leading to the successful biological control of invasive species such as Opuntia spp., and Hypericum perforatum set examples and provided data useful for research programs that would follow. However, this early work failed to become established as a source of applicable principles for later workers in weed biocontrol. Recently, retrospective and parallel studies have been suggested as a means to reengage with earlier work to derive useful ideas and data to enhance future programs in weed biocontrol. Parallel studies by workers in plant community ecology on the nature of feedback elicited by plant species in their invaded and native range have shown the importance of soil microbial communities in effecting feedback. Retrospective reexamination of previous studies would likely provide clues to other insect–plant pathogen interactions in addition to those described by the author and others. The effects of invasive species in profoundly altering soil microbial communities point to the need for further studies on key microbial species contributing to or driving the impact of biocontrol. These collective data suggest that the desired goal of selecting for and utilizing stronger biocontrol agents to reduce nontarget effects and to increase the impact of biological control programs would be best served by prerelease studies that assess the propensity of a candidate agent for direct or indirect interaction with other agents. This could be assessed through the use of survival analysis. Overall, parallel empirical and retrospective studies should be a necessary part of how biological control is practiced.     

Microcomputer programs for DNA sequence analysis.

Computer programs are described which allow (a) analysis of DNA sequences to be performed on a laboratory microcomputer or (b) transfer of DNA sequences between a laboratory microcomputer and another computer system, such as a DNA library. The sequence analysis programs are interactive, do not require prior experience with computers and in many other respects resemble programs which have been written for larger computer systems (1-7). The user enters sequence data into a text file, accesses this file with the programs, and is then able to (a) search for restriction enzyme sites or other specified sequences, (b) translate in one or more reading frames in one or both directions in order to find open reading frames, or (c) determine codon usage in the sequence in one or more given reading frames. The results are given in table format and a restriction map is generated. The modem program permits collection of large amounts of data from a sequence library into a permanent file on the microcomputer disc system, or transfer of laboratory data in the reverse direction to a remote computer system.     

A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11.

A computer package written in Fortran-IV for the PDP-11 minicomputer is described. The package's novel features are: software for voice-entry of sequence data; a less memory intensive algorithm for optimal sequence alignment; and programs that fit statistical models to nucleic acid and protein sequences.     

Collection and analysis of kinetic data from a stopped-flow spectrophotometer using a microcomputer

A method of interfacing an inexpensive microcomputer to a stopped-flow kinetics spectrophotometer is described. It allows software-selectable sampling frequencies between 0.1 ms and 8 s and large numbers of data points to be collected. Machine language routines to use the interface are described and these allow the sampling frequency to be altered during data collection to ensure adequate numbers of points in critical regions of the kinetic profile. BASIC programs for collection and analysis of multicomponent kinetic data using this system are also described. Due to the large number of data points that can be collected and the ability to selectively sample transmittance values in regions where the signal is rapidly changing with time, relatively unsophisticated methods of data analysis can be used. These methods are suitable for use by microcomputers and mean that data analysis and acquisition can be performed on the same microcomputer in real time. To illustrate this, multicomponent analysis of kinetic transients is performed on simulated data and on the dissociation kinetics of the ethidium-DNA complex.     

A program package applicable to the detection of overlaps between restriction maps.

A computer program package for the storage, change, and comparison of restriction maps is described. The programs are intended to detect overlaps between relatively short (about 10-40 kb; abbreviations ref.2) maps and to merge the overlapping fragments into large restriction maps. They run on a 16-bit-microcomputer with limited memory and addressing capability. Due to the restricted reliability of restriction maps compared with DNA sequence data a particular storage method was used. The source code of the programs is freely available (+).