PROBFIND: a computer program for selecting oligonucleotide probes from peptide sequences.

Synthetic oligonucleotides have proven to be extremely useful probes for screening cDNA and genomic libraries. Selection of the appropriate probe can be more easily and accurately achieved with the use of the computer program PROBFIND. The user enters the amino acid sequence from a file or from the keyboard, selects the minimum length allowed for the probe and the maximum allowable degeneracy. The computer prints a list of the sequences of potential probes which meet these minimum specifications and the location of the corresponding sequence in the protein to the screen and to a file. The user may modify the specifications for length and degeneracy at any time during the output of data, which allows for rapid selection of the desired probe. The program is interactive, accepts any file format with only a single modification of the file, is written in BASIC, and requires less than 6 kbytes of memory. This makes the program easy to use and adaptable even to unsophisticated microcomputers.     

MicroMeasure: a new computer program for the collection and analysis of cytogenetic data.

The ability to identify individual chromosomes in cytological preparations is an essential component of many investigations. While several computer software applications have been used to facilitate such quantitative karyotype analysis, most of these programs are limited by design for specific types of analyses, or can be used only with specific hardware configurations. MicroMeasure is a new image analysis application that may be used to collect data for a wide variety of chromosomal parameters from electronically captured or scanned images. Unlike similar applications, MicroMeasure may be individually configured by the end user to suit a wide variety of research needs. This program can be used with most common personal computers, and requires no unusual or specific hardware. MicroMeasure is made available to the research community without cost by the Department of Biology at Colorado State University via the World Wide Web at http://www.biology.colostate.edu/MicroMeasure.     

A web-accessible computer program for calculating electrical potentials and ion activities at cell-membrane surfaces

Aims

Increasing evidence indicates that plant responses to ions (uptake/transport, inhibition, and alleviation of inhibition) are dependent upon ion activities at the outer surface of root-cell plasma membranes (PMs) rather than activities in the bulk-phase rooting medium.

Methods

A web-accessible computer program was written to calculate the electrical potential (ψ) at the outer surface of root-cell PMs (ψ _PM). From these values of ψ _PM, activities of ion I with charge Z ({I ^Z}) can be calculated for the outer surface of the PM ({I ^Z}_PM). In addition, ψ and {I ^Z} in the Donnan phase of the cell walls (ψ _CW and {I ^Z}_CW) can be calculated.

Results

By reanalysing published data, we illustrate how this computer program can assist in the investigation of plant-ion interactions. For example, we demonstrate that in saline solutions, both Ca deficiency and Na uptake are more closely related to {Ca²⁺}_PM and {Na⁺}_PM than to {Ca²⁺}_b and {Na⁺}_b (activities in the bulk-phase media). Additional examples are given for Zn and P nutrition, Ni toxicity, and arsenate uptake.

Conclusions

The computer program presented here should assist others to develop an electrostatic view of plant-ion interactions and to re-evaluate some commonly-held views regarding mechanisms of ion transport, toxicity, competition among ions, and other phenomena.     

HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules.

HYDRO is a program for the calculation of sedimentation and diffusion coefficients, rotational relaxation times, and intrinsic viscosities of rigid macromolecules of arbitrary shape that are represented by bead models. Actually, HYDRO contains various FORTRAN callable subroutines that can be linked to the user's own programs to account for variability of shape or flexibility. Some hints are given for the use of HYDRO in various situations.     

ADEPT: a computer program for prediction of protein antigenic determinants

ADEPT, a program that can be used for prediction of proteinantigenic determinants from the amino acid sequence alone forthe cases of humoral and cellular immune response, is described.Most methods presently utilized for this purpose are implementedin the program along with some original parameters for the caseof humoral immune response. There is also a possibility to combineseveral methods for the case of humoral immune response, whichprovides a means to create new predictive methods. ADEPT alsoincludes a literature-derived database of proteins in the SWISS-PROTstandard with experimentally determined antigenic determinants,so the predictive ability of new methods can be assessed withinthe program and corresponding statistical information is calculated.ADEPT may be useful for solving vamious tasks involving thedelineation of antigenic regions on proteins or characterizationof peptide fragments, arising, for examnple, in protein engineering(e.g. selection of protein portions most suitable for insertionof peptide sequences that are antigenically active or possessingother desired characteristics), and in particular for constructionof vaccines containing B- and/or T-cell epitopes, as well asfor other problems of medico-biological research.     

pH gradients generated by polyprotic buffers. I. Theory and computer simulation

This paper presents the general equations for computing pH, dissociation coefficients, buffering power and ionic strength of pure polyelectrolyte solutions (polyacids, polybases and zwitterionic species with any number of dissociable groups) and mixtures of any number of these species. A program has been written for simulating the behaviour of mixtures containing up to 50 species (including buffers and titrants), each of them with up to 10 dissociable groups. This allowed one to check the equations with the available data on a few oligoprotic species.     

DSLINK: a computer program for gene-centromere linkage analysis in families with a trisomic offspring.

Trisomic individuals provide information for gene-centromere mapping, since two of the four chromatids in a meiotic tetrad can be recovered. When centromeric markers are available, linkage analysis between the centromere and any marker locus can be performed in nuclear families having one or more trisomic offspring. Since conventional linkage programs consider only disomic individuals, we have written a FORTRAN computer program, DSLINK, that performs gene-centromere linkage analysis on the basis of information on trisomic and disomic offspring. This program makes it possible to study the relationship between recombination and chromosome segregation.     

incor: a computer program for testing differences among independent correlations

An interactive fortran program (incor) performs the Paul (1989) procedure for testing the null hypothesis that more than two independent population correlations are equivalent. The program also performs subsequent range tests for comparing all possible pairwise correlations.     

EXCAVATOR: a computer program for efficiently mining gene expression data

Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship among genes in a biological process. We have developed a computer package EXCAVATOR for clustering gene expression profiles based on our new framework for representing gene expression data as a minimum spanning tree. EXCAVATOR uses a number of rigorous and efficient clustering algorithms. This program has a number of unique features, including capabilities for: (i) data- constrained clustering; (ii) identification of genes with similar expression profiles to pre-specified seed genes; (iii) cluster identification from a noisy background; (iv) computational comparison between different clustering results of the same data set. EXCAVATOR can be run from a Unix/Linux/DOS shell, from a Java interface or from a Web server. The clustering results can be visualized as colored figures and 2-dimensional plots. Moreover, EXCAVATOR provides a wide range of options for data formats, distance measures, objective functions, clustering algorithms, methods to choose number of clusters, etc. The effectiveness of EXCAVATOR has been demonstrated on several experimental data sets. Its performance compares favorably against the popular K-means clustering method in terms of clustering quality and computing time.     

Effect of phosphate and ammonium ion concentrations on solvent production in defined medium byClostridium acetobutylicum

Summary Experiments have been performed in batch fermentation, using a defined medium, to investigate the effects of phosphate and ammonium ion concentrations on solvent production usingClostridium acetobutylicum. Solvent production occurred under conditions of either ammonium- or phosphate-limitation, but the optimum conditions were observed to be where both of these nutrients were slightly in excess of growth requirements. A greater excess of nutrients caused the fermentation to be acidogenic rather than solventogenic.     

Oligo Design: a computer program for development of probes for oligonucleotide microarrays

Oligonucleotide microarrays have demonstrated potential for the analysis of gene expression, genotyping, and mutational analysis. Our work focuses primarily on the detection and identification of bacteria based on known short sequences of DNA. Oligo Design, the software described here, automates several design aspects that enable the improved selection of oligonucleotides for use with microarrays for these applications. Two major features of the program are: (i) a tiling algorithm for the design of short overlapping temperature-matched oligonucleotides of variable length, which are useful for the analysis of single nucleotide polymorphisms and (ii) a set of tools for the analysis of multiple alignments of gene families and related short DNA sequences, which allow for the identification of conserved DNA sequences for PCR primer selection and variable DNA sequences for the selection of unique probes for identification. Note that the program does not address the full genome perspective but, instead, is focused on the genetic analysis of short segments of DNA. The program is Internet-enabled and includes a built-in browser and the automated ability to download sequences from GenBank by specifying the GI number. The program also includes several utilities, including audio recital of a DNA sequence (useful for verifying sequences against a written document), a random sequence generator that provides insight into the relationship between melting temperature and GC content, and a PCR calculator.     

Preparation of metal ion buffers for biological experimentation: a methods approach with emphasis on iron and zinc

Transition metal ions are a challenge to study in physiology because of problems associated with solubility, oxidation, binding, and attaining appropriate free activities in solution. This review discusses these problems and potential ways of accommodating them. Special attention is given to iron and zinc ions, but many of the concepts can be applied for studying other transition metals. Selection of reagents appropriate for metal work (including water, salts, noncomplexing pH buffers) is briefly discussed. Calculation of the solubility product (K(sp)) for common iron and zinc precipitates is covered, as well as techniques used to solubilize Fe(3+) with organic chelates. Factors that affect Fe(2+) oxidation are mentioned, and the use of ascorbate as a reducing agent is considered. Measurement of the rate of Fe(2+) oxidation (or Fe(3+) reduction) with the Fe(2+) chromophores ferrozine and BPS is also discussed. Generation of a free metal ion activity through use of metal buffers (chelators) is discussed. Theoretical problems associated with this technique are explored, and selected shareware metal ion buffer calculators are described. Finally, techniques for measuring and minimizing nonspecific binding of iron and zinc ions to biological membranes are considered.     

Intracellular and luminal ion concentrations in sea turtle salt glands determined by x-ray microanalysis

Summary The lachrymal salt glands of hatchlings of the green sea turtle (Chelonia mydas) secrete a hyperosmotic (up to 2000 mosmol·kg^–1) NaCl solution. X-ray microanalysis of frozen-hydrated glands showed that during secretion intracellular Na⁺ concentration in the principal cells increased from 13 to 34 mmol·l^–1 of cell water, whilst Cl^– and K⁺ concentrations remained unchanged at 81 mmol·l^–1 and 160–174 mmol·l^–1, respectively. The high Cl^– concentration and the change in Na⁺ concentration are consistent with the prevailing paradigm for secretion by the structurally and functionally similar elasmobranch rectal gland. Concentrations of Na⁺, Cl^– and K⁺ in the lumina of secretory tubules of secreting (Na⁺ 122, Cl^– 167, K⁺ 38 mmol·l^–1) and non-secreting (Na⁺ 114, Cl^–1 174, K⁺ 44 mmol·l^–1) glands were similar and the fluid was calculated to be approximately isosmotic with blood. In the central canals Na⁺ and Cl^– concentrations were similar but K⁺ concentration was lower (11–15 mmol·l^–1). It is concluded that either a high transepithelial NaCl gradient in secretory tubules and central canals is very rapidly dissipated during the short time between gland excision and freezing, or that ductal modification of an initial isosmotic secretion occurs.     

A computer program for automatic recording and processing of renograms.

A program is described, which performs automatic uptake, plotting and processing of radio-hippuran renograms obtained from a gamma camera, using an on-line minicomputer system. The program is written in machine language for a ND 50/50 system equipped with a PDP8-L processor, but translation for other nuclear medicine EDP system is easy. Minimum configuration requirements are: (i) 4K processor with TTY; (ii) external clock; (iii) magnetic tape transport; and (iv) 4K + 4K buffered camera interface or additional 8K of storage plus camera interface. Camera interface is computer-controlled and includes two AD-converters, a display unit for buffer storage and interest-areas selection facility. Operation starts recording 40 scintiphotographs of 30 sec each. Then, kidney uptake curves are obtained by subtraction of blood and tissue background, and diagnostic parameters, such as the initial slope, the maximum uptake point and 50% activity time, are computed. The only manual intervention required is the computer-assisted selection of interest-areas of kidneys, and blood and tissue background. Time required is 20 min for uptake of renograms and 5 min for processing and output, thus allowing routine execution of good quality renography, including hardcopy printout of both kidney uptake curves and diagnostic paramerers.     

A computer program for long term anticoagulation control.

A computer program is described which calculates suggested daily anticoagulant dose schedules for long term patients. This program is a part of the real-time Information System for Thrombosis Centres. The program requires only the most recent information on the patient from the Information System's data base. This information consists of the latest two measured coagulation times, the previous dose schedule, the target and limiting values set by the physician to the coagulation time, and a very limited number of parameters accounting for the patient's anticoagulation history. A simple dose-response model is used to simulate and predict a coagulation time. By comparing this prediction with the measured coagulation time the program computes the necessary adjustment in the average dose and the appointment period. It gives remarks, if necessary. The Information System is used successfully for the majority of patients of Leiden Thrombosis Centre, where it operates as a part of a real-time Hospital Information System.