Computer monitoring, capture and analysis of gas/liquid chromatograph traces

The work described here is effectively the computerization ofa gas/liquid chromatograph of the pen recorder type using aBBC microcomputer. The output from the g. l. c. can be capturedby the computer in accordance with a series of parameters. Thesampling rate can be altered, as can an averaging facility toreduce noise, and a threshold level to eliminate the storageof irrelevent and space-consuming data. The unprocessed readingsare initially stored on the computer's floppy disk, then laterretrieved and cut into smaller sections to allow maximum resolutionfor on-screen analysis. In the main analysis stage of the systemall processing is shown graphically on the computer monitorat all stages. The principal steps in analysis involve the mathematicalmodelling and elimination of the solvent peak, the fixing ofthe retention time for each subsequent peak and its disentanglingfrom any following peaks, and finally the calculation of thearea under each individual peak. Several alternative methodsare made available for disentangling peaks, which can be triedsuccessively on a single peak then each printed out with commentsfor comparison later. All readings and results in table formand screen dumps of all trace images are available via a dotmatrix printer. Received on October 29, 1985; accepted on June 27, 1986     

Generating precise mechanical stimuli and recording chordotonal organ discharge patterns using a microcomputer

A computer-controlled system for the investigation of the responseproperties of the tibio-femoral chordotonal organ in the locustis described. The computer is used to generate small amplitudesinusoidal movements of the tibia via a small servo-controlledmotor. The resulting response recorded via a suction electrodeis simultaneously detected, processed and stored on disk. Fullconstructional details for all hardware required are given.The software, developed for a BBC microcomputer, in additionto controlling all the hardware, has graphics and analysis routinesenabling the operator to display and manipulate the stored data.     

Programming for the DNA analysis of FCM data on an IBM microcomputer

The analysis of data generated on a flow cytometer (FCM) is often performed on a computer obtained especially for dedicated use with the flow cytometer. This computer component can be expensive and also presents the FCM user with the added burden of mastering specialized programming language or of accepting the secret analytical processes of protected proprietary program routines. We believe that the evolution of more accurate and efficient FCM analyses that have the power to consider complex signal distributions can be assisted by the availability of analysis programs written in languages common to many users. DNA analysis routines written for a relatively inexpensive microcomputer (IBM PC/XT) in Basic and Pascal are described here. The routines can automatically process multiple FCM data files and can provide high-resolution graphic hardcopy. A foreground/background utilization is also described that allows the computer to be available for other uses in the laboratory.     

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.     

Microcomputer monitor and blood sampler for free-diving Weddell seals

The equipment used for the first sampling of arterial blood at depth on free-diving Weddell seals Leptonychotes weddelli is described. Blood was withdrawn through an aortic catheter by a submersible, peristaltic roller pump and stored in a single- or multiple-sample collection device. The multiple sampler allowed up to eight individual blood samples to be collected during a single dive. The blood pump was controlled by a dedicated microcomputer that allowed initiation of blood sampling at flexible combinations of depth and/or time during either the descending or ascending phase of the dive. The dedicated microcomputer also recorded swimming depth, velocity, heart rate, and body temperature at selectable time intervals. These data were transmitted to a laboratory computer, and blood samples were retrieved, when the seal surfaced to breathe.     

Practical applications in molecular biology of sensitive fluorescence detection by a laser-excited fluorescence image analyzer.

A new kind of fluorescence image analyzer was developed for a variety of uses, especially in molecular biology. Compounds labeled with fluorescent groups on a gel or nitrocellulose membrane are excited with 532 nm of light from a green laser. The fluorescence emitted passes through light-collecting fibers to a photomultiplier. Imaging data converted from the emitted light are analyzed by a microcomputer and stored on a magnetic optical disk. Dideoxy DNA sequencing was done with the same amount of DNA used for autoradiography, and the sequencing ladders obtained from gel scanning were automatically converted to sequence data by the analyzer. When an agarose gel was analyzed after electrophoresis, DNA stained with ethidium bromide was detected by the analyzer with higher sensitivity rather than by the conventional photographic method. Nylon and nitrocellulose membranes could be read by the analyzer, so blot hybridization experiments can be done without radioisotopes. High-quality computer storage of the imaging data from gel electrophoresis and hybridized membranes, including pulsed-field gels, make it possible to quantify image intensity and to construct many kinds of databases.     

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.     

Principles and Perspectives for Educational Biology

Computer-aided learning (CAL) techniques are now used at many levels of biological education. Many of these CAL programs are written by teachers because suitable material is unavailable. However, the amount of time required for the design and coding of a reliable CAL program can deter many teachers. Any CAL program can be split into two components: the ‘non-educational’ part, for example, program control structures, input–output routines; and the educational material. The ‘non-educational’ component can be organized into a program shell which can then be used with a wide range of biological topics. A program shell, for use on the BBC microcomputer, is described with an example of an application. The example is ‘LINKAGE’, a genetics teaching program.     

A microcomputer program for establishing and maintaining a database for laboratory culture collections

A computer program that facilitates the creation of a culture collection database has been written for a microcomputer (Apple He with a Z-80 card) using dBASE II® (Ashton-Tate). The Culture Collection Program accommodates up to 250 individual strain records on one 5 1/4" floppy disk. For each strain, information that can be stored includes the name of the micro-organism, culture collection number, antibiotic resistance markers, plasmids, genetic markers, references, growth medium, growth temperature and additional comments. The last date of subculturing can be ascertained and information about the status of the preserved cultures can also be noted. With a menu-driven format which requires no computer programming expertise, the user can readily create new entries, update old ones and search the database for strains with certain common properties.     

生物数据标准化研究进展

随着生物测序技术的快速发展,积累了海量的生物数据。生物数据资源作为生物分析研究及应用的核心和源头,为保证数据的正确性、可用性和安全性,对生物数据资源进行标准化的管理非常重要和迫切。本文综述了目前国内外生物数据标准化研制进展,目前国内外对生物数据缺少一个总体的规划,生物数据语义存在大量的不兼容性,数据格式多种多样,在生物数据收集、处理、存储和共享等方面缺乏统一的标准。国内外生物数据标准化处于起步阶段,但各国生物专家都在努力进行标准研制工作。文章最后从生物数据术语、生物数据资源收集、处理和交换、存储、生物数据库建设和生物数据伦理规范等方面出发,对标准研制工作进行一一探讨,期望能为生物数据标准制定提供一定的参考和依据。     

Visualization of multidimensional spectra in flow cytometry.

Flow data from a cell sorter have been processed by hardwired circuits which include amplification, discrimination, coincidence requirements, peak sensing and holding, A-D conversion, and a computerized pulse height analysis with storage of the spectra obtained. Two dimensional spectra can be stored directly in memory, on tape and disk. Three and four parametric cellular events can be recorded on line during the flow measurement in a sequential mode on tape for subsequent recall. Simple processing of these data can be performed for displaying of two dimensional projections from these multidimensional spaces based on threshold conditions for the remaining parameters. Interfaced transmission of the stored data to a large scale computer enables more sophisticated data analysis. Data reduction by means of a multidimensional probability analysis has been carried out in order to transfer the spectra to a computerized picture system for display. This system creates perspective two-dimensional images from a three-dimensional data space. Frequency can be converted into grey levels. Hard copy in color (color as the third dimension and color intensity as frequency) simplifies the visualization of multiparametric flow data sets.     

A low-cost system for computerized rodent weight logging with statistical analysis

A system comprising a suite of 4 computer programs has been developed for on-line rodent weight data collection and statistical analysis using an IBM personal computer. Data can be collected from up to 3 separate trials simultaneously, and can be stored for later statistical analysis. Mettler balances were used for the animal weighing. A Mettler current loop adapter and a multiplexer were used to interface the balances with the computer.     

Progressive degradation of serum samples limits proteomic biomarker discovery

Preanalytical variables play a key role in discovery of biomarkers. Although the effect of several preanalytical variables on the mass spectral profiles has been studied extensively, little is known about long-term storage of serum samples. This is important because samples used in case-control or epidemiological studies are usually stored for a long time before analysis. Here we evaluated long-term storage effects on mass spectral peak patterns of serum peptides extracted using weak cation exchange magnetic beads. For this, 20 serum samples stored at −80 °C were divided equally into two groups based on their storage time. We found that intensities of 26 mass spectral peaks significantly varied between these two groups. Intensities of these peaks significantly correlated with storage time. Genetic algorithm-based models generated using these 26 peaks could classify 63 additional samples into these two groups with 100% and 96% accuracy, respectively. We also show that storing samples for 10 months at −80 and −20 °C results in the appearance/disappearance or intensity variation of peaks, some of which were previously reported as disease biomarkers.     

Paper-based archiving of mammalian and plant samples for RNA analysis

The ability to archive biological samples for subsequent nucleic acid analysis is essential for tissue specimens and forensic samples. FTA Card is a chemically treated filter paper designed for the collection and room temperature storage of biological samples for subsequent DNA analysis. Its usefulness for the preservation of biological samples for subsequent RNA analysis was tested. Here, we demonstrate that RNA in biological samples stored on FTA Cards is stable and can be used successfully for RT-PCR and northern blot analysis. RNA stability depends on the storage temperature and the type of biological specimen. RNA in mammalian cells stored on FTA Cards is stable for over one year at temperatures at or below -20 degrees C and for two to three months in samples stored at room temperature. For plant leaf, longer storage times (> 5 days) require temperatures at or below -70 degrees C following sample application. FTA Cards may constitute a method not only for convenient collection and storage of biological samples but also for rapid RT-PCR analysis of tissue and cell samples.     

An off-line system for in-time analysis of cardiac catheterization data and for establishment of a cardiological database for retrospective studies.

The system described may be divided in two major parts: (i) automatic analysis of cardiac catheterization data running off-line on a Siemens 305 computer; (ii) storage and retrieval of the results from these analyses and additional data from related departments (thoracic surgery, internal medicine and clinical physiology) in a cardiological database on an IBM 370/155 computer. The first part is described with special regard to (i) operation and control during the phases of data collection, pre-processing, processing and storage of results; (ii) the presentation of the results in a complete and readable form and (iii) the modular design of the software. The results of an evaluation of the computer methods versus manual methods are also presented. The second part has been described with regard to the type of data entered in the cardiological database. The structure of the database and the programs used for storage and retrieval have not been described in detail in the present publication.     

EEG data acquisition and preprocessing by microcomputer satellite system

Recent development in computer technology allows already medium scale EEG data processing to be performed within the clinical neurophysiology department, if a fast minicomputer with adequate mass storage and graphical output facilities is used. Data acquisition, however, should be delegated to a microcomputer which also should take over as much preprocessing as possible. A system is presented, where one or several microcomputer-based satellite units perform analog-digital conversion, Fourier transformation (FFT), calculation of power spectra and crossproducts, as well as event related averaging or other preprocessing procedures. The units are connected to a fast central minicomputer, where a supervisor program loads the microprocessors with their programs, supervises their activity, receives preprocessed data and activates appropriate postprocessing programs to produce the final results.     

Matrix algebra routines for the Acorn Archimedes microcomputer: example applications

A set of matrix algebra routines have been written, as BASICVprocedures, for the Acorn Archimedes microcomputer. It is shownthat these procedures are executed so quickly that programs,which require matrix algebra computations, can be written ininterpreted BASIC. Two example applications, reciprocal averagingand principal components analysis, are demonstrated. Received on January 19, 1988; accepted on February 9, 1988     

Extension of lymphocyte viability for radiation biodosimetry: Potential implications for radiological/nuclear mass casualty incidents

Dicentric chromosome assay (DCA) is routinely used for estimating the absorbed radiation dose in exposed humans. Optimal lymphocyte viability is crucial for reliable dose estimation and most cytogenetic laboratories prefer the receipt of blood samples within 24 to 36 hours after collection. Delays in the shipment/receipt of samples can occur sometimes under certain unforeseen circumstances: (1) Adverse weather conditions, (2) distant location of blood collection sites, and (3) shipping and handling of a large number of samples after radiological/nuclear mass casualty incident(s). To circumvent some of these limitations, we evaluated the suitability of ex vivo irradiated blood samples stored in the presence of phytohemagglutinin (PHA) for 7 days at ambient temperature (22-24°C) for radiation biodosimetry. Blood samples stored in the presence of PHA for up to 7 days showed a higher mitotic index than blood samples stored without PHA. To verify the use of stored blood samples for DCA, frequencies of X-rays induced dicentric chromosomes were analyzed in the blood samples that were cultured either 24 hours after exposure or 7 days later after storage. Our results indicate that storage of ex vivo irradiated blood samples in the presence of PHA at ambient temperature was found optimal for DCA and that the radiation doses estimated by dicentric chromosome frequencies were grossly similar between the fresh and stored blood samples. Our study suggests that reliable and accurate biodosimetry results can be obtained for triage using blood samples stored for up to a week at ambient temperature in the presence of PHA.     

Electronic imaging system for direct and rapid quantitation of fluorescence from electrophoretic gels: application to ethidium bromide-stained DNA

We have built an electronic imaging system based on a modified charge-coupled-device television camera that directly quantitates the distribution of fluorescence from electrophoretic gels, chromatograms, and other stationary sources. Exposure times can exceed 1 min. Unlike the photographic system that it replaces, the response of the camera is directly proportional to the intensity of incident fluorescence, and image data are digitized and stored in computer memory ready for analysis immediately upon completion of an exposure. We describe procedures for the display, normalization, and archival storage of image data and programs that use images of ethidium bromide-stained DNA in alkaline agarose gels to quantitate single-strand breaks in DNA.