Realtime acquisition, storage, and display of correlated three-parameter flow cytometric data

A microprocessor-based system which performs realtime correlated acquisition, storage and display of multiparameter (3-parameter) data from a flow cytometer (FACS-III) is presented. List-mode techniques are not employed. The 3-parameter data is collected and correlated, then displayed along with cell-frequency as a realtime 3-parameter colour scattergram, while the experiment is in progress; in addition, correlated and uncorrelated higher-resolution projections of the 3-parameter data are collected and stored. The data projections may also be displayed: as 1-parameter histograms, or as 2-parameter colour or grey-scale scattergrams. Examples of 2- and 3-parameter colour scattergrams are presented. The speed and some characteristics of the realtime acquisition and display software are examined; methods to increase the realtime speed are discussed.     

Analysis of extracellular potentials using an IBM PC

1. A system has been developed for using IBM PC-compatible computers in combination with a Grafitek Data Logging Interface to record spike trains on magentic discs for later analysis. 2. The times and amplitudes of spikes detected on two input channels are recorded, together with a third channel containing information on computer-generated stimuli and keyboard-activated event markers. In excess of 50,000 spikes can be recorded with a computer having 640 k of Random Access Memory. 3. The recorded spike trains can be reconstructed on the computer monitor and keyboard-controlled window discriminators can be used to select the spikes for analysis by amplitude. 4. The same recorded data can be analysed to produce displays of spike count against time, amplitude histograms, inter-spike interval histograms, peri-stimulus time histograms(PSTH), raster displays and auto- and cross-correlations between activity on the two channels. Each spike is identified by number, allowing easy location of the start and finish of the section of data to be analysed, and the PSTH, raster and correlation analyses allow pretriggering to investigate event occurring before stimulation. 5. The axes of the displays histograms can be adjusted to produce optimum displays, and hard copy can be produced on dot matrix printers or digital plotters. 6. Quantitative analysis enables comparison between different recordings and treatments.     

PIKfyve, a mammalian ortholog of yeast Fab1p lipid kinase, synthesizes 5-phosphoinositides. Effect of insulin.

One or more free hydroxyls of the phosphatidylinositol (PtdIns) head group undergo enzymatic phosphorylation, yielding phosphoinositides (PIs) with key functions in eukaryotic cellular regulation. Two such species, PtdIns 5-P and PtdIns 3,5-P(2), have now been identified in mammalian cells, but their biosynthesis remains unclear. We have isolated a novel mammalian PI kinase, p235, whose exact substrate specificity remained to be determined (Shisheva, A., Sbrissa, D., and Ikonomov, O. (1999) Mol. Cell. Biol. 19, 623-634). Here we report that recombinant p235 expressed in COS cells, like the authentic p235 in adipocytes, displays striking specificity for PtdIns over PI substrates and generates two products identified as PtdIns 5-P and PtdIns 3,5-P(2) by HPLC analyses. Synthetic PtdIns 3-P substrates were also converted to PtdIns 3,5-P(2) but to a substantially lesser extent than PtdIns isolated from natural sources. Important properties of the p235 PI 5-kinase include high sensitivity to nonionic detergents and relative resistance to wortmannin and adenosine. By analyzing deletion mutants in a heterologous cell system, we determined that in addition to the predicted catalytic domain other regions of the molecule are critical for the p235 enzymatic activity. HPLC resolution of monophosphoinositide products, generated by p235 immune complexes derived from lysates of 3T3-L1 adipocytes acutely stimulated with insulin, revealed essentially the same PtdIns 5-P levels as the corresponding p235 immune complexes of resting cells. However, the acute insulin action resulted in an increase of a wortmannin-sensitive PtdIns 3-P peak, suggestive of a plausible recruitment of wortmannin-sensitive PI 3-kinase(s) to p235. In conclusion, mouse p235 (renamed here PIKfyve) displays a strong in vitro activity for PtdIns 5-P and PtdIns 3,5-P(2) generation, implying PIKfyve has a key role in their biosynthesis.     

ePlant and the 3D data display initiative: integrative systems biology on the world wide web

Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org).     

SequenceEditingAligner: a multiple sequence editor and aligner

Here we present the SequenceEditingAligner system for editing multiple, aligned genetic sequences. This is an interactive multi-window color system that displays more than 3500 nucleotides or amino acids. The system handles nucleic acid or protein sequences with or without secondary structure data. More than 300 sequences, each more than 1500 elements in length, may be analyzed together. With the system scientists can classify elements, align sequences, edit them, find consensus patterns, and simultaneously generate oligomer frequency histograms and other statistics.     

A Study of the Biological Preferences of Secondary School Pupils in Israel

An interactive computer simulation was designed as an aid to those teaching evolutionary theory. The simulation was inspired by (tie example of industrial melanism in the peppered moth. A BBC microcomputer is used to present a variegated display overlaid with moth shapes, where the colour of some moths is more like that of the background display than others. The student adopts the role of predator, and uses a mouse-pointer to ‘kill’ as many moths as possible in 18 sec. Surviving moths 'breed' to produce the next generation. Since practical trials demonstrated that moths are killed as an inverse function of degree of crypsis, progressive evolution occurs through the generations. The program also stores moth colour frequency data and, at a point chosen by the user, plots histograms for each generation. Development problems, and the simulation's value as a teaching aid, are discussed.     

Somatotopy of digital nerve projections to the cuneate nucleus in the monkey

Somatotopic arrangements of cells and fibers within the dorsal columns and the dorsal column nuclei have been mapped most precisely by electrophysiological recording methods. This study uses an anatomical approach to evaluate the precision of individual digital nerve projections to the cuneate nucleus (CN) in young macaque monkeys. Digital nerves supplying about one-half the palmar skin of a digit were surgically exposed, cut, and treated with wheatgerm agglutinin conjugated to horseradish peroxidase (WGA:HRP) on 3 successive days. After 2 additional days, animals were killed and medullas were recovered for study of serial sections reacted to display axons labeled by transganglionic transport of label. Labeled afferent fibers from each digit were found within a circumscribed columnar zone extending through the caudal CN and rostrally throughout the pars rotunda of CN. At caudal levels, diffuse projections reach the dorsal edge of the CN; more rostrally, they shift into deeper parts of the nucleus and are heaviest along its ventral and medial edges at levels near the obex. Fibers from the thumb (digit 1) project lateral (and ventral) to those from digit 2, and projections from digit 3 are medial to those from 2. Each digital projection field is closely adjacent to that from the adjacent digit. Few fibers extend to the rostral CN. Projection fields of homologous digits are quite symmetrical on the two sides. Although there do seem to be some differences in the somatotopic arrangement of digital input in macaques compared to other nonprimate mammals studied previously, these observations (precisely organized, circumscribed fields for separate digits) define a system well designed for transmission of data encoding spatial relationships.     

Somatotopy of Digital Nerve Projections to the Cuneate Nucleus in the Monkey

Somatotopic arrangements of cells and fibers within the dorsal columns and the dorsal column nuclei have been mapped most precisely by electrophysiological recording methods. This study uses an anatomical approach to evaluate the precision of individual digital nerve projections to the cuneate nucleus (CN) in young macaque monkeys. Digital nerves supplying about one-half the palmar skin of a digit were surgically exposed, cut, and treated with wheatgerm agglutinin conjugated to horseradish peroxidase (WGA:HRP) on 3 successive days. After 2 additional days, animals were killed and medullas were recovered for study of serial sections reacted to display axons labeled by transganglionic transport of label. Labeled afferent fibers from each digit were found within a circumscribed columnar zone extending through the caudal CN and rostrally throughout the pars rotunda of CN. At caudal levels, diffuse projections reach the dorsal edge of the CN; more rostrally, they shift into deeper parts of the nucleus and are heaviest along its ventral and medial edges at levels near the obex. Fibers from the thumb (digit 1) project lateral (and ventral) to those from digit 2, and projections from digit 3 are medial to those from 2. Each digital projection field is closely adjacent to that from the adjacent digit. Few fibers extend to the rostral CN. Projection fields of homologous digits are quite symmetrical on the two sides. Although there do seem to be some differences in the somatotopic arrangement of digital input in macaques compared to other nonprimate mammals studied previously, these observations (precisely organized, circumscribed fields for separate digits) define a system well designed for transmission of data encoding spatial relationships.     

Applications of microcomputer technology to cytophotometry.

Lack of appropriate software support for microprocessor program development has previously limited the applications of such technology in the field of microspectrophotometry. This paper describes our use of a Vickers M86 integrating microdensitometer coupled through a custom-designed interface circuit to a Processor Technology SOL III microcomputer. W e have developed a series of interactive, user-oriented programs for DNA-Feulgen cytophotometry with this instrument to allow automatic storage of data in files on floppy disks and instant retrieval of sets of measurements for statistical processing. The same data files can also be used to generate graphic displays in the form of bar histograms or plots of linear regressions on a video monitor and to produce hardcopy output of data files and graphic displays through the use of a high speed DIABLO printer.     

Agonist-mediated Ca2+ release in permeabilized UMR-106-01 cells. Transport properties and generation of inositol 1,4,5-trisphosphate

Permeabilized and intact UMR-106-01 cells attached to culture plates or coverslips were used to evaluate compartmentalized generation and the effective concentration of inositol 1,4,5-trisphosphate (In-1,4,5-P3) during agonist-mediated Ca2+ release. In permeabilized cells, Ca2+ release had the following characteristics. In-1,4,5-P3 released approximately 65% of the Ca2+ incorporated into intracellular stores. Prostaglandin F2 alpha (PGF2 alpha), endothelin, or GTP(gamma S) alone released a small amount or no Ca2+. However, the agonists together with GTP(gamma S) were as effective as In-1,4,5-P3 in releasing Ca2+. Both agonist- and In-1,4,5-P3-mediated Ca2+ release required the presence of permeable ion. Agonists, like In-1,4,5-P3, stimulated 45Ca uptake from low Ca2+ medium devoid of permeable ions into Ca2(+)-loaded intracellular stores. The permeabilized cell system was then used to evaluate compartmentalized generation and action of In-1,4,5-P3 during agonist stimulation. Mass measurement shows that in intact resting cells In-1,4,5-P3 concentration was 1.4 microM and was reduced to 0.05 microM following permeabilization. Stimulation with agonists increases In-1,4,5-P3 concentration from 0.05 to 0.34 microM. Ca2+ release by this concentration of In-1,4,5-P3 evenly distributed in the cytosol can account for only part of the agonist-mediated Ca2+ release. However, the effects of saturating In-1,4,5-P3 concentration and agonists were blocked by the specific inhibitor heparin. Measurement of heparin dependency of In-1,4,5-P3-mediated Ca2+ release was used to calculate an affinity for In-1,4,5-P3 of 0.39 microM. Similar measurements with agonists show that In-1,4,5-P3 concentration at the site of Ca2+ release during agonist stimulation is 11.2 microM. Hence, the total increase in In-1,4,5-P3 is reflected in considerably higher localized concentrations. This is interpreted to suggest compartmentalized generation and action of In-1,4,5-P3 during agonist stimulation.     

Phagocytosis in Acanthamoeba: II. Soluble and insoluble mannose-rich ligands stimulate phosphoinositide metabolism

The generation of second messengers during phagocytosis of yeast by Acanthamoeba castellanii was examined. The kinetics of binding and internalization of yeast by Acanthamoeba were measured and this was compared with the generation of known second messengers. We observed stimulated degradation of PI-4, 5-P2 to 1,4,5 IP3 with kinetics similar to that observed for the binding of yeast to amoeba. Similar production of IP3 could be induced upon treatment with a soluble mannosylated glycoprotein. We propose that the Acanthamoeba mannose receptor stimulates the degradation of PI-4, 5-P2 to 1,4,5 IP3 as an initial event in phagocytosis.     

Altered substrate selection of the melibiose transporter (MelY) of Enterobacter cloacae involving point mutations in Leu-88, Leu-91, and Ala-182 that confer enhanced maltose transport

We isolated mutants of Escherichia coli HS4006 containing the melibiose-H(+) symporter (MelY) from Enterobacter cloacae that had enhanced fermentation on 1% maltose MacConkey plates. DNA sequencing revealed three site classes of mutations: L-88-P, L-91-P, and A-182-P. The mutants L-88-P and L-91-P had 3.6- and 5.1-fold greater maltose uptake than the wild type and enhanced apparent affinities for maltose. Energy-coupled transport was defective for melibiose accumulation, but detectable maltose accumulation for the mutants indicated that active transport is dependent upon the substrate transported through the carrier. We conclude that the residues Leu-88, Leu-91 (transmembrane segment 3 [TMS-3]), and Ala-182 (TMS-6) of MelY mediate sugar selection. These data represent the first MelY mutations that confer changes in sugar selection.     

Behavior of crested auklets (<Emphasis Type="Italic">Aethia cristatella</Emphasis>, Charadriiformes,Alcidae) in the breeding season: Visual and acoustic displays

The crested auklet, a highly social planktivorous bird species of the Northern Pacific, is an important component of marine ecosystems. Although visual and acoustic modalities play a major role in the communication of these birds, the available data on the repertoire of their vocal signals and postures are scarce and lack quantitative analysis. This study deals with visual and acoustic displays of crested auklets on their breeding grounds and the occurrence frequencies of certain forms of social behavior in male and female birds. The data were collected on Talan Island (the Sea of Okhotsk) in 1987–1991 and 2008. They show that the rate of contacts between birds is very high and sex-specific: on average, males initiate 1.13 contacts/min, compared to 0.65 contacts/min initiated by females. Directionality of ruff-sniff displays differs depending on the posture of the recipient bird. The duration of the trumpeting display in males depends on their social surroundings. However, the duration of either the trumpeting display or the mutual cackling display during courtship is independent of the behavioral context. Vocalization of crested auklets is characterized by two independent basic frequencies occurring either sequentially or simultaneously. The role of different communicative modalities in the behavior of the crested auklet is discussed.     

Interactive multi-window integration of two-parameter flow cytometric data fields

Integration is necessary to determine the particle content of regions of interest of flow cytometric two-parameter fields. The improved program of the Cytomic 12 analyzer (1) offers: window trace integration for relatively simple window structures. The field of interest is surrounded by an integration trace (window). Eight independent windows can be stored and successively evaluated. It also offers painted field integration for complicated window structures. The pointer or a small window is interactively moved over the structures to be integrated like the brush of a painter. The "painted field" defines the window to be integrated. Window sets and painted fields can be stored on a floppy disk. Painted fields can be added and may also serve as look up tables for sorting.     

Conversion of linear histogram flow cytometry data to a logarithmic display

A routine is described that readily allows the rescaling of linear histographic data to a corresponding logarithmic histogram. This procedure significantly improves data display, particularly where a wide range in the measured parameter is encountered. The logarithmic scale displays peaks with band widths more proportional to their respective coefficients of variation than is the case in a linear display. Rescaling several linear histograms to a common logarithmic scale allows the combination of these linear data even though the linear ranges are different. This routine is presented as a program written in BASIC for execution on a microcomputer.     

SeeDNA： A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts

An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK support. It displays two-dimensionai (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/or its randomized counterpart. It is also capable of showing the difference of K-string distributions between two sequences. The C source code using the GTK package is freely available.     

Regulatory phosphorylation of FXYD2 by PKC and cross interactions between FXYD2, plasmalemmal Ca-ATPase and Na,K-ATPase

FXYD2 is a regulatory peptide associated with the α-subunit of the kidney Na,K-ATPase. FXYD2 can be phosphorylated by PKA, and its phosphorylation activates Na,K-ATPase. Here we show that FXYD2 is phosphorylated by PKC (PKC-FXYD2-P), by PKA (PKA-FXYD2-P) or by PKA and PKC simultaneously (FXYD2-P₂) modulating both the erythrocyte Na,K-ATPase and the plasma membrane Ca²⁺-ATPase (PMCA). In erythrocyte ghosts, the addition of PKA-FXYD2-P activated Na,K-ATPase by 80%, while non-phosphorylated FXYD2 (np) activated only 55%. The addition of np FXYD2 did not affect PMCA basal activity, but FXYD2-P₂ increased the basal PMCA activity by up to 200%. Calmodulin-activated PMCA activity was increased by np FXYD2 (3-fold) or FXYD2-P₂ (2.5-fold). However, PKC-FXYD2-P increased PMCA activity only by 50%. In contrast, when PMCA was treated with PKA-FXYD2-P, the ATPase activity was inhibited by 50%. The effect of all forms of FXYD2-P on calcium uptake from PMCA resembled the pattern observed in ATP hydrolysis. Our results suggest that the FXYD2 anchoring site could be conserved among the P-ATPase family permitting cross regulation. The effects of FXYD2 on calcium uptake and calcium-stimulated ATP hydrolysis suggest a novel role for FXYD2 on PMCA.     

XmMol: An X11 and motif program for macromolecular visualization and modeling

XmMol is a desktop tool designed to provide both interactive molecular graphics on X11 displays and easy interface with external applications. A kernel provides an interactive wire-frame display of macromolecules. It supports depth cueing, 3D clipping, and stereo. Various representations, coloring, and labeling modes are proposed. Docking and interactive back-bone deformation tools are also supported. Communication protocols allow the user to develop new external features or to use XmMol as a visualization tool for external numerical programs.     

Oscillations of intracellular calcium induced by vasopressin in individual fura-2-loaded mesangial cells. Frequency dependence on basal calcium concentration, agonist concentration, and temperature

Intracellular free calcium concentration ([Ca2+]i) was measured in fura-2-loaded single rat mesangial cells by dual wavelength spectrofluorometry. Stimulation with arginine vasopressin (AVP) caused an initial sharp rise of [Ca2+]i followed by repetitive spikes. The frequency of the oscillations was dependent on the concentration of AVP. At 0.1, 1.0, 10.0, and 100.0 nM AVP, the frequencies of oscillations were 0.17 +/- 0.05 (n = 6), 0.32 +/- 0.05 (n = 6), 0.49 +/- 0.05 (n = 6), and 0.48 +/- 0.05 min-1 (n = 5), respectively. Reduction in extracellular [Ca2+] reduced the frequency of AVP-induced oscillations but did not abolish the oscillations. The frequency of calcium oscillations, upon stimulation with 1.0 nM AVP, was directly correlated with the basal [Ca2+]i prior to stimulation. Oscillation frequency increased with increasing temperature. An Arrhenius plot between 24 and 37 degrees C indicated a strong temperature dependency of the oscillations with a Q10 of 3.0. Protein kinase C stimulation by active phorbol esters inhibited AVP-induced calcium oscillations but not the initial [Ca2+] response to AVP. These observations are consistent with a model incorporating a feedback loop linking [Ca2+]i to the mechanism of [Ca2+]i increase. Ca(2+)-induced Ca2+ release may be involved, whereby inositol 1,4,5-trisphosphate (inositol 1,4,5-P3) formation releases Ca2+ from an inositol 1,4,5-P3-sensitive pool, with subsequent Ca2+ uptake and release from an inositol 1,4,5-P3-insensitive pool.     

Interactive and graphic coupling between multiple alignments, secondary structure predictions and motif/pattern scanning into proteins

A computer module that includes multiple alignments, secondarystructure prediction, and site and pattern search has been developedand integrated into our ANTHEPROT software for protein sequenceanalysis. All the programs can be invokeed from within any routine,thus yielding multiple path to obtain final results. All theresults are graphically displayed. The main feature of thismodule is that all methods are connected in an interactive graphicmaimer. This module has been designed to display easily thepotential sites with conserved predicted structures.