New method for the analysis of flow cytometric data

A numerical method for deriving the fractions of cells in different phases of the cell cycle from a single observed DNA histogram is presented. The observed histogram is regarded as a polluted version (containing allocation errors) of the true histogram. A mathematical model is used to describe the pollution process. A theoretical histogram, representing the true histogram, is constructed so that G1 cells are put into one channel and G2M cells into another; the distribution of S cells in between is approximated with a set of harmonic functions. This theoretical histogram is subsequently disturbed with Gaussian dispersion functions to stimulate the pollution, yielding a predicted histogram. Using a maximum likelihood estimation technique, the model parameters are adjusted iteratively, matching the predicted histogram to the actually observed one. With the final parameter values substituted, the corresponding final theoretical histogram is regarded as a reliable reconstruction of the true histogram. From the latter, the required percentages can be read directly. The advantage of this approach over other mathematical analysis methods is that it allows a wide range of different, continuous distributions for relatively few model parameters (thus featuring flexibility and realism and a diminished risk of encountering computational problems). In addition, estimation errors providing a measure of accuracy can be obtained. To test the method, it was used to analyze various observed histograms from the literature that have been obtained by either simulation or actual flow cytometric measurements. The method appeared to perform well, as compared to the reported results of several other methods of analysis applied to the same data.     

A quantitative method for evaluating bivariate flow cytometric data obtained using monoclonal antibodies to bromodeoxyuridine.

A method is presented for analyzing data from bivariate analysis of cell populations exposed to bromodeoxyuridine and subsequently examined both for the presence of BrdUrd and for the cellular DNA content. It is shown that certain features may be defined in the bivariate data which are constant independent both of cell type and, within limits, experimental variability. These landmark features include the ratio of red, DNA, fluorescence of G2 + M cells to G1 cells, the ratio of green fluorescence corresponding to the non-specific binding of unlabeled G2 + M cells to unlabeled G1 cells, and the distribution of green fluorescence in unlabeled cells. The landmarks make it possible to standardize rules for establishing the separation line between-labeled and unlabeled cells as required in these experiments to obtain estimates of cytokinetic parameters. Values obtained for the DNA synthesis time and the potential doubling time which result from different decision rules for distinguishing labeled from unlabeled are compared in two murine tumor lines. The potential doubling time, but not the DNA synthesis time is shown to depend sensitively on the separation line. Suggestions are presented for analyzing clinical data with this procedure.     

A rapid flow cytometric method for bivariate bromodeoxyuridine/DNA analysis using simultaneous proteolytic enzyme digestion and acid denaturation

This report describes an immunocytochemical procedure for the simultaneous quantification of bromodeoxyuridine (BrdUrd) incorporated into cellular DNA and total DNA content in individual cells in suspension. Improvement of existing methods was achieved by combining acid denaturation and proteolytic enzyme digestion (0.2 mg/ml pepsin in 2N HCl for 30 min at room temperature). Acid denaturation preceded by enzyme digestion resulted in a large amount of debris and the occurrence of naked nuclei. In contrast, the simultaneous denaturation/protein digestion procedure did not damage the cellular structure, is rapid and reproducible, and has cell recoveries of more than 85%. Although experimental conditions were tested on human cultured keratinocytes, this method also appeared applicable to bone marrow cells and cells obtained from solid tissues.     

Monoparametric models of flow cytometric karyotypes with spreadsheet software

Summary Theoretical flow karyotypes from both plant and mammalian species have been simply modelled using computer spreadsheet software. The models are based upon published values of relative DNA content or relative lengths of each of the chromosomes. From such data, the histograms of chromosome distribution have been simulated for both linear and logarithmic modules of a flow cytometer, and as a function of the coefficient of variation. Simulated and experimental histograms are compard for Nicotiana plumbaginifolia. This readily accessible exercise facilitates the planning and execution of flow cytometric analysis and sorting of chromosomes.     

Identification of inverted duplicated #15 chromosomes using bivariate flow cytometric analysis

A dual laser FACS IV cell sorter has been used to obtain bivariate flow histograms of human metaphase chromosomes stained with the DNA-specific dyes, 33258 Hoechst and chromomycin A3. Approximately twenty distinct chromosomal fluorescence populations can be resolved using this double staining technique and the flow cytometer which has been modified only by the substitution of a specially designed air-spaced achromat for the standard focusing lens. Metaphase chromosomes from two different cell lines bearing inverted duplicated #15 autosomes have been subjected to bivariate chromosome analysis. In both cases, the inverted duplicated #15 chromosomes have been identified in the bivariate flow histogram. This identification was supported by experiments in which doubly stained chromosomes were counterstained with either netropsin or distamycin A, resulting in a relative increase in the 33258 Hoechst fluorescence intensity of the structurally abnormal #15 chromosomes, compared with the other chromosomes, as predicted by cytological studies. The possibility of identifying and separating small abnormal autosomes using commercially available instrumentation should facilitate the use of recombinant DNA techniques for the construction of libraries which are highly enriched for DNA sequences from limited autosomal subregions important in the study of chromosomal abnormalities such as deletions, translocations and inversion duplications.     

Improved method for computing potential doubling time from flow cytometric data

Relative movement methods use the timed progression of the mean fluorescence of cells which have been labeled with monoclonal antibodies against bromodeoxyuridine and displayed with bivariate flow cytometry according to DNA and label content to compute duration of DNA synthesis, TS. The relative movement is the difference of the mean DNA fluorescence of the labeled undivided cells from the G1 channel relative to the difference between the G1 and G2M channels. In this communication, we show how to extend this method to compute the potential doubling time, Tpot, the time required for a population of cells to double, given quiescent cells but no cell loss. A quantity v is introduced that is a function of the fraction of labeled divided cells and the fraction of labeled undivided cells. We show that v is independent of time and is equal to ln(2)Ts/Tpot so that Tpot (equal to ln(2)Ts/v) can be directly found from the information available in computing the relative movement. The method is applied to Chinese hamster ovary cells to demonstrate its utility.     

A proposal for a flow cytometric data file standard

The increasing complexity of multiparameter data collection and analysis in flow cytometry and the development of relatively inexpensive arc-lamp-based flow cytometers, which increases the probability that laboratories or institutions may have more than one type of instrument, creates a need for shareable analysis programs and for the transport of flow cytometric data files within an installation or from one institution to another. To address this need, we propose a standard file format to be used for all flow cytometric data. The general principles of this proposal are: (1) The data file will contain a minimum of three segments, TEXT, DATA, and ANALYSIS; (2) The TEXT and ANALYSIS segments consist of KEYWORDS, which are the names of data fields, and their values; (3) All TEXT is encoded in ASCII; (4) KEYWORDS and their values may be of any length; (5) Certain KEYWORDS will be standard, i.e., having specified formats to be recognized by all programs. The structure of the DATA segment will be uniquely defined by the values of KEYWORDS in the TEXT area. It may be in any bit resolution, facilitating compatibility between machines with different word length and/or allowing bit compression of the data. The structured nature of the TEXT area should facilitate management of flow cytometric data using existing data base management systems. The proposed file format has been implemented on VAX, PDP-11, and HP9920 based flow cytometry data acquisition systems.     

A simple preservative for flow cytometric DNA analysis

A solution containing citric acid buffered saline (CABS) and 99% ethanol (E) 1:1 was used for preserving cells for flow cytometric DNA analysis. DNA histograms obtained from fine needle biopsy aspirates and preserved in CABS+E had a similar mean coefficient of variation (CV) as was obtained from aspirates taken in CABS (3.3 vs. 3.4%) and a clearly smaller mean CV than was obtained from aspirates preserved in 50% ethanol (mean 4.8%, P less than .0001). Aspirates taken in CABS more often contained a small (less than 3,000) number of cells as compared with aspirates preserved either in CABS+E or ethanol (P less than .0001). Since preservation of cells in CABS+E allows long-term storage of samples and results in a decreased number of insufficient samples as compared with buffered saline and in an enhanced resolution as compared with 50% ethanol, CABS+E is recommended for preservation of cytological samples to be analyzed for DNA content with flow cytometry.     

Interactive display and analysis of data from bivariate flow cytometers.

An interactive computer program, SWELL, displayss and analyzes bivariate distributions generated by flow cytometers. SWELL is modular with options available via a menu, is written in Fortran, and utilizes a video color display system. Data are accumulated as a bivariate distribution that is transferred to the computer as a 64 x 64 matrix. For ease of visualization, matrices are displayed in pseudocolor. The distribution values are broken into eight ranges and each range is represented by a color. Each element of the matrix is then displayed in its assigned color. To allow pooling and comparison, distributions are aligned, edited, and standardized. Unknown samples are pooled or analyzed singly and compared to the normal pool by subtraction. Differences are displayed as pseudocolor matrices of sign, magnitude, or statistical magnitude in units of standard deviation. This latter display, scaled to tolerance limits, readily reveals regions of significant difference between normal and abnormal samples. Counts within such regions can be compared to diagnose samples automatically.     

A new method for the preparation of metaphase chromosomes for flow analysis

A new method for the preparation of metaphase chromosomes for flow analysis has been evaluated. It has been shown that this method, which involves detergent lysis of metaphase cells and polyamines to stabilize the DNA, yields lower coefficients of variation and background levels in the DNA histograms than is currently obtained by hexylene glycol based methods. A conventional flow cytometer (FACS-II) has been used to resolve the human karyotype into about 14 peaks after ethidium bromide staining and excitation with a relatively low level of illumination (0.4 W at 488 nm). Flow karyotypes have also been obtained from suspension cell lines, in particular from the mouse cell line, Friend 707/B10. The only disadvantage of this method is that the chromosomes are highly condensed and therefore banding studies on sorted chromosomes may not be possible.     

A method for calibration of flow cytometric wavelength shift fluorescence measurements

Recently, new fluorescent dyes have been introduced into flow cytometry which alter their spectral characteristics when changes occur in certain cell features, e.g., intracellular pH or calcium ion concentration. Such changes may be determined by measuring the fluorescence intensity ratio in two different wavelength ranges (5). Here a new method is described, which simplifies the use of steadily flowing fluids for calibration. The pulse electronics of a flow cytometer cannot process the static fluorescence signals of a streaming fluid. If, however, the exciting or emitted fluorescence light of a calibration fluid is made pulsating, the flow cytometer electronics can evaluate those pulses. The new calibration procedure uses measurement of two wavelength windows shown in a two-parameter display to generate an absolute calibration scale. Measurement of the spectral shift in calibration fluids under identical instrumental settings provides absolute values that measurements of intracellular concentrations can be referred to.     

A new method for the improvement of data production in phytochemical analysis

Introduction – The use of the average analytical signal for the construction of curves by the least squares method (LSM) over the standard addition method (SAM) is widespread. It would be advantageous, however, to find a way to avoid intermediary averages, which are known to be the cause of significant increases in standard deviations (SD). Objective – To develop a protocol that uses all gathered data to create curves by LSM over SAM. To use Excel^® for the estimation of y = mx + b and R² rather than using LSM equations for the SD of m, x and b. Methodology – The level of lead (II) in the bark (cork) of Quercus suber Linnaeus was determined using differential pulse anodic stripping voltammetry (DPASV). Three current samples were taken for each of the four standard additions. These signals were combined for adjustment by LSM. The results were compared with those obtained after averaging the current for each addition, and the expression of uncertainty in the measurements determined. Results – The new method shows an expanded uncertainty of ± 0.3321 μg/g (nearly 1.42%). The difference between the results obtained by the new and the old method is 0.01 μg/g (23.41 and 23.40 μg/g). The limit of detection changed approximately from 4.8 to 4 μg/g and the relative SD approximately from 9 to 6%. Conclusion – The absence of intermediary averages in curves improved the determination of lead (II) in cork by DPASV. Estimation of SD only with LSM equations produced results that were significantly worse. The changes are large enough to transform an apparently internally non‐validated procedure (repeatability for precision) into an internally validated procedure. Copyright © 2009 John Wiley & Sons, Ltd.     

A rapid and sensitive flow cytometric method for the detection of multidrug-resistant cells

Multidrug-resistant (MDR) cells are characterized by a defect in drug accumulation caused by activity of an energy-dependent rapid drug efflux pump. The action of this drug pump can be inhibited by specific agents, referred to as membrane transport modulating agents (MTMAs), resulting in a restoration of the intracellular drug accumulation. This paper presents a flow cytometric assay for the detection of MDR cells, which is based on the ability of these cells to respond to MTMAs. Daunorubicin net-uptake kinetics were measured of anthracycline-sensitive (A2780/S) and -resistant (A2780/R) human ovarian carcinoma cells in vitro. A2780/R cells accumulated significantly less (about a factor of 5) daunorubicin as compared to A2780/S cells. Addition of verapamil or cyclosporin A to A2780/R cells at steady-state daunorubicin uptake led to a dose-dependent increase in cellular daunorubicin accumulation. The sensitivity of the assay was determined by testing mixtures of A2780/S and A2780/R cells. Analysis of A2780/S cells contaminated with A2780/R cells showed that as few as 2.5% MDR cells could readily be detected in the mixture. In conclusion, this functional assay enables the detection of MDR cells in a heterogeneous cell suspension and is ideally suited for the study of the occurrence of typical MDR in human cancer.     

A new cytometric method for the immunophenotypic characterization of bone-derived human osteoclasts

BACKGROUND: Osteoclast cell function relates to bone resorption. Isolation and characterization of these cells from in vivo sources remain difficult. The aim of this study was to show the feasibility of using flow cytometry to identify and characterize human mature osteoclasts obtained from bone tissues. METHODS: Bone femoral heads obtained as discarded surgical material were used. To check the nature of 121F(+) (a monoclonal antibody specific for human osteoclasts) cells by flow cytometry, we used laser scanning cytometry to analyze simultaneously the immunophenotype and DNA cell content of osteoclast-like cell-enriched bone samples. RESULTS: Results were compared with conventional morphologic and cytochemical studies. The percentage of cells that showed both cytochemical (tartrate-resistant acid phosphatase [TRAP](+)) and immunophenotypic (121F(+)) osteoclast-associated characteristics was very similar (12.5 +/- 6.2 versus 14.7 +/- 11.7; P = 0.46). Laser scanning cytometry showed that 121F(+) cells were bigger (P = 0.04) and they had a higher DNA cell content (P = 0.04) and more nuclei per cell (P = 0.04) than the 121F(-) cells present in the same sample. DISCUSSION: This study relied on the combined use of the 121F(+) antibody and different cytometry-based techniques to characterize the osteoclast populations from human bone.     

A simple method to preserve oceanic phytoplankton for flow cytometric analyses

A simple method was developed to preserve marine phytoplankton populations so that delayed flow cytometric analyses could be performed. The method consisted of immediate fixation with 1% glutaraldehyde (final concentration) followed by storage in liquid nitrogen. The method was tested on individual algal species and on natural samples from both coastal and pelagic waters. In most cases, it caused little cell loss and preserved well both forward angle light scatter and chlorophyll fluorescence, but phycoerythrin fluorescence sometimes was significantly increased. The technique performed best for the small-sized picoplankton (below 2 microns) such as Synechococcus cyanobacteria or the newly discovered oceanic prochlorophytes. For larger-sized cells it had to be applied on a case by case basis as some fragile species, particularly dinoflagellates and cryptophytes, were poorly preserved.     

Automatic identification of algae: neural network analysis of flow cytometric data

The performance of an artificial neural network for automaticidentification of phytoplankton was investigated with data fromalgal laboratory cultures, analysed on the Optical PlanktonAnalyser (OPA), a flow cytometer especially developed for theanalysis of phytoplankton. Data from monocultures of eight algalspecies were used to train a neural network. The performanceof the trained network was tested with OPA data from mixturesof laboratory cultures. The network could distinguish Cyanobacteriafrom other algae with 99% accuracy. The identification of specieswas performed with less accuracy, but was generally >90%.This indicates that a neural network under supervised learningcan be used for automatic identification of species in relativelycomplex mixtures. Incorporation of such a system may also increasethe operational size range of a flow cytometer. The combinationof the OPA and neural network data analysis offers the elementsto build an operational automatic algal identification system.     

Preparation of tissues for DNA flow cytometric analysis

A method for measuring DNA in tissue cells by flow cytometry utilizing a one step combination nuclear isolation-DNA fluorochrome staining procedure is described. A variety of cells and tissues, both in vivo and in vitro, was used to illustrate the universal nature of this technique. These included murine bone marrow, liver testicle, sarcoma brain tumor, rat pancreatic islets, human peripheral blood, colon mucosa, colon cancer, sarcoma and brain tumor tissues. A special nuclear isolation medium, which contained either of the DNA fluorochromes, 4',6-diamidino-2 phenylindole-2 HCl or propidium iodide, was utilized successfully to isolate single suspensions of DNA fluorochrome stained nuclei in a rapid (5-10 min), consistent manner from a variety of tissues and cells. Multiple sampling of the same tissue or comparison between whole tissues and their single cell isolates showed that a representative sample was being obtained.     

Eight-parameter PC-AT based flow cytometric data system

An 8-parameter flow cytometric data system is described using an IBM-AT compatible personal computer (PC) and a commercial analog to digital conversion (ADC) board. A dedicated pulse processing interface adapts the flow cytometric pulses to the ADC board and controls the number of parameters to be taken up and the trigger conditions. The trigger thresholds are automatically held at a level immediately above the noise level. For the timing of kinetic measurements a linear voltage ramp of adjustable rise time is available. A built-in precision voltage source can be used for an overall calibration. The data system is operated by software written in assembly language. Data may be collected and processed in 1-8-parameter listmode or 1-3-parameter histogram mode. Functions are available for graphical color displays, numerical integration, multiparameter gating, and printing.