T-cell antigen-receptor stoichiometry: pre-clustering for sensitivity

The T-cell antigen receptor (TCR x CD3) is a multi-subunit complex that is responsible for triggering an adaptive immune response. It shows high specificity and sensitivity, while having a low affinity for the ligand. Furthermore, T cells respond to antigen over a wide concentration range. The stoichiometry and architecture of TCR x CD3 in the membrane have been under intense scrutiny because they might be the key to explaining its paradoxical properties. This review highlights new evidence that TCR x CD3 is found on intact unstimulated T cells in a monovalent form (one ligand-binding site per receptor) as well as in several distinct multivalent forms. This is in contrast to the TCR x CD3 stoichiometries determined by several biochemical means; however, these data can be explained by the effects of different detergents on the integrity of the receptor. Here, we discuss a model in which the multivalent receptors are important for the detection of low concentrations of ligand and therefore confer sensitivity, whereas the co-expressed monovalent TCR x CD3s allow a wide dynamic range.     

Cell cycle analysis using numerical simulation of bivariate DNA/bromodeoxyuridine distributions

This report describes a mathematical model of cell proliferation for simulation of bivariate DNA/bromodeoxyuridine (BrdUrd) distributions. The model formulates the change with time in the frequency of cells with any DNA content and in the amount of incorporated BrdUrd, according to given cytokinetic parameters, i.e., durations and dispersions of cell cycle phases and DNA synthesis rate during S-phase. We have applied this model to sequential DNA/BrdUrd distributions measured for Chinese hamster ovary cells asynchronously grown in vitro, 1) for 30 min in 10 microM BrdUrd followed by growth in BrdUrd-free medium for 0 to 24 h, or 2) during continuous incubation in 3 microM BrdUrd plus 30 microM thymidine for 2 to 24 h. The matches between the experimental and simulated distributions give the G1, S, G2M, and total cell cycle durations (and coefficients of variation) of 5.6 h (0.08), 7.0 h (0.07), 1.4 h (0.16), and 14.0 h (0.05), respectively. The model is shown to be useful for quantitative interpretation of the bivariate distributions.     

Evaluation of four methods of DNA distribution data analysis based on bromodeoxyuridine/DNA bivariate data

Four published methods of DNA-content histogram analysis (those of Fried, Dean and Jett, simplified Dean, and Fox) were compared using a double labeling of different cell populations. Partially synchronized and asynchronous cell populations were incubated with bromodeoxyuridine (BrdUrd) and then stained with an anti-BrdUrd monoclonal antibody and propidium iodide (PI). The fractions of cells in the G1, S, and G2 + M phases were calculated by each method and compared with those derived from G1, S, and G2 + M areas plotted on BrdUrd/DNA bivariate histograms, taken as the "true" values. This procedure enabled an optimal choice of method for a given cell population.     

Improved bromodeoxyuridine/DNA analysis by anti-BudR monoclonal antibody versus right angle light scatter

Dynamic cell cycle analysis is based on the incorporation of labelled precursors into DNA. Although antibodies to BrdU are very useful for analysing in flow cells which synthesize DNA, this approach has two main limitations. First, the detection of low incorporating cells is often difficult; second, four parameter flow cytometry is not able to correlate cell cycle to any other cellular marker. We have developed a methodology that, employing an IgGH + L as a second antibody and side scatter instead of propidium iodide fluorescence, allows a better discrimination of BudR+ cells. This approach allows the collection of an extra-fluorescent signal, and the analysis of specific cellular markers within the cell cycle.     

Improved bromodeoxyuridine/DNA analysis by anti-BudR monoclonal antibody versus right angle light scatter

Summary Dynamic cell cycle analysis is based on the incorporation of labelled precursors into DNA. Although antibodies to BrdU are very useful for analysing in flow cells which synthesize DNA, this approach has two main limitations. First, the detection of low incorporating cells is often difficult; second, four parameter flow cytometry is not able to correlate cell cycle to any other cellular marker. We have developed a methodology that, employing an IgG_H+L as a second antibody and side scatter instead of propidium iodide fluorescence, allows a better discrimination of BudR⁺ cells. This approach allows the collection of an extra-fluorescent signal, and the analysis of specific cellular markers within the cell cycle.     

Microfluorometric analysis of cellular DNA following incorporation of bromodeoxyuridine.

Bromodeoxyuridine (BrdU) incorporation into cellular DNA has a differential effect on the cell-associated fluorescence of several DNA-specific dyes. After cells were treated with BrdU, flow microfluorometry was used to study the relative increase or decrease influorescence of stained cells. Bromodeoxyuridine incorporation into CHO cells increased the fluorescence of mithramycin-, olivomycin-, or chromomycin-stained cells, decreased that of propidium iodide-stained cells, and had little, if any, effect on the fluorescence of acriflavine Feulgen-stained cells. Changes in relative fluorescence of cell associated dyes are due to changes in the amounts of dye bound to cells with BrdU-substituted DNA. Colorimetric and absorbance measurement of DNA content showed that BrdU does not alter the diploid DNA content of CHO cells; however, BrdU induces perturbations in the distribution of cells about the cell cycle which cause an increase in average DNA content.     

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.     

The utilization of bromodeoxyuridine incorporation into DNA for the analysis of cellular kinetics

Recently developed differential staining techniques based on the incorporation of bromodeoxyuridine (BUdR) into DNA permits the unequivocal identification of metaphase cells which have replicated once, twice, and three or more times. This technique has the potential of being utilized in the examination of kinetics of dividing cell populations. This potential is examined in a phytohemagglutinin-stimulated lymphocyte system. Determinations of the effect of increasing concentrations of BUdR on the distribution of metaphase cells between different generation cycles reveals no inhibition of cellular kinetics below 35 μM. The ability to distinguish third generation metaphase cells from subsequent generations is examined through the determination of “labelled” centromeric regions. The applicability of this system to current cellular kinetics is discussed.     

Simultaneous analysis of cell surface antigens, bromodeoxyuridine incorporation and DNA content

A method has been developed for correlating the presence of cell surface markers with bromodeoxyuridine (BrdUrd) uptake. We have found that paraformaldehyde fixation will maintain immunofluorescent cell surface staining through acid denaturation that is necessary for anti-BrdUrd reactivity to single-stranded DNA. In addition, the forward angle light scattering was maintained, even though the cells had been exposed to 2N HCl and detergent. The protocol was tested on three model systems: mouse thymus, a human cell line (CCRF-SB), and peripheral blood leukocytes. It was found that there was no specific loss of lymphocyte subsets.     

Cell kinetics in mouse epidermis studied by bivariate DNA/bromodeoxyuridine and DNA/keratin flow cytometry.

Hairless mice were injected intraperitoneally with bromodeoxyuridine (Brd-Urd). Basal cells were isolated from epidermis, fixed in 70% ethanol, and prepared for bivariate BrdUrd/DNA flow cytometric (FCM) analysis. Optimum detection of incorporated BrdUrd in DNA was obtained by combining pepsin digestion and acid denaturation. The cell loss was reduced to a minimum by using phosphate-buffered saline containing Ca2+ and Mg2+ to neutralize the acid. The percentage of cells in S phase and the average uptake of BrdUrd per labelled cell in eight consecutive windows throughout the S phase were measured after pulse labelling at intervals during a 24 h period. Furthermore, the cell cycle progression of a pulse-labelled cohort of cells was followed up to 96 h after BrdUrd injection. In general the results from both experiments were in good agreement with previous data from 3H-thymidine labelling studies. The percentage of cells in S phase was highest at night and lowest in the afternoon, whereas the average uptake of BrdUrd per labelled cell showed only minor circadian variations. There were no indications that BrdUrd significantly perturbed normal epidermal growth kinetics. A cell cycle time of about 36 h was observed for the labelled cohort. Indications of heterogeneity in traverse through G1 phase were found, and the existence of slowly cycling or temporarily resting cells in G2 phase was confirmed. There was, however, no evidence of a significant population of temporarily resting cells in the S phase. Bivariate DNA/keratin FCM analysis revealed a high purity of basal cells in the suspensions and indicated that the synthesis of the differentiation-keratin K10 was turned on only in G1 phase and after the last division.     

Cytochemistry and C-values: the less-well-known world of nuclear DNA amounts

BACKGROUND: In the plant sciences there are two widely applied technologies for measuring nuclear DNA content: Feulgen absorbance cytophotometry and flow cytometry (FCM). While FCM is, with good reasons, increasingly popular among plant scientists, absorbance-cytophotometric techniques lose ground. This results in a narrowing of the methodological repertoire, which is neither desirable nor beneficial. Both approaches have their advantages, but static cytophotometry seems to pose more instrumental difficulties and material-based problems than FCM, so that Feulgen-based data in the literature are often less reliable than one would expect. SCOPE: The purpose of this article is to present a selective overview of the field of nuclear DNA content measurement, and C-values in particular, with a focus on the technical difficulties imposed by the characteristics of the biological material and with some comments on the photometrical aspects of the work. For over 20 years it has been known that plant polyphenols cause problems in Feulgen DNA cytophotometry, since they act as major staining inhibitors leading to unreliable results. However, little information is available about the chemical classes of plant metabolites capable of DNA staining interference and the mechanisms of their inhibition. Plant slimes are another source of concern. CONCLUSIONS: In FCM research to uncover the effects of secondary metabolites on measurement results has begun only recently. In particular, the analysis of intraspecific genome size variation demands a stringent methodology which accounts for inhibitors. FCM tests for inhibitory effects of endogenous metabolites should become obligatory. The use of dry seeds for harvesting embryo and endosperm nuclei for FCM and Feulgen densitometry may often provide a means of circumventing staining inhibitors. The importance of internal standardization is highlighted. Our goal is a better understanding of phytochemical/cytochemical interactions in plant DNA photometry for the benefit of an ever-growing list of plant genome sizes.     

Detection of free radical-induced DNA damage with bromodeoxyuridine/Hoechst flow cytometry: implications for Bloom's syndrome

The clinical radiosensitiser bromodeoxyridine (BrdU) was shown to enhance oxygen free radical-mediated growth inhibition. Cells from Bloom's syndrome, a rare autosomal recessive disorder characterized by pre- and post-natal growth deficits, telangiectatic erythema, recurrent respiratory infections and a high incidence of cancer, exhibit in culture a hypersensitivity to BrdU. We analysed disturbed cell kinetics of Bloom's syndrome fibroblasts and permanent B-cell lines with a novel cell kinetic method: BrdU/Hoechst flow cytometry. Fibroblasts show a pattern similar to that of normal cells exposed to a breakdown product of lipid peroxides, whereas B-cells exhibit the cell kinetic disturbance provoked by elevated oxygen concentrations in normal cells. In both cell types the cell kinetic pattern was dependent upon the BrdU concentration in the culture medium. These data suggest an elevated endogenous generation of oxygen free radicals in Bloom's syndrome cells, which may relate to the elevated incidence of malignancies in these patients.     

Inhibition of Friend erythroleukemic cell differentiation by bromodeoxyuridine: correlation with the amount of bromodeoxyuridine in DNA

These studies were undertaken to examine the relationship between the inhibition by 5-bromodeoxyuridine (BrdU) of erythroid differentiation in Friend erythroleukemia cells and the incorporation of BrdU into DNA. Experiments were carried out in which the incorporation of BrdU into DNA and the concentration of BrdU to which the cells were exposed were varied independently of each other. In addition, the ability of deoxycytidine (dC) to reverse the effects of BrdU on hemoglobin production and to reduce the amount of BrdU in DNA was analyzed. Under all the conditions tested, the effects of BrdU were correlated with the amount of BrdU incorporated into nuclear DNA. These results differ from those of recent studies on the inhibition of pigmentation and the induction of mutations by BrdU in Syrian hamster melanoma cells. The results suggest that BrdU may be producing its biological effects by a variety of different mechanisms.     

Detection of free radical-induced DNA damage with bromodeoxyuridine/Hoechst flow cytometry: implications for Bloom's syndrome.

The clinical radiosensitizer bromodeoxyuridine (BrdU) was shown to enhance oxygen free radical-mediated growth inhibition. Cells from Bloom's syndrome, a rare autosomal recessive disorder characterized by pre- and post-natal growth deficits, telangiectatic erythema, recurrent respiratory infections and a high incidence of cancer, exhibit in culture a hypersensitivity to BrdU. We analysed disturbed cell kinetics of Bloom's syndrome fibroblasts and permanent B-cell lines with a novel cell kinetic method: BrdU/Hoechst flow cytometry. Fibroblasts show a pattern similar to that of normal cells exposed to a breakdown product of lipid peroxides, whereas B-cells exhibit the cell kinetic disturbance provoked by elevated oxygen concentrations in normal cells. In both cell types the cell kinetic pattern was dependent upon the BrdU concentration in the culture medium. These data suggest an elevated endogenous generation of oxygen free radicals in Bloom's syndrome cells, which may relate to the elevated incidence of malignancies in these patients.     

Inhibition of biological effects of bromodeoxyuridine by deoxycytidine: correlation with decreased incorporation of bromodeoxyuridine into DNA.

The effects of 5-bromodeoxyuridine (BrdU) on pigmentation, contact inhibition, cell morphology, and tumorogenicity of Syrian hamster melanoma cells are inhibited in the presence of deoxycytidine (dC). The inhibition of these biological effects of BrdU by dC is correlated with a decrease in the incorporation of BrdU into nuclear DNA. The results suggest that the intracellular changes resulting from the addition of dC to cells in the presence of BrdU are comparable to those resulting from a decrease in the concentration of BrdU in the medium.     

Cell cycle perturbation by sodium butyrate in tumorigenic and non-tumorigenic human urothelial cell lines assessed by flow cytometric bromodeoxyuridine/DNA analysis

The effect of sodium butyrate on cell proliferation was studied in eight human urothelial cell lines differing in transformation grade (TGr): Hu 1752 (mortal, TGr I); HCV29 (immortal and tumorigenic, TGr II); HCV29T, T24, T24A, T24B, Hu 961A and Hu 1703He (tumorigenic, TGr III). In all cell lines, except Hu 1752, addition of 4 mm sodium butyrate at 18 h after replating resulted in a significantly decreased population of adherent cells after a further 24–48 h. This might partially be explained by detachment of cells, probably mainly S phase cells, from the substrate in the lines HCV 29, HCV29T, Hu 961A and Hu 1703He. Flow cytometric DNA analysis of the adherent cell population showed that all TGr II and III urothelial cell lines were DNA aneuploid, and that butyrate perturbed the cell cycle distribution in these cell lines, mainly by a decrease of the S phase fraction. Flow cytometric bromodeoxyuridine (BrdUrd)/DNA analysis of continuously BrdUrd labelled cultures, using a ‘washless’ BrdUrd/DNA staining technique, showed that butyrate inhibited the G_0/1-S phase transition, indicated by a delayed depletion of BrdUrd negative G_0/1 cells in the cell lines HCV29, HCV29T, T24B, Hu 961A and Hu 1703He. BrdUrd/DNA analysis further showed that butyrate inhibited the G₂M-G_0/1 phase transition, indicated by a pronounced accumulation of BrdUrd positive G₂M cells in the cell lines HCV29T, T24B, Hu 961A and Hu 1703He. Microscopy of HCV29T and Hu 961A cells indicated that this block did not occur in mitosis. The parental cell line T 24 and the cell line T 24 A did not show an accumulation of BrdUrd negative G_0/1 cells or BrdUrd positive G₂M cells like that occurring in the derived cell line T 24B.     

Gradients in plastid and mitochondrial DNA synthesis inFunaria protonemata: Visualization by bromodeoxyuridine immunohistochemistry

Summary DNA synthesis was investigated by visualizing sites of bromodeoxyuridine incorporation with antibodies in protonemata of the mossFunaria hygrometrica. In apically elongating tip cells a pronounced gradient of organelle DNA synthesis from tip to base was visible, reflecting the distribution of proliferating organelles within the tip cell. Side branch development coincided with reinitiation of replication of plastid and mitochondrial DNA.Abbreviations BrdU 5-bromo-2-deoxyuridine - DABCO diazabicyclol (2,2,2) octan - FITC fluorescein-5-isothiocyanat - HSA human serum albumine - IgG immunoglobulin G - PBS saline phosphate buffer     

Partition-free congruence analysis: implications for sensitivity analysis

A criterion is proposed to compare systematic hypotheses based on multiple sources of information under a diverse set of interpretive assumptions (i.e., sensitivity analysis of Wheeler, 1995 ). This metric, the Meta‐Retention Index (MRI), is the retention index (RI) of Farris calculated over the set of conventional homologous qualitative characters (ordered, unordered, Sankoff, etc.) and molecular fragment characters sensu Wheeler (1996, 1999 ). The superiority of this measure to other similar measures (e.g., incongruence length difference test) comes from its independence from partition information. The only values that participate in its calculation are the minimum, maximum and observed cost (= cladogram cost) of each character. The partition (morphology, gene locus) from which the variant may have come is irrelevant. In the special cases where there is only a single data partition, this measure is equivalent to the conventional RI; and in the case where there are single fragment characters per partition (contiguous molecular loci as data sets) the measure is identical to the complement of the Rescaled Incongruence Length Difference (RILD) of Wheeler and Hayashi (1998 ). The MRI can serve as an optimality criterion for deciding among systematic hypotheses based on the same data, but different sets of analysis assumptions (e.g., character weights, indel costs). The MRI may lose discriminatory power in situations where a minority of highly congruent characters is given high weight. This situation can be detected and seems unlikely to occur frequently in real data sets. © The Willi Hennig Society 2006.