DNA flow cytometry in metastases and a recurrency of malignant melanomas. A comparison of results from fresh and paraffin embedded material

Single cell suspensions from 16 biopsies from 15 patients with metastatic or recurrent malignant melanoma were prepared according to the method described by Vindel?v (1977) and the nuclear DNA content was measured by a laboratory-built flow cytometer. The DNA histograms thus obtained were compared with those obtained from suspensions of single nuclei from the same biopsies after formalin fixation and paraffin embedding, according to the method of Hedley et al. (1983). Linear regression analysis of ploidy values from fresh material compared with those from paraffin blocks showed a strong correlation (R2 = 0.85), while that of the S-phase fraction was somewhat weaker (R2 = 0.66). It is concluded that archival wax preparations of malignant melanoma cell populations are suitable for FCM analysis of ploidy, and to a lesser extent for analysis of fraction of cells in various cell cycle phases.     

ANTIBODY-PRODUCING CELLS: ANALYSIS AND PURIFICATION BY VELOCITY SEDIMENTATION

Velocity sedimentation cell separation is a simple and reproducible method for obtaining highly enriched populations of viable antibody-producing cells. Using suspensions of spleen cells prepared from mice immunized with sheep erythrocytes, fractions containing up to 2% 19S-PFC and 25% 7S-PFC can be obtained. Granulocytes constitute almost all of the remaining cells in these fractions. The sedimentation profile of 7S-PFC is very broad in comparison with that of cell populations known to be homogeneous in size (e.g. mouse erythrocytes). Analysis of the profile of 7S-PFC at different times after immunization suggests that the heterogeneity arises largely from the doubling in cell volume as a cell moves from one mitosis to the next. Early in the immune response, when the majority of the PFC are proliferating, the variation in sedimentation velocities is consistent with such a two-fold variation in cell volume. Late in the response, when most PFC have stopped proliferating, the sedimentation profile is more homogeneous. This analysis suggests that the fractionation procedure is sensitive enough to separate PFC according to their position in the cell cycle. Sedimentation velocities were also measured for several other classes of cells found in spleen. Comparison of these values shows that sedimentation velocity is a useful parameter for characterizing different types of cells.     

Non-invasive analysis of cell cycle dynamics in single living cells with Raman micro-spectroscopy

Raman micro-spectroscopy is a laser-based technique which enables rapid and non-invasive biochemical analysis of cells and tissues without the need for labels, markers or stains. Previous characterization of the mammalian cell cycle using Raman micro-spectroscopy involved the analysis of suspensions of viable cells and individual fixed and/or dried cells. Cell suspensions do not provide cell-specific information, and fixing/drying can introduce artefacts which distort Raman spectra, potentially obscuring both qualitative and quantitative analytical results. In this article, we present Raman spectral characterization of biochemical changes related to cell cycle dynamics within single living cells in vitro. Raman spectra of human osteosarcoma cells synchronized in G(0)/G(1), S, and G(2)/M phases of the cell cycle were obtained and multivariate statistics applied to analyze the changes in cell spectra as a function of cell cycle phase. Principal components analysis identified spectral differences between cells in different phases, indicating a decrease in relative cellular lipid contribution to Raman spectral signatures from G(0)/G(1) to G(2)/M, with a concurrent relative increase in signal from nucleic acids and proteins. Supervised linear discriminant analysis of spectra was used to classify cells according to cell cycle phase, and exhibited 97% discrimination between G(0)/G(1)-phase cells and G(2)/M-phase cells. The non-invasive analysis of live cell cycle dynamics with Raman micro-spectroscopy demonstrates the potential of this approach to monitoring biochemical cellular reactions and processes in live cells in the absence of fixatives or labels.     

Bacterial degradation of EDTA

Degradation of EDTA (ethylenediaminetetraacetic acid) or metal-EDTA complexes by cell suspensions of the bacterial strain DSM 9103 was studied. The activity of EDTA degradation was the highest in the phase of active cell growth and decreased considerably in the stationary phase, after substrate depletion in the medium. Exponential-phase cells were incubated in HEPES buffer (pH 7.0) with 1 mM of uncomplexed EDTA or EDTA complexes with Mg2+, Ca2+, Mn2+, Pb2+, Co2+, Cd2+, Zn2+, Cu2+, or Fe3+. The metal-EDTA complexes (Me-EDTA) studied could be divided into three groups according to their degradability. EDTA complexes with stability constants K below 10(16) (lg K < 16), such as Mg-EDTA, Ca-EDTA, and Mn-EDTA, as well as uncomplexed EDTA, were degraded by the cell suspensions at a constant rate to completion within 5-10 h of incubation. Me-EDTA complexes with lg K above 16 (Zn-EDTA, Co-EDTA, Pb-EDTA, and Cu-EDTA) were not completely degraded during a 24-hour incubation, which was possibly due to the toxic effect of the metal ions released. No degradation of Cd-EDTA or Fe(III)-EDTA by cell suspensions of strain DSM 9103 was observed under the conditions studied.     

Synchronous Arabidopsis suspension cultures for analysis of cell-cycle gene activity

Synchronized suspension cultures are powerful tools in plant cell-cycle studies. However, few Arabidopsis cell cultures are available, and synchrony extending over several sequential phases of the cell cycle has not been reported. Here we describe the first useful synchrony in Arabidopsis, achieved by selecting the rapidly dividing Arabidopsis cell suspensions MM1 and MM2d. Synchrony may be achieved either by removing and re-supplying sucrose to the growth media or by applying an aphidicolin block/release. Synchronization with aphidicolin produced up to 80% S-phase cells and up to 92% G2 cells, together with clear separation of different cell-cycle phases. These synchronization procedures can be used for analysis of gene expression and protein activity. We show that representatives of three CDK gene classes of Arabidopsis (CDKA, CDKB1 and CDKB2) show differential expression timing, and that three CDK inhibitor genes show strikingly different expression patterns during cell-cycle re-entry. We propose that ICK2 (KRP2) may have a specific role in this process.     

Genetic and phenotypic characterization of capsule mutants of Cryptococcus neoformans

Stable mutants with reduced capacity to produce capsules were isolated from suspensions of Cryptococcus neoformans after treatment of the wild type with a mutagen. The mutants could be assigned one of two phenotypes, hypocapsular or acapsular. Hypocapsular mutants were immunochemically and physicochemically indistinguishable from the wild type, whereas acapsular mutants lacked a major capsular antigen and a negatively charged exterior. In genetic analysis, the mutant trait segregated as a Mendelian gene (1:1) when random basidiospores from an outcross were studied, and analysis of products of single meiotic events from outcrossed mutants was likewise consistent with meiotic segregation. Two-factor crosses yielded the expected four classes of progeny, with recombinants equal to parentals. We concluded that chromosomal genes are responsible for synthesis of the cryptococcal capsule and that random basidiospore analysis represents a useful technique for genetic analysis in this species.     

Calcium Ion Impedes Translation Initiation at the Synapse

Abstract: Stimulation of synaptoneurosome suspensions by the neurotransmitter glutamate gives rise to rapid loading of ribosomes onto mRNA and increased incorporation of amino acids into trichloroacetic acid-precipitable polypeptides. Metabotropic glutamate receptors (mGluRs) are responsible for this effect. Although simultaneous Ca²⁺ entry and mGluR stimulation do not change the response, entry of Ca²⁺ 30 s or 3 min before mGluR stimulation markedly depresses the polyribosomal loading. Either NMDA or ionophore (A23187) produces the depression. A calmodulin antagonist, W7, alleviates the effect, suggesting that inactivation of phospholipase A₂ by calcium-calmodulin-dependent kinase II is partially responsible for the phenomenon. Thus, interaction between different classes of glutamate receptors affects the control of protein translation at the synapse. This effect may partially explain recent observations of negative interactions between receptor classes in induction of long-term potentiation.     

Comparison of flow cytometric data obtained using fresh and paraffin-embedded lymphoid tissue

Flow cytometric (FCM) DNA analysis was carried out on 24 lymph nodes: 13 from benign reactive hyperplasias and 11 from non-Hodgkin's lymphomas. FCM was performed on two types of samples: (1) fresh cell suspensions and (2) suspensions prepared from formalin-fixed, paraffin-embedded sections. FCM of fresh samples detected aneuploidy in 23 of the 24 cases while FCM of paraffin-embedded samples detected aneuploidy in only 6 of the 24 cases. Those six cases were lymphomas considered histologically as having a poor prognosis. Only one case, a lymphoma, was euploid with both methods. The coefficients of variance determined in each case for both methods were found to be within "normal ranges," but were greater in the paraffin-embedded specimens. The results suggest that FCM DNA analysis of formalin-fixed, paraffin-embedded sections does not have as great a resolution capacity as does analysis of fresh cell suspensions, since the former failed to detect cell populations that had a small degree of aneuploidy (close to the 2n population).     

Plant regeneration from protoplasts of wild barley (Hordeum murinum L.)

Summary We have produced a large number of plants regenerated from protoplasts originally isolated from embryo-derived cell suspensions of wild barley, Hordeum murinum L.. Suspensions initially allowed protoplast isolation and culture 5.5 to 9 months from the date of callus initiation. Colony formation efficiencies ranged from 1.5 to 3.0 % and from 0.1 to 1.4 % for protoplast cultures with and without nurse cells, respectively. Both nurse and non-nurse techniques allowed efficient embryogenesis and plant regeneration. More than 400 shoots/plantlets have been obtained from 6 independent experiments. Over 150 plants have been transferred to the greenhouse. Protoplasts isolated from the youngest suspensions (5.5 months old) gave rise to the largest number of plants. Protoplasts isolated from suspensions as old as 15 months were also regenerable.Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - BAP 6-benzylaminopurine - NAA naphthaleneacetic acid - L1, L2 medium according to Lazzeri et al. 1991 - L3 medium medium according to Jähne et al. 1991a     

Heat pretreatment increases resolution in DNA flow cytometry of paraffin-embedded tumor tissue

BACKGROUND: Flow cytometry of single-cell suspensions prepared by enzymatic digestion from formalin-fixed, paraffin-embedded tissue suffers from several major drawbacks. The most important factors that influence the results are the high and unpredictable coefficients of variation (CVs) of the G0/G1 peak in the DNA histogram and reduction of propidium iodide (PI) intercalation with DNA, resulting from protein cross-linking by formalin. METHODS: In this study we introduce a heating step (2 h incubation in citrate solution at 80 degrees C) prior to a brief pepsin digestion of tissue sections in the protocol for DNA content analysis of formalin-fixed and paraffin-embedded tissue. This new method is compared with established methods for the preparation of cell suspensions from frozen and paraffin-embedded tissues with respect to cell yield, DNA histogram resolution, DNA dye saturation kinetics, cell cycle parameters, and antigen retrieval in various epithelial and nonepithelial tissues. RESULTS: The recovery of single cells from the paraffin sections was doubled by the heat treatment step, while the limited time of proteolysis resulted in decreased cell debris. Furthermore, an increased fraction of cells became cytokeratin-positive, while these immunocytochemically stained cells also exhibited a higher mean fluorescence intensity. The DNA histograms prepared from cell suspensions obtained according to this new protocol showed a significantly improved resolution, leading to a better identification of peridiploid cell populations. Heat pretreatment of paraffin-embedded archival tissue sections showed PI saturation kinetics similar to, or even better than, those of fresh unfixed tissues, independent of duration of fixation. CONCLUSIONS: This new method, making use of routinely available antigen retrieval principles, thus allows high-resolution DNA analysis of routinely fixed and paraffin-embedded tissue samples. Using external reference cells, inter- and intralaboratory standardization of DNA histograms can be achieved.     

Dynamic light scattering from dilute suspensions of thin discs and thin rods as limiting forms of cylinder, ellipsoid and ellipsoidal shell of revolution

A previous formulation of the field correlation function G1(tau) of light quasielastically scattered from suspensions of rigid rods undergoing anisotropic translational as well as rotational diffusion (T. Maeda and S. Fujime, Macromolecules 17 (1984) 1157) was extended to the cases of suspensions of cylinders (length L and radius R), ellipsoids and ellipsoidal shells of revolution (x2/b2 + y2/b2 + z2/a2 = 1). The present formulation includes that for suspensions of rigid rods in the limit of KR 1 or in the limit of b/a 1 and Kb 1 (an extremely prolate ellipsoid), and also that for suspensions of discs in the limit of KL 1 or in the limit of b/a 1 and Ka 1 (an extremely oblate ellipsoid), where K is the length of the scattering vector. Explicit forms of G1(tau), of the first cumulant Gamma of G1(tau) and of the dynamic form factors will be given, and numerical methods suitable for computation of dynamic form factors will be discussed. The present results can be applied to the analysis of experimental data for dilute suspensions of thin rods and thin discs. When the situation is favorable, our method can provide transport coefficients D1, D3, and Theta from dynamic light-scattering data only, where D(1) and D(3) are, respectively, the translational diffusion coefficients parallel with the x (y) and z axes, and Theta the rotational diffusion coefficient around the x (y) axis.     

Gene prediction and gene classes in Arabidopsis thaliana

Gene prediction methods for eukaryotic genomes still are not fully satisfying. One way to improve gene prediction accuracy, proven to be relevant for prokaryotes, is to consider more than one model of genes. Thus, we used our classification of Arabidopsis thaliana genes in two classes (CU(1) and CU(2)), previously delineated according to statistical features, in the GeneMark gene identification program. For each gene class, as well as for the two classes combined, a Markov model was developed (respectively, GM-CU(1), GM-CU(2) and GM-all) and then used on a test set of 168 genes to compare their respective efficiency. We concluded from this analysis that GM-CU(1) is more sensitive than GM-CU(2) which seems to be more specific to a gene type. Besides, GM-all does not give better results than GM-CU(1) and combining results from GM-CU(1) and GM-CU(2) greatly improve prediction efficiency in comparison with predictions made with GM-all only. Thus, this work confirms the necessity to consider more than one gene model for gene prediction in eukaryotic genomes, and to look for gene classes in order to build these models.     

Plant DNA flow cytometry and estimation of nuclear genome size

BACKGROUND: DNA flow cytometry describes the use of flow cytometry for estimation of DNA quantity in cell nuclei. The method involves preparation of aqueous suspensions of intact nuclei whose DNA is stained using a DNA fluorochrome. The nuclei are classified according to their relative fluorescence intensity or DNA content. Because the sample preparation and analysis is convenient and rapid, DNA flow cytometry has become a popular method for ploidy screening, detection of mixoploidy and aneuploidy, cell cycle analysis, assessment of the degree of polysomaty, determination of reproductive pathway, and estimation of absolute DNA amount or genome size. While the former applications are relatively straightforward, estimation of absolute DNA amount requires special attention to possible errors in sample preparation and analysis. SCOPE: The article reviews current procedures for estimation of absolute DNA amounts in plants using flow cytometry, with special emphasis on preparation of nuclei suspensions, stoichiometric DNA staining and the use of DNA reference standards. In addition, methodological pitfalls encountered in estimation of intraspecific variation in genome size are discussed as well as problems linked to the use of DNA flow cytometry for fieldwork. CONCLUSIONS: Reliable estimation of absolute DNA amounts in plants using flow cytometry is not a trivial task. Although several well-proven protocols are available and some factors controlling the precision and reproducibility have been identified, several problems persist: (1) the need for fresh tissues complicates the transfer of samples from field to the laboratory and/or their storage; (2) the role of cytosolic compounds interfering with quantitative DNA staining is not well understood; and (3) the use of a set of internationally agreed DNA reference standards still remains an unrealized goal.     

Mass isolation of pole cells from Drosophila melanogaster.

Crude cell suspensions were obtained from 3 × 10⁶ pregastrula staged embryos. These cells fractionated into three bands on Renografin density gradients. Using ultrastructural characteristics for identification, pole cells were localized in the two denser bands. EM analyses also revealed a striking difference in the frequency of lipid vacuoles found in the pole-cell cytoplasm versus the cytoplasm of other embryonic cells. This difference has enabled us to identify pole cells by light microscopy using a neutral lipid stain. Through detailed analyses of the Renografin fractions with this stain, we have shown that pole cells resolve into two to three density classes. Evidence is presented which suggests that these density classes reflect different developmental age classes. The size differences between the pole cells and other embryonic cells contained in the enriched pole-cell fractions from the density gradients has enabled us to use sedimentation velocity centrifugation for additional enrichment. A distinct lower band of cells was obtained which consisted of 80% pole cells. Using these procedures, 1–2 × 10⁷ pole cells can be obtained daily.     

Cholesteric-like crystal analogs in glucuronoxylan-rich cell wall composites: Experimental approach of acellular re-assembly from native cellulosic suspension

Summary Many plant cell walls are constructed according to a helicoidal pattern that is analog to a cholesteric liquid crystal order. This raises the question whether the wall assembly passes through a true but temporary liquid crystal state. The paper focuses on experiments performed from aqueous suspensions of extracted quince slime, i.e., a cellulose/glucuronoxylan wall composite that presents a helicoidal order when observed in situ, within the enlarged periplasm of the seed epidermal cells. Experiments carried out in acellular conditions showed that a spontaneous reassociation into a helicoidal order can be obtained from totally dispersed suspensions. The ultrastructural aspect of the reassembled mucilage suspension was different according to the resin used (LR White or nanoplast, a water-soluble melamin resin). It was always typically polydomain, and when an order was visible it was cholesteric-like and similar to the in situ native organization. Transition states with many imperfections expressed the difficulty of the system to reassemble in the absence of constraining surfaces. The possible intervention of glucuronoxylan (GX) in the ordered assembly of the microfibrils was checked by: (1) progressive extraction of GX by trifluoroacetic acid (TFA). The extraction was associated to a control of the fraction by analysis of uronic acid contents and observation at the electron microscope level. Extraction of GX provoked the formation of a flocculent mass, the flocculation being more intense when the TFA was more concentrated; (2) progressive change of pH in order to analyze the influence of pH on flocculation. Low pH (ca. pH 3) led also to a flocculation of the suspension, but the floc was reversibly lost after dialysis against distilled water. The results indicate the antifloc role of the GX due to the anionic charges carried by the side-chains. However, the function of GX as helper twisting agent in the cholesteric-like reassembly must not be ruled out.     

DNA ploidy and cell cycle analysis in ear malignant melanoma by flow and image cytometry.

Sixteen ear malignant melanomas (MM) were studied for ploidy and cell cycle analysis by flow and image cytometry. The results were compared with clinical (age, sex, stage), histologic (depth of invasion, level, type) and prognostic (recurrence, death) parameters. Single nuclear suspensions were obtained from fixed, paraffin-embedded tumor and adjacent normal tissue processed separately according to Hedley's technique. These, a "spiked" specimen of normal tissue and tumor, and a spleen diploid control were analyzed on a FACScan flow cytometer (Becton Dickinson, Mountain View, California, U.S.A.). Feulgen-stained Cytocentrifuge preparations of nuclear suspensions of normal, MM and diploid spleen were analyzed with the CAS 200 Image Analyzer (Cell Analysis Systems, Inc., Elmhurst, Illinois, U.S.A.) against commercial calibration rat hepatocytes defined as diploid. Six (37.5%) MM were diploid, and 10 (62.5%) were aneuploid; 8 (90%) were hypodiploid, for a high frequency. There were no statistically significant correlations between clinical, pathologic, prognostic or cell cycle analysis parameters and ploidy, although poor prognostic features tended to be in aneuploid lesions.     

Cellular composition of fractions of mouse testis cells following velocity sedimentation separation

Identification of cells has been made in stained smears of cell suspensions prepared from mouse testes and separated by velocity sedimentation at unit gravity. Comparison of various methods of producing suspensions demonstrated that the best cell separations were achieved using suspensions prepared with trypsin. Various fractions obtained following separation contained 29% Sertoli cells sedimenting at about 14 mm/h, 17% Leydig cells at 11 mm/h, 73% pachytene spermatocytes at 9.5 mm/h, 54% binucleate spermatids and 14% secondary spermatocytes at 6.7 mm/h, 77% round spermatids at 4.5 mm/h, 21% elongating spermatids and 74% cytoplasmic fragments detached from these spermatids at 2.1 mm/h and 37% late spermatids at 0.75 mm/h. The resolution of different size classes of cells was essentially complete, but separation of different types of cells was limited by the occurrence of multinucleate forms of the cells and by fragments of damaged elongated spermatids. Most cells, however, appeared to be intact on light microscopical examination.     

Differential regulation in tobacco cell suspensions of genes involved in plant-bacteria interactions by pathogen-related signals

Six cDNA clones whose corresponding mRNAs accumulate early during the hypersensitive reaction in tobacco leaves have been classified into 2 groups according to their maximum levels of accumulation in an incompatible versus a compatible interaction withPseudomonas solanacearum. We present evidence that, at least in the first stages of the interaction, tobacco cell suspensions retain the ability to respond differentially to compatible and incompatible isolates ofP. solanacearum.In addition, studies on the effect of a fungal elicitor on the accumulation of the mRNAs corresponding to the cDNA clones in cell suspensions indicate that only one group of genes responds to this treatment.     

Resistance of selected strains of Pseudomonas aeruginosa to low-intensity ultraviolet radiation.

The resistances of 10 strains of Pseudomonas aeruginosa and other microorganisms to an ultraviolet (UV) intensity of 100 muW/cm2 were determined. Organisms were exposed in 2- or 15-ml saline suspensions contained in uncapped polyethylene bottles for increasing periods of time, and the surviving fractions were enumerated. Decimal reduction times were calculated by regression analysis, using the least-squares method. The 10 strains of P. aeruginosa, compared with Micrococcus radiodurans and Candida albicans, were very susceptible to low-intensity UV radiation. Results from this study showed that a UV intensity of 100 muW/cm2 penetrated saline suspensions up to 40 mm deep sufficiently to kill high levels of microbial cells, especially P. aeruginosa cells. These results allowed us to design a system for determining and monitoring the sterilization capability of low-intensity UV radiation. In our particular case, UV proved to be an efficient mode for sterilizing saline suspensions of P. aeruginosa in polyethylene bottles. The significance and application of these findings with regard to supporting UV as a sterilant are discussed.