Cytofluorometric Determination of Nuclear DNA in Living and Preserved Algae

Three DNA-localizing fluorochromes used in conjunction with epi (incident) UV illumination were examined for sensitivity and selectivity for the cytofluorometric determination of nuclear DNA in ten species of six algal genera: Mougeotia, Oedogonium, Sirogonium, Spirogyra and Zygnema among the green algae, and the marine red alga Polysiphonia boldii. In comparison with absorption photometry for the determination of nuclear DNA, the cytofluorometric procedure proved to be simpler and considerably more sensitive. Following staining with 4',6-diamidino-2-phenylindole (DAPI), nuclei fluoresce blue-white, the fluorescence intensity of the DNA-DAPI complex being considerably greater than that of the unbound dye molecule. Algal strains stained with 2,5-bis[4'-aminopheny](1')]-1,3,4-oxadiazole (BAO) also showed brilliant blue-white nuclear fluorescence. Although the BAO schedule requires the use of freshly prepared dye and sulfite water, and careful control of hydrolysis, nuclear fluorescence of the stained specimens does not fade under irradiation of the UV beam as rapidly as it does with certain other fluorochrome procedures. A more useful fluorochrome was the fungal antibiotic mithramycin. Its staining schedule is simple and the bright orange-yellow fluorescence of the nuclei is associated with an exceptional degree of sensitivity and specificity for DNA. Forty-eight-year-old preserved filaments of Spirogyra jatobae, stained with either BAO or mithramycin, exhibited a fluorescence brilliance of nuclear and chloroplast DNA equal to that of fresh specimens of this species. The three schedules, but particularly the one with mithramycin, have proven useful in providing indirect evidence for variation in ploidy level in several of the above algal genera, and in verifying the assumed ploidy level of the gametophyte (haploid) and tetrasporophyte (diploid) of Polysiphonia boldii     

Feulgen-Naphthol Yellow S cytophotometry of liver cells. The effect of formaldehyde induced shrinkage on nuclear Naphthol Yellow S binding.

1. In isolated liver cells, fixed in 4 per cent formaldehyde (NFS) for Feulgen-Naphthol Yellow S (F-NYS) staining of DNA and protein, nuclear shrinkage increases the nuclear concentration of solids to 46 per cent (w/v) before the start of the NYS staining. 2. When a fixative mixture of methanol:acetic acid:formalin (85:5:10 by volume; MAF) is used, the concentration of nuclear solids during NYS staining remain at a physiological level of 19 per cent. 3. By exposing liver cells to NFS for 10 to 120 seconds before fixation in MAF, increasing nuclear shrinkage can be induced with increasing pretreatment in NFS. Nuclear NYS binding decreases in parallel with the decreasing nuclear volume in cells thus treated. As the shrinkage induced reduction in NYS binding may vary with the net charge of nuclear non-histone proteins, MAF fixation must be preferred for quantitative determinations of nuclear non-histone protein in F-NYS stained, isolated cells. 4. Fixation in MAF offers the same advantages as NFS fixation as regards the small loss of proteins during the Feulgen staining procedure and the excellent reproducibility of the F-NYS staining. Storage of MAF fixed cells in the fixative for a few days does not alter their F-NYS staining properties. 5. In MAF fixed, F-NYS stained cells there is no NYS binding to histone basic amino acid residues.     

Photographic densitometry for quantitative DNA analysis of cytologic and histologic specimens.

We found that photographic densitometry (PD) is a useful technique for quantitative determinations of nuclear DNA content in clinical tumor material. Optimum conditions for the use of PD in clinical cytology and histopathology were worked out. A quantitative evaluation of the method was performed, particularly with respect to errors that may appear when measuring clinical tumor material. Our study showed that PD offers accurate DNA measurements in cytologic and histologic specimens. Ploidy level determinations in tumor cell populations in clinical material could be as accurately performed with PD as with scanning microspectrophotometry (SMP). Nuclear DNA content of individual cells as determined by PD correlated highly with nuclear DNA content determined by SMP (correlation coefficient, 0.96). Since the PD method is less influenced by background variation than are other image techniques (due to measurement of a photographic image), it is particularly useful in measurement of histopathologic sections, in which the background variation can introduce considerable errors. The method is also valuable with clinical cytologic smears, in which the presence of blood and other material disturbs the background. PD represents a valid complement to scanning microspectrophotometry and TV imaging systems, particularly for DNA analysis of tissue sections. Moreover, it can be applied easily in the clinical routine. Relevant tissue areas are selected and photographed by the pathologist or cytopathologist, and the measurement is performed by a laboratory technician.     

Signal analysis of slit-scan contour data.

As a method for the preselection of alarms in gynecological cell samples, the Battelle Cytophotometry Research Group uses the slit-scan technique to obtain various cell parameters, such as the N/C ratio and the relative DNA content, from fluorescently stained cells, which are aligned one-dimensionally in the tape system designed at Battelle. The system developed at Battelle Institute analyzes all signals that exceed the background noise. As the first step in processing the slit-scan data, several threshold levels permit the separation of various artifacts. In subsequent steps, the nuclear peak is recognized, the nuclear boundaries are calculated, and seven cell parameters are determined. For the alarm detection at present only one parameter, DNA fluorescence, is used for these determinations. Visual assignment of these data to definite objects on the tape makes it possible to obtain frequency distributions of: (a) all recorded objects within the sample on the tape; (b) all signals that are classified as cells; and (c) all types of objects that preferentially cause alarms.     

Study of the cell cycle-dependent assembly of the DNA pre-replication centres in Xenopus egg extracts.

RPA is a cellular, three-subunit, single-stranded (ss) DNA binding protein, which assists T-antigen in the assembly of the pre-priming complex in the SV40 replication system. By immunodepletion and complementation, we have identified RPA as an essential factor for cellular DNA replication in Xenopus extracts. RPA assembles post-mitotically on the decondensing chromosomes into numerous subnuclear pre-replication centres (preRCs) which serve, upon formation of the nuclear membrane, as RCs for the initiation of DNA synthesis. By a variety of experiments including the use of isolated components, we demonstrate that an inactive cdc2-cyclin B kinase complex is essential to allow post-mitotic assembly of the preRCs. In contrast, the active cdk2-cyclin A kinase does not impede or facilitate the assembly of preRCs. Digestion analysis using the single-strand-specific P1 nuclease as well as competition experiments with ssDNA, reveal that replication-associated unwinding of the DNA, assisted by RPA, requires the formation of the nuclear membrane. The p21 cdk-interacting protein Cip1 appears to inhibit DNA replication prior to the unwinding DNA step, but after assembly of preRC and nuclear reconstruction.     

Mutants of bacteriophage T4 deficient in the ability to induce nuclear disruption. II. Physiological state of the host nucleoid in infected cells

Studies with ndd mutants of phage T4, deficient in the ability to induce nuclear disruption, the movement of the host DNA from a largely central location in the cell into close association with the cell membrane, show that nuclear disruption is not essential for host DNA breakdown. Degradation of prelabeled host DNA to acid-soluble products occurs at the same rate in the absence of nuclear disruption as it does in its presence. Moreover, the absence of nuclear disruption results in an alternative pathway of slow degradation of host DNA independent of phage endonuclease II.M-band analyses of association between DNA andmembrane (Earhart et al., 1968) indicate that endonuclease II is required for the release of host DNA from the membrane when nuclear disruption occurs normally, and that the product of at least one of the genes rIIA, rIIB, D1 or D2a (probably D2a, which is necessary for the synthesis of endonuclease IV) is required for DNA release when nuclear disruption does not occur.Analyses of the sizes of host DNA single strands at various times after infection by means of alkaline sucrose density-gradients show that the presence or absence of nuclear disruption has little, if any, effect on the rate of accumulation of single-strand nicks. Neutral sucrose density-gradient analyses suggest that a limited number of double-strand breaks can accumulate in host DNA when endonuclease IV is active, but few, if any, occur when neither endonuclease II or IV is active.Gentle lysis of ndd-infected cells and subsequent sedimentation analysis of the host DNA in neutral sucrose density-gradients reveal that the host chromosomes become “unfolded” within five minutes after infection. Thin-section electron microscopy shows that the host DNA becomes widely dispersed throughout the cytoplasm of cells at late times after infection with ndd mutants. These observations make it very unlikely that nuclear disruption is a passive process which occurs whenever the forces or structures which maintain the normal state of the Escherichia coli nucleoid are altered.All of our data are consistent with a mechanism of nuclear disruption which involves multiple attachment of the host DNA to the cell membrane under the control of the D2b gene of phage T4. We propose that in ndd-infected cells this multiple attachment does not occur, with the result that a limited number of double-strand breaks release much of the host DNA from the cell membrane.     

A cytochemical and immunocytochemical study of DNA distribution in spermatid nuclei of mouse,rabbit, and bull

Summary DNA distribution in mouse, rabbit and bull spermatids was analyzed by electron microscopy, after using a Feulgen-like HCl-osmium ammine procedure, and after immunocytochemistry with anti-DNA antibodies. In addition, nucleic acids were visualized with the intercalating dye ethidium bromide and phosphotungstic acid. The parts of DNA displaying a beta helix configuration (possibly A-T rich parts) were identified by epifluorescence microscopy after staining with Hoechst 33258. In all 3 species, young spermatid nuclei were seen to have large areas poor in DNA, as well as DNA-rich areas, which were mostly concentrated into a peripheral layer close to the acrosome and into one or several masses, displaying species-specific locations. These DNA-rich areas were stained with Hoechst 33258. Elongating spermatid nuclei contained homogeneously distributed DNA, and this was evident following both immunocytochemistry and nucleic acid histochemistry in all 3 species. However, the distribution appeared more heterogeneous after the Feulgen-like procedure, and was accompanied by a disappearance of Hoechst-fluorescence. In fully elongated spermatids, all nuclear areas stained with Hoechst 33258, while the 3 other techniques labeled either all or species-specific parts of the condensed chromatin. The reasons for these variable reactions are discussed in terms of technique specificities, DNA configuration and nucleoprotein moiety replacements.     

Visualization of intracellular trafficking of exogenous DNA delivered by cationic liposomes

To visualize the intracellular trafficking of exogenous DNAs delivered by cationic liposomes, rhodamine-labeled DNAs were transfected into NIH3T3 cells and observed by confocal laser microscopy. After 0.5- to 1-h incubations, the DNAs reached the nucleus with a much higher frequency than that expected from the cell division rate. This result suggests that DNAs can enter the nucleus in the presence of the nuclear membrane. Interestingly, some DNAs appeared to extend through the nuclear membrane in the aggregated form which were much larger than the nuclear pore complex. The DNAs which have passed through the nuclear membrane were stained with SYTO 24, a DNA labeling reagent. The stained part may be "naked" DNA that is free of lipids or proteins. This observation indicates that a complex containing DNA fuses with the nuclear membrane and then naked DNA is released into the nucleus.     

Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement

The solution structures of two alternating purine-pyrimidine octamers, [d(G-T-A-C-G-T-A-C)]2 and the reverse sequence [d(C-A-T-G-C-A-T-G)]2, are investigated by using nuclear magnetic resonance spectroscopy and restrained molecular dynamics calculations. Chemical shift assignments are obtained for non-exchangeable protons by a combination of two-dimensional correlation and nuclear Overhauser enhancement (NOE) spectroscopy experiments. Distances between protons are estimated by extrapolating distances derived from time-dependent NOE measurements to zero mixing time. Approximate dihedral angles are determined within the deoxyribose ring from coupling constants observed in one and two-dimensional spectra. Sets of distance and dihedral determinations for each of the duplexes form the bases for structure determination. Molecular dynamics is then used to generate structures that satisfy the experimental restraints incorporated as effective potentials into the total energy. Separate runs start from classical A and B-form DNA and converge to essentially identical structures. To circumvent the problems of spin diffusion and differential motion associated with distance measurements within molecules, models are improved by NOE-based refinement in which observed NOE intensities are compared to those calculated using a full matrix analysis procedure. The refined structures generally have the global features of B-type DNA. Some, but not all, variations in dihedral angles and in the spatial relationships of adjacent base-pairs are observed to be in synchrony with the alternating purine-pyrimidine sequence.     

Normal and perturbed Chinese hamster ovary cells: correlation of DNA, RNA, and protein content by flow cytometry

Quantitative, correlated determinations of DNA, RNA, and protein, as well as RNA to DNA and RNA to protein ratios, were performed on three-color stained cells using a multiwavelength-excitation flow cytometer. DNA-bound Hoechst 33342 (blue), protein-fluorescein isothiocyanate (green), and RNA-bound pyronin Y (red) fluorescence measurements were correlated as each stained cell intersected three spatially separated laser beams. The analytical scheme provided sensitive and accurate fluorescence determinations by minimizing the effects of overlap in the spectral characteristics of the three dyes. Computer analysis was used to generate two-parameter contour density profiles as well as to obtain numerical data for subpopulations delineated on the basis of cellular DNA content. Such determinations allowed for analysis of RNA to DNA and RNA to protein ratios for cells within particular regions of the cell cycle. The technique was used to study the interrelationship of DNA, RNA, and protein contents in exponentially growing Chinese hamster ovary cells as well as in cell populations progressing the cell cycle after release from arrest in G1 phase. The sensitivity of the method for early detection of conditions of unbalanced growth is demonstrated in the comparison of the differential effects of the cycle-perturbing agent, adriamycin, on cells treated either during exponential growth or while reversibly arrested in G1 phase.     

Naegleria fowleri: Light and electron microscopy study of mitosis

DAPI and Feulgen stains were used as specific DNA markers for studying the mitosis process in Naegleria fowleri. Both DAPI and Feulgen stains reacted with DNA in the nuclei of the amoebae. Representative figures of N. fowleri mitotic nuclei with a defined arrangement according to the phase of the cell cycle were observed. A notable characteristic is that the nucleolus is present throughout the stages of mitosis. During metaphase, several deeply stained DNA condensations following an elongated pattern were observed, corresponding almost certainly to tightly grouped chromosomes. Ultrastructural observations demonstrated that the nucleus divides by cryptomitosis, a process in which the nuclear membrane does not disappear during the mitosis. Centrioles were not found, and a spindle of microtubules was observed running the length of the nucleus from pole to pole however, they did not come to a focal point.     

Image analysis and DNA content of urothelial cells infected with human polyomavirus

Human polyomavirus (HPV)-infected cells in the urinary sediment are characterized by large homogeneous basophilic nuclear inclusions, which may mimic the nuclear changes in urothelial cancer. The virus is composed of double-stranded DNA and produces intense green fluorescence of nuclei stained with acridine orange. DNA measurements of Feulgen-stained smears of urinary sediment disclosed that HPV-infected cells have aneuploid DNA values and could not be differentiated from cancer cells on the basis of DNA content alone. On the other hand, computer discriminant analysis performed on high-resolution images of HPV-infected and malignant urothelial cells stained by both the Papanicolaou and Feulgen methods showed that excellent discrimination between the two groups of cells could be achieved with either stain. The misclassification rates ranged from 3% to 9%. This differentiation was almost entirely based upon computer features pertaining to the texture of the nuclear chromatin. This study documented still further the diagnostic value of high-resolution image analysis of cells in the human urinary sediment.     

A new sensitive non-isotopic method using sulfonated probes to detect picogram quantities of specific DNA sequences on blot hybridization

The use of non-radioactive systems to detect target DNA or RNA displays many advantages such as safe manipulation, potential use in non-specialized scientific area and prolonged lifetime of the probes (one year or more). We here describe a method we have improved and optimized using sulfonated DNA probes for hybridization on dot and Southern blots. Sulfonation is an easy chemical modification procedure which does not require enzymatic coctail as does nick-translation. Sensitivity of this method has been particularly improved by using a new blocking solution, containing heparin, which allows easy and fast detection of picogram quantities of DNA. This method allows the use of nitrocellulose as well as nylon membranes with very low background. Equal resolution is obtained in comparative experiments involving both sulfonated and 32P-radiolabelled probes. Single copy gene sequences are readily detected in nuclear DNA. These results allow the use of this procedure for restriction fragment length polymorphism (RFLP) studies.     

Increased accuracy and speed of absorption cytometric DNA measurements by automatic corrections for nuclear darkness

We have developed a method of calculating the average local absorbance (ALA) of a nucleus from the integrated nuclear absorbance and area. One can use the ALA, along with nuclear areas measured at different point absorbance thresholds, to determine whether a nucleus is stained too lightly or too darkly for accurate absorption measurements; this allows selection of an optimal light wavelength for the performance of these measurements. The ALA can also be used for automatic and instantaneous correction of integrated absorbance values from darkly stained cells. This allows the rapid measurement of the integrated absorbances of a large number of nuclei that are heterogeneous in stain intensity. Coefficients of variation of approximately 3% are obtained for the integrated absorbances of nuclei of nontransformed G0/G1 cells. This correction method can be applied with any image densitometer that generates both integrated absorbance and area values.     

Correlation of DNA ploidy with c-erbB-2 expression in preinvasive and invasive breast tumors.

Detection of c-erbB-2 oncogene product expression by monoclonal antibody staining (avidin-biotin technique) in formalin-fixed, paraffin-embedded atypical hyperplasias (AH, n = 20), intraductal carcinomas (IDCA, n = 27) and invasive carcinomas (INVCA, n = 48) was compared to ploidy determinations obtained by flow cytometry (INVCA) or image analysis (AH, IDCA). Cytoplasmic membrane staining was present in 11/48 (23%) INVCA and 8/27 (30%) IDCA but none of the AH. Tumors with abnormal DNA content expressed c-erbB-2 more frequently: INVCA, 2/19 (11%) diploid range versus 9/29 (31%) aneuploid; IDCA, 1/7 (14%) diploid range versus 7/20 (35%) aneuploid. Poorly differentiated (nuclear grade) IDCA or INVCA were also more frequently stained (14/35, 40%) than were well or moderately differentiated cases (5/40, 12.5%). Oncogene product expression and DNA content derangements may be related biologic parameters in breast neoplasia, and both are highly associated with cytologic nuclear abnormalities.     

Acetylcholine receptor clusters are associated with nuclei in rat myotubes

Clustered and diffuse acetylcholine receptors are present in cultured myotubes. These clustered AChRs represent regions of myotube membrane containing high receptor density. We have studied the distribution of the AChR clusters and nuclei to determine whether there is an association in the distribution of nuclei beneath AChR clusters. AChR clusters were visualized with alpha-bungarotoxin conjugated to tetramethylrhodamine (alpha BTX-TMR) and the nuclei were stained with bisbenzimide which binds specifically to DNA. This double label procedure, and the computerized analysis of the data allowed us to determine the distribution of nuclei and AChR clusters in the same myotube. During early stages of myotube development the nuclei formed aggregates which were comprised of 4 to 10 nuclei in close apposition to one another. This association of AChR clusters with nuclear aggregates was greatest at Day 4 after plating. As the number of nuclear aggregates associated with clusters decreased the number of nuclei in the aggregates also decreased and the AChR clusters decreased in size as well as number. At all time points examined, the concentration of myotube nuclei in the cells was 3 to 12 times higher beneath areas of AChR clusters than away from clusters. Our computerized analysis shows that there is an association of the AChR clusters with the nuclear region during myotube development.     

Evaluation of the effects of cryopreservation of isolated erythrocytes and leukocytes of largemouth bass by flow cytometry

We examined the effects of separation and freezing on fish leukocyte and erythrocyte morphology by light microscopy and on DNA content as measured by flow cytometry (FCM). Leukocytes and erythrocytes of largemouth bass Micropterus salmoides were isolated by density gradient centrifugation of whole blood, and frozen in liquid nitrogen in a buffer containing DMSO as a cryopreservative. The coefficient of variation (CV) of the G₀/G₁ peak of the cells was used to assess variation in nuclear DNA content within cell populations before and after separation and freezing treatments. In erythrocytes, the CV did not change significantly (P>0.05) when nuclei were isolated and stained without freezing or when erythrocytes were frozen prior to nuclear isolation and staining. In leukocytes, freezing and thawing prior to isolation and staining of nuclei significantly increased the CV (P<0.05), and produced hyperdiploid shoulders of the G₀/G₁ peak. However, the CV of leukocyte nuclei that were isolated and stained prior to freezing and the CV of non-frozen leukocyte nuclei did not differ (P>0.05). Microscopy showed that the freezing protocol had little effect on erythrocyte morphology, but caused irregular swelling in leukocytes. Freezing intact leukocytes also significantly (p<0.05) altered the apparent distribution of cells among the phases of the cell cycle as measured by FCM. The distributions of leukocyte nuclei that were isolated and stained prior to freezing were not different to non-frozen leukocytes. DNA measurements of nucleated blood cells are widely used in physiological, genetic and toxicological studies. Our results suggest that whole blood and erythrocytes for use in such studies can be frozen whole using a simple protocol, but leukocyte nuclei must be isolated and stained before freezing to avoid serious artifacts.     

Involvement of DNA-polymerase activities in mouse-blastocyst differentiation in vitro

Full-grown blastocysts were cultured for 70-92 h in Dulbecco's modified Eagle's medium supplemented with fetal calf serum. They were treated with (1) aphidicolin, a specific inhibitor of eucaryotic DNA polymerase alpha, (2) dideoxythymidine (d2Thd), the precursor of dideoxythymidine triphosphate (d2TTP), a specific inhibitor of DNA polymerase beta and (3) d2TTP itself. Cytophotometric measurements of both the DNA content and the nuclear areas were performed. The results show firstly that trophectoderm differentiation into primary giant trophoblast cells is already irreversibly programmed at the blastocyst stage and does not depend on any DNA replication cycle from that stage onwards. Secondly, the typical enlargement of the trophoblastic nuclei, which occurs at the peri-implantation period, is not related to a proportional increase in DNA content. Thirdly, the onset and progress of DNA endoreduplication in trophoblastic cells is carried out by DNA polymerase alpha during the first part of gestation instead of DNA polymerase beta, as has previously been shown to be the case for mid-gestation rat trophoblast cells.     

Morphometry in surgical pathology

The potential role of morphometry in surgical pathology is discussed. Specific areas in which morphometry could be helpful are in (1) identifying malignant cells in lesions that are largely composed of benign-appearing cells (e.g., follicular thyroid neoplasms), (2) defining reference points in apparent continua (e.g., in the progression from normal colon to adenoma to adenocarcinoma), (3) distinguishing between benign and malignant lesions with similar appearances (e.g., fibromatosis and fibrosarcoma of the soft tissue) and (4) distinguishing between similar-appearing types of malignant neoplasms (e.g., between small-cell carcinoma of the lung and small-cell lymphoma). Morphometric techniques are already being used in DNA ploidy determinations, which frequently bear prognostic information. The measurement of other nuclear and cellular parameters has been used for both diagnostic and prognostic ends; one example is the relation of nuclear roundness to metastatic potential in prostatic carcinomas. Morphometry is now being increasingly applied to histologic sections, as in the prognostic study of lesion thickness in malignant melanoma and the diagnostic study of glandular architecture in colonic adenoma. The use of morphometry can enhance the observation and interpretation of morphologic features, which, combined with the clinical data and the experience of the pathologist, can lead to greater accuracy and precision in surgical pathology diagnoses.