Fluorometric analysis of DNA in cell cultures

A simple, reproducible fluorescent assay has been described which can be used confidently at microgram and submicrogram levels. The method is most suitable for cell cycle and cell growth analysis using [3H]thymidine as the radioactive tracer. A modified method is also described for preparing diaminobenzoic acid hydrochloride.     

Deconvolving sequence variation in mixed DNA populations.

We present an original approach to identifying sequence variants in a mixed DNA population from sequence trace data. The heart of the method is based on parsimony: given a wildtype DNA sequence, a set of observed variations at each position collected from sequencing data, and a complete catalog of all possible mutations, determine the smallest set of mutations from the catalog that could fully explain the observed variations. The algorithmic complexity of the problem is analyzed for several classes of mutations, including block substitutions, single-range deletions, and single-range insertions. The reconstruction problem is shown to be NP-complete for single-range insertions and deletions, while for block substitutions, single character insertion, and single character deletion mutations, polynomial time algorithms are provided. Once a minimum set of mutations compatible with the observed sequence is found, the relative frequency of those mutations is recovered by solving a system of linear equations. Simulation results show the algorithm successfully deconvolving mutations in p53 known to cause cancer. An extension of the algorithm is proposed as a new method of high throughput screening for single nucleotide polymorphisms by multiplexing DNA.     

The autoradiographic test for unscheduled DNA synthesis: a sensitive assay for the detection of DNA repair in the HepG2 cell line

We assessed the DNA-repair capacity of HepG2 cells, which were derived from a human hepatoma, by the unscheduled DNA synthesis assay, using the autoradiography protocol (UDS-AR). We evaluated DNA repair following exposure to direct mutagens (4-nitroquinoline-N-oxide (4-NQO), methyl methanesulfonate (MMS)), to mutagens requiring metabolic activation (benzo[a]pyrene (B[a]P), 2-acetylaminofluorene (2-AAF), N-dimethylnitrosoamine (NDMA)) or to structurally related non-mutagens such as pyrene and 4-acetylaminofluorene (4-AAF). All positive compounds tested induced UDS in HepG2 cells. With 4-NQO and MMS, a concentration-dependent increase in net nuclear grains per cell was observed, with 73 and 90% of cells, respectively, in repair at the highest concentration. B[a]P, 2-AAF and NDMA displayed similar dose-dependent UDS responses, but the percentage of cells in repair was lower (about 45%) than that for 4-NQO and MMS. We assessed the genotoxicity of the compounds tested by determining IC(5NNG): the concentration required to induce 5NNG. The compounds studied were ranked in order of IC(5NNG) as follows: 4-NQO = B[a]P > 2-AAF > MMS > NDMA. The UDS assay discriminated between mutagens and non-mutagens, as pyrene and 4-AAF failed to induce DNA repair. The present study demonstrates that UDS can be used as an endpoint for the detection of DNA damage in HepG2 cells.     

An autoradiographic method of detectingA. laidlawii andM. hyorhinis in cell cultures

Summary The autoradiographic investigation of L cells and Chinese hamster cells for the presence of mycoplasmas (A. laidlawii andM. hyorhinis) using uridine/uracil (UdR/U) testing is a rapid and reliable method suitable for the serial checking of even a small number of cells. It depends on a reduced incorporation of [³H]uridine and an increased uptake of [³H]uracil into the RNA of mycoplasma-infected cells, shown in autoradiograms by the density of the grains and their distribution. Results obtained by the autoradiographic technique correspond approximately to specific activity values of RNA-infected cells after the incorporation of [³H]uridine and [³H]uracil.     

Folate requirement for blast cell transformation in mixed leukocyte cultures.

Mixed leukocyte cultures from normal donors were set up in standard tissue culture media. Blast cell transformation was measured 6 days later by ³H-thymidine uptake and assessed qualitatively with stained smears. Media RPMI 1629 and RPMI 1640 allowed much more intense blastogenesis than Medium 199, the difference being due to the low folic acid content of Medium 199 (0.01 mg/liter) compared with RPMI 1629 (10 mg/liter) and RPMI 1640 (1 mg/liter). Further experiments indicated that folic acid increased the multiplication rate of blast cells but did not promote the induction or initial transformation phases of the mixed leukocyte reaction. The effect of folic acid on the PHA response was entirely different: ³H-thymidine uptake in 3 day PHA cultures was decreased, and there was no apparent effect on the number or percentage of blast cells seen on the smears. The reason for this difference is at present unknown, but some possibilities are discussed.     

Experiments on the induction of antibody dependent macrophage-mediated cellular cytotoxicity in mixed brain cell cultures.

These examinations were based on the discussion whether in demyelinating diseases anti-lipid antibody associated with brain macrophages could have a cytotoxic effect on oligodendrocytes. We used mixed brain cell cultures of newborn rats where, among others, both oligodendrocytes and vacuolated macrophage-like cells were found. On these macrophage-like cells, the presence of Fc-receptors was proven. Besides Fc-receptor-dependent phagocytosis, these cells showed an Fc-receptor-independent type of phagocytosis. The Fc-receptor-bearing cells moved within the culture and adhered to glass fibers. In the cytoplasm of these cells, unspecific esterase, acid phosphatase and peroxidase could be visualized. The vacuolated cells showed strong autofluorescence, expressed a surface marker found on all types of rat leukocytes and were marked by Griffonia simplicifolia lectin. These results definitely characterized the vacuolised cells as macrophages. We saw globular and pleomorphic macrophages. After incubation of anti-GC serum in a highly diluted solution, significantly more macrophages bound to oligodendrocytes than in the controls. In these cases, we found target cell lysis. It could be shown in vitro that anti-GC serum together with macrophages of neonatal brains can induce a cytotoxic effect on oligodendrocytes.     

An autoradiographic screening test for mycoplasmal contamination of mammalian cell cultures

Summary Autoradiographic detection of incorporation of tritiated thymidine into the cytoplasm of cultured mammalian cells has been evaluated as a test of contamination of the cultures by cell-associated microorganisms, which usually are mycoplasmas. Criteria which indicate the presence of cell-associated mycoplasmas have been established, and the reliability of the standardized autoradiographic method has been assessed by testing the same cultures by two colony formation methods of mycoplasmal detection. The autoradiographic method demonstrated cell-associated microorganisms in all cultures from which characteristic colonies were grown on mycoplasma agar. The autoradiographic method did not produce false positive results, and the outcome of this test was evident in 3 days as opposed to 7 to 14 days by agar culture methods. Some applications of the autoradiographic method are shown, and it is suggested that this method be employed for routine surveillance for mycoplasmal contamination in laboratories where facilities for frequent agar culture tests are not easily available. This research was supported by U.S. Public Health Service Grants CA 12351-02 and CA 12334-01 from the National Cancer Institute.     

Communication compartments in mixed cell cultures

Mixed cultures of epithelial (BRL) cells and fibroblasts (BHK), which sort themselves out into separate domains of each cell type, form communication compartments. Electrical coupling, dye coupling and metabolic coupling measurements have been used to show that small ions and molecules can move freely via intercellular junctions between all the cells in a domain, while their movement across the boundaries between domains is severely restricted. Metabolic coupling is the most sensitive method for detecting trans-boundary communication but the results obtained from all three methods are compatible. The data suggest the reduced transfer across the boundaries is due to fewer channels, resulting from a lower frequency of junction formation between heterologous cells, rather than to channels of smaller diameter. Concentration gradients of small cytoplasmic molecules can be established within these communication compartments which are similar to those predicted to explain pattern formation in developing systems. It is suggested that the cell surface features which cause this sorting out are also responsible for the reduced frequency of heterologous junction formation and hence for compartmentalization.     

Cell-cycle analysis of perturbed cell populations: computer simulation of sequential DNA distributions.

A mathematical model is presented that permits simulation of a time sequence of DNA distributions with a single set of cell-cycle parameters. The method is particularly suited to the quantitative analysis of sets of sequential DNA distributions from perturbed cell populations. The model permits determination of the durations and associated dispersions of the phases of the cell cycle as well as the point in the cell cycle at which the perturbing agent exerts its effect. The mathematical details of the simulation technique are presented, and the technique is applied to the analysis of DNA distributions from perturbed cell populations. Three cell populations are modeled: CHO-line cells released from a block at the interface of the G1-and S-phases, 3T3 cells released from a G1-phase block produced by serum starvation, and S49 mouse lymphoma cells responding to a block in the G1-phage produced by N6,02'-dibutyryl adenosine 3':5'-cyclic monophosphate (Bt2cAMP).     

Flow-cytometric analysis of mixed cell populations using intermediate filament antibodies

Using two human tumour cell lines, T24 bladder carcinoma and Molt-4 leukemia, flow-cytometric DNA analysis of pure and mixed cell populations was performed using cellular cytokeratin content to distinguish cytokeratin-containing carcinoma cells from leukemia cells which do not contain cytokeratin. Using cytokeratin content to gate DNA analysis, the same specificity and sensitivity of cellular DNA content and distribution measurement could be achieved by single-pass FCM analysis of a mixture of the two cell types as was seen when analysing pure populations of the two cell lines. This technique has broad applicability to FCM analysis of mixed populations composed of cells from different tissues of origin.     

DNA damage and repair in brain: relationship to aging.

The usefulness of conducting DNA damage and repair studies in a postmitotic tissue like brain is emphasized. We review studies that use brain as a tissue to test the validity of the DNA damage and repair hypothesis of aging. As far as the accumulation of age dependent DNA damage is concerned, the data appear to overwhelmingly support the hypothesis. However, attempts to demonstrate a decline in DNA repair capacity as a function of age are conflicting and equally divided. Possible reasons for this discrepancy are discussed. It is suggested that assessment of the repair capacity of neurons with respect to a specific type of damage in a specific gene might yield more definitive answers regarding the role of DNA repair potential in the aging process and as a longevity assurance system.     

DNA excision repair and transcription: implications for genome evolution

The past two years have seen a substantial increase in knowledge regarding the enzymology of DNA excision repair. These data support a growing body of information which suggests that transcribed nucleotide sequences are preferentially subject to excision repair. It is possible that these mechanisms, or related ones, are relevant to the molecular evolution of sequences that appear not to evolve according to models which do not take into account regional sequence differences in the extent of DNA repair.     

Abnormal recovery of DNA replication in ultraviolet-irradiated cell cultures of Drosophila melanogaster which are defective in DNA repair

Summary Cell cultures prepared from embryos of a control stock of Drosophila melanogaster respond to ultraviolet light with a decline and subsequent recovery both of thymidine incorporation and in the ability to synthesize nascent DNA in long segments. Recovery of one or both capacities is absent or diminished in irradiated cells from ten nonallelic mutants that are defective in DNA repair and from four of five nonallelic mutagen-sensitive mutants that exhibit normal repair capabilities. Recovery of thymidine incorporation is not observed in nine of ten DNA repair-defective mutants. On the other hand, partial or complete recovery of incorporation is observed in all but one repair-proficient mutagen-sensitive mutant.Irradiated cells from two mutants that display no excision capacity exhibit a gradual arrest of thymidine incorporation within 20 h after the initial decline. This arrest of incorporation is not observed in mutants exhibiting only partial defects in excision repair.Recovery of the ability to synthesize nascent DNA in long segments is normal in cells from the two mutants that display no excision capacity, indicating that recovery does not depend upon the excision of pyrimidine dimers from cellular DNA. Recovery of that ability is not observed, however, in cells from one partially excision-defective mutant, two of three postreplication repair-defective mutants, two of four mutants defective in both excision and postreplication repair, and one of five repair-proficient mutagen-sensitive mutants. These results indicate that recovery of normal DNA replication in irradiated Drosophila cells depends upon the activity of several functions.Abbreviation used UV ultraviolet light — principal wavelength 254 nm