The comet assay method: a new approach in genotoxicology research

The comet assay is a fast, simple and sensitive genotoxicological technique for measuring DNA damage in an individual cell of virtually any cell type of animal or plant origin. Electrophoresis of complete cell genome (assuming a comet-like shape) combined with the image analysis systems for comet analysis provide densitometric and geometric parameters describing the complete comet as well as the head and tail. The comet optical density values are used to quantify the total comet fluorescence and hence indicate DNA content and the level of damage. The application of this method in different fields makes it a powerful tool in human genotoxic study as well as in the estimation of environmental pollution.     

Detection of DNA damage in stressed trout nucleated erythrocytes using the comet assay: protection by nitroxide radicals

Because previous literature reports have demonstrated that nucleated trout erythrocytes in conditions of oxidative stress are subjected to both membrane damage and a decrease in the enzymatic defense systems (glutathione peroxidase), which in turn lead to hemolysis, the present study was undertaken to determine whether DNA may be affected too, prior to the hemolytic event. Impairment of DNA in stressed trout erythrocytes was assessed using the comet assay--a rapid and sensitive, single-cell gel electrophoresis technique used to detect primary DNA damage in individual cells. In addition, indolinic and quinolinic nitroxide radicals were included in the study to determine their efficacy as antioxidants against free-radical-induced DNA damage. The parameters, tail length, tail intensity, and tail moment, used as an index of DNA damage, have shown that trout erythrocytes exposed to oxidative stress experience DNA damage prior to hemolysis and that the nitroxides significantly prevent this damage. This result provides further information about the potential use of these compounds as antioxidants in biological systems.     

Supercoiled DNA repair in thymocyte fractions differing in radiosensitivity

Mouse thymocyte fractions were isolated on the basis of buoyant density in a step-gradient of human serum albumin. These fractions were characterized by cell size, radiosensitivity and hydrocortisone sensitivity, and by labelled precursor incorporation into DNA, RNA and proteins. The relative sedimentation of nucleoids in sucrose gradient was also determined. Large and more radioresistant thymocytes were characterized by an increased rate of DNA repair compared with the fraction of radiosensitive small lymphocytes. Nucleoids prepared from the small thymocyte fraction had greater relative sedimentation rates than those derived from large cells. The response of relative sedimentation of nucleoids from large and small thymocyte fractions to ethidium bromide concentration does not permit a conclusion on different superhelix density for DNA in cells of these fractions. At the same time the estimate of the supercoiled domain size for nucleoids of large and small thymocyte fractions showed that in the more radiosensitive small cells domains of greater size were predominant.     

Image analysis of comet assay measurements

In the last decade the 'comet assay' or 'single cell gel electrophoresis assay' has been established as a sensitive method for the detection of DNA damage and the measurement of its recovery. The results published in the literature have often been obtained with different methods for comet structure measurement. In most cases these data are not comparable with each other. Even when using similar systems for the analysis, it is difficult to obtain matching data. This presentation will describe some technical aspects of our measurement equipment and evaluation software. It focuses on necessary experimental conditions to minimize errors in obtaining such data. The software developed here allows the rapid analysis of the microscopic samples (< 2 s per image). The image analysis was designed with respect to the morphological shapes of comet cells, which were investigated with a confocal laser microscope. The system is built with standard components which are commercially available. As a measure of the amount of DNA damage the ratio of fluorescence intensity was used inside the comet tail and the fluorescence intensity of the comet head. Other parameters such as DNA content, comet area, head radius, tail length and tail moment are also determined. The reproducibility of the system has been evaluated in several experiments over a period of 5 years.     

Isolation of two fractions of hepatocytes and characterization of their lipid composition

Two fractions of hepatocytes were isolated from the rat liver by nonfermentative method. These fractions were different for mechanical stability to the action of perfusion factors. It has been shown that cells of these fractions were differently separated in the linear density gradient of sucrose. It was connected with structural and functional heterogeneity of hepatocytes in the liver. Results obtained allow us to confirm that hepatocytes in the liver form at least two classes of cells with different lipid content. The plasmatic membranes of hepatocytes with high content of lipids were inclined to damage in the process of liver perfusion as compared to cells with low lipid content.     

A structure-specific DNA endonuclease is enriched in kinetoplasts purified from Crithidia fasciculata

The mitochondrial DNA (kinetoplast DNA) of the trypanosomatid Crithidia fasciculata consists of minicircles and maxicircles topologically interlocked in a single network per cell. Individual minicircles replicate unidirectionally from either of two replication origins located 180 degrees apart on the minicircle DNA. Initiation of minicircle leading-strand synthesis involves the synthesis of an RNA primer which is removed in the last stage of replication. We report here the purification to near homogeneity of a structure-specific DNA endo-nuclease based on the RNase H activity of the enzyme on a poly(rA).poly(dT) substrate. RNase H activity gel analysis of whole cell and kinetoplast extracts shows that the enzyme is enriched in kinetoplast fractions. The DNA endonuclease activity of the enzyme is specific for DNA primers annealed to a template strand and requires an unannealed 5' tail. The enzyme cleaves 3' of the first base paired nucleotide releasing the intact tail. The purified enzyme migrates as a 32 kDa protein on SDS gels and has a Stoke's radius of 21.5 A and a sedimentation coefficient of 3.7 s, indicating that the protein is a monomer in solution with a native molecular mass of 32.4 kDa. These results suggest that the enzyme may be involved in RNA primer removal during minicircle replication.     

Comet assay demonstrates a higher ultraviolet B sensitivity to DNA damage in dysplastic nevus cells than in common melanocytic nevus cells and foreskin melanocytes

We used the single cell gel electrophoresis assay (comet assay) to study ultraviolet B (UVB)-induced DNA damage in pigment cells. This assay detects DNA damage, mainly DNA strand breaks and alkali labile sites in the DNA molecule. We studied the effect of biologically relevant doses (comparable to 2-3 MED (minimal erythemal dose) for in vivo irradiated full-thickness skin) of monochromatic UVB light of 302 nm on cultured melanocytes derived from foreskin, common melanocytic nevi, and dysplastic nevi. We were able to demonstrate a linear dose-response relationship between UV dose and the migration coefficient of the comet tail in all three types of pigment cells. Nevus cells originating from dysplastic nevi showed the highest sensitivity to UVB irradiation: 65% higher induction of DNA damage compared to the induction in foreskin melanocytes. Common melanocytic nevus cells were most resistant and showed a 30% lower induction of DNA damage in comparison to foreskin melanocytes. Differences in chromatin structure and cell cycle profile may influence the results of the comet assay. Control experiments with x-ray irradiation, which is well known to produce direct DNA strand breaks via radical formation, revealed only small differences between the three types of melanocytic cells. It is unlikely, therefore, that intrinsic nuclear characteristics may account for the observed differences.     

Bacteriophage MX-1: properties of the phage and its structural proteins

Bacteriophage MX-1 is a virulent DNA phage for Myxococcus. The host range includes strains of Myxococcus xanthus, M. fulvus and M. virescens. The phage has a sedimentation coefficient (S degrees 20,w) of 1145S and a density of 1-531 g/ml. By using SDS-polyacrylamide gel electrophoresis, 23 phage proteins with apparent mol. wt. between 10000 and 150000 were resolved. Gel filtration in the presence of non-ionic detergent partially resolved the proteins. The fraction excluded from Sephadex G-100, fraction 1, contains two glycoproteins. Fraction 1 was resolved into three fractions (1-1, 1-2 and 1-3) by chromatography on Sephadex G-200. The glycoproteins were present in fraction 1-2; all the proteins from this fraction were derived from the phage tail. Comparison of the amino-acid, hexosamine and neutral-sugar compositions of the two glycoproteins showed that they are distinct molecular species; the smaller molecule is not a subunit of the larger. The significance of these findings is discussed and compared with the proteins of the tails of T-even phage of Escherichia coli.     

Sacharose density gradient separation of Ehrlich ascites carcinoma and L-5178Y tumor cells in different cell cycle phases

Optimal conditions were determined for the distribution of Ehrlich ascites carcinoma (EAC) and L-5178Y mouse tumor cells, proliferating in vivo, by their age within the cell cycle by sedimentation in a buffered linear sacharose density gradient. Measurements of cell size, DNA content and incorporation of tritiated thymidine in successive parts of the gradient confirmed the actual separation of cells of different age: in the upper fractions there were cells in G1 phase, in the middle fractions in S phase and in the lower layers of the gradient there were cells in G2 and/or M phase.     

DNA-binding properties of the tandem HMG boxes of high-mobility-group protein 1 (HMG1)

High-mobility-group protein 1 (HMG1) is a conserved chromosomal protein with two homologous DNA-binding HMG-box domains, A and B, linked by a short basic region to an acidic carboxy-terminal tail. NMR spectroscopy on the free didomain (AB) shows that the two HMG boxes do not interact. The didomain has a higher affinity for all DNA substrates tested than single HMG-box domains and has a significantly higher ability to distort DNA by bending and supercoiling. The interaction of the didomain with DNA is stabilized by the presence of the basic region (approximately 20 residues, 9 of which are Lys) that links the second HMG box to the acidic tail in intact HMG1; this may be, at least in part, why this region also enhances supercoiling of relaxed circular DNA by the didomain and circularization of short DNA fragments (in the presence of ligase). Competition assays suggest significantly different structure-specific preferences of single and tandem HMG boxes for four-way junction and supercoiled plasmid DNA. Binding to supercoiled DNA appears to be promoted by protein oligomerization, which is pronounced for the didomains. Electron microscopy suggests that the oligomers are globular aggregates, associated with DNA looping. One box versus two (or several) is likely to be an important determinant of the properties of (non-sequence specific) HMG-box proteins.     

Mutational spectra of a 100-base pair mitochondrial DNA target sequence in bronchial epithelial cells: a comparison of smoking and nonsmoking twins

Seventeen separate mitochondrial hot spot mutations in a 100-bp target sequence (mitochondrial bp 10,030-10,130) were detected and measured in bronchial epithelial cell samples isolated from smokers and nonsmokers. Among the individuals sampled were three pairs of monozygotic twins in which one twin had never smoked and had a nonsmoking spouse, and the other had a smoking history of >10 pack-years. Individual point mutations present at frequencies as low as 10(-6) were detected. Partially denaturing electrophoresis was used to separate mutant from nonmutant sequences on the basis of their melting temperatures, and the target sequence was subsequently amplified via high-fidelity PCR with Pfu DNA polymerase. Tests were performed to determine whether mismatch intermediates or DNA adducts present in the cellular DNA were converted to mutants during PCR. Hot spot mutations were clearly observed in bronchial epithelial cells, and the same hot spots were observed consistently in different samples. Significant numerical variability in the mutant fractions for individual mutants was observed among samples and are ascribed to unequal mitochondrial segregation in stem and transition cells. The mutational spectra in smokers' samples did not differ significantly from the mutational spectra in nonsmokers' samples for this 100 bp of mitochondrial DNA. No smoking-specific hot spots were detected. The overall mutant fractions in smokers' samples were not elevated compared to those of nonsmokers. As much variability was observed between two samples from the same individual's lung as between a sample from a smoker and a sample from a nonsmoker. These findings demonstrate that inhaled tobacco smoke does not induce prominent point mutations in this 100-bp target mitochondrial sequence in smokers' bronchial epithelial cells. Endogenous factors (e.g., DNA replication errors or DNA damage by endogenous reactive chemicals) are suggested to be more likely to represent the most important contributors to mitochondrial mutagenesis.     

Genome plasticity in the distal tail fiber locus of the T-even bacteriophage: recombination between conserved motifs swaps adhesin specificity

The adsorption specificity of the T-even phages is determined by the protein sequence near the tip of the long tail fibers. These adhesin sequences are highly variable in both their sequence and specificity for bacterial receptors. The tail fiber adhesin domains are located in different genes in closely related phages of the T-even type. In phage T4, the adhesin sequence is encoded by the C-terminal domain of the large tail fiber gene (gene 37), but in T2, the adhesin is a separate gene product (gene 38) that binds to the tip of T2 tail fibers. Analysis of phage T6 and Ac3 sequences reveals additional variant forms of this locus. The tail fiber host specificity determinants can be exchanged, although the different loci have only limited homology. Chimeric fibers can be created by crossovers either between small homologies within the structural part of the fiber gene or in conserved motifs of the adhesin domain. For example, the T2 adhesin determinants are flanked by G-rich DNA motifs and exchanges involving these sequences can replace the specificity determinants. These features of the distal tail fiber loci genetically link their different forms and can mediate acquisition of diverse host range determinants, including those that allow it to cross species boundaries and infect taxonomically distant hosts.     

Acute cocaine effects on stereotype and defense: an ethoexperimental approach

Germinated barley foodstuff (GBF), derived from the aleurone and scutellum fractions of germinated barley, is rich in glutamine and low-lignified hemicellulose, and increases mucosal protein, RNA, and DNA content in the intestine when fed to normal rats. The aim of this study was to evaluate the effects of feeding GBF or germinated gramineous seeds on experimental ulcerative colitis. Sprague-Dawley rats that received 3% dextran sulfate sodium in their diets were used as an experimental colitis model. The effects of sulfasalazine, a drug used to treat inflammatory bowel disease, were compared with those of GBF. After rats had consumed diets containing GBF or various aleurone and scutellum fractions, mucosal damage; the content of mucosal protein, RNA, and DNA in the colo-rectum; and serum interleukin-8 and alpha1-acid glycoprotein levels were assessed. GBF and germinated seeds more effectively prevented bloody diarrhea and mucosal damage in colitis compared with controls and rats receiving sulfasalazine, but non-germinated samples did not have a protective effect. GBF increased mucosal protein and RNA content in the colitis model. The consumption of GBF appears to prevent inflammation in a colitis model, and its effect seems to be related to the germination process. GBF and germinated seeds have the potential to serve as nutritional therapy for ulcerative colitis.     

The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors

The solution structure of a complex between the DNA binding domain of a fungal GATA factor and a 13 base-pair oligonucleotide containing its physiologically relevant CGATAG target sequence has been determined by multidimensional nuclear magnetic resonance spectroscopy. The AREA DNA binding domain, from Aspergillus nidulans, possesses a single Cys2-Cys2 zinc finger module and a basic C-terminal tail, which recognize the CGATAG element via an extensive network of hydrophobic interactions with the bases in the major groove and numerous non-specific contacts along the sugar-phosphate backbone. The zinc finger core of the AREA DNA binding domain has the same global fold as that of the C-terminal DNA binding domain of chicken GATA-1. In contrast to the complex with the DNA binding domain of GATA-1 in which the basic C-terminal tail wraps around the DNA and lies in the minor groove, the structure of complex with the AREA DNA binding domain reveals that the C-terminal tail of the fungal domain runs parallel with the sugar phosphate backbone along the edge of the minor groove. This difference is principally attributed to amino acid substitutions at two positions of the AREA DNA binding domain (Val55, Asn62) relative to that of GATA-1 (Gly55, Lys62). The impact of the different C-terminal tail binding modes on the affinity and specificity of GATA factors is discussed.     

Density regulation by choice of fractions in vibratory shaping

Conclusions It has been established by experiment that for fine powders of angular particle shape maximum density in two-fraction mixtures is attained at a coarse component content of 60% (the density is the higher, the larger the ratio between the particle sizes of the coarse and fine fractions). The density of such a mixture may exceed the densities of the starting fractions by 26–37%.A simple method of calculation has been developed enabling the densities of mixtures with different combinations of starting fraction contents to be determined from the optimum densities of the fractions and from the result of a single control experiment. The same method can be employed for calculating two probable ratios between the amounts of starting components at which any given mixture density will be attained.Experiments have shown that a three-component system has a dome-shaped density diagram with a maximum density of more than 80% of theoretical; any given density (lower than maximum) can be obtained at various combinations of starting fraction contents, but the lower this density, the larger is the number of possible composition combinations.Translated from Poroshkovaya Metallurgiya, No. 7(187), pp. 26–30, July, 1978.     

A dual mechanism for impairment of GABAA receptor activity by NMDA receptor activation in rat cerebellum granule cells

It has been estimated that over three million workers in the USA are potentially exposed to silica or other mineral dusts. Results of epidemiological studies evaluating whether silica or glass fibers increase lung cancer risk to the exposed workers are inconclusive. Detection of DNA damage in cells exposed to genotoxic agents is being used to assess the carcinogenic potential of environmental agents. The alkaline (pH > 13) single cell gel/comet (SCG) assay was used to determine and compare DNA damage in cultured Chinese hamster lung fibroblasts (V79 cells) and human embryonic lung fibroblasts (Hel 299 cells) exposed to crystalline silica (Min-U-Sil 5), amorphous silica (Spherisorb), carbon black, and glass fibers (AAA-10). V79 or Hel 299 cells were exposed to these mineral dusts for 3 h at various concentrations. Min-U-Sil 5 and AAA-10, at almost all concentrations tested, caused a significant increase in DNA migration measured as tail length in both V79 and Hel 299 exposed cells. However, the increase was much higher in V79 then in Hel 299 cells for Min-U-Sil 5. Tail length was also increased relative to controls after amorphous silica treatment, but not to the same extent as that induced by crystalline silica. Exposure to carbon black did not induce DNA migration at any of the concentrations tested. These results indicate that silica and glass fibers, but not carbon black, can induce DNA damage in mammalian cells, and that crystalline silica has a higher DNA-damaging activity than amorphous silica. For glass fibers, induction of DNA damage in both V79 and Hel 299 cells was observed even at a concentration 10 times lower than silica and the response was similar in both cell lines. These results suggest that the SCG/comet assay is useful for the detection of DNA damage caused by occupationally related dusts/particles.     

Apoptotic process in the monkey small intestinal epithelium: I. Association with glutathione level and its efflux

The apoptotic process in the normal gastrointestinal mucosa is of interest due to its possible role in physiological cell renewal. The aim of this study was to identify the apoptotic process in the monkey small intestine and the association of glutathione level and its efflux in this process. Monkey small intestinal epithelial cells were separated in to different fractions consisting of villus, middle and crypt cells. Apoptosis was identified by DNA ladder pattern and Hoechst staining. The level of glutathione, its efflux and the enzymes involved in its metabolism were quantitated in these fractions. Apoptotic cells were identified predominantly in the villus tip cell fractions by both DNA ladder pattern and Hoechst dye staining. Glutathione level was 7 fold higher in the crypt cells as compared to villus tip cells the middle cells showing a gradual decrease. A similar pattern was seen in mitochondrial content of glutathione. As the cells mature from crypt to villus, there is increased efflux of GSH, which may be responsible for the decreased level of GSH in apoptotic villus cells. In the monkey small intestine, apoptotic cells are seen in the villus tip fractions and the glutathione level and its efflux may play a role in this process.