Validation of an automatic comet assay analysis system integrating the curve fitting of combined comet intensity profiles

In recent years, the single-cell gel electrophoresis (comet) assay has become a reference technique for the assessment of DNA fragmentation both in vitro and in vivo at the cellular level.In order to improve the throughput of genotoxicity screening, development of fully automated systems is clearly a must. This would allow us to increase processing time and to avoid subjectivity brought about by frequent manual settings required for the ‘classical’ analysis systems.To validate a fully automatic system developed in our laboratory, different experiments were conducted in vitro on murine P388D1 cells with increasing doses of ethyl methanesulfonate (up to 5 mM), thus covering a large range of DNA damage (up to 80% of DNA in the tail). The present study (1) validates our ‘in house’ fully automatic system versus a widely used semi-automatic commercial system for the image-analysis step, and versus the human eye for the image acquisition step, (2) shows that computing tail DNA a posteriori on the basis of a curve fitting concept that combines intensity profiles [G. Dehon, P. Bogaerts, P. Duez, L. Catoire, J. Dubois, Curve fitting of combined comet intensity profiles: a new global concept to quantify DNA damage by the comet assay, Chemom. Intell. Lab. Syst. 73 (2004) 235–243] gives results not significantly different from the ‘classical’ approach but is much more accurate and easy to undertake and (3) demonstrates that, with these increased performances, the number of comets to be scored can be reduced to a minimum of 20 comets per slide without sacrificing statistical reliability.     

Validation and implementation of an internal standard in comet assay analysis

The comet assay is widely used to detect DNA damage in single cells. However, only moderate attention has been paid to the experimental variability of this assay, especially during electrophoresis. To take into account this variation and to be able to compare measurements from different electrophoretic runs, as would be necessary when large numbers of samples need to be analysed, it is important to integrate an internal standard into the assay. This study presents a first step in the validation and implementation of an internal standard in the alkaline comet assay. Untreated and ethyl methanesulfonate treated cells (K562 human erythroleukemia cell line) were used as negative and positive internal standards, respectively, in each electrophoresis run. Three steps were followed: (1) assessment of the different levels of variability which may influence the damage levels of the internal standards, (2) evaluation of the variability across separate electrophoresis runs on the quantification of DNA damage in the internal standards by three experimenters involved in different studies and (3) proposal of an adequate calculation system to integrate the internal standards into test sample data. The application of the two proposed models to samples from a human biomonitoring study is presented. The model which calibrates the measurements against the negative internal standard is the most useful since this negative standard was the most stable across experiments and among the three experimenters. The percentage of DNA in the tail is the most appropriate parameter to analyse induced DNA damage, because its interelectrophoresis and interexperimenter variation is less pronounced than that of tail length.     

Automated comet assay analysis.

BACKGROUND: Recently the "comet assay" or "single-cell gel electrophoresis assay" has been established as a sensitive method for the detection of DNA damage and repair. Most of the software now available to quantify various parameters for DNA damage requires the interaction of a human observer. In this report, we describe an automated analysis system that is based on self-developed software and hardware and needs minimal human interaction. METHODS: The image analysis is divided into two parts: 1) automatic cell recognition and comet classification and 2) quantification of desired comet parameters. Image preprocessing, segmentation, and feature classification were developed with algorithms based on mathematical morphology. To enhance evaluation speed, we have introduced parallel processing of data under the Windows NT operating system (Microsoft Corporation, Redmond, WA). Use of an analogue real-time autofocus unit (B?cker et al.: Phys Med Biol 1997;42:1981-1992) allows for faster analysis. RESULTS: Our recognition software shows a sensitivity of 95.2% and a specificity of 92.7% when tested on test samples from routine work with DNA damage by low-dose radiation (0-2 Gy). The parallel hardware and software concept enables us to analyze 100 comets on one slide in less than 15 min. CONCLUSIONS: A comparison of measurements made on the same samples by manual and automated analysis systems revealed that there are no significant differences. The slope of the dose-response curves and the repair kinetics are very similar and demonstrate that automatic comet assay analysis is possible.     

Potential bias in NMR relaxation data introduced by peak intensity analysis and curve fitting methods

We present an evaluation of the accuracy and precision of relaxation rates calculated using a variety of methods, applied to data sets obtained for several very different protein systems. We show that common methods of data evaluation, such as the determination of peak heights and peak volumes, may be subject to bias, giving incorrect values for quantities such as R₁ and R₂. For example, one common method of peak-height determination, using a search routine to obtain the peak-height maximum in successive spectra, may be a source of significant systematic error in the relaxation rate. The alternative use of peak volumes or of a fixed coordinate position for the peak height in successive spectra gives more accurate results, particularly in cases where the signal/noise is low, but these methods have inherent problems of their own. For example, volumes are difficult to quantitate for overlapped peaks. We show that with any method of sampling the peak intensity, the choice of a 2- or 3-parameter equation to fit the exponential relaxation decay curves can dramatically affect both the accuracy and precision of the calculated relaxation rates. In general, a 2-parameter fit of relaxation decay curves is preferable. However, for very low intensity peaks a 3 parameter fit may be more appropriate.     

Application of an automatic integrating system to the recording of spontaneous locomotor activity in small mammals

This paper describes an automatic system in which the rotation of the drum of a rotating activity cage turns by means of a crank, lever, ratchet, worm and gear, the shaft of a precision, linear, continuous-rotation potentiometer across which a constant potential difference is applied. The potential read off by the moving contact of the potentiometer is thus directly proportional to the number of rotations of the activity wheel. This potential is recorded at any desired interval by an automatic printing meter. By using a multi-point instrument a number of rotating cages can be monitored simultaneously.Any activity which can be made to rotate the potentiometer shaft can be recorded in the way described. Thus records can be obtained from bouncing cages, interruptions of light beams, drops, or any electrical contact, and of course the record could be made on magnetic or punched tapes or on punched cards to facilitate computer analysis, as well as on a printed chart as described.     

Impact of the comet assay in radiobiology

Until the development of single cell gel electrophoresis methods in the 1980s, measurement of radiation-induced DNA strand breaks in individual cells was limited to detection of micronuclei or chromosome breaks that measured the combined effects of exposure and repair. Development of methods to measure the extent of migration of DNA from single cells permitted detection of initial radiation-induced DNA breaks present in each cell. As cells need not be radiolabeled, there were new opportunities for analysis of radiation effects on cells from virtually any tissue, provided a single cell suspension could be prepared. The comet assay (as this method was subsequently named) was able to measure, for the first time, the fraction of radiobiologically hypoxic cells in mouse and human tumors. It was used to determine that the rate of rejoining of DNA breaks was relatively homogenous within an irradiated population of cells. Because individual cells were analyzed, heavily damaged or apoptotic cells could be identified and eliminated from analysis to determine "true" DNA strand break rejoining rates. Other examples of applications of the comet assay in radiobiology research include analysis of the inter-individual differences in response to radiation, effect of hypoxia modifying agents on tumor hypoxic fraction, the role of cell cycle position during DNA break induction and rejoining, non-targeted effects on bystander cells, and effects of charged particles on DNA fragmentation patterns.     

Validation of the sigmoid wave curve fitting algorithm on a forest-tundra ecotone in the Northwest Territories,Canada

Ecotones are gradual transitions between two adjacent ecological systems. Ecotones are characterized by their spatial properties which are reflected in an ecotone width and location and the temporal variation across time during succession or environmental change on both a local and a global scale. If only one main environmental factor drives this gradual change the shape of the ecotone is evident as a sigmoid wave. In this paper we explore a two-dimensional sigmoid wave curve fitting algorithm that describes an ecotone and validate it on classified remote sensing data of a forest-tundra ecotone in the Northwest Territories of Canada. The estimated location and width of the forest-tundra ecotone are validated with digital land cover data. We conclude that the algorithm was able to delineate the forest-tundra ecotone based upon the classified remote sensing image and is robust for various algorithm parameter settings.     

A computer system automatic analysis of vectorcardiograms.

This computer system performs the analysis of orthogonal electrocardiograms for vectorcardiographic (VCG) display and classification. The data acquisition can be performed 'on-line' with the complete analysis in 'real-time', or off-line by processing a magnetic tape. The original computational methods for beat averaging and wave recognition are described. Some features, such as the quality of the visual display of the VCG traces, the availability of a measurement matrix allowing the quantitative analysis of the VCG and the use of a data bank for storage, retrieval and statistical studies make this system very efficient for clinical purposes, introducing the concept of 'Computer Assisted Vectorcardiography'.     

Validation of an automatic system (DoubleCage) for detecting the location of animals during preference tests

Preference tests have often been performed for collecting information about animals' acceptance of environmental refinement objects. In numerous published studies animals were individually tested during preference experiments, as it is difficult to observe group-housed animals with an automatic system. Thus, videotaping is still the most favoured method for observing preferences of socially-housed animals. To reduce the observation workload and to be able to carry out preference testing of socially-housed animals, an automatic recording system (DoubleCage) was developed for determining the location of group-housed animals in a preference test set-up. This system is able to distinguish the transition of individual animals between two cages and to record up to 16 animals at the same time (four animals per cage). The present study evaluated the reliability of the DoubleCage system. The data recorded by the DoubleCage program and the data obtained by human observation were compared. The measurements of the DoubleCage system and manual observation of the videotapes are comparable and significantly correlated (P < 0.0001) with good agreement. Using the DoubleCage system enables precise and reliable recording of the preferences of group-housed animals and a considerable reduction of animal observation time.     

Usefulness of combined in vivo skin comet assay and in vivo skin micronucleus test

We have already found that the in vivo skin comet assay is useful for the evaluation of primary DNA damage induced by genotoxic chemicals in epidermal skin cells. The aim of the present study was to evaluate the sensitivity and specificity of the combined in vivo skin comet assay and in vivo skin micronucleus (MN) test using the same animal to explore the usefulness of the new test method. The combined alkaline comet assay and MN test was carried out with three chemicals: 4-nitroquinoline-1-oxide (4NQO), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and benzo[a]pyrene (B[a]P). In the first experiment, we compared DNA- and chromosome-damaging effects of 3 [72, 24 and 3 hours (h) before sacrifice] and 4 applications (72, 48, 24 and 3h before sacrifice) of 4NQO, which induces dermal irritancy. The animals were euthanized and their skin was sampled for the combination test. As a result, the 4-application method was able to detect both DNA- and chromosome-damaging potential with a lower concentration; therefore, in the second experiment, MNNG and B[a]P were topically applied four times, respectively. The animals were euthanized, and then their skins were sampled for combination tests. In the alkaline comet assay, significant differences in the percent of DNA (%DNA) in the tail were observed in epidermal skin cells treated with MNNG and B[a]P. In the MN test, an increased frequency of MN cells (%MN) cells was observed by treatment with MNNG; however, there were no significant increases. In contrast, significant differences in %MN were observed by treatment with B[a]P. From these results, we conclude that the combined in vivo skin comet assay and in vivo MN test was useful because it can detect different genotoxicity with the same sampling time and reduce the number of animals used.     

Validation of GNE:p.M712T identification by melting curve analysis

Hereditary inclusion body myopathy/distal myopathy with rimmed vacuoles is an adult onset autosomal recessive muscle-wasting disease common in people of Iranian-Jewish descent, due to the founder allelic variant GNE:p.M712T. High correlation of disease susceptibility with GNE:p.M712T allows its use as a molecular marker for diagnosis. In this study, we applied and validated the use of melting curve analysis using SimpleProbe technology for detection of this mutation using specimens obtained by mouthwash, buccal swab, and whole blood. The assay was then applied to 43 clinical specimens, and results were validated by additional methods. A probe spanning this mutation in exon 12 accurately discerns two Tm corresponding to its hybridization to wild-type and M712T-derived amplicons. A 10 degrees C divergence in Tm allowed rapid single-tube genotyping of reference and patient samples with 100% accuracy. Distal myopathy constitutes a large heterogeneous group of pathologies with similar physiological manifestations and little molecular markers for distinguishing subtypes. Application of SimpleProbes for detection of GNE:p.M712T on genomic DNA obtained from buccal epithelial cells allows accurate, rapid, and cost-effective identification of this allele in individuals at risk. This procedure is amenable to automated high-throughput applications and can be extended to both clinical and research applications.     

Preservation of comet assay slides: comparison with fresh slides.

The single cell gel electrophoresis assay (comet assay) is an inexpensive, rapid and highly sensitive method for the determination of DNA damage, crosslinks, and alkaline-labile lesions in individual cells. A limitation of the procedure is that the microelectrophoretic gels must be scored rapidly as the comet configuration deteriorates on storage due to dehydration of the agarose and diffusion of DNA. The objectives of this study were firstly to evaluate drying regimes as rapid and simple methods of preservation of the microgels as close to their original fresh state as possible, and secondly to examine the effects of storage of the slides. Human hepatoma (HepG2) cells challenged for 30 min with hydrogen peroxide (H(2)O(2)) were used in the study. Microgel slides were prepared and evaluated immediately, or after drying with or without a methanol fixation step. Microgels that were dried at a variety of temperatures (22-50 degrees C) and re-hydrated did not differ in the values obtained for H(2)O(2)-induced DNA damage when compared to fresh samples. Samples could also be continually dried and re-hydrated over a period of up to 3 months with no obvious loss of information. In conclusion, drying of microgels represents a simple and inexpensive method of preserving comet assay slides.     

Analysis of chromate-induced DNA-protein crosslinks with the comet assay

Modifications of the comet assay have been introduced to measure crosslinks by determining the reduction of induced DNA migration. Our previous results indicated that the modified protocol of the alkaline comet assay is a sensitive tool for the detection of formaldehyde-induced DNA-protein crosslinks. But results for mitomycin C and cisplatin suggested that the modified protocol is not well suited for the evaluation of DNA-DNA crosslinkers. We now used the comet assay to investigate in V79 cells the effect of potassium chromate (K(2)CrO(4)), another DNA-protein crosslinker, to see whether the results obtained for formaldehyde can be generalized. However, chromate did not reduce spontaneous or radiation-induced DNA migration in the alkaline (pH 13) comet assay but led to a small but significant induction of DNA migration. A crosslinking effect of chromate could also not be detected with the alkaline comet assay after postincubation of cells in normal medium after chromate treatment to enable repair of other (migration-inducing) lesions that might mask the crosslinking effect. Exposure of slides to proteinase K further increased DNA migration of chromate-treated cells, thus indicating the presence of DNA-protein crosslinks. In contrast to the alkaline comet assay, a "neutral" version at pH 9 was suited to demonstrate reduced induction of DNA migration after gamma-irradiation of chromate-treated cells. The crosslinking effect was seen immediately at the end of the chromate treatment as well as after a 3h postincubation period. Using the "neutral" protocol in combination with proteinase K, we were able to demonstrate the presence of DNA-protein crosslinks as the probable cause for the migration-reducing effect. Further investigations will have to show whether this protocol can be recommended as a universal approach for the detection of DNA-protein crosslinks and also of DNA-DNA crosslinks with the comet assay.     

Validation of the anthrax lethal toxin neutralization assay.

A validation of the performance characteristics of a toxin neutralization assay is presented. This in vitro assay measures the functional ability of antisera, containing antibodies to anthrax lethal toxin, to specifically protect J774A.1 cells against Bacillus anthracis lethal toxin cytotoxicity. This colormetric assay is based upon the reduction of MTT by living cells. Human and rabbit antisera produced against anthrax vaccine absorbed (AVA) were used to validate the assay. Results showed a high level of repeatability and reproducibility, particularly for a bio-assay. Inter-assay variability in absorbance values was the most prominent negative finding however, an acceptable level was demonstrated with a ratio [neutralization ratio (NR)] of the test serum 50% effective dose (ED(50)) to the reference standard ED(50). Accuracy was maintained, even in samples with minimal neutralizing capacity, and linearity was noted when sample dilutions resulted in accurate prediction of the Y(max)and Y(min). Specificity tests demonstrated that normal sera did not have an observable effect on the ability of the reference standard to neutralize toxin. The assay remained stable against time, temperature, and freeze/thaw effects on the reference standards, but not on the toxin. The assay also remained stable against media and solution storage effects. Cell passage number and cell plating density were two critical parameters identified during the robustness studies that may be responsible for inter-assay variability in absorbance values. The work was performed in accordance with the FDA's Bioanalytical Method Validation Guidance for Industry and the FDA's Good Laboratory Practice for Nonclinical Laboratory Studies (21 CFR Part 58).     

Contribution of apoptosis to responses in the comet assay

Apoptosis, a physiological process of selected cell deletion, leads to DNA fragmentation in typical segments of 180 base pairs. DNA strand breaks are also an effect induced by genotoxic compounds. The aim of this study was to compare these two types of damaging potentials by a known genotoxic substance and an apoptosis-inducing agent in HT-29 colon adenocarcinoma cells. The cells were incubated for 24h with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), a potent DNA damage-inducing agent, staurosporine, an inhibitor of protein kinase C and apoptosis-inducing agent, and hydrogen peroxide, a source of reactive oxygen species. Apoptosis was measured with the Annexin V affinity assay which detects the translocation of phosphatidylserine (PS) from the inner to the outer leaflet of the cytoplasmic membrane, an early event in the apoptotic process. DNA damage as an end point of genotoxicity was detected by single cell microgel electrophoresis, also called "comet assay". The results show that apoptosis does not necessarily need to correlate or coincide with DNA damage observed with genotoxic substances in the comet assay. The representative apoptosis-inducing agent (staurosporine) did not induce strand breaks in the tested concentrations (0.5 and 1.0microM); genotoxic doses of the strand break inducing agent MNNG did not induce apoptosis. Therefore, the comet assay can be used as a specific test for detecting genotoxicity, and the results are not necessarily confounded by concomittant processes leading to apoptosis.     

State of the art in S-LCA: integrating literature review and automatic text analysis

Purpose

Social life cycle assessment (S-LCA) method lacks of standard and code of practice. The aim of the study is to classify the wide variety of contributions on S-LCA for tracking the development of different themes and for defining and classifying the main approaches in a systematic and reproducible way.

Methods

The research addressed to study a collection of 51 articles published between January 2006 and November 2014 using statistical criteria. We used automatic text analysis (ATA) tools related to lexicon analysis to identify keywords useful in tracing the main topics covered in articles published in different periods. We conducted principal component analysis (PCA) to classify the different approaches in the literature and to outline the orientations of the various research groups.

Results and discussion

The results from lexicon analysis showed a rapid succession of different topics covered in the analyzed period. This alternation is strongly affected by the introduction of UNEP/Society of Environmental Toxicology and Chemistry (SETAC) S-LCA guidelines and methodological sheets. PCA analysis enabled to synthesize the information related to the numerous approaches. Results did not show a clear division into groups which indicates the absence of a dominant position on the subject in the literature.

Conclusions

This study attempted to map the state of art in S-LCA integrating literature review with multivariate statistical techniques. The analysis showed a highly fragmented field. These results confirm the existence of a variety of approaches that in part have already been identified by literature reviews on S-LCA. Alignment with the results in the literature confirms ATA to be a suitable instrument for the realization of reviews. Moreover, being systematic and reproducible allows ATA to be applied repeatedly, expanding the number of articles and topics analyzed.

     

Differential staining of DNA strand breaks in dried comet assay slides.

The comet assay involves embedding cells in agarose on microscope slides. After lysis and electrophoresis, staining is usually performed with a fluorescent DNA-binding dye and observation is carried out on fresh wet slides through an epifluorescence microscope. We present here a simple alternative for preservation of the agarose comet slides and a fluorescent staining that allows fine differential analysis of DNA strand breaks under confocal microscopy. Lymphocytes were processed according to previous published methods. Slides were quickly dehydrated in a hot oven at 50C for 20 min. Once the agarose layer was dried and reduced to a thin film, slides were treated with RNase. Image analysis showed higher tail length, total area, and tail moment. Using confocal microscopic optical sectioning, a thickness of approximately 180 microm for wet slides and 12 microm for dehydrated gels was calculated. Acridine orange, used for DNA differential staining, allowed quantitation of metachromasia and orthochromasia with confocal scanning microscopy. Differences between alkaline and neutral comet assay with AO were clear-cut and, in principle, a metachromatic index can be calculated. (J Histochem Cytochem 49:921-922, 2001)     

Application of public-domain statistical analysis software for evaluation and comparison of comet assay data

A novel approach for statistical analysis of comet assay data (i.e.: tail moment) is proposed, employing public-domain statistical software, the R system. The analytical strategy takes into account that the distribution of comet assay data, like the tail moment, is usually skewed and do not follow a normal distribution. Probability distributions used to model comet assay data included: the Weibull, the exponential, the logistic, the normal, the log normal and log-logistic distribution. In this approach it was also considered that heterogeneity observed among experimental units is a random feature of the comet assay data. This statistical model can be characterized with a location parameter m(ij), a scale parameter r and a between experimental units variability parameter theta. In the logarithmic scale, the parameter m(ij) depends additively on treatment and random effects, as follows: log(m(ij)) = a0 + a1x(ij) + b(i), where exp(a0) represents approximately the mean value of the control group, exp(a1) can be interpreted as the relative risk of damage with respect to the control group, x(ij) is an indicator of experimental group and exp(b(i)) is the individual risk effects assume to follows a Gamma distribution with mean 1 and variance theta. Model selection is based on Akaike's information criteria (AIC). Real data coming from comet analysis of blood samples taken from the flounder Paralichtys orbignyanus (Teleostei: Paralichtyidae) and from samples of cells suspension obtained from the estuarine polychaeta Laeonereis acuta (Nereididae) were employed. This statistical approach showed that the comet assay data should be analyzed under a modeling framework that take into account the important features of these measurements. Model selection and heterogeneity between experimental units play central points in the analysis of these data.     

Low sensitivity of the comet assay to detect acetaldehyde-induced genotoxicity

Acetaldehyde (AA) is known to induce DNA-protein cross-links (DPX) and other genotoxic and mutagenic effects in cultured mammalian cells. Compared to formaldehyde (FA), AA is a very weak inducer of DPX and increased DPX levels are only measured at high, cytotoxic concentrations by different methods. Besides DPX, AA also induces DNA-DNA cross-links. Because the comet assay is increasingly used for the detection of cross-linking agents, we characterized the effects of AA in the comet assay in relation to cytotoxicity and other genetic endpoints such as the induction of sister chromatid exchange (SCE) and micronuclei (MN). The standard alkaline comet assay did not indicate induction of DNA strand-breaks by AA in a range of concentrations from 0.2 to 20 mM. AA at a concentration of 20 mM was clearly cytotoxic and reduced cell growth and population doubling to less than 50% of the control. Using the comet assay modification with proteinase K, slightly enhanced DNA migration was measured in comparison to treatment with AA only. No significant induction of cross-links by AA (measured as reduction of gamma ray-induced DNA migration) was determined by the comet assay. A small and reproducible but statistically not significant effect was measured for the AA concentration 20 mM. A clear and concentration-related increase in the frequency of sister chromatid exchange (SCE) and micronuclei (MN) was already measured at lower concentrations (0.2 and 0.5 mM, respectively). These results suggest that the comet assay has a low sensitivity for the detection of AA-induced DNA lesions leading to the induction of SCE and MN.