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Dantas AF, Fascineli ML, José SCBR, Pádua JG, Gimenes MA, Grisolia CK. Loss of genetic integrity in artificially aged seed lots of rice (Oryza sativa L.) and common bean (Phaseolus vulgaris L.). MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 846:403080. [PMID: 31585628 DOI: 10.1016/j.mrgentox.2019.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/27/2019] [Accepted: 07/27/2019] [Indexed: 10/26/2022]
Abstract
Loss of genetic integrity can occur during the long-term conservation of seeds. We have studied these effects in seeds of rice (Oryza sativa L.) and common bean (Phaseolus vulgaris L.) exposed to accelerated aging (elevated temperature and moisture) conditions. Tests of first count, germination, and germination speed index were performed to measure physiological quality; cytogenetic tests and comet assay were used to evaluate genetic integrity. With aging, we observed a decrease in mitotic index and an increase in the frequency of chromosomal alterations in root cells of imbibed seeds, as well as increased DNA damage (comet assay) in dry and imbibed seed embryos of both species. The comet assay can be a useful technique for measuring genetic integrity in seed conservation programs.
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Affiliation(s)
- Alisson F Dantas
- Laboratory of Genetic Toxicology, Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil.
| | - Maria L Fascineli
- Laboratory of Genetic Toxicology, Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
| | - Solange C B R José
- Brazilian Agricultural Research Corporation (Embrapa) - Embrapa Genetic Resources & Biotechnology, Brasilia, Brazil
| | - Juliano G Pádua
- Brazilian Agricultural Research Corporation (Embrapa) - Embrapa Genetic Resources & Biotechnology, Brasilia, Brazil
| | - Marcos A Gimenes
- Brazilian Agricultural Research Corporation (Embrapa) - Embrapa Genetic Resources & Biotechnology, Brasilia, Brazil
| | - Cesar K Grisolia
- Laboratory of Genetic Toxicology, Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasilia, Brasilia, Brazil
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Nikolova T, Marini F, Kaina B. Genotoxicity testing: Comparison of the γH2AX focus assay with the alkaline and neutral comet assays. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2017; 822:10-18. [PMID: 28844237 DOI: 10.1016/j.mrgentox.2017.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Genotoxicity testing relies on the quantitative measurement of adverse effects, such as chromosome aberrations, micronuclei, and mutations, resulting from primary DNA damage. Ideally, assays will detect DNA damage and cellular responses with high sensitivity, reliability, and throughput. Several novel genotoxicity assays may fulfill these requirements, including the comet assay and the more recently developed γH2AX assay. Although they are thought to be specific for genotoxicants, a systematic comparison of the assays has not yet been undertaken. In the present study, we compare the γH2AX focus assay with the alkaline and neutral versions of the comet assay, as to their sensitivities and limitations for detection of genetic damage. We investigated the dose-response relationships of γH2AX foci and comet tail intensities at various times following treatment with four prototypical genotoxicants, methyl methanesulfonate (MMS), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), mitomycin C, and hydrogen peroxide (H2O2) and we tested whether there is a correlation between the endpoints, i.e., alkali-labile sites and DNA strand breaks on the one hand and the cell's response to DNA double-strand breaks and blocked replication forks on the other. Induction of γH2AX foci gave a linear dose response and all agents tested were positive in the assay. The increase in comet tail intensity was also a function of dose; however, mitomycin C was almost completely ineffective in the comet assay, and the doses needed to achieve a significant effect were somewhat higher for some treatments in the comet assay than in the γH2AX foci assay, which was confirmed by threshold analysis. There was high correlation between tail intensity and γH2AX foci for MMS and H2O2, less for MNNG, and none for mitomycin C. From this we infer that the γH2AX foci assay is more reliable, sensitive, and robust than the comet assay for detecting genotoxicant-induced DNA damage.
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Affiliation(s)
- Teodora Nikolova
- Institute of Toxicology, University Medical Center, Mainz, Germany
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center, Mainz, Germany
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany.
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Ganapathy S, Muraleedharan A, Sathidevi PS, Chand P, Rajkumar RP. CometQ: An automated tool for the detection and quantification of DNA damage using comet assay image analysis. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2016; 133:143-154. [PMID: 27393806 DOI: 10.1016/j.cmpb.2016.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/17/2016] [Accepted: 05/31/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND AND OBJECTIVE DNA damage analysis plays an important role in determining the approaches for treatment and prevention of various diseases like cancer, schizophrenia and other heritable diseases. Comet assay is a sensitive and versatile method for DNA damage analysis. The main objective of this work is to implement a fully automated tool for the detection and quantification of DNA damage by analysing comet assay images. METHODS The comet assay image analysis consists of four stages: (1) classifier (2) comet segmentation (3) comet partitioning and (4) comet quantification. Main features of the proposed software are the design and development of four comet segmentation methods, and the automatic routing of the input comet assay image to the most suitable one among these methods depending on the type of the image (silver stained or fluorescent stained) as well as the level of DNA damage (heavily damaged or lightly/moderately damaged). A classifier stage, based on support vector machine (SVM) is designed and implemented at the front end, to categorise the input image into one of the above four groups to ensure proper routing. Comet segmentation is followed by comet partitioning which is implemented using a novel technique coined as modified fuzzy clustering. Comet parameters are calculated in the comet quantification stage and are saved in an excel file. RESULTS Our dataset consists of 600 silver stained images obtained from 40 Schizophrenia patients with different levels of severity, admitted to a tertiary hospital in South India and 56 fluorescent stained images obtained from different internet sources. The performance of "CometQ", the proposed standalone application for automated analysis of comet assay images, is evaluated by a clinical expert and is also compared with that of a most recent and related software-OpenComet. CometQ gave 90.26% positive predictive value (PPV) and 93.34% sensitivity which are much higher than those of OpenComet, especially in the case of silver stained images. The results are validated using confusion matrix and Jaccard index (JI). Comet assay images obtained after DNA damage repair by incubation in the nutrient medium were also analysed, and CometQ showed a significant change in all the comet parameters in most of the cases. CONCLUSIONS Results show that CometQ is an accurate and efficient tool with good sensitivity and PPV for DNA damage analysis using comet assay images.
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Affiliation(s)
- Sreelatha Ganapathy
- Department of Electronics & Communication Engineering, National Institute of Technology Calicut, India.
| | - Aparna Muraleedharan
- Department of Anatomy, Pondicherry Institute of Medical Sciences (PIMS), Kalapet Puducherry, India
| | | | - Parkash Chand
- Department of Anatomy, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, India
| | - Ravi Philip Rajkumar
- Department of Psychiatry, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, India
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Lanier C, Manier N, Cuny D, Deram A. The comet assay in higher terrestrial plant model: Review and evolutionary trends. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 207:6-20. [PMID: 26327498 DOI: 10.1016/j.envpol.2015.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/13/2015] [Indexed: 05/24/2023]
Abstract
The comet assay is a sensitive technique for the measurement of DNA damage in individual cells. Although it has been primarily applied to animal cells, its adaptation to higher plant tissues significantly extends the utility of plants for environmental genotoxicity research. The present review focuses on 101 key publications and discusses protocols and evolutionary trends specific to higher plants. General consensus validates the use of the percentage of DNA found in the tail, the alkaline version of the test and root study. The comet protocol has proved its effectiveness and its adaptability for cultivated plant models. Its transposition in wild plants thus appears as a logical evolution. However, certain aspects of the protocol can be improved, namely through the systematic use of positive controls and increasing the number of nuclei read. These optimizations will permit the increase in the performance of this test, namely when interpreting mechanistic and physiological phenomena.
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Affiliation(s)
- Caroline Lanier
- Université Lille 2, EA 4483, Laboratoire des Sciences Végétales et Fongiques - Faculté des Sciences Pharmaceutiques et Biologiques, B.P. 83, F-59006 Lille Cedex, France; Université Lille 2, Faculté Ingénierie et Management de la Santé (ILIS), EA 4483, 42, Rue Ambroise Paré, 59120 Loos, France
| | - Nicolas Manier
- INERIS, Parc Technologique ALATA, B.P. 2, 60550 Verneuil en Halatte, France
| | - Damien Cuny
- Université Lille 2, Faculté Ingénierie et Management de la Santé (ILIS), EA 4483, 42, Rue Ambroise Paré, 59120 Loos, France
| | - Annabelle Deram
- Université Lille 2, EA 4483, Laboratoire des Sciences Végétales et Fongiques - Faculté des Sciences Pharmaceutiques et Biologiques, B.P. 83, F-59006 Lille Cedex, France; Université Lille 2, Faculté Ingénierie et Management de la Santé (ILIS), EA 4483, 42, Rue Ambroise Paré, 59120 Loos, France.
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Sreelatha G, Muraleedharan A, Sathidevi P, Chand P, Rajkumar R. Quantification of DNA damage by the analysis of silver stained comet assay images. Ing Rech Biomed 2015. [DOI: 10.1016/j.irbm.2015.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ge J, Chow DN, Fessler JL, Weingeist DM, Wood DK, Engelward BP. Micropatterned comet assay enables high throughput and sensitive DNA damage quantification. Mutagenesis 2015; 30:11-9. [PMID: 25527723 DOI: 10.1093/mutage/geu063] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The single cell gel electrophoresis assay, also known as the comet assay, is a versatile method for measuring many classes of DNA damage, including base damage, abasic sites, single strand breaks and double strand breaks. However, limited throughput and difficulties with reproducibility have limited its utility, particularly for clinical and epidemiological studies. To address these limitations, we created a microarray comet assay. The use of a micrometer scale array of cells increases the number of analysable comets per square centimetre and enables automated imaging and analysis. In addition, the platform is compatible with standard 24- and 96-well plate formats. Here, we have assessed the consistency and sensitivity of the microarray comet assay. We showed that the linear detection range for H2O2-induced DNA damage in human lymphoblastoid cells is between 30 and 100 μM, and that within this range, inter-sample coefficient of variance was between 5 and 10%. Importantly, only 20 comets were required to detect a statistically significant induction of DNA damage for doses within the linear range. We also evaluated sample-to-sample and experiment-to-experiment variation and found that for both conditions, the coefficient of variation was lower than what has been reported for the traditional comet assay. Finally, we also show that the assay can be performed using a 4× objective (rather than the standard 10× objective for the traditional assay). This adjustment combined with the microarray format makes it possible to capture more than 50 analysable comets in a single image, which can then be automatically analysed using in-house software. Overall, throughput is increased more than 100-fold compared to the traditional assay. Together, the results presented here demonstrate key advances in comet assay technology that improve the throughput, sensitivity, and robustness, thus enabling larger scale clinical and epidemiological studies.
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Affiliation(s)
- Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Danielle N Chow
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jessica L Fessler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - David M Weingeist
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - David K Wood
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bevin P Engelward
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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Gyori BM, Venkatachalam G, Thiagarajan PS, Hsu D, Clement MV. OpenComet: an automated tool for comet assay image analysis. Redox Biol 2014; 2:457-65. [PMID: 24624335 PMCID: PMC3949099 DOI: 10.1016/j.redox.2013.12.020] [Citation(s) in RCA: 447] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 12/18/2013] [Accepted: 12/22/2013] [Indexed: 11/16/2022] Open
Abstract
Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.
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Affiliation(s)
- Benjamin M Gyori
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; School of Computing, National University of Singapore, Singapore
| | - Gireedhar Venkatachalam
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - P S Thiagarajan
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; School of Computing, National University of Singapore, Singapore
| | - David Hsu
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; School of Computing, National University of Singapore, Singapore
| | - Marie-Veronique Clement
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Sharma AK, Soussaline F, Sallette J, Dybdahl M. The influence of the number of cells scored on the sensitivity in the comet assay. Mutat Res 2012; 749:70-5. [PMID: 22981767 DOI: 10.1016/j.mrgentox.2012.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 06/08/2012] [Accepted: 07/25/2012] [Indexed: 10/27/2022]
Abstract
The impact on the sensitivity of the in vitro comet assay by increasing the number of cells scored has only been addressed in a few studies. The present study investigated whether the sensitivity of the assay could be improved by scoring more than 100 cells. Two cell lines and three different chemicals were used: Caco-2 cells were exposed to ethylmethane sulfonate and hydrogen peroxide in three concentrations, and HepG2 cells were exposed to ethylmethane sulfonate, hydrogen peroxide and benzo[a]pyrene in up to four concentrations, in four to five independent experiments. The scoring was carried out by means of a fully automated scoring system and the results were analyzed by evaluating the % tail DNA of 100-700 randomly selected cells for each slide consisting of two gels. By increasing the number of cells scored, the coefficients of variance decreased, leading to an improved sensitivity of the assay. A two-way ANOVA analysis of variance showed that the contribution from the two variables "the number of cells scored" and "concentration" on the total variation in the coefficients of variance dataset was statistically significant (p<0.05). The increase in sensitivity was demonstrated by the possibility to detect an increase in % tail DNA with statistical significance at lower concentrations. The results indicated that for low levels of DNA damage, below 9% tail DNA, scoring of 600 cells increased the sensitivity compared with scoring of 100 cells. For relatively low levels of DNA damage, about 9-16% tail DNA, scoring of 300 cells increased the sensitivity. Thus, the recommendation for the optimum number of cells scored would be 600 and 300 for low and relatively low levels of DNA damage, respectively. The findings from this study could be particularly important for bio-monitoring studies where small differences in DNA-damage levels could be relevant.
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Affiliation(s)
- Anoop Kumar Sharma
- Technical University of Denmark, National Food Institute, Søborg, Denmark.
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González JE, Romero I, Barquinero JF, García O. Automatic analysis of silver-stained comets by CellProfiler software. Mutat Res 2012; 748:60-4. [PMID: 22771502 DOI: 10.1016/j.mrgentox.2012.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/25/2012] [Accepted: 06/27/2012] [Indexed: 10/28/2022]
Abstract
The comet assay is one of the most widely used methods to evaluate DNA damage and repair in eukaryotic cells. The comets can be measured by software, in a semi-automatic or automatic process. In this paper, we apply the CellProfiler open-source software for automatic analysis of comets from digitized images, reporting the percentage of tail DNA. A side-by-side comparison of CellProfiler with CASP software demonstrated good agreement between the two packages. Our work demonstrates that automatic measurement of silver-stained comets with open-source software is possible, providing significant time savings.
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Affiliation(s)
- J E González
- Laboratorio de Radiobiología, Centro de Protección e Higiene de las Radiaciones, La Habana, Cuba.
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Automated segmentation of comet assay images using Gaussian filtering and fuzzy clustering. Med Biol Eng Comput 2012; 50:523-32. [PMID: 22402889 DOI: 10.1007/s11517-012-0882-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
Abstract
Comet assay is one of the most popular tests for the detection of DNA damage at single cell level. In this study, an algorithm for comet assay analysis has been proposed, aiming to minimize user interaction and providing reproducible measurements. The algorithm comprises two-steps: (a) comet identification via Gaussian pre-filtering and morphological operators; (b) comet segmentation via fuzzy clustering. The algorithm has been evaluated using comet images from human leukocytes treated with a commonly used DNA damaging agent. A comparison of the proposed approach with a commercial system has been performed. Results show that fuzzy segmentation can increase overall sensitivity, giving benefits in bio-monitoring studies where weak genotoxic effects are expected.
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Mukherjee B, Dutta A, Roychoudhury S, Ray MR. Chronic inhalation of biomass smoke is associated with DNA damage in airway cells: involvement of particulate pollutants and benzene. J Appl Toxicol 2011; 33:281-9. [PMID: 22131134 DOI: 10.1002/jat.1748] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 08/26/2011] [Accepted: 08/26/2011] [Indexed: 11/08/2022]
Abstract
This study examined whether indoor air pollution from biomass fuel burning induces DNA damage in airway cells. For this, sputum cells were collected from 56 premenopausal rural women who cooked with biomass (wood, dung, crop residues) and 49 age-matched controls who cooked with cleaner liquefied petroleum gas. The levels of particulate matters with diameters of less than 10 and 2.5 µm (PM(10) and PM(2.5)) in indoor air were measured using a real-time aerosol monitor. Benzene exposure was monitored by measuring trans,trans-muconic acid (t,t-MA) in urine by HPLC-UV. DNA damage was examined by alkaline comet assay in sputum cells. Generation of reactive oxygen species (ROS) and level of superoxide dismutase (SOD) in sputum cells were measured by flow cytometry and spectrophotometry, respectively. Compared with controls, biomass users had 4 times higher tail percentage DNA, 37% more comet tail length and 5 times more Olive tail moment (p < 0.001) in inflammatory and epithelial cells in sputum, suggesting extensive DNA damage. In addition, women who cooked with biomass had 6 times higher levels of urinary t,t-MA and 2-fold higher levels of ROS generation concomitant with 28% depletion of SOD. Indoor air of biomass-using households had 2-4 times more PM(10) and PM(2.5) than that of controls. After controlling potential confounders, positive association was found between DNA damage parameters, particulate pollution, urinary t,t-MA and ROS. Thus, long-term exposure to biomass smoke induces DNA damage in airway cells and the effect was probably mediated, at least in part, by oxidative stress generated by inhaled particulate matter and benzene.
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Affiliation(s)
- Bidisha Mukherjee
- Department of Experimental Hematology, Chittaranjan National Cancer Institute, 37 SP Mukherjee Road, Kolkata 700 026, India
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Genotoxicity testing in vitro – Development of a higher throughput analysis method based on the comet assay. Toxicol In Vitro 2009; 23:1570-5. [DOI: 10.1016/j.tiv.2009.07.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 06/16/2009] [Accepted: 07/06/2009] [Indexed: 11/24/2022]
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