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Journal articles on the topic 'COMET assay'

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Author: Grafiati

Published: 4 June 2021

Last updated: 10 March 2023

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1

DİNÇER, Yıldız, and Selin KANKAYA. "Comet Assay for Determining of DNA Damage: Review." Turkiye Klinikleri Journal of Medical Sciences 30, no. 4 (2010): 1365–73. http://dx.doi.org/10.5336/medsci.2009-15258.

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2

Bivehed, Erik, and Björn Hellman. "Flash-comet assay." MethodsX 7 (2020): 101161. http://dx.doi.org/10.1016/j.mex.2020.101161.

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3

Baert, Philippe, and Patrick Van Oostveldt. "Miniaturizing the comet assay with 3D vertical comets." Cytometry 51A, no. 1 (December 23, 2002): 26–34. http://dx.doi.org/10.1002/cyto.a.10006.

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4

Afiahayati, Edgar Anarossi, Ryna Dwi Yanuaryska, and Sri Mulyana. "GamaComet: A Deep Learning-Based Tool for the Detection and Classification of DNA Damage from Buccal Mucosa Comet Assay Images." Diagnostics 12, no. 8 (August 18, 2022): 2002. http://dx.doi.org/10.3390/diagnostics12082002.

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Comet assay is a simple and precise method to analyze DNA damage. Nowadays, many research studies have demonstrated the effectiveness of buccal mucosa cells usage in comet assays. However, several software tools do not perform well for detecting and classifying comets from a comet assay image of buccal mucosa cells because the cell has a lot more noise. Therefore, a specific software tool is required for fully automated comet detection and classification from buccal mucosa cell swabs. This research proposes a deep learning-based fully automated framework using Faster R-CNN to detect and classify comets in a comet assay image taken from buccal mucosa swab. To train the Faster R-CNN model, buccal mucosa samples were collected from 24 patients in Indonesia. We acquired 275 comet assay images containing 519 comets. Furthermore, two strategies were used to overcome the lack of dataset problems during the model training, namely transfer learning and data augmentation. We implemented the proposed Faster R-CNN model as a web-based tool, GamaComet, that can be accessed freely for academic purposes. To test the GamaComet, buccal mucosa samples were collected from seven patients in Indonesia. We acquired 43 comet assay images containing 73 comets. GamaComet can give an accuracy of 81.34% for the detection task and an accuracy of 66.67% for the classification task. Furthermore, we also compared the performance of GamaComet with an existing free software tool for comet detection, OpenComet. The experiment results showed that GamaComet performed significantly better than OpenComet that could only give an accuracy of 11.5% for the comet detection task. Downstream analysis can be well conducted based on the detection and classification results from GamaComet. The analysis showed that patients owning comet assay images containing comets with class 3 and class 4 had a smoking habit, meaning they had more cells with a high level of DNA damage. Although GamaComet had a good performance, the performance for the classification task could still be improved. Therefore, it will be one of the future works for the research development of GamaComet.

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5

McArt, Darragh G., George McKerr, C. Vyvyan Howard, Kurt Saetzler, and Gillian R. Wasson. "Modelling the comet assay." Biochemical Society Transactions 37, no. 4 (July 22, 2009): 914–17. http://dx.doi.org/10.1042/bst0370914.

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The single-cell gel electrophoresis technique or comet assay is widely regarded as a quick and reliable method of analysing DNA damage in individual cells. It has a proven track record from the fields of biomonitoring to nutritional studies. The assay operates by subjecting cells that are fixed in agarose to high salt and detergent lysis, thus removing all the cellular content except the DNA. By relaxing the DNA in an alkaline buffer, strands containing breaks are released from supercoiling. Upon electrophoresis, these strands are pulled out into the agarose, forming a tail which, when stained with a fluorescent dye, can be analysed by fluorescence microscopy. The intensity of this tail reflects the amount of DNA damage sustained. Despite being such an established and widely used assay, there are still many aspects of the comet assay which are not fully understood. The present review looks at how the comet assay is being used, and highlights some of its limitations. The protocol itself varies among laboratories, so results from similar studies may vary. Given such discrepancies, it would be attractive to break the assay into components to generate a mathematical model to investigate specific parameters.

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6

B�cker, W., W. Rolf, T. Bauch, W. U. M�ller, and C. Streffer. "Automated comet assay analysis." Cytometry 35, no. 2 (February 1, 1999): 134–44. http://dx.doi.org/10.1002/(sici)1097-0320(19990201)35:2<134::aid-cyto5>3.0.co;2-9.

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7

Kawaguchi, Satomi, Takanori Nakamura, Ayumi Yamamoto, Gisho Honda, and Yu F. Sasaki. "Is the Comet Assay a Sensitive Procedure for Detecting Genotoxicity?" Journal of Nucleic Acids 2010 (2010): 1–8. http://dx.doi.org/10.4061/2010/541050.

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Although the Comet assay, a procedure for quantitating DNA damage in mammalian cells, is considered sensitive, it has never been ascertained that its sensitivity is higher than the sensitivity of other genotoxicity assays in mammalian cells. To determine whether the power of the Comet assay to detect a low level of genotoxic potential is superior to those of other genotoxicity assays in mammalian cells, we compared the results of Comet assay with those of micronucleus test (MN test). WTK1 human lymphoblastoid cells were exposed to methyl nitrosourea (MNU), ethyl nitrosourea (ENU), methyl methanesulfonate (MMS), ethyl methanesulfonate (EMS), bleomycin (BLM), or UVC. In Comet assay, cells were exposed to each mutagen with (Comet assay/araC) and without (Comet assay) DNA repair inhibitors (araC and hydroxyurea). Furthermore, acellular Comet assay (acellular assay) was performed to determine how single-strand breaks (SSBs) as the initial damage contributes to DNA migration and/or to micronucleus formation. The lowest genotoxic dose (LGD), which is defined as the lowest dose at which each mutagen causes a positive response on each genotoxicity assay, was used to compare the power of the Comet assay to detect a low level of genotoxic potential and that of MN test; that is, a low LGD indicates a high power. Results are summarized as follows: (1) for all mutagens studied, LGDs were MN test ≦ Comet assay; (2) except for BLM, LGDs were Comet assay/araC ≦ MN test; (3) except for UVC and MNU, LGDs were acellular assay ≦ Comet assay/araC ≦ MN test ≦ Comet assay. The following is suggested by the present findings: (1) LGD in the Comet assay is higher than that in MN test, which suggests that the power of the MN test to detect a low level of genotoxic potential is superior to that of the Comet assay; (2) for the studied mutagens, all assays were able to detect all mutagens correctly, which suggests that the sensitivity of the Comet assay and that of the MN test were exactly identical; (3) the power of the Comet assay to detect a low level of genotoxic potential can be elevated to a level higher than that of MN test by using DNA resynthesis inhibitors, such as araC and HU.

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8

Kennedy, E. K., J. P. McNamee, L. Prud'homme Lalonde, T. Jones, and D. Wilkinson. "Acellular comet assay: a tool for assessing variables influencing the alkaline comet assay." Radiation Protection Dosimetry 148, no. 2 (March 11, 2011): 155–61. http://dx.doi.org/10.1093/rpd/ncr027.

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9

Zee, Yeng Peng, Carmen López-Fernández, F. Arroyo, Stephen D. Johnston, William V. Holt, and Jaime Gosalvez. "Evidence that single-stranded DNA breaks are a normal feature of koala sperm chromatin, while double-stranded DNA breaks are indicative of DNA damage." REPRODUCTION 138, no. 2 (August 2009): 267–78. http://dx.doi.org/10.1530/rep-09-0021.

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In this study, we have used single and double comet assays to differentiate between single- and double-stranded DNA damage in an effort to refine the interpretation of DNA damage in mature koala spermatozoa. We have also investigated the likelihood that single-stranded DNA breakage is part of the natural spermiogenic process in koalas, where its function would be the generation of structural bends in the DNA molecule so that appropriate packaging and compaction can occur. Koala spermatozoa were examined using the sperm chromatin dispersion test (SCDt) and comet assays to investigate non-orthodox double-stranded DNA. Comet assays were conducted under 1) neutral conditions; and 2) neutral followed by alkaline conditions (double comet assay); the latter technique enabled simultaneous visualisation of both single-stranded and double-stranded DNA breaks. Following the SCDt, there was a continuum of nuclear morphotypes, ranging from no apparent DNA fragmentation to those with highly dispersed and degraded chromatin. Dispersion morphotypes were mirrored by a similar diversity of comet morphologies that could be further differentiated using the double comet assay. The majority of koala spermatozoa had nuclei with DNA abasic-like residues that produced single-tailed comets following the double comet assay. The ubiquity of these residues suggests that constitutive alkali-labile sites are part of the structural configuration of the koala sperm nucleus. Spermatozoa with ‘true’ DNA fragmentation exhibited a continuum of comet morphologies, ranging from a more severe form of alkaline-susceptible DNA with a diffuse single tail to nuclei that exhibited both single- and double-stranded breaks with two comet tails.

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10

Teixeira Neto, Paulo Florentino, Ronald Feitosa Pinheiro, and Romélia Pinheiro Gonçalves. "Comet assay in myelodysplastic syndromes." Revista Brasileira de Hematologia e Hemoterapia 34, no. 4 (2012): 317. http://dx.doi.org/10.5581/1516-8484.20120080.

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11

Anderson, D., and M. J. Plewa. "The International Comet Assay Workshop." Mutagenesis 13, no. 1 (January 1, 1998): 67–73. http://dx.doi.org/10.1093/mutage/13.1.67.

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12

Collins, A. R., A. A. Oscoz, G. Brunborg, I. Gaivao, L. Giovannelli, M. Kruszewski, C. C. Smith, and R. Stetina. "The comet assay: topical issues." Mutagenesis 23, no. 3 (February 17, 2008): 143–51. http://dx.doi.org/10.1093/mutage/gem051.

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13

CEMELI, E., A. BAUMGARTNER, and D. ANDERSON. "Antioxidants and the Comet assay." Mutation Research/Reviews in Mutation Research 681, no. 1 (January 2009): 51–67. http://dx.doi.org/10.1016/j.mrrev.2008.05.002.

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14

Kumaravel, T. S., Barbara Vilhar, Stephen P. Faux, and Awadhesh N. Jha. "Comet Assay measurements: a perspective." Cell Biology and Toxicology 25, no. 1 (November 27, 2007): 53–64. http://dx.doi.org/10.1007/s10565-007-9043-9.

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15

Piperakis, S. M. "Comet assay: A brief history." Cell Biology and Toxicology 25, no. 1 (June 13, 2008): 1–3. http://dx.doi.org/10.1007/s10565-008-9081-y.

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16

Choucroun, P., D. Gillet, G. Dorange, B. Sawicki, and J. D. Dewitte. "Comet assay and early apoptosis." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 478, no. 1-2 (July 2001): 89–96. http://dx.doi.org/10.1016/s0027-5107(01)00123-3.

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17

Carvalho, Natália C., Rozilda L. de Souza, Felipe Dal-Pizzol, and Vanessa Moraes de Andrade. "Comet assay in neonatal sepsis." Indian Journal of Pediatrics 77, no. 8 (August 2010): 875–77. http://dx.doi.org/10.1007/s12098-010-0127-9.

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18

Cortés-Gutiérrez, Elva I., Martha I. Dávila-Rodríguez, José Luís Fernández, Carmen López-Fernández, Altea Gosálbez, and Jaime Gosálvez. "New Application of the Comet Assay." Journal of Histochemistry & Cytochemistry 59, no. 7 (May 3, 2011): 655–60. http://dx.doi.org/10.1369/0022155411410884.

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The comet assay is a well-established, simple, versatile, visual, rapid, and sensitive tool used extensively to assess DNA damage and DNA repair quantitatively and qualitatively in single cells. The comet assay is most frequently used to analyze white blood cells or lymphocytes in human biomonitoring studies, although other cell types have been examined, including buccal, nasal, epithelial, and placental cells and even spermatozoa. This study was conducted to design a protocol that can be used to generate comets in subnuclear units, such as chromosomes. The new technique is based on the chromosome isolation protocols currently used for whole chromosome mounting in electron microscopy, coupled to the alkaline variant of the comet assay, to detect DNA damage. The results show that migrant DNA fragments can be visualized in whole nuclei and isolated chromosomes and that they exhibit patterns of DNA migration that depend on the level of DNA damage produced. This protocol has great potential for the highly reproducible study of DNA damage and repair in specific chromosomal domains.

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19

Gajski, Goran, Sabine Langie, and Aliy Zhanataev. "Recent applications of the Comet Assay: A report from the International Comet Assay Workshop 2019." Toxicology Letters 333 (October 2020): 1–3. http://dx.doi.org/10.1016/j.toxlet.2020.07.022.

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20

Seo, Jung-Eun, Se-Wook Oh, Yun-Ji Kim, Nam-Hyouck Lee, Sang-Pill Hong, and Young-Ho Kim. "Study on the Characteristics of DNA Comet Assay for Irradiated Vegetables and Grains." Journal of the Korean Society of Food Science and Nutrition 37, no. 4 (April 30, 2008): 472–76. http://dx.doi.org/10.3746/jkfn.2008.37.4.472.

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21

Collins, A. R. "The comet assay: a heavenly method!" Mutagenesis 30, no. 1 (December 19, 2014): 1–4. http://dx.doi.org/10.1093/mutage/geu079.

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22

Olive, Peggy L. "The Comet Assay in Clinical Practice." Acta Oncologica 38, no. 7 (January 1999): 839–44. http://dx.doi.org/10.1080/028418699432527.

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23

Shaposhnikov, Sergey, Gunnar Brunborg, Amaya Azqueta, Isabel Gaivão, Andrew Smart, and Andrew R. Collins. "Novel formats for the comet assay." Toxicology Letters 221 (August 2013): S189. http://dx.doi.org/10.1016/j.toxlet.2013.05.431.

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24

Pant, K., S. W. Bruce, S. Springer, M. Klug Laforce, L. J. Rausch, and R. Kulkarni. "Comet assay in rat nasal tissue." Toxicology Letters 258 (September 2016): S305—S306. http://dx.doi.org/10.1016/j.toxlet.2016.06.2045.

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25

Rank, Jette, Kristian Syberg, and Klara Jensen. "Comet assay on tetraploid yeast cells." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 673, no. 1 (February 2009): 53–58. http://dx.doi.org/10.1016/j.mrgentox.2008.11.014.

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26

Fairbairn, Daryl W., Peggy L. Olive, and Kim L. O'Neill. "The comet assay: a comprehensive review." Mutation Research/Reviews in Genetic Toxicology 339, no. 1 (February 1995): 37–59. http://dx.doi.org/10.1016/0165-1110(94)00013-3.

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27

Karlsson, Hanna L. "The comet assay in nanotoxicology research." Analytical and Bioanalytical Chemistry 398, no. 2 (July 18, 2010): 651–66. http://dx.doi.org/10.1007/s00216-010-3977-0.

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28

Brunborg, Gunnar. "Reference cells in the comet assay." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 845 (September 2019): 403064. http://dx.doi.org/10.1016/j.mrgentox.2019.05.020.

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29

Brunborg, Gunnar, and Andrew Collins. "Guidance for publishing comet assay results." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 854-855 (June 2020): 503146. http://dx.doi.org/10.1016/j.mrgentox.2020.503146.

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30

Gajendiran, Natarajan, Kimio Tanaka, and Nanao Kamada. "Comet assay to sense neutron ‘fingerprint’." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 452, no. 2 (September 2000): 179–87. http://dx.doi.org/10.1016/s0027-5107(00)00082-8.

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31

Chernigina, I. A., and T. G. Shcherbatyuk. "A New Version of Comet Assay." Sovremennye tehnologii v medicine 8, no. 1 (March 2016): 20–27. http://dx.doi.org/10.17691/stm2016.8.1.03.

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32

Wang, Alexander S. S., B. Ramanathan, Yuan-Hung Chien, C. M. V. Goparaju, and Kun-Yan Jan. "Comet assay with nuclear extract incubation." Analytical Biochemistry 337, no. 1 (February 2005): 70–75. http://dx.doi.org/10.1016/j.ab.2004.10.024.

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33

Møller, Peter, Amaya Azqueta, Elisa Boutet-Robinet, Gudrun Koppen, Stefano Bonassi, Mirta Milić, Goran Gajski, et al. "Minimum Information for Reporting on the Comet Assay (MIRCA): recommendations for describing comet assay procedures and results." Nature Protocols 15, no. 12 (October 26, 2020): 3817–26. http://dx.doi.org/10.1038/s41596-020-0398-1.

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AbstractThe comet assay is a widely used test for the detection of DNA damage and repair activity. However, there are interlaboratory differences in reported levels of baseline and induced damage in the same experimental systems. These differences may be attributed to protocol differences, although it is difficult to identify the relevant conditions because detailed comet assay procedures are not always published. Here, we present a Consensus Statement for the Minimum Information for Reporting Comet Assay (MIRCA) providing recommendations for describing comet assay conditions and results. These recommendations differentiate between ‘desirable’ and ‘essential’ information: ‘essential’ information refers to the precise details that are necessary to assess the quality of the experimental work, whereas ‘desirable’ information relates to technical issues that might be encountered when repeating the experiments. Adherence to MIRCA recommendations should ensure that comet assay results can be easily interpreted and independently verified by other researchers.

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34

Kim, So-Jung, Young-Jae Chung, and Taek-Kyun Lee. "In vivo Comet Assay on Flounder and Clam Exposed to BaP and TBT." Ocean and Polar Research 33, no. 2 (June 30, 2011): 127–33. http://dx.doi.org/10.4217/opr.2011.33.2.127.

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35

Kirilova, Milena, Rumen Ivanov, and George Miloshev. "A novel parameter in comet assay measurements." Genetika 37, no. 2 (2005): 93–101. http://dx.doi.org/10.2298/gensr0502093k.

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Single Cell Gel Electrophoresis (SCGE) or Comet assay is a very sensitive method for assessing damages in DNA on a single cell level. It has found many applications in fields where genotoxic activity could be an issue. In environmental monitoring, health care, food industry Comet assay is used with increasing popularity. For verifying the results obtained by this method many parameters could be monitored. To that end several software packages exist. In the conditions that we are suggesting one more parameter could be measured - comet shape. We argue that this parameter could be an advantage of the Comet Assay when the way of DNA damaging needs to be predicted.

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36

Koppen, Gudrun, Amaya Azqueta, Bertrand Pourrut, Gunnar Brunborg, Andrew R. Collins, and Sabine A. S. Langie. "The next three decades of the comet assay: a report of the 11th International Comet Assay Workshop." Mutagenesis 32, no. 3 (March 4, 2017): 397–408. http://dx.doi.org/10.1093/mutage/gex002.

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37

Møller, Peter, Damian Muruzabal, Tamara Bakuradze, Elke Richling, Ezgi Eyluel Bankoglu, Helga Stopper, Sabine A. S. Langie, et al. "Potassium bromate as positive assay control for the Fpg-modified comet assay." Mutagenesis 35, no. 4 (April 22, 2020): 341–48. http://dx.doi.org/10.1093/mutage/geaa011.

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Abstract The comet assay is a popular assay in biomonitoring studies. DNA strand breaks (or unspecific DNA lesions) are measured using the standard comet assay. Oxidative stress-generated DNA lesions can be measured by employing DNA repair enzymes to recognise oxidatively damaged DNA. Unfortunately, there has been a tendency to fail to report results from assay controls (or maybe even not to employ assay controls). We believe this might have been due to uncertainty as to what really constitutes a positive control. It should go without saying that a biomonitoring study cannot have a positive control group as it is unethical to expose healthy humans to DNA damaging (and thus potentially carcinogenic) agents. However, it is possible to include assay controls in the analysis (here meant as a cryopreserved sample of cells i.e. included in each experiment as a reference sample). In the present report we tested potassium bromate (KBrO3) as a positive comet assay control for the formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay. Ten laboratories used the same procedure for treatment of monocytic THP-1 cells with KBrO3 (0.5, 1.5 and 4.5 mM for 1 h at 37°C) and subsequent cryopreservation. Results from one laboratory were excluded in the statistical analysis because of technical issues in the Fpg-modified comet assay. All other laboratories found a concentration–response relationship in cryopreserved samples (regression coefficients from 0.80 to 0.98), although with different slopes ranging from 1.25 to 11.9 Fpg-sensitive sites (%DNA in tail) per 1 mM KBrO3. Our results demonstrate that KBrO3 is a suitable positive comet assay control.

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38

Olive, P. L., and J. P. Banáth. "Growth fraction measured using the comet assay." Cell Proliferation 25, no. 5 (September 1992): 447–57. http://dx.doi.org/10.1111/j.1365-2184.1992.tb01453.x.

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39

McArt, D. G., G. R. Wasson, G. McKerr, K. Saetzler, M. Reed, and C. V. Howard. "Systematic random sampling of the comet assay." Mutagenesis 24, no. 4 (May 28, 2009): 373–78. http://dx.doi.org/10.1093/mutage/gep020.

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40

Gutzkow, Kristine B., Torgrim M. Langleite, Silja Meier, Anne Graupner, Andrew R. Collins, and Gunnar Brunborg. "High-throughput comet assay using 96 minigels." Mutagenesis 28, no. 3 (March 5, 2013): 333–40. http://dx.doi.org/10.1093/mutage/get012.

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41

McNamee, J. P., J. R. N. McLean, C. L. Ferrarotto, and P. V. Bellier. "Comet assay: rapid processing of multiple samples." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 466, no. 1 (March 2000): 63–69. http://dx.doi.org/10.1016/s1383-5718(00)00004-8.

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42

Burlinson, B. "The comet assay – Peculiarities, pitfalls and interpretation." Toxicology Letters 238, no. 2 (October 2015): S17. http://dx.doi.org/10.1016/j.toxlet.2015.08.175.

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43

OLIVE, P. "Impact of the comet assay in radiobiology." Mutation Research/Reviews in Mutation Research 681, no. 1 (January 2009): 13–23. http://dx.doi.org/10.1016/j.mrrev.2007.11.001.

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44

Baumgartner, A., E. Cemeli, and D. Anderson. "The comet assay in male reproductive toxicology." Cell Biology and Toxicology 25, no. 1 (October 31, 2007): 81–98. http://dx.doi.org/10.1007/s10565-007-9041-y.

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45

Klaude, Maria, Stefan Eriksson, Jonas Nygren, and Gunnar Ahnström. "The comet assay: mechanisms and technical considerations." Mutation Research/DNA Repair 363, no. 2 (June 1996): 89–96. http://dx.doi.org/10.1016/0921-8777(95)00063-1.

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46

Devaux, A., M. Pesonen, and G. Monod. "Alkaline comet assay in rainbow trout hepatocytes." Toxicology in Vitro 11, no. 1-2 (February 1997): 71–79. http://dx.doi.org/10.1016/s0887-2333(97)00004-0.

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47

Gajendran, Natarajan. "Comet assay to monitor cell line aging." Indian Journal of Science and Technology 1, no. 1 (January 30, 2007): 1–4. http://dx.doi.org/10.17485/ijst/2008/v1i1/1.

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48

Kiziltan, Erhan, and Erkan Yurtcu. "Semi-automatic scoring tool for comet assay." Journal of Serbian Society for Computational Mechanics 9, no. 2 (2015): 27–33. http://dx.doi.org/10.5937/jsscm1502027k.

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49

Cotelle, S., and J. F. F�rard. "Comet assay in genetic ecotoxicology: A review." Environmental and Molecular Mutagenesis 34, no. 4 (1999): 246–55. http://dx.doi.org/10.1002/(sici)1098-2280(1999)34:4<246::aid-em4>3.0.co;2-v.

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50

Petersen, Anita B., Robert Gniadecki, and Hans Christian Wulf. "Laser scanning cytometry for comet assay analysis." Cytometry 39, no. 1 (January 1, 2000): 10–15. http://dx.doi.org/10.1002/(sici)1097-0320(20000101)39:1<10::aid-cyto3>3.0.co;2-r.

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