Determination of Genetic Mutation Profile of drpr Gene in Drosophila melanogaster using High-Resolution Melting Analysis
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Keywords:
drpr, High resolution melting, Genetic mutation, Drosophila melanogaster
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Abstract
Genotype determination of experimental animals is generally conducted using sequencing methods that require expensive cost as well as experience and special equipment. This study aimed to determine the presence of drpr gene mutation in Drosophila melanogaster using coupled real time PCR-High Resolution Melting (real time PCR-HRM) as an alternative method. Two types of fly samples, w1118 and drprΔ5 were used as wildtype control and mutant genotype, respectively. The DNA from twenty of each w1118 and mutant drprΔ5 flies were isolated and amplified using real time PCR. The generated amplicons were then further processed by HRM method at the temperature of 60-95°C. This study demonstrated that the real time PCR-HRM method could distinguish wildtype control w1118 and mutant drprΔ5 based on the HRM data with the confidence level was more than 90%. Therefore, this study provides an evidence that real time PCR-HRM method might be beneficial to screen the mutant genotype from its wildtype counterpart based on differences in the melting temperatures due to changes at nucleotide base level
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Determination of Genetic Mutation Profile of drpr Gene in Drosophila melanogaster using High-Resolution Melting Analysis. (2022). Jurnal Biota, 8(1), 11-18. https://doi.org/10.19109/Biota.v8i1.7556
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How to Cite
Determination of Genetic Mutation Profile of drpr Gene in Drosophila melanogaster using High-Resolution Melting Analysis. (2022). Jurnal Biota, 8(1), 11-18. https://doi.org/10.19109/Biota.v8i1.7556
References
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Buckingham, L. (2012). Molecular Diagnostics: Fundamentals, Methods, and Clinical Applications: F.A. Davis Company.
Cagan, R. (2013). Bench to bedside with fruit flies: an interview with Ross Cagan. Disease Models & Mechanisms, 6(3), 567-569. doi:10.1242/dmm.012443
Denayer, T., Stöhr, T., & Van Roy, M. (2014). Animal models in translational medicine: Validation and prediction. New Horizons in Translational Medicine, 2(1), 5-11. https://doi.org/10.1016/j.nhtm.2014.08.001
Dhami, M. K., & Kumarasinghe, L. (2014). A HRM real-time PCR assay for rapid and specific identification of the emerging pest spotted-wing drosophila (Drosophila suzukii). PloS one, 9(6). https://doi.org/10.1371/journal.pone.0098934
Ekowati, H., Arai, J., Putri, A. S. D., Nainu, F., Shiratsuchi, A., & Nakanishi, Y. (2017). Protective effects of Phaseolus vulgaris lectin against viral infection in Drosophila. Drug Discoveries and Therapeutics, 11(6), 329-335. doi:10.5582/ddt.2017.01071
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Gladstone, M., & Su, T. T. (2011). Chemical genetics and drug screening in Drosophila cancer models. Journal of Genetics and Genomics, 38(10), 497-504. doi: 10.1016/j.jgg.2011.09.003
Hughes, J. P., Rees, S., Kalindjian, S. B., & Philpott, K. L. (2011). Principles of early drug discovery. British Journal of Pharmacology, 162(6), 1239-1249. doi:10.1111/j.1476-5381.2010.01127.x
Ishikawa, T., Kamei, Y., Otozai, S., Kim, J., Sato, A., Kuwahara, Y., Todo, T. (2010). High-resolution melting curve analysis for rapid detection of mutations in a Medaka TILLING library. BMC molecular biology, 11, 70-70. doi:10.1186/1471-2199-11-70
Lochlainn, S. Ó., Amoah, S., Graham, N. S., Alamer, K., Rios, J. J., Kurup, S,.Broadley, M. R. (2011). High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes. Plant methods, 7(1), 43-43. doi:10.1186/1746-4811-7-43
Maitra, U., & Ciesla, L. (2019). Using Drosophila as a platform for drug discovery from natural products in Parkinson's disease. MedChemComm, 10(6), 867-879. doi:10.1039/C9MD00099B
Manaka, J., Kuraishi, T., Shiratsuchi, A., Nakai, Y., Higashida, H., Henson, P., & Nakanishi, Y. (2004). Draper-mediated and phosphatidylserine-independent phagocytosis of apoptotic cells by Drosophila hemocytes/macrophages. Journal of Biological Chemistry, 279(46), 48466-48476. doi: 10.1074/jbc.M408597200
Maslov, A. Y., Quispe-Tintaya, W., Gorbacheva, T., White, R. R., & Vijg, J. (2015). High-throughput sequencing in mutation detection: A new generation of genotoxicity tests? Mutation research, 776, 136-143. doi:10.1016/j.mrfmmm.2015.03.014
McGonigle, P., & Ruggeri, B. (2014). Animal models of human disease: Challenges in enabling translation. Biochemical Pharmacology, 87(1), 162-171. doi:10.1016/j.bcp.2013.08.006
Nainu, F., Asri, R. M., Arsyad, A., Manggau, M. A., & Amir, M. N. (2018). In vivo antibacterial activity of green algae Ulva reticulata against Staphylococcus aureus in Drosophila model of infection. Pharmacognosy Journal, 10(5), 993-997. doi:10.5530/pj.2018.5.169
Nainu, F., Asri, R. M., Djide, M. N., Ahsan, M., Arfiansyah, R., Sartini, S., & Alam, G. (2019). Protective effect of green algae Ulva reticulata against Pseudomonas aeruginosa in Drosophila infection model. HAYATI Journal of Biosciences, 26(4), 163-171. doi:10.4308/hjb.26.4.163
Nainu, F., Djide, M. N., Subehan, S., Sartini, S., Roska, T. P., Salim, E., & Kuraishi, T. (2020). Protective Signatures of Roselle (Hibiscus sabdariffa L.) Calyx Fractions against Staphylococcus aureus in Drosophila Infection Model. HAYATI Journal of Biosciences, 27(4), 306-313. doi:10.4308/hjb.27.4.306
Nainu, F., Nakanishi, Y., & Shiratsuchi, A. (2019). Fruit fly as a model organism in the study of human diseases and drug discovery. Journal of Center for Medical Education Sapporo Medical University (10), 21-32. doi:10.15114/jcme.10.21
Nainu, F., Rahmatika, D., Emran, T. B., & Harapan, H. (2020). Potential Application of Drosophila melanogaster as a Model Organism in COVID-19-Related Research. Frontiers in Pharmacology, 11(1415). doi:10.3389/fphar.2020.588561
Nainu, F., Tanaka, Y., Shiratsuchi, A., & Nakanishi, Y. (2015). Protection of insects against viral infection by apoptosis-dependent phagocytosis. Journal of Immunology, 195(12), 5696-5706. doi:10.4049/jimmunol.1500613
Nurhamidah, S., Djide, M. N., Arfiansyah, R., & Nainu, F. (2018). Deteksi Salmonella enterica serovar Typhimurium dalam produk pangan siap saji menggunakan metode PCR, Melt Curve, dan analisis HRM. Majalah Farmasi dan Farmakologi, 22(1), 20-26. doi:https://doi.org/10.20956/mff.v22i1.5721
Palandri, A., Martin, E., Russi, M., Rera, M., Tricoire, H., & Monnier, V. (2018). Identification of cardioprotective drugs by medium-scale in vivo pharmacological screening on a Drosophila cardiac model of Friedreich's ataxia. Disease Models & Mechanisms, 11(7). https://doi.org/10.1242/dmm.033811
Pandey, U. B., & Nichols, C. D. (2011). Human disease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery. Pharmacological Reviews, 63(2), 411-436. https://doi.org/10.1124/pr.110.003293
Song, J., & Tanouye, M. A. (2008). From bench to drug: human seizure modeling using Drosophila. Progress in Neurobiology, 84(2), 182-191. doi:10.1016/j.pneurobio.2007.10.006
Tung, T. T., Nagaosa, K., Fujita, Y., Kita, A., Mori, H., Okada, R., Nonaka, S., & Nakanishi, Y. (2013). Phosphatidylserine recognition and induction of apoptotic cell clearance by Drosophila engulfment receptor Draper. Journal of Biochemistry, 153(5), 483-491. https://doi.org/10.1093/jb/mvt014
Ugur, B., Chen, K., & Bellen, H. J. (2016). Drosophila tools and assays for the study of human diseases. Disease Models & Mechanisms, 9(3), 235-244. doi:10.1242/dmm.023762
Willoughby, L. F., Schlosser, T., Manning, S. A., Parisot, J. P., Street, I. P., Richardson, H. E., Brumby, A. M. (2013). An in vivo large-scale chemical screening platform using Drosophila for anti-cancer drug discovery. Disease Models & Mechanisms, 6(2), 521-529. doi:10.1242/dmm.009985
Yadav, A K., Srikrishna, S., & Gupta, S. C. (2016). Cancer drug development using Drosophila as an in vivo tool: From bedside to bench and back. Trends in Pharmacological Sciences, 37(9), 789-806. doi:10.1016/j.tips.2016.05.010
Akasaka, T., & Ocorr, K. (2009). Drug discovery through functional screening in the Drosophila heart. In H. Koga (Ed.), Reverse Chemical Genetics: Methods and Protocols (pp. 235-249). Totowa, NJ: Humana Press. Doi:10.1007/978-1-60761-232-2_18
Alberts, B., Johnson, A., Lewis, J., Morgan, D., Raff, M., Roberts, K., & Walter, P. (2017). Molecular Biology of the Cell (5th Edition ed.): W.W. Norton.
Bancerz-Kisiel, A., Lipczyńska, K., Szczerba-Turek, A., Gospodarek, E., Platt-Samoraj, A., & Szweda, W. (2014). The use of the HRM method for identifying possible mutations in the ymoA gene region and evaluating their influence on the enterotoxic properties of Y. enterocolitica strains. BMC Veterinary Research, 10(1), 207. https://doi.org/10.1186/s12917-014-0207-6
Breyer, M. D., Look, A. T., & Cifra, A. (2015). From bench to patient: model systems in drug discovery. Disease Models & Mechanisms, 8(10), 1171-1174. doi: 10.1242/dmm.023036
Buckingham, L. (2012). Molecular Diagnostics: Fundamentals, Methods, and Clinical Applications: F.A. Davis Company.
Cagan, R. (2013). Bench to bedside with fruit flies: an interview with Ross Cagan. Disease Models & Mechanisms, 6(3), 567-569. doi:10.1242/dmm.012443
Denayer, T., Stöhr, T., & Van Roy, M. (2014). Animal models in translational medicine: Validation and prediction. New Horizons in Translational Medicine, 2(1), 5-11. https://doi.org/10.1016/j.nhtm.2014.08.001
Dhami, M. K., & Kumarasinghe, L. (2014). A HRM real-time PCR assay for rapid and specific identification of the emerging pest spotted-wing drosophila (Drosophila suzukii). PloS one, 9(6). https://doi.org/10.1371/journal.pone.0098934
Ekowati, H., Arai, J., Putri, A. S. D., Nainu, F., Shiratsuchi, A., & Nakanishi, Y. (2017). Protective effects of Phaseolus vulgaris lectin against viral infection in Drosophila. Drug Discoveries and Therapeutics, 11(6), 329-335. doi:10.5582/ddt.2017.01071
Farrar, J. S., & Wittwer, C. T. (2017). Chapter 6 - High-Resolution Melting Curve Analysis for Molecular Diagnostics. In G. P. Patrinos (Ed.), Molecular Diagnostics (Third Edition) (pp. 79-102). https://doi.org/10.1016/B978-0-12-802971-8.00006-7
Freeman, M. R., Delrow, J., Kim, J., Johnson, E., & Doe, C. Q. (2003). Unwrapping glial biology: Gcm target genes regulating glial development, diversification, and function. Neuron, 38(4), 567-580. doi:10.1016/s0896-6273(03)00289-7
Gladstone, M., & Su, T. T. (2011). Chemical genetics and drug screening in Drosophila cancer models. Journal of Genetics and Genomics, 38(10), 497-504. doi: 10.1016/j.jgg.2011.09.003
Hughes, J. P., Rees, S., Kalindjian, S. B., & Philpott, K. L. (2011). Principles of early drug discovery. British Journal of Pharmacology, 162(6), 1239-1249. doi:10.1111/j.1476-5381.2010.01127.x
Ishikawa, T., Kamei, Y., Otozai, S., Kim, J., Sato, A., Kuwahara, Y., Todo, T. (2010). High-resolution melting curve analysis for rapid detection of mutations in a Medaka TILLING library. BMC molecular biology, 11, 70-70. doi:10.1186/1471-2199-11-70
Lochlainn, S. Ó., Amoah, S., Graham, N. S., Alamer, K., Rios, J. J., Kurup, S,.Broadley, M. R. (2011). High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes. Plant methods, 7(1), 43-43. doi:10.1186/1746-4811-7-43
Maitra, U., & Ciesla, L. (2019). Using Drosophila as a platform for drug discovery from natural products in Parkinson's disease. MedChemComm, 10(6), 867-879. doi:10.1039/C9MD00099B
Manaka, J., Kuraishi, T., Shiratsuchi, A., Nakai, Y., Higashida, H., Henson, P., & Nakanishi, Y. (2004). Draper-mediated and phosphatidylserine-independent phagocytosis of apoptotic cells by Drosophila hemocytes/macrophages. Journal of Biological Chemistry, 279(46), 48466-48476. doi: 10.1074/jbc.M408597200
Maslov, A. Y., Quispe-Tintaya, W., Gorbacheva, T., White, R. R., & Vijg, J. (2015). High-throughput sequencing in mutation detection: A new generation of genotoxicity tests? Mutation research, 776, 136-143. doi:10.1016/j.mrfmmm.2015.03.014
McGonigle, P., & Ruggeri, B. (2014). Animal models of human disease: Challenges in enabling translation. Biochemical Pharmacology, 87(1), 162-171. doi:10.1016/j.bcp.2013.08.006
Nainu, F., Asri, R. M., Arsyad, A., Manggau, M. A., & Amir, M. N. (2018). In vivo antibacterial activity of green algae Ulva reticulata against Staphylococcus aureus in Drosophila model of infection. Pharmacognosy Journal, 10(5), 993-997. doi:10.5530/pj.2018.5.169
Nainu, F., Asri, R. M., Djide, M. N., Ahsan, M., Arfiansyah, R., Sartini, S., & Alam, G. (2019). Protective effect of green algae Ulva reticulata against Pseudomonas aeruginosa in Drosophila infection model. HAYATI Journal of Biosciences, 26(4), 163-171. doi:10.4308/hjb.26.4.163
Nainu, F., Djide, M. N., Subehan, S., Sartini, S., Roska, T. P., Salim, E., & Kuraishi, T. (2020). Protective Signatures of Roselle (Hibiscus sabdariffa L.) Calyx Fractions against Staphylococcus aureus in Drosophila Infection Model. HAYATI Journal of Biosciences, 27(4), 306-313. doi:10.4308/hjb.27.4.306
Nainu, F., Nakanishi, Y., & Shiratsuchi, A. (2019). Fruit fly as a model organism in the study of human diseases and drug discovery. Journal of Center for Medical Education Sapporo Medical University (10), 21-32. doi:10.15114/jcme.10.21
Nainu, F., Rahmatika, D., Emran, T. B., & Harapan, H. (2020). Potential Application of Drosophila melanogaster as a Model Organism in COVID-19-Related Research. Frontiers in Pharmacology, 11(1415). doi:10.3389/fphar.2020.588561
Nainu, F., Tanaka, Y., Shiratsuchi, A., & Nakanishi, Y. (2015). Protection of insects against viral infection by apoptosis-dependent phagocytosis. Journal of Immunology, 195(12), 5696-5706. doi:10.4049/jimmunol.1500613
Nurhamidah, S., Djide, M. N., Arfiansyah, R., & Nainu, F. (2018). Deteksi Salmonella enterica serovar Typhimurium dalam produk pangan siap saji menggunakan metode PCR, Melt Curve, dan analisis HRM. Majalah Farmasi dan Farmakologi, 22(1), 20-26. doi:https://doi.org/10.20956/mff.v22i1.5721
Palandri, A., Martin, E., Russi, M., Rera, M., Tricoire, H., & Monnier, V. (2018). Identification of cardioprotective drugs by medium-scale in vivo pharmacological screening on a Drosophila cardiac model of Friedreich's ataxia. Disease Models & Mechanisms, 11(7). https://doi.org/10.1242/dmm.033811
Pandey, U. B., & Nichols, C. D. (2011). Human disease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery. Pharmacological Reviews, 63(2), 411-436. https://doi.org/10.1124/pr.110.003293
Song, J., & Tanouye, M. A. (2008). From bench to drug: human seizure modeling using Drosophila. Progress in Neurobiology, 84(2), 182-191. doi:10.1016/j.pneurobio.2007.10.006
Tung, T. T., Nagaosa, K., Fujita, Y., Kita, A., Mori, H., Okada, R., Nonaka, S., & Nakanishi, Y. (2013). Phosphatidylserine recognition and induction of apoptotic cell clearance by Drosophila engulfment receptor Draper. Journal of Biochemistry, 153(5), 483-491. https://doi.org/10.1093/jb/mvt014
Ugur, B., Chen, K., & Bellen, H. J. (2016). Drosophila tools and assays for the study of human diseases. Disease Models & Mechanisms, 9(3), 235-244. doi:10.1242/dmm.023762
Willoughby, L. F., Schlosser, T., Manning, S. A., Parisot, J. P., Street, I. P., Richardson, H. E., Brumby, A. M. (2013). An in vivo large-scale chemical screening platform using Drosophila for anti-cancer drug discovery. Disease Models & Mechanisms, 6(2), 521-529. doi:10.1242/dmm.009985
Yadav, A K., Srikrishna, S., & Gupta, S. C. (2016). Cancer drug development using Drosophila as an in vivo tool: From bedside to bench and back. Trends in Pharmacological Sciences, 37(9), 789-806. doi:10.1016/j.tips.2016.05.010