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Submitted
September 17, 2021
Accepted
November 8, 2021
Published
November 30, 2021
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Abstract

Brown rat or commonly called sewer rat (Rattus norvegicus) meat is one of ingredients that is usually used to counterfeit beef meatballs to reduce the production prices. These issues can be very detrimental to consumers, in terms of health and halal reasons. Thus, this condition has prompted the development of test methods to detect sewer rat meat in processed foods. Several method developments in detecting the content of sewer rat meat in processed food have been carried out. One of the simplest and fastest methods to identify sewer rat meat is Polymerase Chain Reaction (PCR). Most method developments for detecting sewer rat meat have used endpoint PCR, but this method still has several shortcomings in terms of specificity and promptness in obtaining results. Therefore, developing a sewer rat meat detection method using real-time PCR and combined with a more sensitive and specific TaqMan probe can be an alternative for detecting sewer rat meat in processed foods. Primer and probe design is the first and crucial step in the development of detection methods with real-time PCR. This study aims to design primers and probes for the detection of the mt-CoI gene in sewer rats. The mt-CoI gene sequence of Rattus norvegicus (NC_001665.2) was obtained from the National Center of Biotechnology Information (NCBI) database. Primer was designed using Primer3Plus software. Then, several candidates of primers and probes were analyzed in silico for specificity of the mt-CoI gene using software, including Primer-BLAST and Nucleotide-BLAST. The result of this study is primers and probes which are specific to the mt-CoI gene in sewer rats (Rattus norvegicus), with the sequence of forward primer (5’-ATGAGCAAAAGCCC ACTTTG-3’), reverse primer (5’-CGGCCGTAAGTGAGATGAAT-3’), and probe (5’-GCAGGGATACCTCGTCGTTA-3’). The result can be used to develop methods for detecting sewer rat meat in meatballs or other processed foods using real-time PCR and TaqMan probes.

Keywords

real-time PCR, in silico, primer, probe, detection, Rattus novergicus, mt-Co1, Primer3Plus real-time PCR in silico, primer Rattus norvegicus mt-Co1

Article Details

How to Cite
Sihotang, M. A. E. D., Erwinda, Y. E., Suwarni, E., & Lusianti, E. (2021). Short Communication: Desain Primer dan Analisis in Silico untuk Amplifikasi Gen mt-Co1 pada Tikus got (Rattus norvegicus). Eruditio : Indonesia Journal of Food and Drug Safety, 1(2), 20–29. https://doi.org/10.54384/eruditio.v1i2.82
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References

  1. Ahamad, M. N. U., Ali, M. E., Hossain, M. A. M., Asing, A., Sultana, S., & Jahurul, M. H. A. (2017).
  2. Multiplex PCR assay discriminates rabbit, rat and squirrel meat in food chain. Food Additives and Contaminants - Part A Chemistry, Analysis, Control, Exposure and Risk Assessment, 34(12), 2043–2057.
  3. Akimkin, V., Beer, M., Blome, S., Hanke, D., Hoper, D., Jenckel, M., & Pohlmann, A. (2016). New chimeric porcine coronavirus in swine feces, Germany, 2012. Emerging Infectious Diseases, 22(7), 1314–1315. doi: 10.3201/eid2207.160179
  4. Ali, M. E., Razzak, M. A., Hamid, S. B. A., Rahman, M. M., Amin, M. Al, Rashid, N. R. A., & Asing. (2015). Multiplex PCR assay for the detection of five meat species forbidden in Islamic foods. Food Chemistry, 177, 214–224.
  5. Borah, P. (2011). Primer designing for PCR. Science Vision, 11(3), 134–136.
  6. Bobrov, A. G., Kirillina, O., Vadyvaloo, V., Koestler, B. J., Hinz, A. K., Mack, D., … Perry, R. D. (2015). The Yersinia pestis HmsCDE regulatory system is essential for blockage of the oriental rat flea (Xenopsylla cheopis), a classic plague vector. Environmental Microbiology, 17(4), 947–959. doi: 10.1111/1462-2920.12419
  7. Bustin, S., & Huggett, J. (2017). qPCR primer design revisited. Biomolecular Detection and Quantification, 14(November), 19–28.
  8. Cahyadi, M., Wibowo, T., Pramono, A., & Abdurrahman, Z. H. (2020). A novel multiplex-pcr assay to detect three non-halal meats contained in meatball using mitochondrial 12s rrna gene. Food Science of Animal Resources, 40(4), 628–635.
  9. Centers for Disease Control and Prevention. (2017). Diseases directly transmitted by rodents. https://www.cdc.gov/rodents/diseases/direct.html
  10. Chen, X., Ran, D., Zeng, L., Xin, M., (2020). Immunoassay of cooked wild rat meat by ELISA with a highly specific antibody targeting rat heat-resistant proteins. Food and Agricultural Immunology, 31 (1), https://doi.org/10.1080/09540105.2020.1740180
  11. Debode, F., Marien, A., Janssen, É., Bragard, C., & Berben, G. (2017). The influence of amplicon length on real-time PCR results Frédéric.pdf. 21(1), 3–11.
  12. Estalilla, O. C., Medeiros, L. J., Manning, J. T., & Luthra, R. (2000). 5’ → 3’ Exonuclease-based real-time PCR assays for detecting the t(14;18)(q32;21): A survey of 162 malignant lymphomas and reactive specimens. Modern Pathology, 13(6), 661–666.
  13. Geller, J., Meyer, C., Parker, M., & Hawk, H. (2013). Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys. Molecular Ecology Resources, 13(5), 851–861.
  14. Herrero, B., Madriñán, M., Vieites, J. M., & Espiñeira, M. (2010). Authentication of atlantic cod (Gadus morhua) Using real time PCR. Journal of Agricultural and Food Chemistry, 58(8), 4794–4799.
  15. Holm, W. Van, Ghesquière, J., Boon, N., Verspecht, T., Bernaerts, K., Zayed, N., Chatzigiannidou, I., & Teughels, W. (2021). A Viability Quantitative PCR Dilemma: Are Longer Amplicons Better? Applied and Environmental Microbiology, 87(5), 1–11.
  16. Hung, J. H., & Weng, Z. (2016). Designing polymerase chain reaction primers using Primer3Plus. Cold Spring Harbor Protocols, 2016(9), 821–826.
  17. Kerfeld, C. A., & Scott, K. M. (2011). Using BLAST to teach “E-value-tionary” concepts. PLoS Biology, 9(2), 1–4. https://doi.org/10.1371/journal.pbio.1001014
  18. Lorenz, T. C. (2012). Polymerase chain reaction: Basic protocol plus troubleshooting and optimization strategies. Journal of Visualized Experiments, 63, 1–15.
  19. Newell, P. D., Fricker, A. D., Roco, C. A., Chandrangsu, P., & Merkel, S. M. (2013). A Small-Group Activity Introducing the Use and Interpretation of BLAST. Journal of Microbiology & Biology Education, 14(2), 238–243.
  20. Nuraini, H., Primasari, A., Andreas, E., & Sumantri, C. (2012). The use of cytochrome b gene as a specific marker of the rat meat (Rattus norvegicus) on meat and meat products. Media Peternakan, 35(1), 15–20.
  21. Purcell, R. V., Pearson, J., Frizelle, F. A., & Keenan, J. I. (2016). Comparison of standard, quantitative and digital PCR in the detection of enterotoxigenic Bacteroides fragilis. Scientific Reports, 6(September), 1–8.
  22. Rodrigues, M. S., Morelli, K. A., & Jansen, A. M. (2017). Cytochrome c oxidase subunit 1 gene as a DNA barcode for discriminating Trypanosoma cruzi DTUs and closely related species. Parasites and Vectors, 10(1), 1–18.
  23. Rodríguez-Lázaro, D., Cook, N., & Hernández, M. (2013). Real-time PCR in food science: PCR diagnostics. Current Issues in Molecular Biology, 15(2), 39–44.
  24. Rodríguez, A., Rodríguez, M., Córdoba, J. J., & Andrade, M. J. (2015). Design of Primers and Probes for Quantitative Real-Time PCR Methods. Methods in Molecular Biology (Clifton, N.J.), 1275, vii.
  25. Roswiem, A. P., & Septiani, T. (2018). Identifikasi Daging Tikus Pada Produk Baso Dengan Metode Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE). Jurnal Kedokteran YARSI, 26(2), 058–065.
  26. Saraswati, H., Seprianto, S., & Dwi Wahyuni, F. (2019). Desain Primer Secara In Silico untuk Amplifikasi Gen cryIII dari Bacillus thuringiensis Isolat Lokal. Indonesian Journal of Biotechnology and Biodiversity, 3(1), 33–38.
  27. Shen, Z., Qu, W., Wang, W., Lu, Y., Wu, Y., Li, Z., Hang, X., Wang, X., Zhao, D., & Zhang, C. (2010). MPprimer: A program for reliable multiplex PCR primer design. BMC Bioinformatics, 11.
  28. Su, Y., Wang, S., Guo, J., Xue, B., Xu, L., & Que, Y. (2013). A TaqMan real-time PCR assay for detection and quantification of sporisorium scitamineum in sugarcane. The Scientific World Journal, 2013.
  29. Suparman, S. (2016). Desain Primer PCR Secara In Silico Untuk Amplifikasi Gen COI Pada Kupu-Kupu Papilio ulysses Linnaeus Dari Pulau Bacan. Jurnal Pendidikan Matematika Dan IPA, 7(1), 14.
  30. Timón-Gómez, A., Nývltová, E., Abriata, L. A., Vila, A. J., Hosler, J., & Barrientos, A. (2018). Mitochondrial Cytochrome c Oxidase Biogenesis: Recent Developments. Physiology & Behavior, 176(3), 139–148.
  31. Tobe, S. S., Kitchener, A., & Linacre, A. (2009). Cytochrome b or cytochrome c oxidase subunit I for mammalian species identification-An answer to the debate. Forensic Science International: Genetics Supplement Series, 2(1), 306–307.
  32. VanGuilder, H. D., Vrana, K. E., & Freeman, W. M. (2008). Twenty-five years of quantitative PCR for gene expression analysis. BioTechniques, 44(5), 619–626.
  33. Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., & Madden, T. L. (2012). Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics, 13(134).