Quality and quantity of Aspergillus niger DNA isolation using filter-based kit and cooling method

Renatasya Silviana Herningtyas; Muhammad Taufiq Qurrohman

doi:10.31101/ijhst.v6i1.3274

Authors

Renatasya Silviana Herningtyas Sekolah Tinggi Ilmu Kesehatan Nasional, Indonesia
Muhammad Taufiq Qurrohman Sekolah Tinggi Ilmu Kesehatan Nasional, Indonesia

DOI:

https://doi.org/10.31101/ijhst.v6i1.3274

Keywords:

Aspergillus niger; cooling method; filter-based kit

Abstract

Polymerase Chain Reaction (PCR) is an important technique to improve sensitivity in the detection of fungal infections, such as those caused by Aspergillus niger. The availability of pure DNA and DNA isolation techniques are important factors in implementing PCR. This study aims to compare the quality and quantity of DNA isolation of Aspergillus niger using the Filter Based Kit method and cooling. The experimental research design was used with a qualitative test of DNA isolate using Agarose Gel Electrophoresis (1.5%) and a quantitative DNA test using a UV-Vis Spectrophotometer (wavelengths of 260 nm and 280 nm). Data analysis compared the qualitative and quantitative results of DNA isolates from both methods. The results showed the presence of DNA bands in both isolation methods, with thicker bands in the Filter Based Kit method. The average concentration of DNA after isolation using the Filter Based Kit (6,478 ng/μl) was higher than that of the cooling method (5,994 ng/μl). The purity of DNA was also higher in the filter-based kit (1.7) than in the cooling method (1.1). The Filter Based Kit method contains chemical components that support the successful isolation of DNA. It can be concluded that the filter-based kit method produces Aspergillus niger DNA isolate with better quality and quantity than the cooling method. The implication of these findings is that the Filter Based Kit could be a better option for the isolation of Aspergillus niger DNA in laboratory applications.

References

Barac, A., Vujovic, A., Drazic, A., Stevanovic, G., Paglietti, B., Lukic, K., Stojanovic, M., & Stjepanovic, M. (2023). Diagnosis of Chronic Pulmonary Aspergillosis : Clinical , Radiological or Laboratory ? Journal of Fungi, 9(11), 1–11.

Barqly, H. H. A. kahfi, Risandiansyah, R., & Aini, N. (2021). Perbandingan Kuantitas Dan Kualitas Isolat DNA Aspergillus niger Menggunakan Filter Based Kit, Alkaline Lysis Dan Heat Treatment. Jurnal Bio Komplementer Medicine, 8(2), 1–9.

Chabi, M. L., Goracci, A., Roche, N., Paugam, A., Lupo, A., & Revel, M. P. (2015). Pulmonary aspergillosis. Diagnostic and Interventional Imaging, 96(5), 1–8. https://doi.org/10.1016/j.diii.2015.01.005

Couto, M. C. M., Sudre, A. P., Lima, M. F., & Bomfim, T. C. B. (2013). Comparison of techniques for DNA extraction and agarose gel staining of DNA fragments using samples of Cryptosporidium. Veterinarni Medicina, 58(10), 535–542. https://doi.org/10.17221/7085-VETMED

Dairawan, M., & Shetty, P. J. (2020). The Evolution of DNA Extraction Methods. American Journal of Biomedical Science & Research, 8(1), 39–45. https://doi.org/10.34297/ajbsr.2020.08.001234

Denning, D. W., Pleuvry, A., & Cole, D. C. (2013). Global burden of chronic pulmonary aspergillosis complicating sarcoidosis. European Respiratory Journal, 41(3), 621–626. https://doi.org/10.1183/09031936.00226911

Despois, O., Chen, S. C.-A., Gilroy, N., Jones, M., Wu, P., & Beardsley, J. (2022). Chronic Pulmonary Aspergillosis : Burden , Clinical Characteristics and Treatment Outcomes at a Large Australian Tertiary Hospital. Journal of Fungi, 8(110), 1–13.

Djurhuus, A., Port, J., Closek, C. J., Yamahara, K. M., Romero-Maraccini, O., Walz, K. R., Goldsmith, D. B., Michisaki, R., Breitbart, M., Boehm, A. B., & Chavez, F. P. (2017). Evaluation of filtration and DNA extraction methods for environmental DNA biodiversity assessments across multiple trophic levels. Frontiers in Marine Science, 4(OCT), 314. https://doi.org/10.3389/fmars.2017.00314

Donastin, A., Koentjoro, M. P., Hidayat, M. T., & Prasetyo, E. N. (2022). Perbandingan Tiga Metode Isolasi DNA Asperigilus niger. Metamorfosa: Journal of Biological Science, 9(1), 69–78. https://doi.org/10.24843/metamorfosa.2021.v09.i01.p07

Dwiyitno, Hoffman, S., Parmentier, K., & Keer, C. Van. (2018). Method Comparison of DNA Method Comparison of DNA Isolation and Quantification for Fish and Seafood Authenticity Determination. Squalen Bull. of Mar. and Fish. Postharvest and Biotech, 13(3), 115–124.

Fadllan, F., Djuminar, A., Hardiana, A. T., Dermawan, A., & Ernawati. (2019). Perbandingan Ekstraksi DNA Salmonella typhi Dari Kultur Darah Metode Spin Column dan Alcohol Based. Jurnal Riset Kesehatan Poltekkes Depkes Bandung, 11(2), 232–243.

Goldschmidt, P., Degorge, S., Merabet, L., & Chaumeil, C. (2014). Enzymatic treatment of specimens before DNA extraction directly influences molecular detection of infectious agents. PLoS ONE, 9(6), 1–6. https://doi.org/10.1371/journal.pone.0094886

Gupta, N. (2019). DNA extraction and polymerase chain reaction. Journal of Cytology, 36(2), 116–117. https://doi.org/10.4103/JOC.JOC_110_18

Hermansyah, H., Sutami, N., & Miksusanti, M. (2018). Amplifikasi PCR Domain D1/D2 28S rDNA Menggunakan Primer ITS1 Dan ITS4 Sampel DNA Dari Candida tropicalis Yang Diisolasi Dengan Metode Pendinginan. Indonesian Journal of Pure and Applied Chemistry, 1(1), 1. https://doi.org/10.26418/indonesian.v1i1.26037

Hollingshead, C., Luttmann, K., Sitta, E. A., & Elsaghir, H. (2020). Aspergillus niger fungemia secondary to chronic pulmonary aspergillosis in a patient with invasive squamous cell carcinoma. BMJ Case Rep, 13(3), 1–2. https://doi.org/10.1136/bcr-2020-234843

Jakribettu, R. P., George, T., Abraham, S., Fazal, F., Kinila, S., & Baliga, M. S. (2019). Clinical and laboratory profile of chronic pulmonary aspergillosis : a retrospective study. Egypt J Bronchol, 13, 109–113. https://doi.org/10.4103/ejb.ejb

Kumar, M. C., & Mugunthan, M. (2018). Evaluation of three DNA extraction methods from fungal cultures. Medical Journal Armed Forces India, 74(4), 333–336. https://doi.org/10.1016/j.mjafi.2017.07.009

Lamoth, F., & Calandra, T. (2022). Pulmonary aspergillosis : diagnosis and treatment. European Respiratory Review Series, 31(166), 1–15. https://doi.org/10.1183/16000617.0114-2022

Larkin, P. M. K., Multani, A., Beaird, O. E., Dayo, A. J., Fishbein, G. A., & Yang, S. (2020). A Collaborative Tale of Diagnosing and Treating Chronic Pulmonary Aspergillosis , from the Perspectives of Clinical Microbiologists , Surgical Pathologists , and Infectious Disease Clinicians. Journal Fungi, 6(3), 1–27.

Latif, A. A., & Osman, G. (2017). Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods, 13(1), 1–9. https://doi.org/10.1186/s13007-016-0152-4

McFall, S. M., Neto, M. F., Reed, J. L., & Wagner, R. L. (2016). Filtration isolation of nucleic acids: A simple and rapid DNA extraction method. Journal of Visualized Experiments, 2016(114), 2–7. https://doi.org/10.3791/54289

Nieman, C. C., Yamasaki, Y., Collier, T. C., & Lee, Y. (2015). A DNA extraction protocol for improved DNA yield from individual mosquitoes. F1000Research, 4, 1–8. https://doi.org/10.12688/f1000research.7413.1

Rachmawati, Y., & Khoiriyah, R. A. (2018). Comparison of DNA Isolation Results using Simple Methods and Kits in Samples of Psidium guajava Leaves. BIOTROPIC The Journal of Tropical Biology, 2(2), 93–99.

Rana, S., Kumar, K., Singh, M., & Lal, R. (2018). Optimization of protocol for DNA isolation from filamentous fungi and its identification. International Journal of Basic and Applied Research, 8(5), 226–231.

Rozaliyani, A., Rosianawati, H., Handayani, D., & Agustin, H. (2020). Chronic Pulmonary Aspergillosis in Post Tuberculosis Patients in Indonesia and the Role of LDBio Aspergillus ICT as Part of the Diagnosis Scheme. Journal of Fungi, 6(4), 1–10.

Šarkanj, B., Bošnjak, Z., Perić, M., Kovač, T., & Džijan, S. (2018). DNA Isolation from Aspergillus flavus: Optimal method selection. Croatian Journal of Food Science and Technology, 10(2), 157–163. https://doi.org/10.17508/CJFST.2018.10.2.02

Setiani, N. A., Tritama, E., & Tresnawulansari, A. (2021). Optimasi Optical Density (OD) pada Isolasi Genom Salmonella typhi Menggunakan Genomic DNA Purification Kit. Jurnal Sains Dan Teknologi Farmasi Indonesia, 10(1), 35–43.

Setianingrum, F., Rozaliyani, A., Syam, R., & Adawiyah, R. (2020). Evaluation and comparison of automated and manual ELISA for diagnosis of chronic pulmonary aspergillosis ( CPA ) in Indonesia. Diagnostic Microbiology & Infectious Disease, 98(3), 1–6. https://doi.org/10.1016/j.diagmicrobio.2020.115124

Shi, R., Lewis, R. S., & Panthee, D. R. (2018). Filter paper-based spin column method for cost-efficient DNA or RNA purification. PLoS ONE, 13(12), 1–14. https://doi.org/10.1371/journal.pone.0203011

Sophian, A., Purwaningsih, R., Muindar, Igirisa, E. P. J., & Amirullah, M. L. (2021). Short Communication : Analysis of purity and concentration of DNA extracted from intron patho gene-spin extraction on processed crab food product samples. ASIAN J TROP BIOTECHNOL, 18(1), 28–31. https://doi.org/10.13057/biotek/c180103

Sutanta, M., Wulan, D. T., Nabila, Y., & Sophian, A. (2021). Short Communication: Application of Double Wash Technique for Species DNA Isolation in Soft Capsule Shell Samples. ERUDITIO, 2(1), 14–19.

Wickes, B. L., & Wiederhold, N. P. (2018). Molecular diagnostics in medical mycology. Nature Communications, 9, 1–13. https://doi.org/10.1038/s41467-018-07556-5

Wilopo, B. A. P., Richardson, M. D., & Denning, D. W. (2019). Diagnostic Aspects of Chronic Pulmonary Aspergillosis : Present and New Directions. Current Fungal Infection Reports, 13, 292–300.

Yahya, A., Firmansyah, M., Arlisyah, A., & Risandiansyah, R. (2017). Comparison of DNA Extraction Methods Between Conventional, Kit, Alkali and Buffer-Only for PCR Amplification on Raw and Boiled Bovine and Porcine Meat. The Journal of Experimental Life Sciences, 7(2), 110–114. https://doi.org/10.21776/ub.jels.2017.007.02.09