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Isolasi DNA pada Produk Otak-Otak Ikan Bandeng Utaminingsih, Sri; Utami, Sofia Dyah; Sophian, Alfi
Muhammadiyah Journal of Nutrition and Food Science (MJNF) Vol 3, No 1 (2022): Muhammadiyah Journal of Nutrition and Food Science (MJNF)
Publisher : Faculty of Medicine and Health Universitas Muhammadiyah Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24853/mjnf.3.1.36-41

Latar belakang: Analisis mutu DNA hasil isolasi merupakan teknik analisis yang digunakan untuk mengetahui kualitas DNA hasil isolasi sehingga meminimalkan kegagalan proses amplifikasi dalam analisis molekuler. Tujuan: Tujuan dilakukan penelitian ini adalah untuk melihat mutu DNA hasil isolasi pada produk pangan olahan ikan berupa otak-otak ikan bandeng. Prosedur ekstraksi DNA mengikuti protokol ekstraksi manual kit yang digunakan. Analisis mutu DNA hasil isolasi diukur menggunakan nanophotometer, dimana analisis mutu berdasarkan nilai konsentrasi dan kemurnian DNA hasil isolasi. Analisis data dilakukan menggunakan uji rata-rata nilai konsentrasi dan kemurnian. Hasil: Berdasarkan hasil analisis mutu DNA diperoleh hasil konsentrasi DNA berada pada kisaran 9.6 – 18.5 dengan nilai rata-rata DNA hasil isolasi berada pada nilai 13.4 ng/µL, sedangkan nilai kemurnian yang dibaca pada panjang gelombang A260/A28 berada pada kisaran 1.64 – 1.87, dengan nilai rata-rata berada pada nilai 1.79. Simpulan: Sehingga dapat disimpulkan bahwa DNA hasil isolasi yang dilakukan pada sampel produk pangan olahan otak-otak ikan bandeng menunjukkan nilai konsentrasi dan kemurnian yang masuk dalam kategori hasil isolasi DNA yang baik.

Analisis Nilai Kemurnian DNA Menggunakan Nano Fotometer pada Rasio 260/230 yang Diisolasi dari Produk Nugget Sophian, Alfi; Yustina, Yustina
Muhammadiyah Journal of Nutrition and Food Science (MJNF) Vol 3, No 2 (2022): Muhammadiyah Journal of Nutrition and Food Science (MJNF)
Publisher : Faculty of Medicine and Health Universitas Muhammadiyah Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24853/mjnf.3.2.82-86

Latar belakang: Parameter nilai kemurnian yang dianalisis dari panjang gelombang dengan rasio 260/230 merupakan parameter validasi sekunder yang digunakan untuk melakukan analisis mutu DNA hasil isolasi pada produk nugget ayam. Tujuan: Tujuan dari dilakukannya penelitian ini adalah untuk memberi informasi tentang nilai analisis kemurnian DNA hasil isolasi yang dibaca pada rasio 260/230. Dengan diperolehnya informasi dari hasil penelitian ini diharapkan dapat memberi manfaat terhadap penelitian sejenis yang relevan. Metode: Metode yang digunakan dalam penelitian ini adalah metode isolasi DNA menggunakan teknik spin kolom, kemudian DNA hasil isolasi yang diperoleh dibaca menggunakan nano fotometer pada rasio 260/230. Hasil: Hasil pengukuran kemudian dihitung nilai rata-rata dan standar deviasinya. Berdasarkan hasil pengukuran DNA hasil isolasi diperoleh hasil kemurnian yang dibaca pada rasio A260/A230 berada pada kisaran 1,98 – 2,10, dengan nilai rata-rata berada pada nilai 2,043. Simpulan: Berdasarkan hasil tersebut maka dapat disimpulkan bahwa DNA hasil isolasi yang diperoleh menunjukkan kualitas DNA yang baik berdasarkan syarat mutu nilai kemurnian DNA pada rasio 260/230 yaitu pada kisaran 2,0 – 2,2.

Detection of Porcine DNA in Cosmetic Products using Real-Time PCR Method: A Review of Method and Applications Sari, Miftiana Nugraha; Sophian, Alfi; Nawwaruddin, Hazza Hammam; Rumiyati, Rumiyati; Rohman, Abdul
Journal of Food and Pharmaceutical Sciences Vol 13, No 2 (2025): J.Food.Pharm.Sci
Publisher : Integrated Research and Testing Laboratory (LPPT) Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jfps.20332

For Muslim customers, the halal validity of cosmetics is a major concern. In cosmetics industry, one critical aspect is the contamination of porcine derivatives in halal cosmetic products. This review method discusses the application of real-time PCR (RT-PCR) for the detection of porcine DNA in cosmetic products, including the principle of the method, DNA extraction protocol, primers and probes design, and method application in various types of cosmetic products. DNA extraction from the cosmetic matrix samples requires optimization due to the complexity of the material and the possibility of DNA degradation during the cosmetic production process. The precise primers and probes design is also crucial to ensure specificity towards porcine DNA. The application of the RT-PCR method has been successful in various forms of cosmetics such as creams, lotions, lipsticks, and soaps, although each type of cosmetic product has unique challenges. Performance evaluation of the RT-PCR method showed good repeatability and reproducibility with coefficients of variation (CV) below 10% in numerous studies. The main challenges of the method include extraction of DNA due to the DNA degradation during the cosmetics production process, interference from cosmetic ingredients to RT-PCR analysis, and the need for method standardization. Solutions that have been developed such as the use of short gene targets, PCR additives to overcome inhibitors, and amplification techniques such as digital PCR to improve sensitivity. The recent development has led to the integration of protein-based methods and international standardization to support cosmetic halal certifications.

Detection of Porcine DNA in Cosmetic Products using Real-Time PCR Method: A Review of Method and Applications Sari, Miftiana Nugraha; Sophian, Alfi; Nawwaruddin, Hazza Hammam; Rumiyati, Rumiyati; Rohman, Abdul
Journal of Food and Pharmaceutical Sciences Vol 13, No 2 (2025): J.Food.Pharm.Sci
Publisher : Integrated Research and Testing Laboratory (LPPT) Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jfps.20332

For Muslim customers, the halal validity of cosmetics is a major concern. In cosmetics industry, one critical aspect is the contamination of porcine derivatives in halal cosmetic products. This review method discusses the application of real-time PCR (RT-PCR) for the detection of porcine DNA in cosmetic products, including the principle of the method, DNA extraction protocol, primers and probes design, and method application in various types of cosmetic products. DNA extraction from the cosmetic matrix samples requires optimization due to the complexity of the material and the possibility of DNA degradation during the cosmetic production process. The precise primers and probes design is also crucial to ensure specificity towards porcine DNA. The application of the RT-PCR method has been successful in various forms of cosmetics such as creams, lotions, lipsticks, and soaps, although each type of cosmetic product has unique challenges. Performance evaluation of the RT-PCR method showed good repeatability and reproducibility with coefficients of variation (CV) below 10% in numerous studies. The main challenges of the method include extraction of DNA due to the DNA degradation during the cosmetics production process, interference from cosmetic ingredients to RT-PCR analysis, and the need for method standardization. Solutions that have been developed such as the use of short gene targets, PCR additives to overcome inhibitors, and amplification techniques such as digital PCR to improve sensitivity. The recent development has led to the integration of protein-based methods and international standardization to support cosmetic halal certifications.

The Role of Alcohol in the DNA Isolation Process: A Comprehensive Review Sophian, Alfi
Kupang Journal of Food and Nutrition Research Vol. 6 No. 2 (2025): Kupang Journal of Food and Nutrition Research
Publisher : Poltekkes Kemenkes Kupang

Show Abstract | Download Original | Original Source | Check in Google Scholar

DNA isolation is a fundamental step in various molecular biology applications, with its success highly dependent on the purity and integrity of the isolated DNA. This review article aims to highlight the vital role of alcohol, particularly ethanol and isopropanol, in the DNA isolation process from various biological sources. This comprehensive review explores the biophysical principles underlying DNA precipitation by alcohol, where the reduction of the solution's dielectric constant and disruption of the hydration layer lead to DNA precipitation. The article also evaluates the application of alcohol in different DNA isolation protocols, including the classic phenol-chloroform extraction method, commercial silica column-based kits, and salting-out techniques. Recent advancements in optimizing alcohol precipitation parameters indicate that process efficiency can be enhanced by adjusting the type of alcohol, incubation time, and salt concentration. Current research trends also point toward the development of environmentally friendly approaches that minimize alcohol usage, as well as alternative alcohol-free methods such as magnetic-based technology and paper-based DNA isolation systems.The future prospects of DNA isolation are projected to integrate traditional alcohol-based methods with advanced technologies such as automation, nanomaterials, and microfluidic systems. A deeper understanding of alcohol’s role in DNA isolation is expected to optimize existing protocols and drive innovation in DNA isolation techniques for applications ranging from diagnostics to genomic research.

Bibliometric Analysis of Foodborne Pathogen Research in the Year Range 2013-2023 Based on Scopus Web Data Sophian, Alfi; Purwaningsih, Ratna
FoodTech: Jurnal Teknologi Pangan Vol 6, No 2 (2023): October
Publisher : Universitas Tanjungpura

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26418/jft.v6i2.80411

Bibliometric analysis is a methodology that can be used to investigate patterns in publications based on data cited from academic literature. This research is conducted to comprehensively analyze selected topics. This paper presents the evolution and structure of the chosen research topic. The goal is to obtain an overview of information about the foodborne pathogen research that has been conducted, with the hope that this information can provide insights and guidance for further research related to foodborne pathogens. This paper is also expected to open up new opportunities for identifying gaps in the analysis of potential innovations in foodborne pathogen research, which can serve as a reference for future studies. Bibliometric literature analysis is centred around the main components using Bibliometrics and VOSviewer. This analysis is based on articles published in Scopus journals from 2013 to 2023. Data extracted from the Scopus web shows an increasing trend year by year, with the United States having the highest number of articles, totalling 3,109, and 22 countries with the lowest number of articles. As for the categories based on the source of information, they can be grouped into journals, books, book series, conference proceedings, and undefined sources. The visualization network shows five different colours, with each colour representing the number of clades generated from the analysis. Based on this, it can be concluded that a significant amount of research related to foodborne pathogens has been conducted, with many studies focusing on pathogens in animals, food microbiology, food control, antibiotic resistance, and pathogens in non-human subjects.

DNA isolation in processed goat meat products (tongseng) Sophian, Alfi
Asia Pacific Journal of Sustainable Agriculture, Food and Energy Vol. 13 No. 1 (2025): June 2025
Publisher : Asia Pacific Network for Sustainable Agriculture, Food and Energy Network (SAFE Network)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36782/apjsafe.v13i1.477

DNA isolation from processed goat meat products (tongseng) was conducted to evaluate the quality of DNA extracted from these processed meat products. This study is intended to serve as a reference for similar research and to support the development of specific DNA detection assays using real-time PCR or authentication tests. The methodology employed in this study utilized standard testing procedures, with DNA quality parameters including concentration and purity measured using a nanophotometer at an A260/A280 ratio. The DNA isolation results are presented in Table 1 below. The table demonstrates that the isolated DNA concentration values ranged from 695,4 ng/µL to 708,4 ng/µL, with a mean concentration of 701,5 ng/µL. The purity values, measured at the A260/A280 ratio, ranged from 2,07 to 2,08, with an average purity value of 2,08. Based on the research findings, it can be concluded that the DNA isolated from processed goat meat food products exhibited good quality, as evidenced by the mean concentration value of 701,5 ng/µL and purity of 2,08. For future research, it is recommended to conduct similar studies on food products from other categories to obtain comprehensive information that can support species DNA identification assays or product authentication tests.

DNA isolation from processed shrimp food products (shrimp tempura) Sophian, Alfi
Asia Pacific Journal of Sustainable Agriculture, Food and Energy Vol. 13 No. 1 (2025): June 2025
Publisher : Asia Pacific Network for Sustainable Agriculture, Food and Energy Network (SAFE Network)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36782/apjsafe.v13i1.478

DNA isolation is an important step that must be carried out in research or testing the identification of DNA species based on molecular techniques using PCR or real-time PCR. The purpose of this study was to determine the quality of DNA isolated from shrimp processed food products in shrimp tempura preparations. One of the benefits of this research is that it can be a source of information and reference for similar research. The method used in this research is the DNA isolation method using the spin column technique. Analysis of the quality of the isolated DNA was based on the parameters of the concentration value and DNA purity measured by a nanophotometer at the ratio of A260/A280. Data analysis was carried out by calculating the average concentration and purity values obtained from measurements using a nanophotometer and then calculating the standard deviation values and comparing them. Based on the results of the research conducted, it was concluded that the DNA isolated from the results showed the value of concentration and purity of DNA which was included in the good DNA category. The results of statistical tests on data uniformity show that the data analyzed in this study are homogeneous.

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