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All Journal Indonesian Journal of Biotechnology Biosaintifika: Journal of Biology & Biology Education
Afif Pranaya Jati
Masyarakat Bioinformatika Dan Biodiversitas Indonesia (MABBI), Ruang 613, Lantai 6, Program Studi Bioteknologi, Universitas Esa Unggul, Jl. Arjuna Utara No. 9, Jakarta Barat 11510, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Immunology & microbiology Materials Science & Nanotechnology

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The design of Indonesian SARS‐CoV‐2 primers based on phylogenomic analysis of the SARS‐CoV‐2 clades Tsania Taskia Nabila; Ata Rofita Wasiati; Afif Pranaya Jati; Annisa Khumaira
Indonesian Journal of Biotechnology Vol 27, No 1 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.66854

Abstract

Molecular detection needs to be augmented for COVID‐19 detection in Indonesia using the PCR method with primer‐based gene analysis. This is necessary because the RNA of the SARS‐CoV‐2 virus, the causative infectious agent of the pandemic, has been mutated. Therefore, this study aimed to develop a primer design for determining SARS‐CoV‐2 clades in Indonesia using phylogenomic analysis. Data were obtained from 38 GISAID (Global Initiative on Sharing All Influenza Data) viruses and the relationships were analyzed using maximum likelihood (ML) phylogenomic analysis with a substitution model of generalized time‐reversible (GTR) to construct the tree topology. The results showed that the five types of SARS‐CoVs‐2 clades in Indonesia were L, G, GH, GR, and O. It also indicated that the GH region had the highest rate of clade at 50%, with the S clade affecting its formation. Furthermore, the genome sequences of the GH type used to design its primer were based on three genes, namely RdRp, S, and N. The RdRp and N genes were found to be conserved and hardy mutants, while the S gene occurred repeatedly. Several previous studies have stated that the designed primers produced missense mutations compared to another in silico. Therefore, three sets of primers were achieved from the GC contents and clamps, Tm range, and structural secondary indicator standards.
Insertion of Three Genes Encoding Polyhydroxybutyrate into Escherichia coli BL21 as the First Host: A Preliminary Exploration of Plasmid Transformant Ganies Riza Aristya; Azizah Tyas Nugrahanty; Lucia Arum Sekar Meysari; Bagas Alfian Dwiaryanda; Arief Muammar; Afif Pranaya Jati; Muhammad Fauzi Arif; Abdul Rahman Siregar; Imam Bagus Nugroho; Hong-Wei Yen
Biosaintifika: Journal of Biology & Biology Education Vol. 18 No. 1 (2026): April 2026
Publisher : Universitas Negeri Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15294/biosaintifika.v18i1.33054

Abstract

The use of biodegradable plastics presents a sustainable option as concerns about the environmental effects of petroleum-based plastics grow. PHB (polyhydroxybutyrate) is one of the biodegradable biopolymers, which can be produced by Escherichia coli encoded by the PhaA, PhaB, and PhaC genes. This research aims to determine and study the ability of E. coli BL21 as a host in transforming the PhaA, PhaB, and PhaC genes encoding PHB, and characterizing successful E. coli BL21 carrying each gene. Recombinant plasmids carrying PhaA, PhaB, and PhaC genes were constructed by cloning into a pUC57 vector and transformed into E. coli BL21 by electroporation. The positive transformants were analyzed using colony-PCR, restriction digestion, and Sanger Sequencing to confirm the successful insertion of the target. Recombinant plasmids were isolated, purified, and verified, obtaining target fragments of 1195bp for PhaA, 752bp for PhaB, and 1786bp for PhaC. The results showed that E. coli BL21 bacteria could act as a transformation host for the recombinant plasmid carrying the PhaA, PhaB, and PhaC genes, which was confirmed through growth on ampicillin LB medium. The PhaA, PhaB, and PhaC genes were successfully transformed with recombinant E. coli BL21 and showed a gene size of 1195 bp, 752 bp, and 1786 bp, respectively. Based on sequences analyses showed a high percent identity and query cover against the reference gene database (KP681582, KP681583, and KP681584). The entire PhaA, PhaB, and PhaC gene sequence has been inserted into recombinant cells, with the result of cutting according to the gene band size and the pUC57 plasmid size. This study provides a foundation for the optimal expression of PHB in recombinant bacteria and serves as a reference in designing genetic transformation strategies for E. coli BL21. The method is also of industrial relevance for replacing or reducing conventional plastics, thereby boosting the circular bioeconomy and directly contributing to the UN Sustainable Development Goals, especially in SDG 9 which focuses in industry, innovation, and infrastructure and SDG 12 which focuses in responsible consumption and production.
Co-Authors Abdul Rahman Siregar Annisa Khumaira Arief Muammar Ata Rofita Wasiati Azizah Tyas Nugrahanty Bagas Alfian Dwiaryanda Ganies Riza Aristya Hong-Wei Yen Imam Bagus Nugroho Lucia Arum Sekar Meysari Muhammad Fauzi Arif Tsania Taskia Nabila