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All Journal Jurnal Ilmu Kedokteran (Journal of Medical Science) Jurnal Ners Indonesia Majalah Kedokteran Bandung Ethos Jurnal Kesehatan Andalas Proceeding International Conference on Global Resource Conservation Jurnal Kedokteran Gigi Universitas Padjadjaran Jurnal Kedokteran Anatomica (Anatomica Medical Journal) Jurnal Surya Masyarakat Acta Biochimica Indonesiana Majalah Kedokteran Andalas Jurnal Surya Masyarakat Nusantara Science and Technology Proceedings Prosiding Seminar Nasional Unimus
Rahmat Azhari Kemal
Fakultas Kedokteran Universitas Riau
Religion Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Dentistry Economics, Econometrics & Finance Education Engineering Environmental Science Health Professions Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Nursing Public Health Veterinary Other

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Journal : Acta Biochimica Indonesiana

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Computational design of ancestral and consensus sequence of apical membrane antigen 1 (AMA1) of Plasmodium spp Rizky Nurdiansyah; Rahmat Azhari Kemal
Acta Biochimica Indonesiana Vol. 2 No. 2 (2019): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.v2i2.40

Abstract

Background: It is important to design a malaria vaccine targeting all human malaria parasites as well as non-human primate parasites to eradicate malaria and prevent zoonotic malaria. Apical membrane antigen 1 (AMA1) protein is shared by human-infecting Plasmodium species. Ancestral sequence reconstruction (ASR) and consensus sequence construction on AMA1 might be able to overcome the antigenic distinction between those species. Objective: We aimed to computationally design the ancestral and consensus sequence of Plasmodium AMA1 protein and analyze the sequences for its putative immunogenicity. Methods: We utilized bioinformatics software to computationally design ancestral and consensus sequences of AMA1 protein. AMA1 protein sequences of human-infecting Plasmodium and non-human primate Plasmodium were retrieved from PlasmoDB. ASR was designed using MEGA X while consensus was inferred using UGENE. Phylogenetic tree consisting of existing Plasmodium sequences and the ancestral sequence was constructed using IQTREE webserver and visualized with FigTree. Results: Phylogenetic analysis showed that Plasmodium spp. were divided into 2 major groups, P. falciparum (Clade F) and non-falciparum (Clade NF) thus three ancestral and consensus sequences were designed based on each clade and both clades at once. Reconstructed ancestral sequences were located as sister branch for naturally occurring strains. On the contrary, consensus sequences are located within the branch of corresponding naturally occurring strains. Sequence analysis showed the presence of CD8+ T cell epitope in all computationally-designed sequences. Conclusion: Ancestral and consensus AMA1 sequences are potential for further studies as a malaria vaccine candidate.
Optimization of multiplex PCR composition to screen for SARS-CoV-2 variants of concern Maya Savira; Enikarmila Asni; Rahmat Azhari Kemal
Acta Biochimica Indonesiana Vol. 4 No. 2 (2021): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.58

Abstract

Background: The ongoing COVID-19 pandemic has led to the emergence of several variants of concern. To rapidly identify those variants, screening samples for whole-genome sequencing (WGS) prioritization could be performed. Objective: We optimized the polymerase chain reaction (PCR) screening method to identify the mutation in spike and ORF1a regions. Methods: We adopted primers targeting mutation in spike and ORF1a region from another study. We optimized the PCR screening method using kits readily available in Indonesia. Firstly, we compared N1 and N2 primers as internal positive control. We also compared GoTaq® 1-Step RT-qPCR System and Indonesia TFRIC-19 BioCOV-19 for the multiplex reaction. We used the optimized composition to screen SARS-CoV-2 positive samples from April – June 2021. Samples with spike and/or ORF1a target failure were subjected to whole genome sequencing (WGS). Results: The results demonstrated the N2 BioCOV-19 reaction as the optimized multiplex PCR composition for spike and ORF1a mutations screening. Whole-genome sequencing has shown that a sample with spike and ORF1a targets failure to be Alpha variant, while other samples with single target failure as non-variants of concern. Therefore, a multiplex RT-PCR composition has been optimized to detect mutation in spike and ORF1a regions. Conclusion: We have optimized a multiplex RT-PCR composition to detect mutation in spike and ORF1a regions.
Co-Authors Agung Ramadhan Arfianti Arfianti Arfianti Arfianti Arfianti Arfianti Ariza Julia Paulina Astrid Faradisty Bayu Fajar Pratama Bayu Fajar Pratama Bebe Gani Carlo Manuel Perangin-angin Dani Rosdiana Dedi Afandi Dina Br Nababan Dita Kartika Sari Donel S Eka Bebasari Elita Rafni Enikarmila Asni Fajri Marindra Siregar Fajri Marindra Siregar Fajri Marindra Siregar Fauzia Andrini Djojosugito Huriatul Masdar Ika A. Rini, Ika A. Ika Agus Rini, Ika Agus Indah Oktaviani Jefrizal Jefrizal Ligat Pribadi Sembiring Ligat Pribadi Sembiring Maya Savira P Purwanto Paramita W.N. Islamiah, Paramita W.N. Reni Oktora Resty Yuwandari Riki Sukiandra Rita Endriani Rizky Nurdiansyah Ruli Fatmawati, Ruli Sitti Zuhairah Sri Intan Agusmai Suyanto Suyanto Tina Lusiany, Tina Tutut Ismi Wahidar Ulfah Ulfah Winarto Winarto Yossi Maryanti Zulharman