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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Jurnal Riset Biologi dan Aplikasinya
Ardana, I Kade Karisma Gita
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Immunology & microbiology Medicine & Pharmacology

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The Comparison of SARS-CoV-2, SARS-CoV, and MERS-CoV Genome and Spike Protein Variations Fikriani, Choirun Nita; Ardana, I Kade Karisma Gita; Listyorini, Dwi
Jurnal Riset Biologi dan Aplikasinya Vol 3, No 1 (2021)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v3n1.p38-44

Abstract

SARS-CoV-2 is a virus that has caused COVID-19 pandemic. This virus is a new variant of the SARS-CoV virus and also closely related to MERS-CoV, which caused similar acute respiratory infections. All these viruses recognize target cells by binding to the Receptor Binding Domain (RBD) on Spike protein with receptors. This study aimed to determine the SARS-CoV-2, MERS-CoV, and SARS-CoV genome structure, Spike protein sequence differences, and variations of RBD’s Receptor Binding Motif (RBM). This research was using data mining approach. Genome sequences were downloaded from NCBI, except for Indonesian samples were downloaded from GISAID. Genomic structures, Spike sequence, and RBD structure were analyzed using Bioedit, followed by protein modelling using SwissModel and PyMol applications. The result showed that the SARS-CoV-2, MERS-CoV, and SARS-CoV genome shared the same genes yet in different numbers and length. SARS-CoV-2 Spike protein sequence was quite similar to SARS-CoV Spike protein, but very different to the Spike protein of MERS-CoV. There were variations of RBD’s RBM structure due to the mutations occurred among these viruses. It is suggested that these differences may increase the affinity between SARS-CoV-2 Spike protein to its hACE2 receptor which caused SARS-CoV-2 becomes more infective and spread wider than SARS-CoV and MERS-CoV, in turn. This result expected to be basic information for the development of SARS-CoV-2 introduction inhibition agent and spreading prevention.
Mutation Analysis and Single Nucleotide Polymorphism of TP53 Gene in Breast Cancer in East Java Radhiyah, Rizqa; Ardana, I Kade Karisma Gita; Wisnubroto, Wisnubroto; Listyorini, Dwi; Susanto, Hendra
Journal of Tropical Life Science Vol 11, No 3 (2021)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.11.03.12

Abstract

The Incidence of Indonesia breast cancer case in 2018 was reported at 20.7% or 160,653 in number. The factors that caused breast cancer is TP53 gene mutation and Single Nucleotide Polymorphism (SNP). This study aimed to determine the mutation and Single Nucleotide Polymorphism (SNP) of TP53 gene in breast cancer. Samples of this study were 9 people chosen based on a purposive technique. The methods include total DNA isolation, DNA quantification, PCR, and sequencing. The results of the sequencing were then analyzed using alignment and blast. The SNP is browsed by the SNP finder on NCBI both followed by protein modeling. The results of this study indicate the existence of mutation in the exon and intron regions. Substitution of Guanine (G) to base Adenine (A) is occur in codon 496 which is a coding region. SNP was also obtained in exon of sample 12. The conclusion of this study is breast cancer can be caused by mutations that occur in the exon and altered the structur of protein structure, so then affect the binding affinity between p53 and its target domain. Tp53 gene mutation is not the only cause of breast cancer staging development, there are other genes that also contribute to the development of cancer stage. In addition, Single Nucleotide Polymorphism in the TP53 gene can be used as a predisposition marker of breast cancer that has potential to be inherited
Co-Authors Dwi Listyorini Fikriani, Choirun Nita Hendra Susanto Radhiyah, Rizqa Wisnubroto, Wisnubroto