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All Journal Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology Research Fair Unisri
Hayatun Fuad
Prodi Administrasi Kesehatan Universitas Mbojo Bima
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Economics, Econometrics & Finance Education Environmental Science Immunology & microbiology Law, Crime, Criminology & Criminal Justice Social Sciences Other

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DETECTION OF VIRULENCE GENES phoP AND phoQ IN Salmonella spp. USING IN SILICO POLYMERASE CHAIN REACTION Stalis Norma Ethica; Hayatun Fuad; Nur Hidayah; Sri Sinto Dewi; Aditya Rahman Ernanto; Ayu Rahmawati Sulistyaningtyas; Richard David Silvestre; Sri Darmawati
RESEARCH FAIR UNISRI Vol. 4 No. 1 (2020): RESEARCH FAIR UNISRI
Publisher : Universitas Slamet Riyadi

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (701.748 KB) | DOI: 10.33061/rsfu.v4i1.3414

Abstract

Detection of Salmonella bacteria based on their virulence genes is among essential steps in the eradication of clinical infection by bacteria. In this study, two pair of primers, PhoPF-PhoPR: 5’- CCGCGCAGGAAAAACTCAAA-3’ and 5’-ATCTGTTCCAGCATCACCGG -3’ as well as PhoQF-PhoQR: 5’-AGAGATGATGCGCGTACTGG-3’ and 5’- CAGACGCCCCATGAGAACAT-3’, had been successfully designed using Primer3Plus to detect the presence of phoP and phoQ genes in Salmonella spp. Using genomic DNA of 44 genomic data of Salmonella spp. as templates, PhoPF-PhoPR could produce 520-bp amplicon, while PhoQF-PhoQR could result in 598-bp amplicon. Results of in silico PCR showed that both pairs of primers PhoPF-PhoPR and PhoQF-PhoQR could detect only Salmonella enterica species, and no Salmonella bongori species could be detected based on phoP and phoQ sequences. Both pairs of PhoPF-PhoPR and PhoQF-PhoQR primers were also able to detect the virulence genes in most of the studied subspecies of Salmonella enterica available in silico database unless Arizona subspecies. As conclusion, based on this in silico study, phoP and phoQ genes appeared to be biomarkers for Salmonella enterica species. Both pairs of primers designed in this study has potential to be used as detection tool to differentiate species Salmonella enterica from Salmonella bongori, and also to distinguish S.enterica subsp. enterica from subsp. Arizonae.Keywords: Gene detection, bacterial virulence, phoP, phoQ, Salmonella spp.
Detection of rtxA Gene as a Biomarker of Seafood-Borne Pathogen Vibrio cholerae using In Silico PCR Assay Stalis Norma Ethica; Nur Hidayati; Hayatun Fuad; Chaerul Arham; Rivana Ariyadi; Ellyka Purwaningrum; Kazi Mohammad Zillur Rahman
Squalen, Buletin Pascapanen dan Bioteknologi Kelautan dan Perikanan Vol 15, No 2 (2020): August 2020
Publisher : Research and Development Center for Marine and Fisheries Product Processing and Biotechnol

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15578/squalen.v15i2.417

Abstract

Seafood-borne outbreaks caused by Vibrio cholerae have led to the increased need for food safety risk assessment of marine products. An in silico investigation about the potential of virulence gene of V. cholerae, rtxA, as a DNA biomarker of the toxigenic bacterium has been carried out. The aim of this study was to use the bacterial DNA biomarker sequence as a tool to facilitate early rapid detection of cholera infection. Five specific pairs of primers were designed from the rtxA open reading frame DNA of V. cholerae O1 biovar El Tor str. N16961 genomic DNA using Primer3Plus. Next, in silico Polymerase Chain Reaction (PCR) assay was carried out using the newly designed primers and 25 genomic DNA of vibrio spp. retrieved from the in silico database. One of the five designed pairs of primers, RtxAOF-RtxAOR: ‘5-CGCAAAACAGTTTCAGCCGA-3’ and 5’-AGGTTGGTCTTTTGTGGCCA-3’, could result in single DNA amplicon sized 518 bp only from V. cholerae species. No amplicon bands were produced from 17 other vibrio genomes studied using similar RtxAF-RtxAR primers. A further check showed that the amplicon was indeed part of the rtxA gene of V. cholerae. Based on this in silico study, rtxA gene appeared to be a DNA biomarker of V. cholerae, which is potential to facilitate rapid diagnosis of the virulence bacterium using in silico PCR assay.
Co-Authors Aditya Rahman Ernanto Arham, Chaerul Ayu Rahmawati Sulistyaningtyas Ellyka Purwaningrum Kazi Mohammad Zillur Rahman Nur Hidayah Nur Hidayati Richard David Silvestre Rivana Ariyadi Sri Darmawati Sri Sinto Dewi Stalis Norma Ethica