Streptolysin Encoding Genes sagC and sagD as Biomarkers of Fish Pathogen Streptococcus iniae: An In Silico Study

Ethica, Stalis Norma; Darmawati, Sri; Dewi, Sri Sinto; Nurrahman, Nurrahman; Sulistyaningtyas, Ayu Rahmawati

doi:10.15578/squalen.v15i1.416

Cited by 3 publications

(2 citation statements)

References 24 publications

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“…genomes stored in the program database. In silico PCR can be done by choosi ng "PCR Amplification" from the main page of the website, and once it opens, inserts the primers, then click "amplify" (Bikandi, Millán, Rementeria, & Garaizar, 2004; San Millán, Martínez-Ballesteros, Rementeria, Garaizar, & Bikandi, 2013); Ethica, Sulistyaningtyas, & Darmawati, 2019;Ethica, Darmawati, Dewi, Nurrahman, & Sulistyaningtyas, 2020). The nucleotide database used in the in silico PCR website comes from National Center of Bioinformatics Institute (NCBI) database.…”

Section: Methodsmentioning

confidence: 99%

Detection of rtxA Gene as a Biomarker of Seafood-Borne Pathogen Vibrio cholerae using In Silico PCR Assay

Ethica

Hidayati

Fuad

et al. 2020

Squalen Bull. Marine Fisheries Postharvest Biotech.

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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.

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Section: Methodsmentioning

confidence: 99%

Detection of rtxA Gene as a Biomarker of Seafood-Borne Pathogen Vibrio cholerae using In Silico PCR Assay

Ethica

Hidayati

Fuad

et al. 2020

Squalen Bull. Marine Fisheries Postharvest Biotech.

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“…Selanjutnya, sekuen fasta gen digunakan sebagai bahan untuk desain primer menggunakan Primer3Plus (Ethica, Hidayati, et al, 2020). Dipilih pasangan primer yang tidak memiliki kemungkinan terjadi formasi hairpin, self-complementarity, dan dimerization (Ethica, Darmawati, et al, 2020). Desain primer yang baru dirancang dari Primer3Plus digunakan sebagai masukan untuk in silico PCR berbasis web yang dijalankan dari http://insilico.ehu.es/PCR/ menggunakan semua genom Corynebacterium yang diambil dari sumber database.…”

Section: Metodeunclassified

Desain Primer untuk Deteksi Gen Diphtheria Toxin Repressor (dtxR) sebagai Biomarker Bakteri Corynebacterium diphtheriae Menggunakan In Silico PCR

Nastiti,

Kuncara

2023

JLM

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Corynebacterium diphtheriae is the bacteria that causes diphtheria. The virulence factor of C. diphtheriae comes from the bacteria's ability to produce bacterial toxins. Toxin production is regulated by a set of genes called tox/dtx genes and is regulated by the dtxR gene. The aim of this study was to design primers used to evaluate the dtxR gene using bacterial DNA sequences. This research is experimental research with a literature study approach using the In silico Polymerase Chain Reaction (PCR), NCBI (National Center for Biotechnology Information), Primer3Plus, and Oligo Calculator applications. The sample obtained from genbank NCBI was C. diphtheriae dtxR gene M80337.1. In silico PCR examination was carried out using newly designed primers from Primer3Plus with 50 genomic DNA of Corynebacterium spp. taken from the In silico PCR database. The dtxR primer pair: '5-ACAGTTAGCCAAACCGTTGC-3' and 5'-TGCGTTCAACTTCGTCACTC-3' can produce a single DNA amplicon measuring 226 bp specifically for C. diphtheria types and no amplicon bands were generated from other Corynebacterium genomes. Based on the study results, this pair of specific primers can be used for in vitro PCR testing and can be used to develop rapid detection of diphtheria.

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Food-grade protease producing bacteria isolated from Indonesian soybean tempe gembus and red oncom after prolonged fermentation

Sulistyaningtyas

Baldivia

Mukaromah

et al. 2021

IOP Conf. Ser.: Earth Environ. Sci.

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The search of food-grade proteases allowing broad application in food industry and protein modification is on increase worldwide due to pressure on the market of these enzymes as commodity product, both on price reduction and increasing performance. This paper reports nine protease-producing bacterial strains as new sources of food-grade protease from bacteria isolated from two Indonesian fungal fermented foods, soybean Tempe gembus and red oncom. Isolation was conducted on every other day within 5 days of storing (post fermentation) and protease production tests were then carried out on skim milk media agar. Cells of the isolated proteolytic strains were morphologically identified using SEM (Scanning Electron Microscope) and a bacterial phylogenetic tree was constructed using MEGA 7 program based on partial sequences of 16S rRNA genes of these bacteria. Based on taxa analysis and plate-based pathogenicity test, B. megaterium IROD3 and, B. amyloquefaciens IROD2, B. tequilensis ISTD3, and S. carnosus IROD4 appeared to be the potential candidates of food-grade proteolytic enzyme producers. This study concluded that prolonged fungal fermentation of soybean Tempe gembus and red oncom allowed growth of known low - nonpathogenic protease producing bacteria.

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Streptolysin Encoding Genes sagC and sagD as Biomarkers of Fish Pathogen Streptococcus iniae: An In Silico Study

Cited by 3 publications

References 24 publications

Detection of rtxA Gene as a Biomarker of Seafood-Borne Pathogen Vibrio cholerae using In Silico PCR Assay

Detection of rtxA Gene as a Biomarker of Seafood-Borne Pathogen Vibrio cholerae using In Silico PCR Assay

Desain Primer untuk Deteksi Gen Diphtheria Toxin Repressor (dtxR) sebagai Biomarker Bakteri Corynebacterium diphtheriae Menggunakan In Silico PCR

Food-grade protease producing bacteria isolated from Indonesian soybean tempe gembus and red oncom after prolonged fermentation

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