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All Journal Indonesia Medicus Veterinus Biology, Medicine, & Natural Product Chemistry Aceh Journal of Animal Science Medical Laboratory Technology Journal JMM (Jurnal Masyarakat Mandiri) Global Health Management Journal Oceana Biomedicina Journal Jurnal Sains dan Teknologi Peternakan Community Empowerment OISAA Journal of Indonesia Emas Journal of Experimental and Clinical Pharmacy (JECP) Pengabdian Kampus: Jurnal Informasi Kegiatan Pengabdian Pada Masyarakat Kontribusi: Jurnal Penelitian dan Pengabdian Kepada Masyarakat Oceana Biomedicina Journal International Journal of Sustainable Applied Sciences (IJSAS) Media Kesehatan Politeknik Kesehatan Makassar Barigas: Jurnal Riset Mahasiswa Tropis: Jurnal Riset Teknologi Laboratorium Medis Mosaic: Jurnal Pengabdian Kepada Masyarakat Al-Musthalah: Jurnal Riset dan Penelitian Multidisiplin
Rian Ka Praja
Program Studi Kedokteran, Fakultas Kedokteran Universitas Palangka Raya
Agriculture, Biological Sciences & Forestry Arts Humanities Biochemistry, Genetics & Molecular Biology Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Dentistry Economics, Econometrics & Finance Education Engineering Environmental Science Health Professions Immunology & microbiology Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Nursing Public Health Social Sciences Veterinary Other

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Journal : Aceh Journal of Animal Science

 1 
In silico SYBR® green-based qPCR primer design for virulent protein C gene of Edwardsiella tarda Rian Ka Praja; Reny Rosalina
Aceh Journal of Animal Science Vol 6, No 3 (2021): November 2021
Publisher : Syiah Kuala University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13170/ajas.6.3.19989

Abstract

Edwardsiella tarda infection in fish results in economic losses in aquaculture industries worldwide. Besides, this pathogen is also a zoonotic agent causing gastrointestinal disease in humans. Detection of virulence factors expressed by E. tarda is a key for molecular diagnosis. This study aimed to design SYBR®Green-based quantitative PCR (qPCR) primer for E. tarda virulent protein C (EvpC) gene. A sequence of EvpC with accession number AY424360.4:6500-6991 obtained from GenBank NCBI was selected as the basis for qPCR primer design. qPCR primers were designed using Primer3 online software. Further analysis related to the secondary structure of each primer was carried out using Beacon Designer Free Edition. Five pairs of qPCR primers were successfully designed with Primer3. Based on the results of Primer3 and Beacon Designer analysis, F primer pair 1 (5'-GAATCCACCGACGATAAGCACAAA-3') and R primer pair 1 (5'-GACACGCAGCACCGACATCA-3') were the most favorable primer set since this primer met the criteria in terms of length, melting temperature, GC content, and self complementarity. In addition, this primer set had the highest (closest to zero) -ΔG value of cross dimer, self dimer, and hairpin. It can be concluded that SYBR® Green-based qPCR primer set for EvpC has been successfully designed. However, laboratory optimization experiments are essential for this designed primer set.
Co-Authors Akmal, Rizqy Fajar Syaikhul Amanda, Nadia Keisha Andra Ari P., Eko Marwanto Heru Mulyantoro Dwi Hermayantiningsih Angeline Novia Toemon, Angeline Novia Anggita Ratri Pusporini Anwar, Muhammad Naufa Arif Rahman Jabal Arini Ratnasari Astrid Ekkelsia Saputri Astrid Ekklesia Saputri Auliazar, Tarra Austin Bertilova Carmelita, Austin Bertilova Balyas, Abi Bakring Bustomi, Qonita Sari Cereymo Ewaldo Cici Meriliyani Cici Meyriliani Sensia Cristin, Mery Enjelica Decenly, Decenly Dinda Ananda Sulistina Dwi Putri Safnurbaiti Dwijayanti, Rts. Sherly Elsa Trinovita Estilia Ledyani Ewaldo, Cereymo Frethernety, Agnes Furtuna, Dewi Klarita Habib, Yusril Hanasia Hanasia Hanasia Hanasia, Hanasia Harianja, Henrigen Hartoyo, Riccardo Hasan, Muhamad Umar Muhtar Herlina Eka Shinta I Dewa Gede Sandhikarana I Dewa Made Sukrama I Wayan Muda Suta Arta I Wayan Suardana Jessica Elisabeth Suharis Kahanjak, Donna Novina Karamo, Beatrice Benita Komang Januartha Putra Pinatih Kurniawan, Mutiara Lauren Maretha Lavefolia, Raissa Amanda Ledyani, Estilia Lusi Ulina Simanungkalit Maretha, Lauren Margaretha Yayu Indah Anugerahny Marta Monika Simamora Mery Enjelica Cristin Muhammad Naufa Anwar Muhammad Naufa Anwar Muhammad Naufal Al-Firas Muhammad Ricko Fahrizal Nabilatul Zhofiroh Nadia Keisha Amanda Nadia Kesiha Amanda Br Ginting Nadiah Romadhona Putri Nasywa Putri Rahmadina Natalia Sri Martani Nawan Nawan, Nawan Nazhifah, Annida Kholifatun Ni Nengah Dwi Fatmawati Ni Nengah Dwi Fatmawati Ni Nyoman Sri Yuliani Nuha, Alya Firyal Nur Khalifah Putri Utami Nurul Ilma Haryono Permatasari, Silvani Purba, Yohana Catherine Debyola Putri, Nadiah Romadhona Qonita Sari Bustomi Rahmadina, Nasywa Putri Raissa Amanda Lavefolia Ranintha BR Surbakti Ranti, Dalia Reny Rosalina Reny Rosalina Reny Rosalina, Reny Riccardo Hartoyo Rizki Rachmad Saputra Rizqy Fajar Syaikhul Akmal Salma Fathinah Salsabila, Ivah Sandhikarana, I Dewa Gede Saputri, Astrid Ekklesia Sensia, Cici Meyriliani Simamora, Marta Monika Simanungkalit, Lusi Ulina Sintice Dhea Valerie Suharis, Jessica Elisabeth Suma, Joy Angel Aria Tarra Auliazar Teresa, Astrid Trisia, Adelgrit Turnip, Oktaviani Naulita Utami, Nur Khalifah Putri Valerie, Sintice Dhea Wahyu Hidayati Widayati, Ratna Widhiyanto, Hendrykus Theo Damar Widiarti, Astri Yan Antonio Yohana Catherine Debyola Purba Ysrafil, Ysrafil Yusril Habib