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All Journal Jurnal Perikanan dan Kelautan Jurnal Kelautan dan Perikanan Terapan (JKPT)
Khumaira Puspasari
Ministry of Marine Affairs and Fisheries
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Decision Sciences, Operations Research & Management Environmental Science

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Optimum Koi Herpesvirus DNA Extraction from the Aquaculture Water Khumaira Puspasari; Ishaaq Saputra; Agustina Kristina Sibuea; Zulhan Efendi Lubis; Firma Firma
Jurnal Perikanan dan Kelautan Vol 11, No 2 (2021)
Publisher : JURNAL PERIKANAN DAN KELAUTAN

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33512/jpk.v11i2.12527

Abstract

Koi Herpesvirus (KHV) is one of the viral fish disease in the common carp aquaculture. At present, KHV diagnoses is performed using Polymerase Chain Reaction (PCR) method. However, the effort to extract DNA viruses from environmental samples depends on two fundamental problems: inhibition of the extraction and amplification processes and a very small number of viruses. The small amount of virus load in the water requires a concentration process before further molecular analysis. In this study, the sensitivity of three methods of extraction and purification of viral genetic material from the water, namely deposition with PEG, filtration-elution, and flocculation with antibodies for the detection of KHV from the water with the PCR method was performed. Water samples were collected from Cirata reservoir, West Java which is a site location for carp aquaculture. The organic flocculation cannot be carried out in the present study because anti-KHV antibodies cannot be produced. This is because the amount of virus in the sample used by the vaccine is low. Meanwhile, the precipitation method with PEG cannot produce DNAextract’s although quantity and purity are good enough to be amplified. For the filtration-elution method, both with and without the reconcentration process, a clear band of DNA can be produced after amplification. In conclusion, the filtration-elution method is considered as the most suitable method in obtaining KHV DNA’s taken from the water samples.
Pemetaan Genomik Daerah RNA2 (Coat Protein) Betanodavirus Penyebab Penyakit Viral Nervous Necrosis (VNN) Khumaira Puspasari; Zakiyah Widowati; Freddy Riatmono; Ade Nurdin; Hasriani Hasriani; Ishaaq Saputra
Jurnal Kelautan dan Perikanan Terapan (JKPT) Vol 3, No 2 (2020): JKPT Desember 2020
Publisher : Politeknik Ahli Usaha Perikanan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15578/jkpt.v3i2.9375

Abstract

Ikan kerapu dan kakap merupakan komoditas ikan penting di Indonesia yang memiliki berbagai jenis spesies maupun hasil silangannya. Salah satu permasalahan dalam kegiatan budidaya kelompok ikan ini yaitu adanya ancaman serangan virus Viral Necrosis Virus (VNN). Pada penelitian ini, dilakukan upaya pemetaan Betanodavirus sebagai penyebab VNN pada sentra budidaya ikan kerapu maupun kakap di wilayah Indonesia.  Pemetaan genomik daerah RNA2 (coat protein) Betanodavirus dilakukan berdasarkan pada sejumlah 355 ekor ikan sampel dengan berbagai ukuran. Pengujian Betanodavirus dilakukan dengan metode Reverse Transcriptase – Nested PCR. Sedangkan untuk mengetahui sekuen dan hubungan kekerabatan lebih detail dilakukan sekuensing DNA dan analisa filogenetik. Hasil penelitian menunjukkan bahwa Betanodavirus yang ditemukan pada sampel yang diperoleh merupakan golongan dari Red-spotted Grouper Nervous Necrosis Virus (RGNNV). Selain itu, dari sejumlah sampel yang diperoleh dapat dikategorikan menjadi delapan sekuen utama. Berdasarkan analisa filogenetik yang telah dilakukan, Betanodavirus dari sampel ikan dapat digolongkan menjadi tiga kluster utama dengan tingkat kemiripan masing-masing kluster adalah 99.0%, 99.0% dan 96.02%.
Co-Authors Ade Nurdin Agustina Kristina Sibuea Firma Firma Freddy Riatmono Hasriani Hasriani Ishaaq Saputra Ishaaq Saputra Zakiyah Widowati Zulhan Efendi Lubis