Judul: Identification of Orange-spotted Grouper (Epinephelus  coioides) with DNA Isolation Methods in The Cytochrome B Gene DNA Mini  Barcode Technique
Abstrak: Kasus mislabeling kerap terjadi pada produk perikanan. Keragaman spesies dan kemiripan morfologi yang cukup tinggi pada kerapu merupakan suatu tantangan yang dihadapi dalam identifikasi spesies. Autentikasi spesies berbasis DNA dapat digunakan untuk mencegah terjadinya kasus mislabeling. Beberapa penelitian menyatakan adanya ambiguitas dalam penggunaan gen COI untuk analisis taksonomi kerapu Epinephelus. Penelitian ini bertujuan memperoleh primer spesifik PCR dengan gen target cytochrome B, dan menentukan kondisi amplifikasi optimum untuk aplikasi pada spesies-spesifik kerapu lumpur (E. coioides). Tahapan penelitian dilakukan dengan pembuatan primer forward dan reverse E. coioides, preparasi sampel, isolasi DNA dengan kit, uji konsentrasi dan kemurnian hasil, elektroforesis hasil isolat DNA, amplifikasi DNA, dan visualisasi hasil amplifikasi. Pasangan primer spesifik E. coioides dengan marka gen cytochrome B berhasil diperoleh. Optimasi suhu annealing pada primer hasil rancangan dilakukan dengan tiga suhu yang berbeda dan telah berhasil diperoleh suhu annealing optimal pada suhu 65°C., Cases of mislabeling occur in fishery products frequently. The high diversity of species and morphological similarity in grouper is a challenge in species identification. Species authentication based on DNA can be used to prevent cases of mislabeling. Several studies have shown ambiguity in the use of the COI gene for the taxonomic analysis of Epinephelus grouper. This study aims to obtain primer-specific PCR with cytochrome B target genes, and determine the optimum amplification conditions for species-spesific application of Orange-spotted grouper (E. coioides). The phases of the research were carried out by making forward and reverse E. coioides primers, sample preparation, DNA isolation using kit, testing the concentration and purity, electrophoresis of the isolated DNA results, DNA amplification, and electrophoresis of the amplification results. Specific primer pairs for E. coioides with cytochrome B gene markers were obtained. Optimization of the annealing temperature on the designed primer was carried out at three different temperatures and was obtained optimally at 65°C.
Keyword: DNA barcoding, Epinephelus coioides, PCR, Primer

Judul: Species Identification in Fisheries Products using Genetic Molecular Marker Cytochrome B Minibarcode
Abstrak: Fish is one of the largest food commodities, so market demand for fish is high. Fish with high economic value is one of the high market demands, this causes fraud in the sale of fish. DNA barcoding is used to identify fishery processed products as well as the authenticity of raw materials so as to reduce food safety problems. The isolation method used was Cetyltrymethyl Ammonium Bromide (CTAB) with concentration and purity testing using a Nanodrop spectrophotometer. The 25 samples consisting of frozen fish fillets, processed fishery product, and salted fish fillets from traditional and supermarket in Jabodetabek. DNA isolates have a concentration of 4,65-3172,6 ng/μL, with a purity of 1,067-2,125. An electrophoregram showed 7 samples sampled on a target DNA of 200-300bp. Analysis using BLAST showed samples detected as Makaira nigricans, Rachycentron canadum, Lates calcarifer, Priacanthus tayenus, Lepidocybium flavobrunneum, and Salmo salar. Phylogeny analysis showed the samples formed a group corresponding to database from Genbank., Ikan menjadi salah satu komoditi pangan yang cukup besar, sehingga permintaan pasar terhadap ikan menjadi tinggi. Ikan dengan nilai ekonomis tinggi menjadi salah satu permintaan pasar yang tinggi, hal tersebut menyebabkan terjadinya kecurangan dalam penjualan ikan. DNA barcoding dengan penanda genetik cytochrome b digunakan untuk mengidentifikasi produk olahan perikanan serta keaslian bahan baku sehingga dapat mengurangi permasalahan keamanan pangan. Metode isolasi yang digunakan adalah Cetyl Trymethyl Ammonium Bromide (CTAB) dengan pengujian konsentrasi dan kemurnian menggunakan spektrofotometer Nanodrop. Sampel berjumlah 25 terdiri dari filet ikan beku, produk olahan perikanan, dan filet ikan asin yang didapat dari pasar tradisional dan swalayan di Jabodetabek. Isolat DNA memiliki konsentrasi 4,65-3172,6 ng/µL, dengan kemurnian 1,067-2,125. Elektroforegram menunjukan 7 sampel teramplifikasi pada DNA target 200-300bp. Hasil analisis menggunakan BLAST menunjukan sampel terdeteksi sebagai Makaira nigricans, Rachycentron canadum, Lates calcarifer, Priacanthus tayenus, Lepidocybium flavobrunneum, dan Salmo salar. Analisis filogeni menunjukan sampel membentuk kelompok yang sesuai dengan basis data dari Genbank.
Keyword: Cytochrome b, DNA barcoding, fishery products, PCR

Judul: Hamiltonian formulation for linear waves motion in two layers fluid
Abstrak: The surface wave could be considered as a wave that separates two fluids, namely water and air. Based on this assumption, it is introduced the interfacial wave, a wave between two layers of fluid with different density. The formulation of interfacial waves motion begins with deriving the base equation of irrotational ideal fluid. Furthermore, according to irrotational fluid assumption, the base equation can be stated in velocity potential. In this derivation, the fluids domain is assumed to be restricted by rigid lid boundary conditions, both at the upper and lower limit. Therefore, the interfacial waves motion can be explained in a hamiltonian formulation. In the hamiltonian formulation, total energy is defined as the sum of kinetic and potential energy. The hamiltonian system is obtained from reduction of kinetic energy by using the Dirichlet Neumann Operator. The resulted kinetic energy equation is nonlinear. Therefore, this form is linearized by first part of the Taylor expansion. This linearization gives a dispersion relation of linear wave. Based on this dispersion relation, the phase speed of the linear wave depends on the density ratio of the two layers fluid.
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