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: Molecular Marker Gen Cytochrome B to Detect Species in Processed Fish Products
Abstrak: DNA barcoding dengan penanda genetik cytochrome b (cyt b) serta autentifikasi berbasis PCR digunakan untuk mengidentifikasi produk olahan perikanan serta keaslian bahan baku sehingga dapat mengurangi permasalahan keamanan pangan. Penelitian ini bertujuan untuk mendeteksi dan melihat ketertelusuran produk olahan perikanan. Sampel berjumlah 25 terdiri dari fillet ikan beku, asin, dan produk olahan perikanan yang diisolasi serta gen diperbanyak dengan primer universal. Isolat DNA memiliki konsentrasi 1,1-3.786,96 ng/μL dengan kemurnian 0,4-2,08. Primer universal berhasil mengamplifikasi gen cyt b sebanyak 22 dari 25 produk perikanan. Hasil analisis menunjukkan sampel terdeteksi sebagai Salmo salar, Lates calcarifer, Thunnus albacares. Hasil penelitan menunjukkan; Mislabelling untuk spesies Pangasianodon sp. yang dipasarkan sebagai produk fillet ikan dori dan kemudian Psettodes erumei yang dipasarkan sebagai ikan kerapu; serta dalam sampel terdeteksi juga ikan yang terancam punah yaitu spesies Carcharhinus falciformis, Sphyrna mokarran dan Himantura chaophraya., PCR-based DNA barcoding with genetic marker cytochrome b (cyt b) can be used to identify species in processed products as well as the authenticity of raw materials. This study aims to detect and see the traceability of fishery processed products. Twenty-five samples consisting of frozen fish fillets, salted fish fillets, and processed fishery product were isolated and their gene was amplified using universal primer. The DNA isolates had a concentration of 1.1-3,786.96 ng/μl, with a purity of 0.4-2.08. The universal primer was successfully amplified the cyt b gene in 22 out of 25 fish products. Analysis showed samples detected as Salmo salar, Lates calcarifer, Thunnus albacares. The results showed; Mislabelling for Pangasionodon sp. species which is marketed as a Dori fish fillet product and then Psettodes erumei which is marketed as Grouper fish fillet; And in the sample detected also endangered fish namely the species Carcharhinus falciformis, Sphyrna mokarran, and Himantura chaophraya.
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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