Judul: Identifikasi Keragaman SNP g.1117G>A Gen HSP70 pada Sapi Pedaging menggunakan Teknik PCR-RFLP
Abstrak: Indonesia memiliki sumber daya genetik ternak (SDGT) yang melimpah, termasuk ternak sapi. Sapi lokal mempunyai potensi produksi yang baik pada kondisi lingkungan yang minimal dan mampu memanfaatkan pakan berkualitas rendah serta mempunyai daya reproduksi yang baik. Daerah tropis sering mengalami perubahan suhu di atas zona nyaman yang mengakibatkan tenak mengalami stres dan dapat berdampak pada produksi dan reproduksi. Salah satu kandidat gen yang mempengaruhi toleransi terhadap heat stres adalah gen Heat Shock Protein 70 (HSP70). Penelitian ini bertujuan untuk mengidentifikasi polimorfisme SNP g.1117G>A gen HSP70 (HSP70|BanI) menggunakan metode PCR-RFLP. Penelitian ini menggunakan 65 sampel DNA 4 bangsa sapi yang terdiri dari 20 ekor sapi PO, 20 ekor sapi Madura, 12 ekor sapi kuantan dan 13 ekor sapi pesisir yang telah dikoleksi oleh Laboratorium Genetika Molekuler Ternak Fakultas Peternakan IPB. Analisa keragaman gen HSP70 dengan metode PCR-RFLP. Enzim yang digunakan untuk pemotongan adalah BanI primer forward 5'-GAAAGGAAAAAAGAGACAGA-3' dan primer reverse 5'-AATACGCAGGAGTAGGTGGT-3'. Keragaman genetik dari gen HSP70 dianalisis menggunakan frekuensi alel, frekuensi genotipe, derajat heterozigositas. Keseimbangan Hardy-Weinberg diuji dengan uji Chi Kuadrat menggunakan aplikasi PopGen 32. Hasil penelitian menunjukkan bahwa Amplifikasi gen HSP70 terletak di 5’UTR dengan suhu annealing 61 ⁰ C selama 15 detik dengan panjang produk 539 pb. Keragaman gen HSP70 pada bangsa sapi pedaging lokal bersifat polimorfik dengan frekuensi alel G sebesar (0,565) lebih tinggi dibanding frekuensi alel A (0,435)., Indonesia has abundant livestock genetic resources, including cattle. Local cattle have good production potential in minimal environmental conditions and are able to utilize low-quality feed and have good reproductive. The tropics often experience changes in temperature above the comfort zone which causes livestock to experience stress and will have an impact on production and reproduction. One candidate gene that affects tolerance to heat stress is the Heat Shock Protein 70 (HSP70) gene. This study aims to identify the SNP g.1117G>A HSP70 gene polymorphism (HSP70|BanI) using the PCR-RFLP method. This study used 65 DNA samples from 4 breeds of cattle consisting of 20 heads of PO cattle, 20 heads of Madura cattle, 12 heads of Kuantan cattle and 13 heads of Pesisir cattle that have been collected by the Laboratory of Animal Molecular Genetics, Faculty of Animal Science IPB. Analysis of the HSP70 gene diversity was done by using the PCR- RFLP method. The enzyme used for cutting was BanI with forward primer 5'-GAAAGGAAAAAAGAGACAGA-3 'and reverse primers 5'-AATACGCAGGAGTAGGTGGT-3'. The variation of the HSP gene was analyzed using allele frequency, genotype frequency, and degree of heterozygosity. Hardy-Weinberg equilibrium was tested by Chi-Square test using PopGen 32 application. The results showed that the HSP70 gene amplification was located at 5’UTR with an annealing temperature of 61 ⁰ C for 15 seconds with a product length of 539 bp. The HSP70 gene in local beef cattle was polymorphic with the allele frequency G (0,565) higher than the A allele frequency (0,435).
Keyword: HSP70, genetic polymorphism, PCR-RFLP, local beef cattle

Judul: Analysis of SNP Diversity g.1117G>A HSP70 Gene in Limousine, Belgian Blue, Wagyu, and FH Cattle Using PCR-RFLP Method
Abstrak: Gen HSP70 merupakan salah satu gen yang berfungsi untuk mengatasi cekaman panas. Penelitian ini bertujuan untuk menganalisis keragaman gen HSP70 menggunakan metode PCR-RFLP dengan ezim pemotong BanI. Sampel DNA yang digunakan sebanyak 79 sampel sapi Bos taurus yang terdiri dari 58 ekor tipe pedaging (limousine, belgian blue, wagyu) dan 21 ekor tipe perah (FH). Keragaman genetik gen HSP70 dihitung frekuensi genotipe dan alel, nilai heterozigositas, serta keseimbangan Hardy-Weinberg menggunakan program PopGen32. Amplifikasi fragmen gen HSP70 pada daerah 5’UTR dengan suhu annealing 61 oC selama 15 detik menghasilkan panjang produk PCR sebesar 539 bp dan diperoleh 2 macam alel (A dan G) dan 3 macam genotipe (GG, AG, AA). Panjang produk genotipe yang dihasilkan yaitu GG (369 bp dan 106 bp), AG (475 bp, 369 bp, dan 106 bp), dan AA (475 bp). Hasil menunjukkan bahwa keragaman gen HSP70 pada sapi Bos taurus tipe pedaging dan perah bersifat polimorfik dan berada dalam keseimbangan Hardy-Weinberg., The HSP70 gene is one of the genes that functions to overcome heat stress. This study aimed to analyze the diversity of the HSP70 gene using the PCR-RFLP method with the BanI cutting enzyme. The DNA samples used were 79 samples of Bos taurus cattle consisting of 58 beef breeds (limousine, belgian blue, wagyu) and 21 dairy cows (FH). The genetic diversity of the HSP70 gene was calculated for genotype and allele frequencies, heterozygosity values, and Hardy-Weinberg balance using the PopGen32 program. Amplification of the HSP70 gene fragment in the 5'UTR region with annealing temperature of 61 oC for 15 seconds resulted in a PCR product length of 539 bp and 2 alleles (A and G) and 3 genotypes (GG, AG, AA) were obtained. The length of the genotype products produced were GG (369 bp and 106 bp), AG (475 bp, 369 bp, and 106 bp), and AA (475 bp). The results showed that the diversity of the HSP70 gene in beef and dairy Bos taurus cattle was polymorphic and was in Hardy-Weinberg equilibrium.
Keyword: Bos taurus cattle, genetic diversity, HSP70, PCR-RFLP

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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