Judul: Genetic Diversity of Promoter and 5’ Untranslated Region of HSP70 Gene in Beef Cattle
Abstrak: Indonesia memiliki beragam jenis sapi baik asli, lokal, maupun eksotik yang berpotensi sebagai sumber protein hewani. Pemanasan global telah menjadi ancaman bagi produktivitas ternak yang berdampak negatif pada pertumbuhan, reproduksi, produksi susu, dan sifat karkas ternak. Adaptasi adalah mekanisme penting bagi ternak jika pemicu stres lingkungan berlangsung dalam kurun waktu yang lama. Salah satu mekanisme adaptasi adalah heat shock protein, termasuk HSP70 (heat shock protein 70) yang merupakan biomarker penting dalam mekanisme biokimia terhadap stres panas. Penelitian ini bertujuan untuk mengidentifikasi keragaman daerah promotor dan 5' UTR (untranslated region) gen HSP70 pada sapi pedaging di Indonesia. Total sampel yang digunakan adalah sebanyak 86 sampel darah yang terdiri dari sapi bali, madura, PO (peranakan ongole), limosin, dan belgian blue. DNA Sampel selanjutnya dianalisis menggunakan metode direct sequencing. Hasil genotyping menunjukkan adanya lima SNP (single nucleotide polymorphism) di daerah promotor (g.-393T>C, g.- 343C>A, g.-202T>C, g.-69T>G) dan tiga SNP di 5' UTR (g.19A>G, g.45C>T, g.100_101ins31). Frekuensi alel yang ditemukan pada sapi PO, limosin dan belgian blue berada dalam keseimbangan Hardy-Weinberg, sedangkan pada populasi sapi bali dan sapi madura frekuensi alelnya disequilibrium. Secara umum keragaman alel yang diamati berkisar rendah hingga tinggi (0.26-1.00), SNP g.19A>G merupakan SNP yang memiliki keragaman tertinggi. Ditemukan bahwa SNP g.-69T>G berikatan dengan faktor transkripsi dari NF-Y dan CAAT box. Selain itu, ditemukan insersi 30 pb (pasang basa) (g.100_101ins31) pada sapi bali dan sapi madura yang belum pernah dilaporkan sebelumnya., Global warming has become a threat of livestock productivity by negatively affecting growth, reproduction, milk yield, and carcass traits of the livestock. Adaptation is a crucial mechanism for animals if the environmental stressor is present for an extended period. One of the mechanisms regulations of adaptation is Heat shock protein, include HSP70 (Heat Shock Protein 70), which is an essential biomarker as a biochemical mechanism against heat shock. This study aims to identify genetic diversity in the promoter area and 5' UTR (untranslated region) HSP70) gene in several beef cattle in Indonesia. A total of 86 blood samples of bali, madura, PO (peranakan ongole), limousine, and BB (belgian blue) cattle were used in this study. The extracted DNA of all blood samples was then analyzed using the direct sequencing method. The genotyping results showed the presence of five SNP (Single Nucleotide Polymorphism) in the promoter region (g.-393T>C, g.-343C>A, g.-202T>C and g.-69T>G) and three SNPs at 5' UTR (g.19A>G, g.45C>T, and g.100_101ins31). The frequency of SNP alleles found in PO, limousine, and BB cattle was in equilibrium, but in bali and madura cattle populations, the allele frequency was disequilibrium. In general, the level of diversity of observed alleles ranged from low to high (0.26-1.00), where SNP g.19A>G had the highest diversity. It was successfully revealed in this analysis that the SNP g.-69T > G binds to both the NF-Y and CAAT box transcription factor. In addition, the 30 bp (base pair) insertions (g.100_101ins31) that were identified in bali and madura cattle have never been reported in previous research studies.
Keyword: 5’-UTR, HSP70, promotor, sapi pedaging, SNP

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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