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: 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: 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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