Judul: Analysis of 5’ and 3’UTR Region Polymorphism of Calpain Gene and Its Relationship with Growth and Meat Quality in Beef Cattle
Abstrak: Bali cattle (Bos javanicus) are native cattle that originally specified from domestication of banteng (Bibos banteng). Bali cattle have the potential to be developed as a premium beef producer. Genes that have important role in meat quality are calpain genes (CAPN). Calpains are classified as Ca2+ dependent intracellular cysteine proteases, including the ubiquitously expressed μ-calpain (CAPN1) and m-calpain (CAPN2). The objective of this study was to analyze 5’ and 3’UTR region polymorphism of calpain gene in beef cattle and its association with growth traits, meat quality in bali cattle using ultrasound. The blood samples of beef cattle used was 113 cattle consist of bali cattle (n=52 cattle) obtained from obtained from BPTU-HMT Denpasar Bali Province, Belgian Blue (n=30 cattle), Limousine (n=14 cattle) from BPTU Padang Mangatas, Wagyu (n=7 cattle), and PO (n=10 cattle) from BET Cipelang Bogor, West Java Province. Carcass include longissimus dorsi thickness (LDT), backfat thickness (BFT) and meat include marbling score (MS), intramuscular fat percentage (PIMF) characteristics were measured using ultrasound images and the USG result data was performed by Image-J NIH software. Polymorphism of 5’UTR and 3’UTR regions in CAPN1 gene were analyzed by PCR-RFLP and DNA direct sequencing respectively. Frequencies of genotype and allele, heterozygosity, and HardyWeinberg equilibrium (ꭓ2) were analyzed using PopGen 1.32 program. The association SNPs polymorphism in CAPN1 gene with growth traits namely weaning weight, body weight at 365 days, body weight at 730 days, and body weight gain, carcass and meat characteristics were performed by General Linier Model (GLM) procedure using SAS 9.4 software. The result shows that CAPN1 g.232 G>T SNP at 5’UTR region was polymorphic in bali cattle and PO, however monomorphic in Belgian Blue, Limousine, and Wagyu. The total of six SNPs at 3’UTR region which were g.15284 C>T, g.15347 T>G, g.15525 G>A, g.15853 G>A, g.15905 G>A, and g.15915 G>A were polymorphic in bali cattle, however monomorphic in Belgian Blue, Limousine, Wagyu and PO. The 3’UTR region was also found indel mutation g.15795–g.15802DelCTCCCTCC which was polymorphic in bali cattle and PO, Belgian Blue, and Limousine, however monomorphic in Wagyu. The polymorphism of g.232 G>T SNP in 5’UTR was associated with body weight at 730 days, however in 3’UTR region were not associated with growth traits in bali cattle. The g.232 G>T SNP in 5'UTR in bali cattle was associated (P <00.5) with marbling score and intramuscular fat percentage. The 3’UTR of g.15525 G>A SNP was associated with back fat thickness. These results further suggest that CAPN1 is a strong candidate gene influencing body weight at 730 days , marbling score, and intramuscular fat percentage in bali cattle., Sapi bali (Bos javanicus) merupakan salah satu ternak asli hasil domestikasi banteng (Bibos banteng). Sapi bali berpotensi untuk dikembangkan sebagai penghasil daging sapi premium. Salah satu gen yang berperan penting dalam kualitas daging adalah gen calpains (CAPN). Calpains diklasifikasikan sebagai protease sistein intraseluler yang diaktivasi oleh Ca2+, termasuk μ-calpain (CAPN1) dan m-calpain (CAPN2). Tujuan dari penelitian ini adalah menganalisis keragaman daerah 5’ dan 3’UTR gen CAPN1 pada sapi pedaging dan asosiasinya dengan sifat pertumbuhan, kualitas daging khususnya pada sapi bali menggunakan citra ultrasonografi.
Keyword: bali cattle, CAPN1 gene, growth traits, meat quality, SNP

Judul: The Polymorphisms of Calpastatin Gene (CAST) and Its Association with Meat Characteristics and Growth Traits in Bali Cattle
Abstrak: Bali cattle (Bos javanicus) is known as one of Indonesian native cattle that domesticated from banteng. Bali cattle was registered by the Ministry of Agriculture of Republic Indonesia (325/Kpts/OT.140/1/2010) is native Indonesian cattle. High adaptability to the environment is one of the traits belong to bali cattle. As one of the local native cattle, bali cattle have the potential to produce high quality meat. One of the factors that affecting the meat quality is genetic factor. The calpastatin gene (CAST) is one of the genes that play an important role in meat quality. The aim of this study was to analyze the polymorphisms of SNP g.41139G>A in the CAST gene using PCR-RFLP and its association with meat charactheristics and growth traits in bali cattle. Bali cattle (n=52) in this study were from BPTU-HPT Sapi Bali Denpasar. Belgian Blue cattle (n=30) from BPTU-HPT Padang Mangatas, West Sumatra Province; Wagyu cattle (n=7) and Limousin cattle (n=14) from BET Cipelang, West Java Province; PO cattle (n=30) from VBC Kebumen were used as comparison. The SNP g.41139G>A polymorphisms on CAST gene were identified by the PCR-RFLP method. Allelic frequency, genotypic frequency, and heterozygosity were analyzed to find out the genetic diversity of bali cattle. The genetic equilibrium in the population was analyzed using the Hardy-Weinberg equilibrium test (χ2) using the PopGen 1.32 program. The association of SNP g.41139G>A polymorphisms on CAST gene with meat characteristics (BFT, LDT, MS, and PIMF) using ultrasound method and growth traits (BW, WW, WT12, WT18, WT24, WT30, and ADG) were analyzed by the t test using SAS program 9.4. The SNP g.41139G>A on CAST gene was specific only found in bali cattle. The SNP g.41139G>A was polymorphic and produced GA genotype and GG genotype, while genotype AA was not found in bali cattle. The SNP g.41139G>A were monomorphic in the other Indonesian beef cattle (Belgian Blue cattle, Wagyu cattle, PO cattle, and Limousin cattle) because only found GG genotype. The results of the SNP association study of g.41139G>A on the CAST gene did not significantly effect with meat characteristics and growth traits in bali cattle., Sapi Bali (Bos javanicus) dikenal sebagai salah satu sapi asli Indonesia hasil domestikasi banteng. Sapi Bali telah ditetapkan oleh Kementerian Pertanian Republik Indonesia (325/Kpts/OT.140/1/2010) sebagai sapi asli Indonesia. Sebagai salah satu sapi asli Indonesia, sapi Bali memiliki potensi sebagai penghasil daging yang cukup berkualitas. Salah satu faktor yang memengaruhi kualitas daging yaitu faktor genetik. Gen calpastatin (CAST) merupakan salah satu gen yang berperan penting terhadap karakteristik dan kualitas daging. Penelitian ini bertujuan menganalisis keragaman SNP g.41139G>A pada gen CAST dengan menggunakan PCR-RFLP serta hubungannya dengan karakteristik daging dan pertumbuhan pada sapi Bali. Sapi Bali (n=52 ekor) yang digunakan berasal dari BPTU-HPT Sapi Bali Denpasar. Sebagai perbandingan digunakan sapi Belgian Blue (n=30 ekor) yang berasal dari BPTU-HPT Padang Mangatas, sapi Wagyu (n=7 ekor) dan Limousin (n=14 ekor) yang berasal dari BET Cipelang, sapi PO (n=30 ekor) dari VBC Kebumen. Karakteristik daging meliputi tebal lemak punggung (BFT), tebal Longissimus dorsi (LDT), marbling score (MS), dan persentase intramuscular fat (PIMF) diukur dengan menggunakan teknik ultrasonografi dan hasil ultasonografi dianalisis
Keyword: bali cattle, CAST gene, polymophisms, ultrasonography

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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