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: Analysis of Meat Quality Determinants Genes as Markers of Premium Meat  Producing  in  Bali  Cattle
Abstrak: Bali cattle are native Indonesian livestock genetic resources (AnGR) that have been domesticated from Banteng. Bali cattle should be maintained and preserved for future use because they have the potential to become premium quality beef cattle. Bali cattle's potential can be increased through selection based on genetic markers or marker-assisted selection (MAS), which produces more accurate, effective, and efficient results. The process can be applied to candidate genes related to meat quality. Calpain1 (CAPN1), fatty acid banding protein-4 (FABP4), sterol regulating element binding protein-1 (SREBF1), and scavenger receptor class B member 1 (SCARB1). The purpose of this study is to analize candidate genes that determine beef quality through analysis of gene diversity using DNA sequencing methods and to associate gene diversity with quality characteristics of Bali beef from Kupang, as well as to analyze CAPN1 gene expression. In this study, 95 Bali cattle were used. Meat samples were used for physical analysis and fatty acid composition, and blood samples were used to identify the diversity of the CAPN1, FABP4, SREBF1, and SCARB1 genes using the direct-sequencing method. Analysis of CAPN1 gene expression in Bali cattle liver and blood tissue. Six novel SNPs were discovered for the CAPN1 gene, four for the FABP4 and SREBF1 genes, and five for the SCARB1 gene in Bali cattle as a result of the analysis of gene diversity. The marbling score, intramuscular fat, pH, meat color, tenderness (WBSF), and fatty acid composition were associated with the CAPN1 gene (g.5327C>T, g.5869T>C, and g.5959C>T), according to the results of the association analysis. The FABP4 gene (g.5002C>T) was significantly associated with carcass characteristics including longissimus dorsi thickness (TLD). SREBF1 gene (g.12629T>C, g.12731T>C, g.12881A>G, and g.12986C>T) had an association with fatty acid composition. The SCARB1 gene (g.72219C>T, g.72380C>A, g.72400A>G, g.72517G>A and g.72607C>T) were significantly associated with fatty acid composition. The results of gene expression analysis showed that the low tenderness value (WBSF) was characterized by a higher CAPN1 gene expression level. The results of this study can be concluded that the CAPN1, FABP4, SREBF1, and SCARB1 genes are potential candidate genes to be used as genetic markers for selection of meat quality traits in Bali cattle., Sapi Bali merupakan sumber daya genetik ternak (SDGT) asli indonesia yang telah mengalami proses domestikasi dari Banteng. Sapi Bali berpotensi untuk dikembangkan sebagai sapi pedaging kualitas premium, oleh karena itu perlu dipertahankan dan dilestarikan untuk dimanfaatkan secara berkelanjutan. Potensi sapi Bali dapat ditingkatkan melalui seleksi berdasarkan marka genetik atau marker assisted selection (MAS) yang hasilnya lebih akurat, efektif dan efisien. Proses seleksi dapat dilakukan pada kandidat gen-gen yang berkaitan dengan kualitas daging. Beberapa gen yang potensial untuk diseleksi antara lain: gen calpain1 (CAPN1), gen fatty acid banding protein-4 (FABP4), gen sterol regulating element binding protein-1 (SREBF1), dan scavenger reseptor class B member 1 (SCARB1). Penelitian ini bertujuan menganalisis karakteristik karkas dan daging berdasarkan teknik ultrasonografi, sifat fisik, dan profil asam lemak daging sapi Bali, mengkarakterisasi kandidat gen penentu kualitas daging sapi melalui analisis keragaman gen dengan metode sekuensing DNA dan mengasosiasikan keragaman gen dengan sifat kualitas daging sapi Bali dari Kupang, serta menganalisis ekspresi gen
Keyword: bali cattle, gene expression, meat quality, ultrasound

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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