Judul: Identification of Polymorphisms in Exon 3 of Myglobin (MB) Gene in Ayam Cemani and IPB-D1 Chicken
Abstrak: Ayam cemani merupakan ayam asli Indonesia asal Temanggung, Jawa Tengah yang memiliki keseluruhan fenotipik berwarna hitam. Daging ayam cemani memiliki potensi sebagai pangan fungsional berkadar Fe tinggi bagi penderita anemia. Kandungan Myoglobin (MB) memiliki korelasi positif terhadap kadar Fe dalam daging. Hal tersebut digunakan sebagai landasan untuk menjadikan Gen MB sebagai gen kandidat yang diduga memiliki pengaruh terhadap kadar Fe dalam daging. Penelitian ini bertujuan mengidentifikasi keragaman ekson 3 gen MB pada ayam cemani yang berasal dari PT Sumber Unggas Indonesia (SUI), Balai Penelitian Ternak (Balitnak), serta ayam IPB-D1 sebagai pembanding. Sebanyak 45 sampel berhasil dilakukan sekuensing DNA menggunakan jasa Macrogen (Seoul, Korea Selatan). Hasil penelitian menunjukkan bahwa pada daerah ekson 3 gen MB terdapat 1 SNP yaitu di posisi basa g.3385T>C. SNP yang diperoleh bersifat polimorfik dan konsisten ditemukan pada ketiga populasi, sehingga SNP tersebut dapat digunakan untuk analisis lanjutan menuju proses seleksi. Sebanyak enam mutasi lainnya juga ditemukan pada daerah 3’UTR yaitu di posisi basa g.3497C>T, g.3549C>T, g.3583G>A, g.3749C>T, g.3800G>A, dan g.3814G>A., Ayam cemani is an Indonesian native chicken from Temanggung, Central Java which has a black phenotypic color. Ayam Cemani has the potential as a functional food with high Fe content for anemia sufferers. The existence of myoglobin has a positive correlation with Fe content in meat. This was used to make the MB gene as a candidate gene that has a role in Fe content in meat. This study aimed to identify the polymorphisms in exon 3 of MB gene in ayam cemani from PT Sumber Unggas Indonesia (SUI), Balai Penelitian Ternak (Balitnak), as well as IPB-D1 chickens as a comparison. A total of 45 samples were successfully DNA-sequenced using Macrogen services (Seoul, South Korea). The results showed that in exon 3 of MB genes there was 1 SNP at position g.3385T>C. The SNP obtained were polymorphic and consistently found in three populations so that the SNP could be used for further analysis towards the selection process. Other six mutations were also found in the 3'UTR region, i.e: g.3497C>T, g.3549C>T, g.3583G>A, g.3749C>T, g.3800G>A, and g.3814G>A.
Keyword: Cemani, MB gene, DNA sequencing

Judul: Analysis of Fibromelanosis Gene for Detection of Cemani Chicken Purity
Abstrak: Ayam cemani merupakan salah satu jenis ayam kedu hitam yang memiliki warna hitam diseluruh tubuhnya akibat mutasi gen fibromelanosis. Fibromelanosis ini disebabkan adanya duplikasi yang tidak seimbang pada kromosom 20 dan salah satu daerah duplikat mengandung gen EDN3. Penelitian ini bertujuan menganalisis variasi batas duplikasi pada daerah fibromelanosis pada kromosom 20 untuk mengetahui kemurnian ayam cemani. Penelitian ini menggunakan metode Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) pada 76 ekor ayam terdiri dari 32 ekor ayam cemani PT. Sumber Unggas Indonesia, 40 ekor ayam cemani Balai Penelitian Peternakan, dan 4 ekor ayam IPB-D1 sebagai pembanding. Hasil penelitian menyatakan ayam cemani memiliki alel ganda yaitu alel Fm, fm+, dan fm-. Ayam cemani (homogisot) memiliki genotipe Fm/Fm dengan dua pita pada 664 bp dan 588 bp. Ayam cemani heterosigot memiliki genotipe Fm/fm+ dengan empat pita pada 664 bp, 588 bp, 400 bp, dan 264 bp. Ayam cemani wildtype memiliki genotipe fm-/fm- dengan satu pita pada 664 bp. Ayam IPB-D1 (wildtype) memiliki dua genotipe yaitu fm+/fm- (pita 664bp,400 bp, dan 264 bp) dan fm+/fm+ (pita 400 bp dan 264 bp). Keragaman ayam cemani rendah dan besifat polimorfik. Ayam cemani SUI berada dalam keseimbangan Hardy-Weinberg kecuali pada ayam cemani Balitnak., Cemani chicken is a type of black kedu chicken that has black color all over its body due to fibromelanosis gene mutation. Fibromelanosis is caused by an unbalanced duplication of chromosome 20 and one of the duplicated regions contains the EDN3 gene. This study aimed to analyze the variation of the duplication limit in the fibromelanosis region on chromosome 20 to determine the purity of cemani chicken. This study used the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method on 76 chickens consisting of 32 cemani chickens PT. Source of Indonesian Poultry, 40 cemani chickens from the Animal Husbandry Research Institute, and 4 IPB-D1 chickens for comparison. The results showed that cemani chickens had multiple alleles, namely Fm, fm+, and fm- alleles. Chicken cemani (homogizot) has a genotype of Fm/Fm with two bands at 664 bp and 588 bp. Heterozygous cemani chickens had Fm/fm+ genotype with four bands at 664 bp, 588 bp, 400 bp, and 264 bp. The wildtype cemani chicken had a genotype of fm-/fm- with one band at 664 bp. IPB-D1 (wildtype) chickens have two genotypes, namely fm+/fm- (bands 664bp, 400 bp, and 264 bp) and fm+/fm+ (bands 400 bp and 264 bp). The diversity of cemani chickens is low and polymorphic. Cemani SUI chickens were in Hardy-Weinberg equilibrium except for cemani Balitnak chickens.
Keyword: cemani chickens, EDN3, fibromelanosis, PCR-RFLF

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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