Judul: Identification of the THY1 Gene Polymorphisms in Candidate IPB-D2 Chicken Line
Abstrak: Gen THY1 merupakan anggota superfamili imunoglobulin yang memiliki kemiripan pada berbagai spesies. Fungsi dari gen THY1 belum sepernuhnya diketahui, namun berperan penting dalam respon imun yaitu berpartisipasi pada aktivasi sel T. Penelitian ini dilakukan untuk mengidentifikasi keragaman gen THY1 pada calon galur ayam IPB-D2 G0 yang dapat dijadikan sebagai kandidat marka genetik sifat ketahanan tubuh terhadap penyakit pada ayam. Penelitian ini dilakukan dengan teknik PCR dan sekuensing DNA. Hasil penelitian menemukan 2 titik SNP pada intron yaitu posisi basa g.2752 C>T dan g.3155 A>G, serta 1 titik SNP pada ekson 3 yaitu posisi basa g.2835 G>A. Kombinasi 3 SNPs membentuk 7 haplotipe. SNP g.2835 G>A merupakan synonymous mutation, bersifat polimorfik, berada pada keseimbangan Hardy-Weinberg, dan beragam. SNP g.2752 C>T dan g.3155 A>G bersifat polimorfik, namun tidak berada pada keseimbangan Hardy-Weinberg, dan keragamannya rendah., The THY1 gene is a member of the immunoglobulin superfamily which has the similarities in various species. The function of the THY1 gene is not fully known, but it plays an important role in the immune response, namely the activation of T cells. This study was conducted to identify the polymorphism of the THY1 gene in candidate IPB-D2 G0 chickens line which can be used as candidates for immunoresistance genetic markers chicken. This research was conducted by PCR techniques and DNA sequencing. The results of the study found 2 SNP points on the intron namely base position g.2752 C> T and g.3155 A> G, and 1 SNP point on exon 3 namely base position g.2835 G> A. The combination of 3 SNPs formed 7 haplotypes. SNP g.2835 G> A is an synonymous mutation, polymorphic, Hardy-Weinberg equilibrium, and varied. SNP g.2752 C> T and g.3155 A> G were polymorphic, but not in the Hardy-Weinberg equilibrium, and the diversity is low.
Keyword: immunity, IPB-D2 Chickens, polymorphisms, SNP, THY1 gene

Judul: Identifikasi Keragaman Gen BG1 Sebagai Kandidat Gen Pengontrol Ketahanan Penyakit Pada Ayam IPB-D2
Abstrak: Ayam IPB-D2 adalah ayam IPB-D1 yang diseleksi berdasarkan konsentrasi IgY dan titer antibodi yang tinggi sebagai parameter ketahanan penyakit ayam. Gen BG1 merupakan salah satu gen yang berperan dalam ketahanan penyakit. Gen BG1 berada di wilayah MHC dan sangat polimorfik. Tujuan penelitian ini adalah mengidentifikasi Single Nucleotide Polymorphism (SNP) gen BG1 pada ayam IPBD2 menggunakan metode direct-sequencing. Penelitian ini menggunakan 46 sampel darah ayam IPB-D2. Hasil sequencing dianalisis untuk memperoleh nilai frekuensi genotipe, frekuensi alel, nilai heterosigositas dan keseimbangan HardyWeinberg (uji chisquare). Penelitian ini ditemukan 8 SNP yaitu g.4817 G>T, g.4865 C>A, g.4944 C>T, g.5040 C>T, g.5069 T>C, g.5075 T>C, g.5089 G>A , g.5367 A>G dan delesi g.5086 – g.5087DelAT. Kombinasi 8 SNP membentuk 6 haplotipe. SNP yang mengubah susunan asam amino yaitu SNP g.4817 G>T cys>phen , SNP g.4865 C>A ser>tyr dan SNP g.5089 G>A gly>glu. Mutasi basa g.4944 C>T beragam dan berada dalam kesetimbangan Hardy Weinberg., IPB-D2 chickens were IPB-D1 chickens that were selected based on high IgY concentrations and ND antibody titer as a parameter of body resistance to disease. BG1 gene is one of the gene that play a role in disease resistance. BG1 gene resides in the MHC region and is highly polymorphic. The purpose of this study was to identify the Single Nucleotide Polymorphism (SNP) of BG1 gene in IPB-D2 chickens using direct-sequencing method. This study used 46 blood samples of IPB-D2 chickens. The sequencing results were analyzed to obtain genotype frequency, allele frequency, heterozygosity and Hardy Weinberg's equilibrium (chisquare test). This results found 8 SNPs that is g.4817 G> T, g.4865 C> A, g.4944 C> T, g. .5040 C>T, g.5069 T>C, g.5075 T>C, g.5089 G>A , g.5367 A>G dan indel mutation g.5086 – g.5087DelAT. The combination of 8 SNPs forms 6 haplotypes. SNPs that changed the amino acid composition were SNP g.4817 G> T cys> phen, SNP g.4865 C> A ser> tyr and SNP g.5089 G> Agly> glu. Mutations g.4944 C> T were diverse and was in Hardy Weinberg equilibrium.
Keyword: BG1 gene, disease resistance, diversity, IPB-D2 Chicken, mutation

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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