Judul: Konstruksi pustaka genom dan sekuensing genom total Kakao (Theobroma cacao L.)
Abstrak: The availability of reference genome sequence of cocoa (Theobroma cacao L.) allows the full potential of the other cocoa plant genetic variation to be read and used for breeding through whole genome reading by next generation sequencing (NGS). This study describes a modification of CTAB method for extracting genomic DNA contains high polysaccharides and polyphenols, genomic library construction and whole genome sequencing using methods by Illumina. High quality of genomic DNA indicated by integrity of the molecule have been produced. Genomic libraries have been constructed were 314-485 bp in size. Base generated reach 391.93 Gbp, with genome size reach 566.9 Mbp. The quality of readings by NGS high enough with 67.9-81.3% of reading has quality value above Q30. Error rate occurs at 0.20-1.14%. Genomic library have been constructed possesses good quality and the data from sequencing were ready for further analysis.
Keyword: Bogor Agricultural University (IPB), Theobroma cacao L., next generation sequencing, genome library, DNA extraction

Judul: Konstruksi dan Analisis Kualitas Pustaka Genom Kedelai (Glycine max (L.) Merr.) untuk Sekuensing Genom Total
Abstrak: Soybean is one of the most important agricultural commodities in the supply of food in Indonesia. However, the low of the national soybean productivity is a constraint in soybean cultivation in Indonesia. National soybean productivity can be increased by genetic improvement of plants. Whole genome sequencing and genomic analysis of soybean is one way to accelerate soybean breeding progress and improve understanding of genetic and genomic information of soybean. Purposes of this research were to construct genomic library of three Indonesian soybean genotypes (Tambora, B3293 and Grobogan) and analyze the quality of the genomic library on whole genome sequencing result. Construction of genomic libraries was carried out in vitro by attaching an adapter to the end of DNA fragments. Clasterization and sequencing of genomic library in this research were conducted by using cBOT claster generation dan Next Generation Sequencing HiSeq2000. Genomic libraries were constructed successfully sized 400 bp with a concentration of 23.20 ng/μL (Tambora), 64.50 ng/μL (B3293), and 21.20 ng/μL (Grobogan). Size and concentration of the constructed genomic libraries were suitable for whole genome sequencing. The total yield of bases generated from the sequencing was 50.1 x 109 bp. Cluster library produced during the process of genome sequencing was Q scores value above 30 was 88.6%. Error rate of base reading during the sequencing was 0.97%. Values of the cluster density, percent cluster PF, the intensity of the base, phasing percent, and prephasing percent generated from this research showed that the cluster quality of genomic libraries was of ideal category.
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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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