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 Jagung (Zea mays (L.)) untuk Sekuensing Genom Total
Abstrak: Whole genome sequencing and analysis of the maize genome is one of the ways to accelerate the increase in corn breeding and to improve the understanding of the genetic and genomic information maize. The purpose of this study is to construct genomic libraries of four maize genotypes in Indonesia (Sp010BB-3-2- 2-1-B, LK2-45, PSG59-8 (early maturing) and LBP54-50 (pulut)) and analyze the quality of the results of genomic libraries total genome sequencing. Genomic library construction performed in vitro by attaching adapters to the ends of DNA fragments. Clasterization and sequencing of genomic library in this research were conducted by using cBOT claster generation and Next Generation Sequencing HiSeq2000. The amount of base produced during the sequencing process as many as 287.1 Gbp. Cluster genomic library generated with Q values above 30 scores ranged from 80.8 – 87.9%. Base reading error rate during the sequencing process was 0.32 – 0.51%. Over all sequencing results showed that quality of the genomic library cluster was belong to the ideal category.
Keyword: Bogor Agricultural University (IPB), Next Generation Sequencing (NGS)., Whole Genome Sequencing, Genomic Library, Maize (Zea mays (L.))

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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