Judul: Variasi Genetik Rotan Berdasarkan Penanda DNA Barcode matK, rbcL dan ITS Pada Pangkalan Data GenBank.
Abstrak: Species identification of rattan is usually done by assessing morphological characteristics. Along with the development of science and technology, biomolecular science began to be applied as a complementary tool identification, one of which is DNA barcoding technique. In the forestry both are still rarely applied as complementary to each other because of limited molecular data. This study was aimed to analyze the genetic structure of various rattan by three DNA Barcode markers that are available in the genetic database (NCBI), namely matK, rbcL and ITS. Data processing was performed using software MEGA and DnaSP. The results showed that markers of ITS have a longer sequence that is above 500 bp and higher GC content (%) 63.1% compared to the others. Constructed phylogeny trees do not show the most accurate marker in discriminating species because different species are still grouped into one clade. Nucleotide variation analysis was conducted to determine more accurate marker based on genetic variation approach to differentiate Calamus and non-Calamus. However, uncertainty in discriminating species was still observed.
Keyword: DNA Barcode, genetic markers, moleculer analysis, rattan

Judul: Utilization of DNA Barcode Markers for Species Identification of Selected Genera in Fabaceae
Abstrak: Fabaceae is an invaluable plant family with considerable ecological and economic importances due to its high value and benefits as food sources, soil fertilization agent, and medicinal plants. However, Fabaceae has been overexploited in Indonesia and several species belong to this family are critically endangered. Due to morphological similarity, rapid and accurate identification of Fabaceae species is essential to support its conservation efforts. Nowadays, species identification through DNA barcoding has become an effective taxonomic classification tool. This study was aimed to evaluate the effectiveness of chloroplast markers, matK and rbcL and the combination (matK+rbcL), as DNA barcodes for the identification of seleted genera in Fabaceae. The results showed that the length of the DNA sequences produced from the samples in this study was 568 bp for matK, 479 bp for rbcL, and 1,047 bp for matK+rbcL. Different sequence lengths at each locus are useful as early identification to differentiate species. The highest percentage of varied loci was obtained from the matK (56,69%). The matK+rbcL and matK loci had the highest identification rates (90% and 82,05%) at the species level. In addition, matK has the highest mean of interspecific distance (0,314) and intraspecific distance (0,003). The matK and the matK+rbcL combination have a better ability for species identification or species confirmation up to the species level than the rbcL, so the matK and the matK+rbcL combination are more recommended for Fabaceae plant identification. In the barcoding gap analysis, the average value of the interspecific distance is higher than the intraspecific distance. The mean value of rbcL intraspecific value is smaller than the matK. This is presumably because rbcL, which plays a role in encoding the RuBisCO protein, is thought to have a low mutation rate so that the level of similarity between species is high. In phylogenetic tree reconstruction, the neighbor joining method has a high monophyletic percentage and this method is quite effective for large datasets and is more informative in phylogenetic tree reconstruction.
Keyword: DNA barcode, Fabaceae, phylogenetic, matK, rbcL

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.
Keyword: