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: Referensi Awal DNA Barcode pada Famili Anacardiaceae
Abstrak: Anacardiaceae merupakan salah satu famili penting di Indonesia yang keberadaan sumberdaya genetiknya mulai terancam akibat dari kerusakan alam, namun identifikasi jenis secara molekuler pada famili tersebut belum menyeluruh. Tujuan penelitian ini adalah untuk mendapatkan penanda genetik yang sesuai dan efektif dalam mengidentifikasi famili Anacardiaceae dengan metode DNA barcoding. Penanda genetik yang digunakan adalah penanda tunggal yaitu matK dan rbcL, serta penanda kombinasi matK+rbcL. Penelitian ini menggunakan data EFForTS sebanyak 28 sampel dengan penanda matK dan 31 sampel menggunakan penanda rbcL. Selain itu juga ditambahkan data dari Genbank sebanyak 24 sampel dengan penanda matK dan 19 sampel dengan penanda rbcL. Akurasi identifikasi pada tingkat spesies tertinggi dengan penanda matK yaitu sebesar 28.57%, sedangkan rbcL sebesar 22.58%, dan matK+rbcL sebesar 19.23%. Dalam penelitian ini, penanda matK, rbcL, dan matK+rbcL tidak dapat membentuk barcoding gap yang jelas, namun hasil t-test menunjukkan bahwa intraspesifik dan interspesifik dengan kedua penanda tersebut berbeda secara signifikan. Penanda matK dan rbcL berhasil membentuk grup-grup monofiletik dalam pohon filogeni untuk masing-masing spesies.
Keyword: anacardiaceae, DNA barcoding, 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.
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