Judul: Long-read Sequences Analysis on Bisbul (Diospyros blancoi A.DC.), Sawo Duren (Chrysophyllum cainito L.) and Gandaria (Bouea macrophylla Griff.)
Abstrak: Tingginya laju deforestasi hutan di Indonesia berpengaruh pada penurunan keanekaragaman hayati dan ketersediaan sumber daya genetik. Bisbul (Diospyros blancoi), Sawo Duren (Chrysophyllum cainito) dan Gandaria (Bouea macrophylla) merupakan tiga jenis tanaman buah yang memiliki potensi ekonomi yang populasinya mulai menurun di Indonesia. Penelitian ini bertujuan untuk mendapatkan data genomik dari jenis D. blancoi, C. cainito dan B. macrophylla serta menganalisis hubungan kekerabatan menggunakan pohon filogenetik. Hasil sekuensing pada D. blancoi, C. cainito dan B. macrophylla didapatkan sekuens partial genome dengan ukuran panjang masing-masing secara berurutan 155.282 bp, 84.370 bp dan 54.120 bp. Ukuran sekuens D. blancoi dinyatakan cukup sebagai partial genome dan dilakukan analisis filogeni. Analisis filogeni menggunakan marka rbcL diperoleh cabang terdekat dengan D. oblonga dengan nilai bootsrap sangat lemah (34%) sedangkan filogeni dengan marka matK menunjukkan sekuens D. blancoi memiliki kekerabatan dekat dengan D. discolor dan D. philipinensis dengan nilai bootstrap pada kategori tinggi (91%)., Deforestation and forest degradation have caused biodiversity loss including the plant genetic resources. Bisbul (Diospyros blancoi), Sawo Duren (Chrysophyllum cainito), and Gandaria (Bouea macrophylla) are three species of fruit trees that have economic values where their population sizes are decreasing in Indonesia. This study aims i) to obtain genomic data of D. blancoi, C. cainito, and B. macrophylla and ii) to analyze the species relatedness using phylogenetic trees. Sequencing works resulted on partial genome with size of 155.282 bp, 84.370 bp. and 54.120 bp, from D. blancoi, C. cainito, and B. macrophylla, respectively. Sequence size of D. blancoi is sufficient only to assembled partial chloroplast genome that can be used for subsequent phylogetic analysis. Phylogenetic analysis using the rbcL marker showed that the closest branch for D. blancioi was to D. oblonga but with a very weak bootstrap value (34%). On the other hand the phylogeny using the matK marker showed that D. blancoi sequences were closely related to D. discolor and D. philippinensis with a high bootstrap value (91%).
Keyword: Bouea macrophylla, Diospyros blancoi, Chrysophyllum cainito, Sequences, matK

Judul: Analysis of Long-Read Sequences DNA on Merbau (Intsia bijuga), Sandalwood (Santalum album), and Moringa (Moringa oleifera)
Abstrak: Informasi genetik dapat digunakan dalam upaya konservasi dengan menduga keragaman genetik melalui penggunaan marka genetik. Sekuens DNA dapat diperoleh melalui tahap ekstraksi, isolasi, dan sekuensing. Sekuensing dapat dilakukan menggunakan mesin dengan teknologi terbaru seperti teknologi ONT, namun jarang sekali diaplikasikan pada pohon hutan. Penelitian ini bertujuan untuk mendapatkan sekuens DNA dan melakukan analisis filogenetik beberapa jenis pohon hutan, yaitu merbau (Intsia bijuga), cendana (Santalum album), dan kelor (Moringa oleifera). Tahapan penelitian mencakup perolehan data hasil sekuensing dan basecalling, quality check, assembly, polishing, anotasi, analisis kekerabatan, serta konstruksi pohon filogenetik. Analisis kekerabatan dilakukan menggunakan DNA sekuens berupa intergenic spacer trnH-psbA, accD, dan matK. Hasil analisis kekerabatan menunjukkan bahwa pohon filogenetik jenis merbau, cendana, dan kelor memiliki nilai bootstrap yang bervariasi yaitu masing-masing sebesar 0,965 (96,5%), 0,509 (50,9%), dan 0,798 (79,8%).
Keyword: accD, analisis filogenetik, long-read sequence, matK, trnH-psbA

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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