Judul: Long-read Sequences Analysis With MinION Oxford Nanopore Technology on Matoa species (Pometia pinnata (J.R. Forst & G. Forst))
Abstrak: Matoa (Pometia pinnata (J.R & G.forst) merupakan tanaman hutan asli Indonesia yang menghasilkan buah dan juga kayu komersial bernilai ekonomi. Akan tetapi, ketersediaan data genetik dan genomik serta analisis kekerabatan tanaman masih terbatas. Penelitian ini bertujuan untuk menghasilkan data genomik dan kekerabatan terdekat Matoa (Pometia pinnata (J.R & G.forst)) dari Famili Sapindaceae. Penelitian terdiri dari beberapa tahapan yaitu i) ekstraksi DNA dengan metode CTAB, ii) uji kualitas dan kuantitas DNA dengan nanophotometer N80 dan qubit 1.0 fluorometer, iii) sekuensing DNA menggunakan alat MinION ONT serta iv) rekonstruksi kekerabatan dengan pohon filogenetik menggunakan barcode rbcL, matK dan kombinasi rbcL+matK. Hasil menunjukkan bahwa proses sekuensing pada jenis matoa (P. pinnata) menghasilkan sekuens dengan panjang urutan basa sebesar 149.661 bp. Penggunaan kombinasi kedua lokus mampu mengklasifikasikan intraspesies dan antarspesies dengan lebih baik., Matoa (Pometia pinnata (JR & G.forst) is a native Indonesian forest plant that produces fruit as well as economically valuable commercial timber. However, the availability of genetic and genomic data and analysis of this plant relationship is still limited. This study aimed to generate genomic data and the phylogenic relationship between Matoa (Pometia pinnata (JR & G.forst)) within the Sapindaceae family. The research consisted of several stages, namely i) DNA extraction using the CTAB method, ii) quality and quantity testing of DNA with nanophotometer N80 and qubit 1.0 fluorometer, iii) DNA sequencing using the MinION ONT tool and iv) reconstruction of phylogenetic trees using barcodes rbcL, matK and a combination of rbcL + matK. The results showed that the sequencing process of the matoa species (P. pinnata) generated sequence lengths of 149,661 bp. The use of a combination of the two loci can better classify intra- species and inter-species.
Keyword: genome, locus, MinION, phylogenetic, Pometia pinnata

Judul: Long-Read Sequences Analysis with MinION Oxford Nanopore Technology of Balsa (Ochroma pyramidale (Cav. ex Lam.) Urb.)
Abstrak: Balsa (O. pyramidale) merupakan salah satu spesies tanaman hutan cepat tumbuh bernilai ekonomi yang diintroduksi ke Indonesia dengan informasi genetik yang masih terbatas. Penelitian ini bertujuan untuk menghasilkan data genomik dan menganalisis hubungan kekerabatan balsa (O. pyramidale) berbasis long-read sequences dengan teknologi Oxford Nanopore (ONT). Penelitian terdiri dari beberapa tahapan yaitu ekstraksi DNA, uji kualitas dan kuantitas DNA, proses sekuensing DNA menggunakan mesin MinION ONT, dan analisis bioinformatik. Hasil penelitian menunjukkan bahwa proses sekuensing pada balsa (O. pyramidale) menghasilkan sekuen partial whole genome kloroplas sebesar 155.430 bp yang dapat digunakan untuk analisis hubungan kekerabatan berbasis DNA barcode pada genom kloroplas. Analisis filogeni menunjukkan bahwa jenis balsa (O. pyramidale) secara genetik (multi-genotipe) berada satu clade dengan sesama jenis O. pyramidale pada setiap penggunaan gen atau marka baik rbcL, matK, maupun kombinasi gen rbcL dan matK. Jenis gen atau marka yang cocok digunakan dalam analisis hubungan kekerabatan pada balsa (O. pyramidale) dapat menggunakan matK dan kombinasi rbcL dan matK., Balsa (O. pyramidale) is one of the fast-growing forest plant species with high economic value and was introduced to Indonesia, but there is not much genetic information available. The main objective of this research was to generate genomic data and analyze the phylogeny of balsa (O. pyramidale) based on long-read sequences with Oxford Nanopore Technology (ONT). The research consisted of several steps: i) DNA extraction, ii) testing the quality and quantity of DNA, iii) the DNA sequencing process using a machine MinION ONT, and vi) bioinformatic analysis. Research results showed that the sequencing process in balsa (O. pyramidale) produced partial whole-genome chloroplast of 155,430 bp which can be used for relationship analysis based on DNA barcodes on the genome. Phylogeny analysis showed that balsa (O. pyramidale) genetically (multi-genotype) is positioned in the same clade with other O. pyramidale deposited samples in every use of genes or markers rbcL, matK, or a combination of genes rbcL and matK. MatK or a combination of both rbcL and matK can be recommended to be used for analysis phylogeny of balsa (O. pyramidale).
Keyword: matK, MinION, Ochroma pyramidale, phylogenetic, 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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