Judul: Long-read Sequences Analysis with MinION Oxford Nanopore Technology of Ulin, Eboni, and Gaharu
Abstrak: Ulin (Eusideroxylon zwageri T. et B.), eboni (Diospyros rumphii), dan gaharu (Aquilaria beccariana) merupakan tiga jenis asli Indonesia yang menurut Redlist IUCN ketiga jenis ini berstatus kekurangan data dan rawan. Sehingga perlu upaya untuk melakukan rintisan sekuensing genom pohon dengan MinION Oxford Nanopore Technology (ONT). Penelitian ini bertujuan untuk mendapatkan data sekuens whole genome atau sebagian dari E. zwageri, D. rumphii, dan A. beccariana, kemudian digunakan untuk menganalisis kekerabatan genetik E. zwageri. Prosedur penelitian mencakup tahapan isolasi DNA dan proses sekuensing hingga analisis bioinformatika. Hasil menunjukkan bahwa sekuensing DNA E. zwageri, D. rumphii, dan A. beccariana menghasilkan urutan basa DNA yang terbaca sebesar 305,5 Mb, 3,25 Gb, dan 525,1 Mb dengan genom parsial kloroplas sebesar 109.485 bp, 144.351 bp, dan 157.265 bp. Analisis kekerabatan menunjukkan E. zwageri dengan menggunakan marka intergenic spacer psbA-trnH berada pada satu clade dengan genus Eusideroxylon lainnya sedangkan dengan marka trnK, E. zwageri asal Indonesia mempunyai kedekatan dengan genus Dahlgrenodendron dan Aspidostemon asal Afrika.
Keyword: DNA-seq, Eusideroxylon zwageri, MinION, psbA-trnH, trnK

Judul: Analysis of Long-read Sequences with MinION Technology on Kapur (Dryobalanops aromatica C.F Gaertn).
Abstrak: Salah satu spesies penting dari famili Dipterokarpa adalah kayu kapur (D. aromatica C.F Gaertn) dengan status konservasi rentan (vulnerable). Status tersebut mencerminkan perlunya upaya konservasi genetik berbasis sains yang didukung dengan teknologi baru, salah satunya adalah Oxford Nanopore Technology (ONT) MinION yang mampu menyajikan analisis long-read DNA sequences yang terjangkau. Saat ini penggunaan ONT masih jarang dilakukan pada pohon hutan asli Indonesia. Penelitian ini bertujuan untuk mendapatkan data sekuens whole genome liputan rendah (low coverage) dan memanfaatkannya untuk menganalisis kekerabatan D. aromatica. Prosedur penelitian mencakup tahapan isolasi dan sekuensing DNA hingga analisis bioinformatika. Hasil menunjukkan bahwa sekuensing DNA D. aromatica dengan pembacaan urutan basa DNA long-read 1,55 Gb dengan genom parsial kloroplas D. aromatica 148.856 bp. Analisis kekerabatan menunjukan D. aromatica berkerabat dekat dengan D. rappa dengan marka kombinasi gen (matK dan rbcL) lebih direkomendasikan untuk digunakan dalam analisis lanjutan D. aromatica., One important species of the dipterocarps is kapur (D. aromatica C.F. Gaertn) with a vulnerable conservation status. This status indicates the need for science based conservation through new technology, among other Oxford Nanopore Technoloy (ONT) MinION, that is able to provide affordable analysis for long-read DNA sequences. Nowadayas, the use of ONT is still rare being applied to native Indonesian forest trees. The objective of this study was to generate long- read sequence data of the whole genome with low coverage and use it to analyze genetic relationship D. aromatica. The research procedure included DNA isolation and sequencing to bioinformatics analysis. The results showed that DNA sequencing of D. aromatica resulted in 1,55 Gb of DNA base long read sequences in which a partial chloroplast genome length was constructed with a total of 148.856 bp. The genetic relationship analysis showed that D. aromatica was closely related to D. rappa with a combined marker of matK and rbcL are recommended for future use of phylogenetic analysis of D. aromatica.
Keyword: Dryobalanops aromatica, genome, markers, MinION, sequencing

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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