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: Validation of Microsatellite Molecular Markers on Matoa (Pometia pinnata)
Abstrak: Indonesia adalah negara yang kaya akan keanekaragaman hayati dengan berbagai jenis spesies tumbuh-tumbuhan. Keanekaragaman tersebut terdiri dari tanaman buah yang salah satunya berasal dari buah Matoa (Pometia pinnata). Matoa merupakan tanaman dari famili Sapindaceae yang tersebar di wilayah tropis. Tanaman matoa banyak dimanfaatkan sebagai obat-obatan tradisional yang diketahui mengandung kelompok senyawa diantaranya flavonoid, tanin, dan saponin. Analisis keragaman genetik matoa menjadi informasi dasar untuk pelaksanaan kegiatan seleksi dan persilangan lanjutan dalam program pemuliaan matoa. Marka mikrosatelit merupakan salah satu metode analisis marka molekuler kodominan. Tujuan dari penelitian ini untuk melakukan seleksi primer untuk analisis kekerabatan 10 aksesi matoa Dramaga dengan 4 matoa Banjarmasin melalui pendekatan marka mikrosatelit. DNA diisolasi menggunakan CTAB (Cetyl Trimethyl Ammonium Bromide). Sepuluh primer mikrosatelit yang digunakan adalah Pp.e.6402, Pp.e.66857, Pp.e.80271, Pp.e.89451, Pp.e.115726, Pp.e.161167, Pp.e.186462, Pp.e.187105, Pp.e.238124, Pp.e.287861. Amplifikasi mengacu pada protokol DreamTaq Green PCR Master Mix. Hasil penelitian menunjukkan bahwa primer yang digunakan mampu mengamplifikasi 20-30% aksesi yang digunakan, dan hanya 2 aksesi yang dapat diamplifikasi pada 9 pasang primer yang digunakan, yaitu aksesi IPBA8, IPBA9. Sembilan primer dapat digunakan untuk analisis molekuler, kecuali primer Pp.e.287861 yang tidak mampu mengamplifikasikan 14 aksesi yang digunakan., Indonesia is a country rich in biodiversity with various types of plant species. One of the diversity of fruit plants comes from the Matoa fruit plant (Pometia pinnata). Matoa is a plant from the Sapindaceae family which is spread throughout the tropics. The matoa plant is widely used as a traditional medicine which is known to contain a group of compounds including flavonoids, tannins and saponins. Analysis of matoa genetic diversity is the basic information for implementing selection and crossbreeding activities in matoa breeding programs. Microsatellite markers are one of the codominant molecular marker analysis methods. This study aims to conduct primary selection for kinship analysis of 10 Dramaga matoa accessions with 4 Banjarmasin matoa using a microsatellite marker approach. DNA was isolated using the CTAB (Cetyl Trimethyl Ammonium Bromide). The ten microsatellite primers used were Pp.e.6402, Pp.e.66857, Pp.e.80271, Pp.e.89451, Pp.e.115726, Pp.e.161167, Pp.e.186462, Pp.e.187105, Pp.e.238124, Pp.e.287861. SSR marker analysis using PCR DreamTaq Green Master Mix. The results showed that the primers used were able to amplify 20- 30% of the accessions used, and only 2 accessions could be amplified in the 9 pairs of primers used, namely IPBA8, IPBA9 accessions. Nine primers could be used for molecular analysis, except for the primer Pp.e.287861 which was unable to amplify the 14 accessions used.
Keyword: allele, biodiversity, codominant, fruit plants, genetic

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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