Judul: Isolasi dan Kloning Gen Sitokinin Oksidase (OsCKX) Pengendali Sifat Produktivitas dari Padi Varietas Ciherang
Abstrak: Gn1a/OsCKX gene (grain number 1a/Cytokinin Oxidase) of rice (Oryza sativa L.) that encodes cytokinin oxidase has been identified as a quantitative trait loci that contribute to an increase in the number of grains of rice. This study aimed to isolate an OsCKX gene from rice cv. Ciherang. Amplification of OsCKX gene was done by PCR (Polymerase Chain Reaction) technique using specific primer pairs and cDNA template of rice cv. Ciherang. Subsequently, OsCKX gene fragment was cloned into a cloning vector pGEM-T Easy using T4-ligase enzyme and transformed into competent cell Escherichia coli Dh5α through heat shock method, and grown on LB agar medium containing ampicillin. Result showed that amplification with specific primers of OsCKX gene generated an amplicon fragment with size of ± 2000 bp. The gene fragment was succesfully cloned into pGEM-T vector and transformed into cells of E. coli Dh5α. Verification of recombinant clone by cutting using two restriction enzymes SmaI and KpnI regenerated two bands of 3015 bp (pGEM-T Easy vector) and 2000 bp (OsCKX gene fragment).
Keyword: rice (Oryza sativa L.), restriction enzymes, pGEM-T Easy vector, OsCKX gene, gene isolation, Cloning

Judul: Phylogenetic Analysis and Design sgRNA of Gn1a Gene Encoding Cytokinin Oxidase/Dehydrogenase in Rice (Oryza sativa L.) Japonica Group
Abstrak: Gn1a adalah gen yang menyandi sitokinin oksidase/dehidrogenase (CKX) pada padi. Adanya regulasi sitokinin menyebabkan tanaman memiliki jumlah malai yang banyak. Jumlah malai menjadi karakter agronomi penting dalam menentukan tingkat produktivitas padi. Genotipe padi dapat dibagi menjadi dua tipe berdasarkan jumlah malai yang dihasilkan yaitu genotipe padi malai banyak dan malai sedikit. Padi dengan genotipe malai sedikit dapat dimanipulasi secara genetik dengan merekayasa gen utama terkait malai, salah satunya gen Gn1a. Oleh karena itu, penelitian ini bertujuan menganalisis filogeni sekuen protein CKX di dalam famili Poaceae serta mendesain guide-RNA CRISPR/Cas9 (sgRNA) dari sekuen gen Gn1a untuk penyuntingan gen pada padi. Penelitian ini dilakukan dengan pendekatan bioinformatika dengan menguji disimilaritas gen dan protein CKX pada berbagai aksesi padi beserta menganalisis potensi sekuen fungsional gen Gn1a untuk dijadikan kandidat sgRNA. Hasil penelitian ini menunjukkan bahwa gen Gnla secara filogeni terbukti menyandi sitokinin oksidase/dehidrogenase, sehingga gen Gnla pada padi grup Japonika dapat dipilih sebagai target posisi mutasi untuk menghilangkan fungsi dari sitokinin oksidase/dehidrogenase. Berdasarkan hasil desain sgRNA pada gen Gnla diperoleh 3 kandidat terbaik untuk dikontruksi ke vektor CRISPR/Cas9 yaitu sgRNA pada peringkat 2, 4, dan 8., Gn1a is a gene encoding cytokinin oxidase/dehydrogenase in rice (CKX). The presence of cytokinin regulation causes plants to have high number in panicles. The number of panicles is an important agronomic character in determining the rice productivity. Rice genotypes can be divided into two types based on the number of panicles produced, i.e.: high and low panicle rice genotypes. Rice with low panicle genotype can be genetically manipulated by engineering the main panicle-related gene, one of which is Gn1a. Therefore, this study aimed to analyze the phylogeny of the CKX protein in the Poaceae family and to design the CRISPR/Cas9 (sgRNA) guide-RNA from the Gn1a gene for gene editing in rice. This research was carried out using a bioinformatics approach by analyzing the dissimilarity of the Gn1a gene and CKX protein sequences in rice and analyzing the potential functional sequence of the Gn1a gene to be a candidate for sgRNA design. The results of the study showed that the Gnla gene is phylogenically proven to encode cytokinin oxidase/ dehydrogenase, so that the Gnla gene in Japonika Group rice can be selected as a mutation target to eliminate cytokinin dehydrogenase function. Based on the results of the sgRNA design on the Gnla gene, we found the 3 best candidates for sgRNA sequence targets to be incorporated into the CRISPR/Cas9 vector, i.e. sgRNA numbers 2, 4, and 8.
Keyword: CRISPR/Cas9, Gn1a, Japonika, malai, sgRNA

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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