Judul: Isolasi dan Karakterisasi Gen SiCCR1 terkait Biosintesis Lignin pada Hotong (Setaria italica [L.] Beauv) untuk Sifat Toleransi terhadap Cekaman Abiotik
Abstrak: Hotong (Setaria italica [L.] Beauv) merupakan tanaman penghasil karbohidrat bernutrisi baik dengan toleransi terhadap cekaman kekeringan dan salinitas. Kandungan lignin di akar dan batang telah dilaporkan sebagai salah satu mekanisme penting toleransi tanaman terhadap cekaman kekeringan dan salinitas, dimana lignin berperan dalam ketegaran mekanik tanaman serta transportasi air dan solut melalui jaringan pembuluh. Cinnamoyl-CoA reductase (CCR) merupakan salah satu enzim kunci dalam lintasan biosintesis lignin. Penelitian ini bertujuan mengisolasi dan mengkarakterisasi gen penyandi CCR, SiCCR1, dari empat genotipe hotong dengan toleransi berbeda terhadap cekaman kekeringan dan salinitas. Gen SiCCR1 berhasil diisolasi dari DNA genom satu genotipe hotong toleran (ICERI-6) dan tiga genotipe hotong peka (NTB-1, Mauliru-2, dan Buru) dengan panjang basa nukleotida 2.293-2.296 pb. Pensejajaran dengan gen SiCCR1 referensi dari hotong kultivar IC-403579 menunjukkan terdapat synonymous SNP di intron 1 (basa 40, 41, 42) dan intron 4 (basa 1.398), dan satu non-synonymous SNP di ekson 6 (basa 2.336). SNP yang teridentifikasi pada gen SiCCR1 dari keempat genotipe hotong dalam penelitian ini belum dapat membedakan dengan konsisten genotipe toleran dan peka terhadap cekaman kekeringan dan salinitas., Foxtail millet (Setaria italica [L.] Beauv) is one of the nutritious carbohydrate-producing crops with comparable tolerance to drought and salinity stresses. Lignin content in the roots and stems has been reported as one important mechanism in the tolerance to drought and salinity stresses, where lignin plays a role in the mechanical robustness of plants and facilitates the transportation of water and solutes through vascular tissue. Cinnamoyl-CoA reductase (CCR) is one of the key enzymes in the lignin biosynthesis pathway. This study aimed to isolate and characterize the CCR encoding gene, SiCCR1, from four foxtail millet genotypes differing in their drought- and salinity tolerance. SiCCR1 genes were successfully isolated from the genomic DNA of one tolerant genotype (ICERI-6) and three sensitive genotypes (NTB-1, Mauliru-2, and Buru) with the nucleotide length ranging from 2.293-2.296 bp. Alignment with the reference sequence of SiCCR1 from cv. IC-403579 (tolerant) showed synonymous SNPs in intron 1 (nt. 40, 41, and 42) and intron 4 (nt. 1.398), and a non-synonymous SNP in exon 6 (nt. 2.336). None of the identified SNPs were consistently associated with the tolerance level of the foxtail millet genotypes.
Keyword: filogenetik, kloning gen, marka molekuler, polimorfisme, SNP

Judul: Isolation and Characterization of Lignin Biosynthesis Gene, SiCOMT1, from Four Foxtail Millet (Setaria italica (L.) Beauv.) Genotypes as Biomass Source
Abstrak: Hotong (Setaria italica (L.) Beauv.) adalah tanaman famili Poaceae yang berpotensi dikembangkan sebagai sumber biomassa lignoselulosa. Lignin merupakan metabolit sekunder yang diproduksi melalui jalur biosintesis yang melibatkan banyak enzim, salah satu enzim yang berperan adalah asam kafeik O-Metiltransferase (COMT). Penelitian ini bertujuan mengisolasi dan mengkarakterisasi gen SiCOMT1 terkait biosintesis lignin dari empat genotipe hotong asal Indonesia, yaitu genotipe NTB-1, Buru, Mauliru-2, dan ICERI-6. Penelitian ini berhasil mengamplifikasi fragmen gen SiCOMT1 dari DNA genom keempat genotipe hotong dengan rentang 2.085-2.126 pb. Pensejajaran basa nukleotida fragmen SiCOMT1 dari keempat genotipe hotong dan hotong kultivar IC-403579 menunjukkan adanya perbedaan basa nukleotida tunggal (SNP) tipe synonymous sejumlah 22 SNP pada daerah UTR, intron 1, dan intron 2, serta tujuh non-synonymous SNP pada daerah ekson 1, 2, dan 3. Gen SiCOMT1 dari keempat genotipe hotong berkerabat dekat dengan rentang similaritas 97,9%-99,4% dan berada dalam satu klaster bernilai bootstrap 100%. Translasi gen SiCOMT1 dari keempat genotipe hotong diprediksi memiliki domain dimerisasi dan domain O-metiltransferase., Foxtail millet (Setaria italica (L.) Beauv) is a graminaceous crop that has the potential to be developed as a source of lignocellulosic biomass. Lignin is a secondary metabolite produced by a biosynthesis pathway involving various enzymes, including Caffeic acid O-methyltransferase (COMT). This study aimed to isolate and characterize the SiCOMT1 gene related to lignin biosynthesis from four Indonesian foxtail millet genotypes, namely NTB-1, Buru, Mauliru-2, and ICERI-6. This study successfully amplified SiCOMT1 fragments ranging from 2,085 to 2,126 bp from the genomic DNA of four foxtail millet genotypes. Nucleotide sequence alignment of the isolated SiCOMT1 from the four foxtail millet genotypes and IC-403579 cultivar showed single nucleotide polymorphisms (SNPs) with 22 synonymous SNPs in the UTR regions, intron 1, and intron 2, and seven non-synonymous SNPs in exon 1, 2 and 3. The SiCOMT1 gene from four foxtail millet genotypes is closely related in one cluster with similarity ranging from 97.9% to 99.4% with a bootstrap value of 100%. The translated SiCOMT1 from four foxtail millet genotypes were predicted to have a dimerization and O-Methyltransferase domains.
Keyword: gene characterization, conserved domain, SNP, Phylogenetics

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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