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, SiCOMT2, from Foxtail Millet (Setaria italica [L.] Beauv) for  Lodging Resistance
Abstrak: Hotong (Setaria italica (L.) Beauv) merupakan salah satu tanaman serealia yang berpotensi dikembangkan sebagai pangan fungsional karena memiliki kandungan gizi yang tinggi. Cekaman rebah adalah salah satu faktor yang mempengaruhi produktivitas hotong. Ketahanan rebah pada hotong dilaporkan berasosiasi dengan kandungan lignin. Caffeic acid O-methyltransferase (COMT) merupakan salah satu enzim kunci dalam jalur biosintesis lignin. Penelitian ini bertujuan mengisolasi dan mengkarakterisasi gen penyandi COMT, SiCOMT2, dari empat genotipe hotong, yaitu NTB-1, Buru, Mauliru-2, dan ICERI-6. Gen SiCOMT2 berhasil diisolasi dari DNA genom empat genotipe hotong dengan panjang basa nukleotida 2.023-2.050 pb. Pensejajaran dengan SiCOMT2 referensi dari hotong kultivar IC-403579 menunjukkan terdapat sepuluh synonymous SNP di intron 1, dua non-synonymous SNP di ekson 1 (basa 322 dan 337), dan tiga non-synonymous SNP di ekson 2 (basa 1.444, 1.663, dan 1.897)., Foxtail millet (Setaria italica [L.] Beauv) is one of the cereal crops potentially developed as a functional food due to its high nutritional value. Lodging stress is one of the detrimental factors limiting the productivity of foxtail millet. Lodging resistance in foxtail millet has been reported to be associated with lignin content. Caffeic acid O-methyltransferase (COMT) is one of the key enzymes in the lignin biosynthesis pathway. This study aimed to isolate and characterize the COMT encoding gene, SiCOMT2, from four foxtail millet genotypes namely NTB-1, Buru, Mauliru-2, and ICERI-6. SiCOMT2 genes were successfully isolated from the genomic DNA of the four foxtail millet genotypes with the nucleotide length ranging from 2.023-2.050 bp. Alignment with the reference sequence of SiCOMT2 from cv. IC-403579 showed ten synonymous SNPs in intron 1, two non-synonymous SNPs in exon 1 (nt. 322 and 337), and three non-synonymous SNPs in exon 2 (nt. 1.444, 1.663, and 1.897).
Keyword: gene cloning, molecular marker, phylogenetics, polymorphism, SNP

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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