Judul: Keragaman genetik Bacillus sp. Rizobakteri pemacu pertumbuhan tanaman berdasarkan sekuen gen 16S rRNA dan amplified rDNA restriction analysis
Abstrak: Sebelas isolat Bacillus sp. rizobakteri pemacu pertumbuhan tanaman telah berhasil diketahui keragaman genetiknya melalui metode sekuens gen 16s rRNA dan ARDRA. Hasil BlastN menunjukkan bahwa tidak terdapat dominansi spesies Bacillus sp. yang digunakan. Penggunaan empat enzim restriksi yaitu HaeIII, CfrI, dan Hinfl telah berhasil menunjukkan keragaman genetik pada Bacillus sp. Penggunaan enzim restriksi RsaI menunjukkan keseragaman pada semua isolat. Hasil dari ARDRA terdiri atas filotipe yaitu Filotipe I (Bacillus sp. Cr24, Cr33, Cr64, dan Cr68), filotipe I1 (Bacillus ps. '2131 dan Cr66), filotipe 111 (Bacillus sp. Cr44 dan Cr71), dan filotipe IV (Bacillus sp. Cr67, Cr 28, dan Cr69) yang dibuat pohon filogenetiknya dengan metode neighbor-joining menggunakan program Treecon 1.3b. Hasil filogenetik menggunakan sekuens gen 16s rRNA juga menunjukkan kekerabatan antar spesies yang digunakan. ARDRA dapat digunakan untuk melihat keragaman spesies berdasarkan situs pemotongannya.
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Judul: Genetic Diversity of Antifungal-Producing Rhizobacteria of Bacillus sp. Based on Amplified rDNA Restriction Analysis (ARDRA) and 16S rRNA Sequence
Abstrak: Genus Bacillus has indirectly mechanism to induce the growth of soybean plant by growth suppression of pathogen through production of antibiotic. The objective of this research was to analyze the diversity of 22 antifungal-producing rhizobacteria of Bacillus sp. strain Cr isolated from rhizosphere of soybean plant based on 16S rRNA Sequence and Amplified rDNA Restriction Analysis (ARDRA). ARDRA was a tool to measure and analyze the diversity of 22 isolates through digestion of 16S rRNA gene by restriction enzymes i.e. HinfI, HaeIII, and RsaI. Based on this analysis, genetic diversity of 22 Bacillus Cr isolates were classified into eight different groups by ARDRA analysis. Moreover, six isolates selected randomly from each ARDRA group that have strong activity to suppress fungal growth were compared with reference strains based on 16S rRNA partial sequence. The distributions of 22 isolates were genetically diverse on several species of Bacillus sp. such as B. subtilis, B. cereus, and B. fusiformis. Therefore, ARDRA is a reliable technique to analyze genetic diversity of huge bacterial community.
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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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