Judul: Karakterisasi Enzim dan Kloning Gen Penyandi Mananase dari Bacillus subtilis Asal Tempe
Abstrak: Nutrition value and characteristics of tempe are primarily derived from enzymatic activities derived from complex microorganisms community during its fermentation. As a rich source of bacterial diversity, tempe could be explored for its potential to yield enzyme, such as mannanase. This study was intended to isolate mannanase producing bacteria derived from a number of tempe samples from Java (Bogor, Surabaya, Malang, Kediri, Lamongan, and Wonogiri); characterize its enzyme; and clone its mannanase gene into E. coli. Crude enzyme from each isolate was prepared for characterization. Showed the highest specific activity (0,41 U/mg protein), isolate N mannanase was further characterized. Nmannanase crude enzyme showed optimum activity at 60oC and pH 5.0. This enzyme has better activity in palm kernel meal (PKM) as its substrate with average activity 1.13 U/ml compared to soybean meal (SBM) (0.43 U/ml) and copra meal (CM) (0.48 U/ml). This enzyme was also stable at 60oC for 4 hours, in wide range of pH (4-10) for 1 hour, and various metal ions. SDS-PAGE and Zymogram analysis showed that this mannanase has molecular weight approximately 39.8 kilodalton. Isolate N was identified having 98% similarity with Bacillus subtilis (Genebank access JN644507) employing 16S rRNA sequence analysis. The B. subtilis N-mannanase gene was successfully isolated and cloned into E.coli. Recombinant’s mannanase activity was detected in E. coli intra- (8.82 U/ml) and extracellular (6.39 U/ml) extracts.
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Judul: Karakterisasi enzim endo b 1,4 mananase dari Nonomuraea jabiensis ID06-379 dan kloning gen penyandinya
Abstrak: sampel tanah di Taman Nasional Kutai. Media yang dioptimasi dapat meningkatkan produksi enzim kasar mananase Nonomuraea jabiensis ID06-379. Produksi β-mananase Nonomuraea jabiensis ID06-379 tertinggi (5.33 U mg-1) dicapai pada medium optimasi (Vogel’s minimal medium) dengan penambahan nutrisi sebagai berikut: 0.5% locus bean gum, 1% ekstrak malt dan 0.05% (NH4)2HPO4, menggunakan fermentasi terendam dengan pengocokan pada 120 rpm, 28 oC selama 2 hari inkubasi. Analisis filogenetik dari urutan gen utuh (1491 bp) 16S rDNA, analisis kemotaksonomi mengungkapkan bahwa galur ID06-379 termasuk dalam genus Nonomuraea dan memiliki 99% kesamaan dengan spesies Nonomuraea jabiensis A4036T berdasarkan pencarian BLAST. Galur tersebut memiliki ciri-ciri kemotaksonomi yang umum bagi genus Nonomuraea, di antaranya pada dinding sel mengandung meso-diaminopimelic acid; kandungan gula dinding selnya terdiri dari manosa, glukosa, ribosa (mayor), madurosa (gula diagnostik, Tipe B), dan galaktosa (minor); fosfatidilkolin, fosfatidilinositol dan fosfatidilgliserol sebagai kandungan fosfolipida tipe P III; dan sebagai menakinon utama adalah MK-9(H4). Kandungan G+C sebesar 71.1%. Pengamatan morfologis dari miselia vegetatif menunjukkan hifa bercabang banyak dan terfragmentasi berbentuk batang. Galur ID06-379 membentuk cabang yang dekat dalam pohon filogenetik dengan spesies terdekatnya yaitu Nonomuraea jabiensis A4036T. Dapat disimpulkan bahwa galur tersebut termasuk dalam kelompok genus Nonomuraea. Namun berdasarkan pada karakteristik fenotipik dan kemotaksonominya, galur ID06-379 memiliki beberapa karakter yang berbeda dengan galur Nonomuraea jabiensis A4036T. Hasil ini menunjukkan bahwa galur ID06-0379 mungkin merupakan spesies baru dalam kelompok genus Nonomuraea. Untuk mengkonfirmasi bahwa isolat tersebut sebagai spesies baru, diperlukan penelitian lebih lanjut seperti hibridisasi DNA-DNA dengan spesies terdekat yang termasuk dalam genus Nonomuraea. Sampai dapat dibuktikan perbedaannya melalui DNA-DNA hibridisasi, sementara ini galur ID06-379 dinamakan sebagai Nonomuraea jabiensis ID06-379 berdasarkan kedekatan homologi gen 16S rRNAnya dengan Nonomuraea jabiensis A4036T. Penelitian ini telah berhasil mengisolasi dan menganalisis secara struktural gen endo-β-1, 4-mananase dari aktinomiset Nonomuraea jabiensis ID06-379. Deteksi gen mananase ini dilakukan menggunakan polymerase chain reaction (PCR) dengan metode LA Taq Invitro Cloning. Hasil penelitian menunjukkan bahwa keselarasan dari beberapa fragmen parsial urutan gen mananase N. jabiensis ID06-379 memberikan urutan suatu segmen DNA sepanjang 2100 pasang basa. Segmen ini berisi gen utuh β-mananase dari N. jabiensis ID06-379. Urutan dari gen β-mananase N. jabiensis ID06-379 matang terdiri atas 1338 bp yang mengkodekan polipeptida sebanyak 446 asam amino. Tempat pemotongan sinyal peptidase berada diantara posisi Ala26-Ser27-Ala28 dan Ala29-Ala30,...dst
Keyword: aktinomiset Indonesia, endo-1, 4-β-mananase, kloning gen, Nonomuraea jabiensis ID06-379, S. lividans 1326

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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