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Articles by Ocky Karna Radjasa
Total Records ( 6 ) for Ocky Karna Radjasa
  Zeily Nurachman , Sari Dewi Kurniasih , Ferra Puspitawati , Sarwono Hadi , Ocky Karna Radjasa and Dessy Natalia
  Problem statement: An Indonesian marine bacterial isolate, Bacillus amyloliquefaciens PSM 3.1 was isolated for hydrolyzing cellulose. A 1500-bp nucleotide fragment was amplified from the chromosomal DNA by the use of primers directed against the conserved sequence of Bacilli endoglucanase genes obtained from GenBank. Approach: The fragment was cloned and expressed in Escherichia coli. Results: The endoglucanase gene (eglII gene) had an open reading frame of 1500 nucleotides encoding a protein of 499 amino acids. The EglII protein belonged to Glycosyl Hydrolase family 5 (GH5) with a Cellulose Binding Module 3 (CBM 3). The structure model of the EglII protein revealed that the catalytic residues seemed to be Glu169 (as proton donor) and Glu257 (as nucleophile) and the catalytic triad residues were Thr256, His229 and Glu169. The EglII endoglucanase exhibited an optimum pH of 6.0 and temperature of 50°C and the enzyme tolerated to high salt concentration. Conclusion/Recommendations: This EglII endoglucanase is a promising candidate for many applications in biomass degradation.
  Zeily Nurachman , Alfredo Kono , Ocky Karna Radjasa and Dessy Natalia
  Problem statement: Bacteria from the surface of the tropical marine hard coral Acropora sp. were screened for producing raw-starch-degrading-α-amylase. Approach: Based on its 16s rDNA sequence, a bacterium that produced the highest amylolitic activity was identified as Bacillus amyloliquifaciens ABBD. The bacterial isolate secreted a α-amylase extracellularly and then the enzyme was partially purified by ammonium sulfate precipitation followed by anion exchange chromatography. Results: Electrophoresis results both SDS-PAGE and native PAGE suggested that the enzyme was a heterodimeric protein (97 kDa) consisting of 45 and 55 kDa subunits. The α-amylase had an optimum pH of 7.0 and temperature of 60°C. More than 80% activity of the enzyme was retained under high salt conditions (up to 20% NaCl). The enzyme remained stable at 50°C for 1 h. Starch hydrolysis by the enzyme at 70°C yielded oligosaccharides (G2-G4) and at room temperature yielded glucose/maltose (G1 and G2). Conclusion: The B. amyloliquifaciens ABBD α-amylase was capable of degrading various raw starch granules from corn, rice, cassava and sago at room temperature.
  Ocky Karna Radjasa , Siti Isrina Oktavia Salasia , Agus Sabdono , Jutta Weise , Johannes F. Imhoff , Christop Lammler and Michael J. Risk
  A marine bacterium associated with soft coral Sinularia polydactyla collected from Bandengan water, Jepara, North Java Sea, Indonesia, was successfully screened for antibacterial activity against pathogenic bacterium Streptococcus equi subsp. zooepidemicus K6.72 isolated from infected monkey of the island of Bali and identified based on morphological, biochemical and molecular methods. Marine bacterium was identified as Pseudomonas sp. based on its 16S rDNA and was found to amplify gene fragments of Non-ribosomal peptide synthetase (NRPS). Cloning and subsequent sequencing, a 360 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved signature regions for peptide synthetases and revealed a high similarity of 61.1% to genes peptide synthetase of Bacillus subtilis.
  Sukarmi and Ocky Karna Radjasa
  The occurrence of large scale of bioactive compounds is not common to all living organisms, but restricted to certain taxonomic groups. Among marine animals, reef`s invertebrates are the most prolific producers of secondary metabolites and have become sources of great interest to natural product chemistry, since they provide a large proportion of bioactive compounds with different biological activities. Perhaps the most significant problem that has hampered the investigation of secondary metabolites is their low concentration. In marine invertebrates many highly active compounds contribute to < 10-6% of the body-wet weight. Providing sufficient amounts of these biologically active substances, hence, may be a difficult task. In addition, it has often proven extremely difficult and some cases impossible, to provide from invertebrates sufficient amounts of many of these substances due to limited amounts found in the producing organism, or to limited quantity of the organism itself, or to geographic, seasonal or sexual variations in the amounts and in the nature of produced secondary metabolites. There has an increasing concerns regarding the collecting reef`s organisms for the discovery and development of pharmaceuticals since it has been perceived variously as sustaining and threatening conservation. There is an urgent need to take into account the bioethical considerations in anticipating the potential consequences of these activities and proposing management options for sustainable use of reef`s invertebrates as the sources of bioactive compounds.
  Ocky Karna Radjasa , Dewi Nasima , Agus Sabdono , Kumiko Kita-Tsukamoto and Kouichi Ohwada
  In this study we isolated marine bacteria from seawaters of Makasar Strait, Indonesia and tested for low temperature adaptation profiles. A total of 27 bacterial isolates represented the most dominant colonies in ZoBell agar plates were selected and tested for low-temperature adaptation, in which all isolates were able to grow at 4 and 20°C incubation indicating that they are psychrotrophic bacteria. A rapid grouping by using repetitive PCR was carried to estimate the richness of the isolates. Following sequencings, it was shown that psychrotrophic bacteria belonged to the members of genera Psychrobacter, Pseudomonas and Vibrio.
  Ocky Karna Radjasa , Torben Martens , Hans-Peter Grossart , Thorsten Brinkhoff , Agus Sabdono and Meinhard Simon
  A coral-associated bacterium was successfully screened for secondary metabolite production based on biological activity and PCR amplification of the non-ribosomal peptide synthetase (NRPS) gene and was identified as closely related to Pseudoalteromonas luteoviolacea based on its 16S rDNA. The bacterium was found to inhibit the growth of other coral-associated bacteria and pathogenic bacteria. To characterize the inhibiting metabolite, a 279 bp long DNA fragment was obtained and the deduced amino acid sequence showed conserved signature regions for peptide synthetases and revealed a high similarity to NosD (40% identity), a multifunctional peptide synthetase from Nostoc sp. GSV224 and NdaB (44% identity), a peptide synthetase module of Nodularia spumigena. To estimate the possible role of secondary metabolites, analyses on the quantitative proportion of Pseudoalteromonas was carried out. The results revealed that Pseudoltermonas group was indeed present within surfaces of coral Acropora sp.
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