Judul: NRPS-PKS Gene Detection and Analysis in Biopigment Producing Actinomycetes
Abstrak: Biopigmen yang dihasilkan mikrob terutama aktinomisetes memiliki beragam fungsi seperti antioksidan, antimikrob, dan antikanker. Biopigmen merupakan metabolit sekunder, beragam metabolit sekunder dihasilkan melalui jalur sintesis protein non ribosomal dan poliketida sintetase (NRPS-PKS). Penelitian ini bertujuan untuk menganalisis domain adenilasi (A) dari NRPS dan domain ketosintase (KS) dari PKS pada aktinomiset penghasil biopigmen. Terdapat lima isolat yang digunakan dalam penelitian ini yaitu HV 4, HV 11, JSN 1.9, JSN 28, dan NTB 42. Genom dari kelima isolat diekstrasi, domain A diamplifikasi dan diklon, kemudian hasil klon di sekuen dan dilakukan analisis bioinformatika. JSN 1.9, JSN 28, dan NTB 42 memiliki amplikon domain A yang memiliki ukuran ±750 pb. Hasil alignment domain A dari JSN 1.9, JSN 28, dan NTB 42 menunjukkan bahwa terdapat 208 nukleotida yang termasuk ke dalam daerah terkonservasi. Model protein dibuat dari hasil sekuen ketiga isolat dan menunjukkan kualitas model yang baik. Dari lima isolat domain A hanya ditemukan pada tiga isolat., Bio-pigments produced by microbes especially actinomycetes have shown various function such as antioxidant, antimicrobe, and anticancer. Bio-pigments are secondary metabolite, a wide variety of them are produced through non ribosomal protein and polyketide synthase (NRPS-PKS) pathway. This study aims to detect and analyze adenylation (A) domain from NRPS and ketosynthase (KS) domain PKS in biopigment producing bacteria. There are five isolates used in this research, which are HV 4, HV 11, JSN 1.9, JSN 28, and NTB 42. Genome was extracted from the isolates, A domain gene was amplified and cloned. Furthermore, recombinant plasmids were sequenced and bioinformatic analysis was done. A domain amplicon was found in JSN 1.9, JSN 28, and NTB 42, with the size of ±750 bp. JSN 1.9, JSN 28, and NTB 42 adenylation domain alignment result shows that there are 208 nucleotides belong to conserved region. Protein models constructed from three sequenced adenylation domain are predicted to have good qualities and displayed behavior similar to that in nature. From five isolates A domain was only found in three isolates.
Keyword: actinomycetes, biopigment, clone, NRPS

Judul: Potensi Biopigment Asal Streptomyces sebagai Antioksidan, Antibakteri dan Antikanker
Abstrak: Actinomycetes, are known for their abilities to produce diverse secondary metabolites. About 100,000 active compounds of secondary metabolites are known to be produced by actinomycetes. This amount includes 45% of all active compounds of secondary metabolites produced by microorganisms. Streptomyces, one of the actinomycetes genus are able to produce various types of pigment. Pigments, as one of the secondary metabolites, have different biological activities such as antioxidant, anticancer, and antimicrobial activity. Soil actinomycetes ARK19 and ARK86 produced pink-purple and yellow intracellular pigment which potentially has pharmaceutical properties. Here, we assessed the antioxidant, antibacterial and anticancer activity of the crude pigment extract and its active fraction and the detection of polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) genes. In our study, ARK19 has the closest similarity with Streptomyces yangpuensis fd-2tb (99%). The actinomycetes showed the best growth and pigment production in ISP4 medium supplemented with starch as a carbon source. The pigment extracts were extracted using methanol solvent resulted yield 7.54% and 6.21% (w/w) for S. yangpuensis ARK19 and S. polychromogenes ARK86, respectively. Based on the UV-Vis analysis, the S. yangpuensis ARK19’s pink-purple pigment was indicated as prodigiosin, while the S. polychromogenes ARK86’s yellow pigment indicated as carotenoid. The crude pigment extracts were tested for their cytotoxic activity by Brine Shrimp Lethality Test (BSLT). The LC50 of each extract was recorded at 182.88 μg/ml and 116 μg/ml for S. yangpuensis ARK19 and S. polychromogenes, respectively. The result suggests that the pigment extracts were classified as a cytotoxic compound and might have anticancer activity. These findings were supported by a cytotoxicity test by MTT assay against a human breast cell line. S. polychromogenes crude pigment extract showed the best cytotoxic activity with an IC50 value of 289.07 μg/mL and 271.27 μg/mL for MCF-7 and MCF-12A cell lines, respectively. Furthermore, to understand the possible chemical compounds involved in their biological activities, we identified the chemical composition of the pigment extracts by GC-MS analysis. Our result revealed that the most dominant compound in the crude pigment extract were 6-Octadecanoid acid and 2-p-nitrophenyl-1,3,4-oxadiazol-5- in S. yangpuensis ARK19 and S. polychromogenes ARK86, respectively. The active fraction was obtained by Thin-Layer Chromatography separation. The antioxidant and antibacterial active fractions of the extracts was determined by bioautography test followed by preparative-TLC. Our result showed that the crude pigment extract as well as their active fraction have in vitro antioxidant activity against DPPH radical. The antibacterial activity was assayed by the disc diffusion method exhibited broad spectrum activity against Bacillus subtilis, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. The active fraction of S. polychromogenes ARK86 extract resulted changes in morphology of B. subtilis as a result of antibacterial activity. Metabolite profiling using LC-MS analysis showed that active fraction of S. yangpuensis ARK19 was rich in dextromethorphan, while S. polychromogenes ARK86 major compounds was morphine. This compound was reported to have anti-oxidative stress and antiproliferative activity. Moreover, PCR-based gene detection revealed the presence of marker genes of both PKS and NRPS clusters, the common secondary metabolite synthesis mechanism in microbes. The results showed that the crude pigment extract and the active
Keyword: Antibacterial, Anticancer, Antioxidant, Biopigment, NRPS/PKS

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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