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: Characterization of Pigmented Actinobacteria through Several Polyphasic Taxonomic Approaches
Abstrak: Aktinobakteri berpotensi menghasilkan komponen metabolit sekunder salah satunya pigmen. Karakterisasi aktinobakteri berpigmen dapat dilakukan melalui pendekatan taksonomi polifasik. Aktinobakteri berpigmen yang dimiliki Laboratorium Mikrobiologi, Departemen Biologi FMIPA IPB diketahui dapat menghasilkan metabolit sekunder pigmen berkhasiat antioksidan. Namun, karakter dari isolat tersebut belum diketahui secara keseluruhan. Penelitian ini bertujuan mengkarakterisasi aktinobakteri berpigmen koleksi Laboratorium Mikrobiologi, Departemen Biologi FMIPA IPB melalui beberapa pendekatan taksonomi polifasik. Tahapan penelitian meliputi purifikasi, pertumbuhan dan karakterisasi morfologi koloni aktinobakteri pada berbagai media, kemampuan tumbuh pada berbagai sumber karbon, identifikasi gen 16S rRNA serta analisis bioinformatika. Lima isolat mampu tumbuh optimal pada media ISP 2. Morfologi koloni kelima isolat berbeda pada setiap media. Empat isolat termasuk genus Streptomyces, sedangkan satu isolat lainnya termasuk rare-actinobacteria non Streptomyces. Setiap isolat memiliki kemampuan tumbuh pada sumber karbon yang berbeda-beda. Hasil identifikasi molekuler gen 16S rRNA isolat HVB menunjukkan ukuran amplikon ~1465 pb yang memiliki kemiripan sebesar 91.62% dengan spesies Rhodococcus wratislaviensis strain G119. Kata kunci: aktinobakteri, molekuler, pigmen, rare-actinobacteria, taksonomi polifasik, Actinobacteria have the potential to produce secondary metabolite components such as pigment. Characterization of pigmented actinobacteria can be carried out using a polyphasic taxonomic approach. Pigmented actinobacteria belonging to the Microbiology Laboratory, Department of Biology FMIPA IPB are known to produce pigment secondary metabolites with antioxidant properties. However, the character of this isolate is not fully known. This research aims to characterize pigmented actinobacteria from the collection of the Microbiology Laboratory, Department of Biology FMIPA IPB through several polyphasic taxonomic approaches. The research stages include purification, growth and morphological characterization of actinobacterial colonies on various media, ability to grow on various carbon sources, identification of the 16S rRNA gene and bioinformatics analysis. Five isolates were able to grow optimally on ISP 2 media. The colony morphology of the five isolates was different on each medium. Four isolates belonged to the genus Streptomyces, while the other one belonged to rare-actinobacteria non-Streptomyces. Each isolate has the ability to grow on different carbon sources. The results of molecular identification of the 16S rRNA gene of HVB isolates showed an amplicon size of ~1465 bp which had a similarity of 91.62% to the species Rhodococcus wratislaviensis strain G119. Key words: actinobacteria, molecular, pigment, polyphasic taxonomy, rare actinobacteria
Keyword: actinobacteria, Molecular, pigment, polyfasic taxonomy, rare actinobacteria

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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