Judul: Screening of Actinomycetes Producing Endo-β-1,3-Glucanase Enzymes from The Maize Rhizosphere and Detection of The Encoding Genes
Abstrak: Aktinomiset rizosfer merupakan salah satu mikroorganisme yang berpotensi sebagai agen biokontrol terhadap cendawan fitopatogen, salah satunya melalui produksi enzim mikolitik seperti glukanase. 11 isolat aktinomiset telah berhasil diisolasi dari rizosfer jagung, dan telah diketahui memiliki aktivitas pemacu pertumbuhan dan biokontrol antifungi, namun belum diketahui potensinya dalam menghasilkan glukanase. Penelitian ini bertujuan untuk menyeleksi aktinomiset rizosfer jagung penghasil glukanase dan mendeteksi keberadaan gen endo-β-1,3-glukanase. Berdasarkan uji kualitatif pada medium yang mengandung 0,5% beta glukan, seluruh isolat mampu menghasilkan enzim glukanase yang beragam yaitu berkisar antara 1,63±0,18 - 2,00±0,24. Tiga isolat dengan indeks glukanolitik tertinggi yaitu ARJ 32 (2,00±0,24), ARJ 38 (1,97±0,12), dan ARJ 23 (1,88±0,14). Amplifikasi PCR menggunakan primer Bgl16F dan Bgl16R menunjukkan bahwa seluruh isolat memiliki gen endo-β-1,3-glukanase dengan pita berukuran ± 160 pb. Analisis lebih lanjut diperlukan untuk menentukan potensinya sebagai agen biokontrol terhadap cendawan fitopatogen., Rhizosphere actinomycetes are one of the microorganisms that have the potential as biocontrol agents against phytopathogenic fungi by producing mycolityc enzymes such as glucanase. A total of 11 isolates of maize rhizosphere actinomycetes were used in this study. Previously, these isolates have been studied to have potential in promoting plant growth and in inhibiting fungal growth, but their potential in producing glucanase is not studied yet. Based on the qualitative test on the medium containing 0.5% β-glucan, all isolates were able to produce the glucanase enzyme with various glucanolytic indexes ranging from 1,63±0,18 to 2,00±0,24 three highest indexes showed by ARJ 32 (2.00±0.24), ARJ 38 (1.97±0.12), and ARJ 23 (1.88±0.14). In addition, all isolates have been detected to have gene encoding glucanase with amplicon size ± 160 bp, as amplified by using Bgl16F and Bgl16R primers. In conclusion, this study showed these isolates attributed with glucanase activity are potential to be further developed as biocontrol candidates.
Keyword: Aktinomiset, β-1,3-glukanase, PCR, penapisan

Judul: Enzyme Activity of β-1,3-Glucanase from Streptomyces spp. Rhizosphere and Cloning of its Encoding Gene
Abstrak: Enzim β-1,3-glukanase merupakan salah satu enzim yang mampu menghidrolisis glukan penyusun dinding sel cendawan fitopatogen. Aktinomiset rizosfer jagung dari kelompok Streptomyces spp. diduga mampu memproduksi enzim yang memiliki aktivitas glukanolitik dan berpotensi untuk dikembangkan sebagai agen biokontrol cendawan fitopatogen. Penelitian ini bertujuan menganalisis aktivitas enzim glukanase secara kuantitatif dua isolat Streptomyces spp. dengan indeks glukanolitik tertinggi pada penelitian sebelumnya dan mengidentifikasi gen penyandinya. Metode penelitian yang dilakukan meliputi uji aktivitas glukanase secara kuantitatif, amplifikasi gen endo-β-1,3-glukanase (bglS), kloning, konfirmasi hasil kloning, sekuensing, analisis fenetik, dan prediksi model protein. Aktivitas spesifik enzim isolat S. collinus ARJ38 lebih tinggi dari S. tritolerans ARJ32, yakni sebesar 41,599 U/mg pada waktu inkubasi hari ke-8. Keberadaan gen penyandi bglS pada kedua isolat berhasil diamplifikasi dan dikloning. Hasil sekuensing gen bglS parsial dari kedua isolat potensial teridentifikasi sebagai endo-β-1,3-glukanase dari kelompok glycoside hydrolase (GH) family 16. Model struktur tiga dimensi yang dikonstruksi dari sekuens asam amino bglS parsial memiliki parameter kualitas serta kemiripan yang tinggi dengan model protein eksperimental endo-β-1,3-glukanase parsial dari Nocardiopsis sp. F96., The β-1,3-glucanase enzyme is one of the enzymes capable of hydrolyzing the glucan components of phytopathogenic fungal cell walls. Streptomyces spp. isolated from the maize rhizosphere are suspected to produce enzymes with glucanolytic activity and have the potential to be developed as biological controlling agents against phytopathogenic fungi. This study aims to quantitatively analyze the enzymatic activity of glucanase in two Streptomyces spp. isolates with the highest glucanolytic index from previous research, and to identify their encoding genes. The research methods include quantitative analyze of the glucanase activity, amplification of the endo-β-1,3-glucanase (bglS) gene, cloning, confirmation of cloning results, sequencing, phenetic tree analysis, and protein model prediction. The specific activity enzyme of S. collinus ARJ38 was higher than that of S. tritolerans ARJ32, with a value of 41.599 U/mg on the 8th day of incubation. The presence of the bglS gene in both isolates was successfully amplified and cloned. The sequencing results of the bglS gene from both potential isolates were identified as endo-β-1,3-glucanase from the glycoside hydrolase family 16. The three-dimensional structure model constructed from the partial bglS amino acid sequence exhibited high-quality parameters and high similarity with the experimental protein model of partial endo-β-1,3-glucanase from Nocardiopsis sp. F96.
Keyword: glucanase, phenetic analysis, protein model, rhizosphere actinomycetes, TA cloning, aktinomiset rizosfer, fenetik, glukanase, model protein

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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