Judul: Isolation and Identification of ACC Deaminase-Containing Rhizobacteria from Rhizosphere of Stressed Pineapple along with Detection, Expression, and Abundance of acdS Gene
Abstrak: ACC deaminase merupakan enzim sitoplasma yang berperan penting dalam menekan kadar etilen berlebih tanaman yang dilanda cekaman dengan cara menghidrolisis senyawa pembentuknya, ACC. Penelitian ini bertujuan untuk mendapatkan isolat dan identitas bakteri penghasil ACC deaminase, primer gen acdS, tingkat ekspresi gen acdS, dan kelimpahan gen acdS pada tanah rizosfer nanas yang dilanda cekaman. Empat jenis sampel tanah asal bakteri diperoleh meliputi tanah dengan cekaman herbisida, cekaman Phytopthora spp., cekaman genangan, dan tanah noncekaman. Penelitian ini diawali dengan mengisolasi bakteri rizosfer pada media umum TSA (Tryptic Soy Agar) kemudian ditumbuhkan kembali pada media selektif DF (Dworkin-Foster) mengandung senyawa ACC. Bakteri yang tumbuh pada media selektif ini diindikasikan memiliki enzim ACC deaminase yang disandi oleh gen acdS. Tahap selanjutnya adalah melakukan identifikasi molekuler isolat bakteri tersebut berdasarkan gen 16S rRNA. Selanjutnya, tahap ekstraksi DNA dan RNA isolat bakteri serta DNA bakteri total tanah dilakukan sebagai template pada sistem deteksi berbasis real time PCR. Sebanyak 49 isolat bakteri berhasil tumbuh pada media TSA dan hanya 7 isolat yang mampu tumbuh pada media selektif DF mengandung 3 mM L-1ACC. Hasil identifikasi gen 16S rRNA menunjukkan bahwa keempat isolat 3, 2A, 5B, dan 1E dengan pertumbuhan terbaik termasuk ke dalam Stenotrophomonas maltophilia, Burkholderia territorii, Pseudomonas oryzihabitans, dan Bacillus tropicus. Sepasang primer 105F-acdS 5’-TGCCAAGCGTGAAGACTGC-3’ and 244R-acdS 5’-GGGTCTGGTTCGACTGGAT-3’ berhasil mengamplifikasi sekuens parsial acdS sepanjang 140 pb pada isolat 3, 2A, 5B, dan 1E dengan suhu disosiasi berturut-turut 86, 89, 87, dan 89.5oC berdasarkan analisis kurva melt peak dan dikonfirmasi dengan pelacakan BlastN dan BlastX. Berdasarkan analisis filogenetik, sekuens acdS isolat 2A dan 1E memiliki kemiripan yang lebih tinggi dibandingkan dengan isolat 3 dan 5B. Sedangkan tingkat ekspresi gen acdS pada keempat bakteri berturut-turut adalah B. tropicus (17.24), B. territorii (17.86), P. oryzihabitans (20.87), dan S. maltophilia yang tidak menunjukkan nilai Cq. Analisis DNA sampel tanah menyimpulkan bahwa kelimpahan gen acdS tanah noncekaman berbeda signifikan terhadap tanah cekaman herbisida dan Phytopthora spp. kecuali pada tanah cekaman genangan. Kelimpahan gen acdS antarcekaman secara umum berbeda signifikan kecuali pada sampel CPB terhadap CGB. Sedangkan kelimpahan gen acdS antara sampel tanah tanaman sehat dan sakit tidak berbeda signifikan kecuali pada sampel cekaman Phytopthora spp. Hasil penelitian ini menggambarkan bahwa bakteri rizosfer asal rizosfer nanas memliki gen acdS yang menyandi ACC deaminase dan diduga mampu meregulasi kadar etilen tanaman dalam merespon berbagai cekaman lingkungan., ACC deaminase is a cytoplasmic enzyme which play an important role in lowering overproduced ethylene in stressed plant by cleaving its precursor, ACC. The aim of this study was to obtain ACC deaminase-encoding rhizobacterial isolates and identity, acdS gene primers, acdS gene expression among bacterial isolates, and acdS gene abundance in stress soil of pineapple rhizosphere. Four types of soil samples where bacterial isolates obtained include herbicide-stress soil, flooding-stress soil, Phytopthora spp.-stress soil and nonstress soil. This study was initiated by isolating rhizobacteria on the TSA (Tryptic Soy Agar) medium and then re-growing on DF (Dworkin-Foster) selective medium containing 3 mM L-1ACC compound. Bacteria that grow on this selective medium were indicated to have ACC deaminase enzyme encoded by acdS gene. Following the purified isolates, the selected isolates were then
Keyword: Ethylene, AcdS Gene, Rhizosphere, Pineapple Plant, Uji Gram Bakteri, Plant Ethylene, Enzim Sitoplasma

Judul: Penapisan Deteksi PCR ACC Deaminase dan Analisis Produksi Auksin Rhizosfer Tanaman Padi Daerah Pesisir
Abstrak: Salinity and drought stress results in the production of ethylene. Rhizosphere bacterial activity suppresses the production of ethylene through the activity of 1-aminocycopropane-1-carboxylate (ACC) deaminase. In this study, a sampel of rhizosphere bacteria from coastal rice plant area was tested. The method used was acc deaminase activity test performed on Dworkin - Foster (DF) media and PCR acdS gene using specific primers of ACC and a quantitative analysis of the production of auxin (IAA). Of 47 isolates obtained, 8 were positively have acdS activity. The positive result was indicated by the presence of 1080 bp amplicon. Quantitative analysis showed the highest yield of 10.6 ppm of auxin. The results prove that there are some bacteria originated from coastal rice plant area which have acc deaminase activity.
Keyword: Bogor Agricultural University (IPB), rice, rhizosfere bacteria, salinity, drought, auxin, ACC deaminase

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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