Judul: Detection of Biosynthetic Genes for Secondary Metabolites and Evaluation of Antibacterial Activity from Endophytic Bacteria Isolated from Syzygium cumini
Abstrak: Eksplorasi aktivitas antibakteri dari bakteri endofit yang berasosiasi dengan duwet (Syzygium cumini) perlu dilakukan untuk mengatasi kasus resistensi bakteri patogen terhadap antibiotik. Penelitian ini bertujuan mendeteksi keberadaan gen-gen biosintetik metabolit sekunder dan mengevaluasi aktivitas antibakteri dari bakteri endofit duwet. Berdasarkan teknik PCR, 9 dari 15 isolat bakteri endofit duwet (60%) membawa minimal satu gen biosintetik metabolit sekunder. Dual-culture assay menunjukkan bahwa empat dari 15 isolat bakteri endofit tanaman ini memiliki aktivitas antibakteri terhadap 2 atau 1 bakteri target Staphylococcus aureus ATCC 6538 dan Bacillus subtilis ATCC 19659. Isolat B2 dan D1 merupakan 2 isolat dengan aktivitas antibakteri terbaik. Secara konsisten, ekstrak kasar kedua isolat tersebut juga dapat menghambat S. aureus ATCC 6538 dan B. subtilis ATCC 19659 dengan zona hambat berkisar antara 8–12,33 mm. Nilai minimum inhibitory concentration (MIC) dan minimum bactericidal concentration (MBC) telah ditentukan menggunakan teknik microbroth-dilution. Nilai MIC ekstrak kasar kedua isolat lebih aktif terhadap B. subtilis ATCC 19659, dibandingkan dengan S. aureus ATCC 6538. Kedua ekstrak tersebut memiliki nilai MBC yang lebih tinggi dibanding nilai MIC-nya. Analisis Liquid Chromatography Quadrupole-tandem Mass Spectrometry (LC-MS/MS) menunjukkan bahwa ekstrak bakteri endofit duwet mengandung beberapa senyawa antibakteri, seperti cyclo(tyrosyl-propyl) dan cyclo(prolylvalyl)., Exploration of antibacterial activity from endophytic bacteria associated with Syzygium cumini is necessary to provide new sources of antibiotics to overcome resistance in pathogenic bacteria. This study aimed to detect the presence of antibiotic-biosynthetic genes and evaluate the antibacterial activity of endophytic bacteria isolated from S. cumini. Based on PCR screening, 9 out of 15 isolates (60%) carried at least one antibiotic-biosynthetic gene. Furthermore, the dual-culture assay showed that four out of 15 isolates showed remarkable antibacterial activity against either one or both target bacteria, including Staphylococcus aureus ATCC6538 and Bacillus subtilis ATCC19659. Endophytic bacteria coded as B2 and D1 exhibited the most promising antibacterial activity against both strains. Consistently, crude extracts of these isolates could inhibit the growth of B. subtilis ATCC19659 and S. aureus ATCC6538, with inhibition zone diameters ranging from 8 to 12.33 mm. According to microbroth-dilution assay, the minimum inhibitory concentration (MIC) values of these isolates were more active against B. subtilis ATCC19659 compared to S. aureus ATCC6538. Both extracts had minimum bactericidal concentration (MBC) higher than their MIC values. Liquid chromatography quadrupole-tandem mass spectrometry (LC-MS/MS) analysis showed the crude extracts derived from these isolates contained several antimicrobial compounds, such as cyclo (tyrosyl-propyl) and cyclo (prolylvalyl).
Keyword: antibacterial, Bacillus subtilis, biosynthetic genes, Staphylococcus aureus, Syzygium cumini

Judul: Antibacterial Activity and Identification of Endophytic Bacteria Isolated from Ziziphus sp.
Abstrak: Penyakit infeksi yang disebabkan oleh bakteri patogen resistan antibiotik menjadi permasalahan utama kesehatan global. Bakteri endofit bidara (Ziziphus sp.) dapat menjadi sumber alternatif penghasil antibiotik baru. Penelitian ini bertujuan menganalisis aktivitas antibakteri isolat bakteri endofit bidara, mengidentifikasi isolat potensial melalui pendekatan molekuler, dan mengidentifikasi profil kimia dari isolat-isolat potensial. Sebanyak 21 isolat bakteri endofit telah berhasil diisolasi dari akar, batang, dan daun bidara. Dual-Culture Agar Diffusion Assay menunjukkan dua dari 21 isolat bakteri memiliki aktivitas antibakteri terhadap empat bakteri target. Estrak kasar metabolit sekunder kedua isolat potensial (80 mg/ml) mampu menghambat semua bakteri target dengan diameter zona hambat berkisar 8,3–15,0 mm. Nilai minimum inhibitory concentration (MIC) dan minimum bactericidal concentration (MBC) yang ditentukan dengan teknik microdilution menunjukkan bahwa kedua ekstrak tersebut memiliki nilai MIC berkisar antara 468,75–>30.000 µg/ml, dan MBC berkisar antara 468,75–>30.000 µg/ml. Berdasarkan analisis gen 16S rRNA, dua isolat potensial yaitu BBSB3 dan BDSB4 masing-masing memiliki kemiripan sekuens tertinggi dengan Pseudomonas aeruginosa strain DSM 50071 dan Pseudomonas aeruginosa strain N. Kedua isolat tersebut terdeteksi memiliki gen polyketide synthase I (PKS I) yang umumnya terlibat dalam biosintesis senyawa poliketida. Analisis liquid chromatograohy tandem mass spectrometry (LC-MS/MS) kedua ekstrak kasar menunjukkan keduanya memiliki berbagai senyawa aktif antibakteri., Infectious diseases caused by antibiotic-resistant pathogenic bacteria are one of the significant health problems worldwide. Exploring the antibacterial activity of endophytic bacteria associated with Ziziphus sp. may provide an alternative source of new antibiotics. This study aims to evaluate the antibacterial activity of endophytic bacteria isolated from Ziziphus sp., identify potential isolates through molecular approaches, and identify the chemical profiles of potential isolates. In previous research, 21 endophytic bacterial isolates were successfully isolated from Ziziphus sp. Antagonism assay showed that two of the 21 bacterial isolates had antibacterial activity against four target bacteria. At a concentration of 80 mg/ml, the crude extract of secondary metabolites of the two potential isolates could inhibit all target bacteria with inhibition zone diameters ranging from 8.3-15.0 mm. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of both extracts ranged from 468.75–>30,000 µg/ml. Based on their 16S rRNA sequences, the selected isolates were closely similar to Pseudomonas aeruginosa strain DSM 50071, and Pseudomonas aeruginosa strain N. Both isolates were also detected to have the PKS I gene, which is generally involved in the biosynthesis of polyketide compounds. LC-MS/MS analysis of the two crude extracts showed both to have various antibacterial active compounds.
Keyword: 16S rRNA, LC-MS/MS, MIC, Pseudomonas aeruginosa, Gen PKS I

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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