Judul: Comparative Analysis of the Total Genome Sequence from Bacillus cereus DCN1 and Detection of Gene Clusters for Secondary Metabolite Synthesis
Abstrak: Bakteri endofit Bacillus cereus DCN1 asal tanaman cengkeh (Syzygium aromaticum L.), memiliki potensi menghasilkan berbagai senyawa metabolit sekunder, termasuk antioksidan. Pengetahuan genomik B. cereus DCN1 membantu dalam analisis sintesis antioksidan. Penelitian ini bertujuan mendeteksi klaster ortolog melalui analisis komparatif dan klaster gen sintesis metabolit sekunder dari sekuen genom total B. cereus DCN1. Sekuen genom total isolat DCN1 diperoleh melalui teknik Whole Genome Sequencing (WGS) menggunakan platform MGI DNBSEQ-G400. Hasil WGS menunjukkan kualitas yang baik dengan depth of coverage sebesar 30x, number of contigs sebanyak 774, dan nilai N50 sebesar 24 kb. Nilai Q20 sebesar 97,55% dan Q30 sebesar 92,75% menunjukkan tingkat kesalahan rendah dan kualitas sekuen yang tinggi. Analisis data menggunakan Orthovenn3 mengidentifikasi 2003 klaster ortolog diantara lima spesies bakteri endofit genus Bacillus, serta mendeteksi adanya perubahan materi genetik akibat simbiosis dengan tanaman inang. B. cereus DCN1 ditemukan memiliki 8 klaster gen biosintesis metabolit sekunder, yaitu Nonribosomal Peptide Synthetases (NRPS), Linear Azo(line) Containing Peptides (LAP), NI-siderophore, NRP-metallophore, batalactone, 2 Ribosomally Synthesized and Posttranslationally Modified Peptides (RiPP), dan terpene yang berpotensi menghasilkan senyawa bioaktif.
Keyword: Bacillus cereus DCN1, biosintesis, cengkeh, Whole Genome Sequencing

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: 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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