Judul: Identification of Bacterial Communities in Eastern Little Tuna (Euthynnus affinis) from Traditional and Modern Market Locations with Metagenomic Analysis
Abstrak: Penanganan pasca panen dengan penerapan rantai dingin dan higiene yang baik merupakan tahapan penting untuk dapat menjaga kualitas ikan dan keamanan pangan. Perbedaan tingkat higiene yang diterapkan pada pasar tradisional dan modern akan mempengaruhi komunitas bakteri pada ikan tongkol. Penelitian ini bertujuan mengisolasi DNA bakteri dan mengidentifikasi komunitas bakteri dengan analisis metagenomik. Tahapan penelitian terdiri dari pengumpulan sampel, inkubasi bakteri, isolasi DNA bakteri dengan kit komersial, permurnian isolat DNA, Next Generation Sequencing dengan target gen 16S rRNA wilayah variabel V3-V4, dan analisis data dengan program bioinformatika. Kelimpahan sekuens bakteri pada ikan tongkol yang berasal dari pasar tradisional sebanyak 42.829 sekuen sedangkan dari pasar modern sebanyak 30.989 sekuen. Filum bakteri yang mendominasi pada kedua sampel tersebut yaitu Fusobakteriota, Bakteroidota, dan Patescibakteria. Komunitas bakteri pada ikan tongkol pasar tradisional memiliki kelimpahan relatif tertinggi pada genus Myroides (42,3%) sedangkan dari pasar modern pada genus Cetobacterium (80,2%)., Post-harvest handling, which includes the use of cold chain and proper hygiene, is a critical in maintaining fish quality and food safety. The bacterial community in eastern little tuna will be affected by differences in the level of hygiene used in traditional and modern markets. This study aims to isolate bacterial DNA and identify bacterial communities by metagenomic analysis. The research stages consisted of sample collection, bacterial incubation, isolation of bacterial DNA with commercial kits, purification of DNA isolates, NGS with the target gene for 16S rRNA V3-V4 variable region, and data analysis using bioinformatics programs. The sequence abundance of bacteria in eastern little tuna from traditional markets was 42.829 sequences while those from modern markets were 30.989 sequences. Fusobakteriota, Bacteroidota, and Patescibakteria were the most predominant bacterial phyla in both samples. Traditional market eastern little tuna had the highest relative abundance in the genus Myroides (42,3%), while the modern had the highest relative abundance in the genus Cetobacterium (80,2%).
Keyword: 16S rRNA, Next Generation Sequencing, Bacterial communities, Eastern Little Tuna, Hygiene

Judul: Cold Chain System Simulation Effect on Bacterial Community and Quality of Eastern Little Tuna (Euthynnus affinis).
Abstrak: Penanganan pascapanen dan tingkat higienis hasil perairan sangat mempengaruhi kualitas dan tingkat keamanan. Pengendalian rantai dingin menjadi salah satu faktor penentu kualitas ikan dan komunitas bakteri yang tumbuh pada ikan tersebut. Identifikasi jenis bakteri pembusuk dan patogen pada hasil perairan perlu dilakukan karena menentukan kualitas fisik dan kimiawi. Metode identifikasi molekuler dengan sensitivitas yang tinggi menjadi solusi. Penelitian ini bertujuan mengidentifikasi kualitas ikan dan komunitas bakteri yang tumbuh. Prosedur penelitian yang dilakukan meliputi pengumpulan sampel, pengukuran pH, pengukuran drip loss, perlakuan transportasi dan penyimpanan suhu dingin, ekstraksi DNA, sekuensing DNA, analisis sekuen dan analisis bioinformatika. Kesimpulan yang diperoleh dari penelitian ini adalah simulasi sistem rantai dingin yang diterapkan pada ikan tongkol tidak berpengaruh nyata terhadap perubahan nilai aw, pH dan drip loss. Perubahan yang tidak signifikan menunjukkan sampel ikan tongkol masih memiliki kualitas yang baik. Analisis bioinformatika yang dilakukan menunjukkan keragaman dan kelimpahan bakteri dari ordo Clostridiales tertinggi pada sampel dengan perlakuan suhu 10oC., Post-harvest handling and hygienic level of aquatic products greatly affect the quality and level of safety. Cold chain control is one of the determining factors for the quality of fish and the bacterial community that grows on the fish. Identification of the types of spoilage bacteria and pathogens in aquatic products needs to be done because it determines the physical and chemical quality. A molecular identification method with high sensitivity is one of the alternative methods. This study aimed to identify the quality of fish and bacterial communities that grow. The research procedures carried out included sample collection, pH measurement, drip loss measurement, transportation and cold storage treatment, DNA extraction, DNA sequencing, sequence analysis and bioinformatics analysis. The conclusion obtained from this study is that the simulation of the cold chain system applied to tuna does not significantly affect changes in the value of aw, pH and drip loss. The insignificant change indicates that the tuna samples still have good quality. The bioinformatics analysis performed showed the highest diversity and abundance of bacteria from the order Clostridiales in the samples treated at 10oC.
Keyword: bioinformatics analysis, DNA isolation, metagenomic, NGS

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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