Judul: Determination of Bacterial Communities in Processing Plants of the Blue Swimming Crab Meat Pasteurized Industry with Metagenomic Techniques
Abstrak: Komunitas bakteri yang ada di lingkungan produksi berpengaruh terhadap kualitas dan kemanan produk. Program sanitasi dilakukan untuk mengendalikan bakteri pada ruang produksi. Pengujian bakteri secara konvensional hanya mengidentifikasi bakteri yang dapat dikultur, sehingga pengujian metagenomik menjadi solusi untuk mengidentifikasi seluruh bakteri. Penelitian ini bertujuan mengidentifikasi komunitas bakteri saat proses produksi dan setelah prosedur sanitasi. Prosedur penelitian meliputi pengambilan sampel, inkubasi bakteri, perhitungan bakteri, isolasi DNA bakteri, sekuensing DNA, dan analisis bioinformatika. Sampel selama proses produksi memiliki kelimpahan absolut dan yang lebih tinggi dibanding sampel setelah prosedur sanitasi dilakukan dengan penurunan kelimpahan absolut sebesar 5,26%. Genus yang mendominasi yaitu Bacillales dengan kelimpahan relatif saat proses produksi (16,7%) dan mengalami penurunan setelah program sanitasi (4,7%). Pengujian molekuler dapat melengkapi pengujian konvensional dengan mengidentifikasi seluruh bakteri, The bacterial community in the production environment affects the quality and safety of the product. Sanitation programs can control the bacterial community in the production environment. Conventional method can only identify bacteria that can be cultured, so metagenomic method is a solution to identify all bacteria. This study aimed to identify bacterial communities during the production and after sanitation procedures. The research procedures included sample collection, bacterial incubation, bacterial counting, bacterial DNA isolation, DNA sequencing, and bioinformatics analysis. Samples during production had higher absolute abundance than after sanitation with decreased 5.26%. Genus that dominates is Bacillales with a relative abundance during the production (16.7%) and decreased after the sanitation (4.7%). Molecular method can complement conventional method by identifying all bacterial.
Keyword: lingkungan produksi, metagenomik, NGS, prosedur sanitasi, rajungan kaleng

Judul: Identification of Bacterial Community in Vannamei Shrimp (Litopenaeus vannamei) from Two Different Market Locations Using Metagenomic Technology
Abstrak: Udang merupakan komoditas hasil perairan yang mudah mengalami proses kemunduran mutu, salah satunya disebabkan oleh aktivitas bakteri. Penggunaan media kultur dalam proses identifikasi komunitas bakteri menjadi kurang optimal, karena proses kultivasi tidak dapat menumbuhkan semua jenis bakteri. Penelitian ini bertujuan untuk mengidentifikasi komunitas bakteri yang terdapat pada komoditas udang segar dengan teknik metagenomik. Proses identifikasi bakteri dilakukan melalui tahap pengusapan permukaan udang, kemudian isolasi DNA bakteri menggunakan Wizard Genomic DNA Purification Kit dan amplifikasi menggunakan primer universal 16S rRNA dengan wilayah V3-V4. Proses sekuensing dilakukan menggunakan teknik Next Generation Sequencing. Komunitas bakteri yang teridentifikasi didominasi oleh filum Bacteroidota, Patescibacteria, Firmicutes, Fusobacteriota, Campilobacteriota, Actinobacteriota, dan Proteobacteria. Potensi kelompok bakteri patogen dan pembusuk pada udang teridentifikasi berasal dari genus Myroides, Flavobacterium, Pseudomonas, Aeromonas, Escherichia, Shigella dan Shewanella, Shrimp is an aquatic product that is prone to deterioration in quality, one of which is caused by bacterial activity. The use of culture media in the identification process of bacterial communities is less than optimal because the cultivation process cannot grow all types of bacteria. This study aims to identify the bacterial community found in fresh shrimp commodities with a metagenomic approach. The bacterial identification process was carried out by swabbing the surface of the shrimp, then isolating bacterial DNA using the Wizard Genomic DNA Purification Kit and amplification using a universal 16S rRNA primer with a V3-V4 region. The sequencing process was carried out using Next Generation Sequencing. The identified bacterial community was dominated by the phyla Bacteroidota, Patescibacteria, Firmicutes, Fusobacteriota, Campilobacteriota, Actinobacteriota, and Proteobacteria. Potential groups of pathogenic and spoilage bacteria in shrimp were identified from the genera Myroides, Flavobacterium, Pseudomonas, Aeromonas, Escherichia, Shigella, and Shewanella
Keyword: amplicon sequence variants, bakteri, DNA, udang

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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