Judul: Optimasi polymerase chain reaction (PCR) untuk deteksi Salmonella spp. pada udang segar
Abstrak: Shrimp is an important protein source and non-oil commodity for foreign trade in Indonesia. Increase in the production volume for export and domestic demand is frequently challenged with rejection of shrimp exports to the importing country. This rejection is caused by many reasons, especially quality and sanitation, antibiotic residue and environmental issues. Presence of Salmonella spp. in shrimp has been frequently reported in Indonesia and worldwide. Within the last 5 years, USFDA recorded that 65% of the refusal of fishery products from Indonesia was due to Salmonella spp. The Indonesian National Standard 01-2728.1-2006 requires that Salmonella spp. on fresh shrimp should be negative in 25 g, because the bacteria are pathogenic and can cause health problems. Testing of Salmonella spp. in seafood is generally done using conventional methods that take 5 days. Various attempts were made to speed up the detection time of Salmonella spp., including by PCR. Variation of detection limits and accuracy for the detection of Salmonella spp. has been observed with different primers i.e. primers oriC targeting the replication gene of Salmonella spp., invA and invE (virulence genes), ompC which encodes outer membrane proteins and hns a DNA binding protein gene. This study aims to develop a PCR procedure for the detection of Salmonella spp. in shrimp, and compare it with conventional methods. The research was conducted in the following three phases: (a) optimization of PCR method with different annealing temperature (b) sensitivity and specificity assays of the PCR method and (c) detection of Salmonella spp. from shrimp using the PCR method selected and a conventional method. The results show that an annealing temperature of 640C is optimum to detect the 284 bp fragment of Salmonella invA gene. The PCR based detection method has a limit detection of 27.81 μg/mL and 1 cfu/mL of viable salmonellae with 100% specificity. The PCR based assay could detect 6 different Salmonella serovars (S. Enteritidis, S. Hadar, S. Heidelberg, S. Kentucky, S. Paratyphi and S. Typhimurium) and none of the non salmonellae isolates. Application of the PCR assay to detect Salmonella in shrimp after selective enrichment step suggested that all 16 samples are positive for Salmonella. Meanwhile the conventional method only detected 3 samples as positive for Salmonella. Use of a primer targeting invA gene is potential for detection of salmonellae in shrimp.
Keyword: detection, Salmonella spp, shrimp, primer, PCR

Judul: Deteksi Salmonella Hadar, Salmonella Typhimurium, dan Salmonella Enteritidis Menggunakan Polymerase Chain Reaction (PCR)
Abstrak: Sebagai upaya penanganan kasus keracunan pangan, metode deteksi Salmonella dalam waktu yang singkat dan akurat perlu dikembangkan. Penelitian ini bertujuan untuk melakukan verifikasi metode polymerase chain reaction (PCR) untuk mendeteksi Salmonella spp., S. Enteritidis dan S. Typhimurium pada karkas ayam. Tahapan uji adalah konfirmasi kultur Salmonella, ekstraksi DNA, optimasi suhu annealing primer, uji spesifisitas primer, penentuan limit deteksi PCR, dan uji coba pada sampel. Berdasarkan hasil penelitian, kemurnian DNA hasil ekstraksi berada dalam rentang standar (1.8 – 2.0). Primer yang digunakan untuk mendeteksi keberadaan 3 serovar tersebut adalah InvAc, STM4497c, dan Prot6E. Suhu annealing yang digunakan untuk ketiga primer adalah 52 °C dan limit deteksi PCR dengan konsentrasi primer 0.5 μM untuk ketiga target gen, masing-masing sebesar 1.9 x 104 sel (InvA), 4.0 x 104 sel (STM4497), 2.0 x 103 sel (Prot6E). Pengujian pada sampel masih perlu dikembangkan karena batas limit deteksi yang masih rendah, yaitu sebesar 4.0 x 104 sel.
Keyword: karkas ayam, PCR, Salmonella spp., S. Enteritidis, S. Typhimurium

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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