Judul: Deteksi Bakteri Salmonella spp. pada Berbagai Produk Sushi Komersial dan Eksplorasi Kandidat Biosensor DNA.
Abstrak: Keracunan makanan dapat disebabkan oleh berbagai faktor, salah satunya kontaminasi bakteri patogen yaitu Salmonella spp. Metode berbasis molekuler membutuhkan waktu yang cepat, lebih sensitif, dan spesifik. Tujuan penelitian ini adalah mengaplikasikan metode berbasis DNA molekuler untuk mendeteksi bakteri Salmonella spp. pada produk sushi komersial dan merancang serta mengidentifikasi oligonukleotida spesifik dari Salmonella spp. Primer yang digunakan untuk gen invA Salmonella spp. memiliki panjang amplifikasi 941 bp. Terdapat dua sampel produk sushi komersial yang mengandung Salmonella spp. Sampel yang positif mengandung Salmonella spp. yaitu sampel S2.1 dan S2.3. Primer spesifik Salmonella spp. dirancang dalam penelitian ini untuk menciptakan suatu primer spesifik dan berukuran lebih kecil yang diharapkan efisien untuk digunakan sebagai marka deteksi dengan PCR atau sebagai bioreseptor pada kit nukleosensor.
Keyword: DNA molekuler, invA, kontaminasi, nukleosensor, Salmonella, sushi

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: Thermal Characteristics and Dynamics of Tropical Cyclone over Western North Pacific Ocean: A Case Study of Typhoon Songda (Chedeng) 2011
Abstrak: The frequent occasion of Tropical Cyclone (TC) over Western North Pacific (WNP) Ocean lies from 10˚N to 26˚N and 121˚E to 170˚E. Sources of TC development come from warm ocean temperature where latent heat is released during condensation processes and subsequently concentrated in the boundary layer. Relative humidity at 850-700 hPa is responsible to produce the most intense storm. Meanwhile, weak vertical wind shear between 850-200 hPa is one of the dynamical factors that lead to the development of TC. Pressure level of 850-200 hPa is chosen to minimize the thermodynamic effect in the lower troposphere. Typhoon Songda (Chedeng in the Philippines) or TSC lasted from May 18th to 30th, 2011 and strengthened into powerful Super Typhoon stage between May 24th and 27th. Long curving track and the exhibition of all sequences of TC life cycle, TSC is then considered as an ideal case of TC. The objective of the study with case of TSC is to investigate the role of thermal characteristics and dynamics on TC intensity. The research is carried out by using Advanced Research of Weather Research and Forecasting model (WRF ARW model) version 3.3. Two domains are employed in the model. The first domain situate from 02˚N to 40˚N and 118˚E to 149˚E and cover spatial resolution () of 33.1 km. The second domain situate from 09˚N to 27˚N and 119˚E to 132˚E with of 11 km. Timestep of the model () is 120 seconds. The model is supported by the following physical parameterization, i.e., Yonsei University Scheme (YSU) in the boundary layer, Kain-Fritsch scheme (KF) in the cumulus, and WRF Single-Moment 3-class scheme in the microphysics. Initial meteorological condition prior to the formation of the cyclone is generated using WRF ARW standard-release model. Sensitivity of the model output is obtained from a selected single-parameter change scenarios, namely, 10 % to 20 % decrease and increase of wind shear initial data at 850-200 hPa, and by 10 % to 20 % decrease of relative humidity initial data at 850-700 hPa. The result showed that the negative correlations between wind shear and intensity are found in wind shear scenarios. Wind shears of 10 ms-1 which lead to strengthening of the wind intensity in the early period of Typhoon development are found in wind shear scenarios. The effect of wind shear changes on wind intensity is statistically significant in the 20 % wind shear scenarios. During mature stage, weak wind intensity occurred when wind shear increase as given in the WRF standard-release and the 20 % decreasing scenario. Different situation is found in the 20 % increasing scenario where wind shear tend to weak and lead to strong wind intensity at this stage. Meanwhile, the reduction of moisture supply at 850-700 hPa resulting from 20 % decreasing relative humidity play a major role in the weakening of wind intensity and reduces mechanical energy of the cycle process as much as 300 J kg-1.
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