Judul: Identification of Pig DNA Fragments in Meat Bone Meal Samples Using Real Time Polymerase Chain Reaction
Abstrak: Meat Bone Meal (MBM) adalah bahan pakan yang memiliki sumber protein, energi, dan mineral yang baik untuk hewan. Pakan MBM diperoleh dari olahan produk samping hewan ternak yang mudah untuk dicampur dengan bahan yang berasal dari produk babi. Importir atau produsen lokal yang curang dapat mencampurkan produk babi ke dalam MBM karena produk babi memiliki harga yang relatif murah dan dapat ditemukan di beberapa negara. Penelitian ini bertujuan untuk mengidentifikasi fragmen DNA babi pada sampel MBM menggunakan metode Real Time Polymerase Chain Reaction (qPCR). Proses identifikasi fragmen DNA babi pada sampel MBM dimulai dari ekstraksi DNA, kuantifikasi DNA (nilai konsentrasi dan kemurnian) dengan spektrofotometer 2000c, dan amplifikasi DNA dengan qPCR berbasis probe. Proses identifikasi DNA babi pada sampel MBM dideteksi menggunakan kit komersial Mericon Pig Kit dengan primer dan probenya sudah termasuk di dalam master mix spesifik. Hasil penelitian menunjukkan bahwa 81 sampel dari 198 sampel MBM teridentifikasi mengandung DNA babi. Sampel DNA babi yang positif dapat diketahui dengan nilai cycle threshold (Ct<45) pada hasil amplifikasi qPCR. Real time PCR dapat dijadikan sebagai metode pengujian untuk mengidentifikasi keberadaan fragmen DNA babi pada sampel MBM., Meat and bone meal (MBM) is a valuable source of protein, energy, and minerals in animal feed production. The MBM feed is obtained from livestock by-products that are easily mixed with pig products. Fraudulent importers or local producers can mix pig products into MBM because they are relatively inexpensive and can be found in several countries. This research aim was to identify pig DNA fragment in MBM samples using Real Time Polymerase Chain Reaction (qPCR). The process of identifying porcine DNA fragments in MBM samples was started from DNA extraction, DNA quantification (concentration and purity values) with spectrofotometer 2000c, and DNA amplification with qPCR based on probes. The process of detection porcine DNA in MBM samples was used a commercial Mericon Pig kit which the primer and probe were inserted into a specific master mix. The results showed that 81 samples were positive for porcine DNA from 198 samples of MBM. Positive samples of porcine DNA can be identified by cycle threshold value (Ct<45) on the result of amplification qPCR. Real time PCR methods can be used to identify the presence of porcine DNA in MBM samples.
Keyword: DNA, MBM, pork, qPCR

Judul: Validation method of the Buffalo (Bubalus bubalis) DNA Identification using Real-time Polymerase Chain Reaction
Abstrak: Banyak kasus pemalsuan produk pangan berbahan dasar daging yang dijumpai di masyarakat. Penambahan daging dengan daging spesies lain yang tidak terjamin mutunya, biasanya dengan kualitas lebih rendah dapat berdampak pada ekonomi dan kesehatan. Identifikasi spesies melalui penggandaan molekul DNA target dalam satu reaksi dapat dilakukan dengan metode real-time PCR. Penelitian ini bertujuan untuk memvalidasi metode real-time Polymerase Chain Reaction (qPCR) dalam identifikasi DNA kerbau pada produk pangan asal hewan. Metode qPCR dengan SYBR green melting curve analysis digunakan sebagai pengujian validasi metode DNA kerbau dengan menggunakan kit komersial QIAGEN DNeasy Food Mericon Kit. Parameter validasi metode yang digunakan dalam penelitian ini meliputi repeatability,reproducibility, limit of detection, dan spesifisitas. Hasil penelitian pada parameter validasi repeatability yaitu sampel positif teramplifikasi 100% sedangkan untuk sampel negatif tidak teramplifikasi. Hasil uji t terhadap nilai Ct dan Tm pada parameter reproducibility DNA kerbau menunjukkan bahwa tidak terdapat perbedaan yang nyata dalam mendeteksi DNA kerbau pada dua pengujian dengan menggunakan metode qPCR, nilai limit deteksi untuk PCR spesifik kerbau sebesar 0,0625%, serta tidak terdapat reaksi silang antar DNA spesies pada pengujian spesifisitas. Metode qPCR dapat dijadikan sebagai metode pengujian untuk mengidentifikasi DNA spesies yang tidak dikehendaki pada pangan asal hewan yang beredar di masyarakat, khususnya terkait pemalsuan daging., There are many cases of fraud meat-based food products found in society. Meat substitution with an unsecured meat, usually of less quality, could have economic and health repercussions. Identification of species utilizing the multiplication of target DNA molecules in a single reaction can be carried out by real-time PCR. This research was aimed to validate the real-time polymerase chain reaction (qPCR) method for identifying buffalo DNA on animal food product. The qPCR method with SYBR green melting curve analysis was used as a validation test for the buffalo DNA. The validation parameters used in this study were repeatability, reproducibility, limit of detection, and specificity. The results showed that on repeatability validation parameters were 100% on positive and negative samples. The t test results on the Ct and Tm values of buffalo DNA reproducibility parameters showed that there was no significant difference in detecting buffalo DNA in two examination with using the qPCR method. The limit of detection (LOD) for buffalo using this method was 0,0625%, and there was no cross-reaction between DNA species in the specificity test. The qPCR method can be used as a testing method to identify the DNA of unwanted species in food of animal origin circulating in the community, especially related to meat adulteration.
Keyword: adulteration, buffalo, DNA, PCR, validation

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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