Judul: Primer Design for Detection Dickeya spp. and Pectobacterium spp. in Potato with Multiplex PCR
Abstrak: Potato (Solanum tuberosum L.) is an important horticultural crop both on industrial need and household consumption. The high demand of potatoes is fulfilled by importation. The importation of potatoes carried out by the Indonesian government has a potential threat such as pathogens from outside that do not yet exist in Indonesia or OPTK A1. There are several OPTK A1 potatoes, Dickeya dadantii, Dickeya solani, Dickeya zeae, Pectobacterium atrosepticum and Pectobacterium wasabiae. This research aims to design multiplex PCR primers associated with OPTK A1 in Dickeya spp. and Pectobacterium spp.. The research was carried out by conducting scientific research in stages including 16S rRNA homology analysis, pelI and maeA gene homology analysis, pelI and maeA gene polymorphism analysis, primers design, and secondary primer structure analysis. Five pairs of primary candidates match to the criteria. Five pairs candidate primers were successfully designed for detection of Dickeya spp. and Pectobacterium spp. respectively: WD2F 5'-agccagttccgagtgtaagc-3' and WD2R 5'-ggtttctgcttgtcgctgtc-3' (D. dadantii); JD1F 5'-tgaacgcatcgccgtact-3' and JD1R 5'-gccaacgatggtgagggtt-3' (D. zeae); FA2F 5'-cgtcattagccgcccaaac-3' and FA2R 5'-gcagttgccgctttcacag-3' (D. solani); SA2F 5'-ggtgccctgaatgtcatcg-3' and SA2R 5'-cgtctgaacgatccgctgta-3' (P. atrosepticum); GI1F 5'-cgggttagacagtggcatca-3' and GI1R 5'-cgtcgcacagatgaaatccg-3' (P. wasabiae). Five primers candidate have primer lengths from 18 to 21 Mer, Tm values from 59.57 to 60.39 ˚C, % GC from 55% to 57% and do not have any potential secondary structure. Furthermore, each primer candidate generates 108, 445, 500, 213, and 316 bp amplicons. These candidate primers have the potential to be used in multiplex PCR detection and need further in vitro testing to prove the effectiveness., Kentang (Solanum tuberosum L.) merupakan tanaman hortikultura yang dibutuhkan baik dalam skala industri maupun skala rumah tangga, tetapi pemenuhan kebutuhan kentang nasional pemerintah Indonesia masih melakukan importasi. Importasi kentang yang dilakukan oleh pemerintah Indonesia memiliki potensi ancaman masuknya patogen dari luar yang belum ada di Indonesia atau OPTK (Organisme Penganggu Tanaman Karantina) A1 . OPTK A1 kentang diantaranya yaitu, Dickeya dadantii, Dickeya solani, Dickeya zeae, Pectobacterium atrosepticum dan Pectobacterium wasabiae. Penelitian ini bertujuan mendapatkan rancangan primer untuk mendeteksi Dickeya spp. dan Pectobacterium spp. pada kentang dengan multiplex PCR. Penelitian melalui beberapa tahapan yaitu analisis homologi 16S rRNA, analisis homologi gen pelI dan maeA, analisis polimorfisme sekuen gen pelI dan maeA, perancangan primer, dan analisis struktur sekunder. Lima pasang primer didapatkan sesuai dengan kriteria untuk digunakan dalam deteksi menggunakan teknik multiplex PCR. Lima pasang primer yang berhasil dirancang untuk deteksi Dickeya spp. dan Pectobacterium spp. diantaranya yaitu WD2F 5'-agccagttccgagtgtaagc-3' and WD2R 5'-ggtttctgcttgtcgctgtc-3' (D. dadantii); JD1F 5'-tgaacgcatcgccgtact-3' and JD1R 5'-gccaacgatggtgagggtt-3' (D. zeae); FA2F 5'-cgtcattagccgcccaaac-3' and FA2R 5'-gcagttgccgctttcacag-3' (D. solani); SA2F 5'-ggtgccctgaatgtcatcg-3' and SA2R 5'-cgtctgaacgatccgctgta-3' (P. atrosepticum); GI1F 5'-cgggttagacagtggcatca-3' and GI1R 5'-cgtcgcacagatgaaatccg-3' (P. wasabiae). Lima kandidat primer memiliki panjang primer 18 hingga 21 mer, nilai Tm berkisar 59,57-60,39 ˚C, %GC berkisar 55%-57%, dan tidak ditemukan nilai energi bebas gibs lebih dari -9 kcal/mol. Masing-masing kandidat primer menghasilkan amplikon sebesar 108, 445, 500, 213, dan 316 bp. Lima kandidat primer merupakan primer spesifik. Kandidat primer tersebut memiliki potensi untuk digunakan dalam deteksi dengan multiplex PCR dan perlu pengujian lebih lanjut secara in vitro untuk membuktikan keefektifannya.
Keyword: multiplex pcr, optk a1, potato, primer design

Judul: Genetic Engineering of Potato (Solanum tuberosum L.) cv IPB CP1 with LYZ-C Gene to Control Bacterial Wilt Disease
Abstrak: Kentang (Solanum tuberosum L.) merupakan salah satu tanaman pangan pokok penting selain padi, gandum dan jagung serta menempati urutan ketiga berdasarkan tingkat konsumsi secara global. Kentang kultivar IPB CP1 merupakan kultivar yang dikembangkan dari mutasi kentang kultivar Atlantik dan memiliki karakteristik umbi yang sesuai sebagai olahan keripik kentang (potato chips). Infeksi penyakit layu bakteri yang disebabkan oleh bakteri Ralstonia solanacearum menjadi salah satu kendala dalam budidaya tanaman kentang di Indonesia. Infeksi bakteri patogen tersebut pada tanaman dapat berdampak serius terhadap kehilangan hasil panen. Perakitan tanaman kentang yang resisten terhadap penyakit bakteri dapat dilakukan melalui rekayasa genetik. Lisozim merupakan enzim-enzim glikosida yang dapat mengkatalisis pemutusan ikatan antara molekul N-asetil-D-glukosamin (NAG) dan asam N-asetil-D-muramat (NAM) sebagai penyusun peptidoglikan pada dinding sel bakteri. Ekspresi gen LYZ-C penyandi lisozim pada tanaman dapat meningkatkan resistensi tanaman terhadap infeksi bakteri patogen. Agrobacterium tumefaciens strain LBA4404 yang mengandung plasmid pCXSN-Lys(+) digunakan untuk mengintroduksikan gen LYZ-C ke dalam genom tanaman kentang kultivar IPB CP1. Tranformasi genetik pada kentang kultivar IPB CP1 terhadap 200 eksplan ruas batang telah berhasil dilakukan. Pembentukan kalus dan regenerasi kalus menjadi tunas berhasil diinduksi pada media MS yang mengandung IAA 1 mg/l, trans-zeatin 3 mg/l dan GA3 0,5 mg/l. Pada penelitian ini efisiensi transformasi dan efisiensi regenerasi yang diperoleh sebesar 35,1% dan 54,7%. Hasil analisis PCR menggunakan primer Lys114-F dan Nost2-R terhadap 10 tanaman transgenik putatif menunjukkan 6 tanaman mengandung transgen LYZ-C yang ditandai dengan adanya amplikon berukuran 565 pb. Uji resistensi secara in vitro pada 4 klon tanaman transgenik dan 1 tanaman non-transgenik, menunjukkan bahwa klon tanaman transgenik memiliki resistensi yang lebih baik terhadap infeksi R. solanacearum penyebab layu bakteri dibandingkan dengan tanaman CP1 non-transgenik. Hal ini menunjukkan bahwa gen LYZ-C yang diintroduksikan ke dalam tanaman kentang kultivar IPB CP1 meningkatkan resistensi tanaman terhadap penyakit layu bakteri. Pada penelitian ini klon CP1L3 merupakan tanaman transgenik yang paling resisten terhadap R. solanacearum dan memiliki nilai indeks penyakit terendah., Potato (Solanum tuberosum L.) is the most important crops besides rice, wheat, corns and includes in the third world crop plants in terms of global consumption. IPB CP1 cultivar is a derivative of radiated Atlantic cultivar and produce suitable tuber characteristics for potato chips. In Indonesia, bacterial wilt infection caused by Ralstonia solanacearum is one of the problems in potato cultivation. Infection of this patohegen has a serious effect to the yield losses. Assembly of transgenic potato resistant to bacterial wilt could be realize through genetic engineering. Lysozyme belongs to the glycoside enzymes that catalyze the cleavage of peptidoglican components of bacterial cell wall. LYZ-C gene expression can enhance the plant resistance against pathogenic bacteria. Agrobacterium tumefaciens strain LBA4404 harboring the pCXSN-Lys(+) used to introduces LYZ-C gene into the plant genome. Genetic transformation of IPB CP1 cultivar by using 200 internodes as the explants was done successfully. Callus formation and regeneration were induced successfully on MS medium containing IAA 1 mg/l, trans-zeatin 3 mg/l dan GA3 0,5 mg/l. In this study, the transformation efficiency and regeneration efficiency were 35,1% and 54,7%, respectively. Based on PCR analysis to 10 putative transgenic plants with Lys114-F and Nost2-R primers, confirmed that
Keyword: Agrobacterium tumefaciens, gen LYZ-C, kentang kultivar IPB CP1, penyakit layu bakteri, transformasi genetik

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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