Judul: Identifikasi dan Variasi Sekuen Nukleotida Begomovirus Penyebab Penyakit Mosaik Kuning pada Beberapa Tanaman
Abstrak: Begomovirus is one of genera in the family Geminiviridae that has been reported globally to cause significant yield losses on crops production. Its infection causess typical symptoms, such as curling, yellow mosaic, and yellowing on the leaf. In Indonesia, yellow mosaic diseases associated with various Begomoviruses have been reported on chili pepper, yard long bean, cucumber and eggplant. Therefore, the aims of this study are (i) to detect Begomoviruses infecting chili pepper, yard long bean, cucumber, and eggplant and (ii) to analyze their genetic variation to determine the dynamics of Begomovirus development in Indonesia in the last ten years. Leaf samples were collected from infected plants (chili pepper, yard long bean, cucumber, and eggplant) in Bogor (West Java) and Brebes (Central Java). In addition, Begomovirus nucleic acid from the collection of Plant Virology Laboratory were used as comparison. These samples were isolated ten years ago from Bogor (West Java) and Magelang, Klaten, and Brebes (Central Java). Begomovirus detection was carried out by polymerase chain reaction (PCR) method using a universal primer pair (SPG1/SPG2) followed by nucleotide sequence analysis. DNA samples were successfully amplified from both field and laboratory samples. Three Begomovirus species were identified, i.e., Pepper yellow leaf curl Indonesia virus (PYLCIV) on chili pepper, Mungbean yellow mosaic India virus (MYMIV) on yard long bean and Tomato leaf curl New Delhi virus (ToLCNDV) on cucumber and eggplant. Phylogenetic tree analysis showed that all samples from the field and laboratory were grouped in one cluster. However, nucleotide base differences were found in each Begomovirus species. This finding indicates a change in the nucleotide sequence of the virus over a period of time., Begomovirus adalah salah satu genera dalam famili Geminiviridae yang telah dilaporkan secara global dapat menyebabkan kehilangan hasil yang nyata pada produksi tanaman. Gejala infeksi Begomovirus umumnya menimbulkan gejala khas, seperti keriting, mosaik kuning, dan daun menguning. Di Indonesia, penyakit mosaik kuning yang diasosiasikan dengan berbagai Begomovirus telah dilaporkan terjadi pada tanaman cabai, kacang panjang, mentimun, dan terung. Oleh karena itu, penelitian ini bertujuan untuk (i) mendeteksi Begomovirus yang menginfeksi tanaman cabai, kacang panjang, mentimun, dan terung, dan (ii) menganalisis variasi genetiknya untuk mengetahui dinamika perkembangan Begomovirus di Indonesia dalam sepuluh tahun terakhir. Sampel daun dikumpulkan dari tanaman yang terinfeksi (cabai, kacang panjang, mentimun, dan terung) di Bogor (Jawa Barat) dan Brebes (Jawa Tengah). Selain itu, sampel asam nukleat Begomovirus dari koleksi Laboratorium Virologi Tumbuhan digunakan sebagai pembanding. Sampel tersebut diisolasi sepuluh tahun yang lalu dari tanaman cabai, kacang panjang, mentimun, dan terung dari beberapa lokasi. Deteksi Begomovirus dilakukan dengan metode polymerase chain reaction (PCR) menggunakan pasangan primer universal (SPG1/SPG2) yang dilanjutkan dengan analisis sekuen nukleotida. Sampel DNA berhasil diamplifikasi dari sampel lapangan dan laboratorium. Tiga spesies Begomovirus berhasil diidentifikasi, yaitu Pepper yellow leaf curl Indonesia virus (PYLCIV) pada cabai, Mungbean yellow mosaic India virus (MYMIV) pada kacang panjang, dan Tomato leaf curl New Delhi virus (ToLCNDV) pada mentimun dan terung. Analisis pohon filogenetik menunjukkan bahwa semua sampel dari lapangan dan laboratorium mengelompok dalam satu klaster. Namun, perbedaan basa nukleotida ditemukan pada setiap spesies Begomovirus. Temuan ini mengindikasikan adanya perubahan sikuen nukleotida
Keyword: Geminiviridae, genetic diversity, PCR, phylogenetic analysis, universal  primer

Judul: Karakterisasi Begomovirus Penyebab Penyakit Daun Keriting pada Mentimun (Cucumis sativus L.)
Abstrak: Cucumber (Cucumis sativus L.) is an important vegetable crops in Indonesia. Productivity of cucumber affected by inefficient and ineffective cultural practices in addition to the problems with pests and diseases. One of important disease on cucumber that has the potential to effect the production is leaf curl disease caused by Begomovirus. Leaf curl diseases caused by Begomovirus has been reported on several crops in Indonesia and become a serious concern effecting yield loss. Tobacco plantation in East Java suffered 30% damage from infection of Tobacco leaf curl begomovirus in 1984. Since early 2000 infection of Pepper yellow leaf curl begomovirus on chillipepper has been reported in West and Central Java and disease management for this yellow disease on chillipepper has not been achieved successfully. Tomato yellow leaf curl begomovirus was also reported to cause epidemic on tomato plants in West and Central Java. Recently, leaf curl disease was observed in cucumber plants especially in Klaten, central Java. Similar disease was reported earlier since 1996, and virus identification showed that nucleotide sequence of the virus has high similarity with Tomato leaf curl New Delhi begomovirus (TLCV-New Delhi). Infection of Begomovirus on Cucurbitaceae has actually became problems in several countries, for instance Squash leaf curl begomovirus caused leaf curl disease on squash (Cucurbita maxima) and Watermelon curly mottle begomovirus caused yellow leaf and dwarfing on melon (C. melo) in United States. Begomovirus is only transmitted by whitefly (Bemisia tabaci) as its insect vector and whitefly is known to have a broad host range and capable to colonize a number of plants. Identification and characterization of Begomovirus causing leaf curl disease of cucumber in Java has not been done despite its importance. Studies on host range and transmission of Begomovirus is important in order to develop disease management strategy. The aims of this research is to detect viruses infecting cucumber plants, to identify Begomovirus infected cucumber, to study transmission efficiency of Begomovirus by vector B. tabaci, and to determine the host range. Field observation and samples collection was conducted in West Java (Bogor, Subang), Central Java (Tegal, Sukoharjo), and Yogyakarta (Sleman). Leaves showing typical symptoms of leaf curling, mosaic, blistering and yellowing were collected for further identification. Infection of Begomovirus, SqMV, ZyMV, and CMV was detected from all samples, but no infection of TRSV nor WMV was detected. Mix infection was found, for instance samples from Bogor and Sleman (Kalasan dan Ngemplak) were infected by 4 viruses (Begomovirus, SqMV, ZyMV, dan CMV) and showed more severe symptoms i.e. leaf curling, mosaic, yellowing and blistering. Nucleotide sequences obtained from sequencing of DNA fragments as the amplicon using polymerase chain reaction (PCR) method ranging from 1474 to 1633 bp for TEGAL, KALASAN, NGEMPLAK, SUKOHARJO, and BOGOR isolates. Begomovirus genome amplified using universal primer pAL1v1978/pAR1c715 covers part of replication gene, coat protein gene and common region which is the region of the genome commonly used for identification of Begomovirus. Sequence homology among the five isolates ranging from 96.1% to 99.3%, indicated close relationship. BOGOR isolate showed different symptoms from other isolates and its relationship is not as close
Keyword: Efficiency of transmission, Geminivirus, host range, insect vector, sequence analysis

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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