Judul: Tungro Disease in Indonesia: detection, genetic variability, and suitability map of tungro resistant varieties
Abstrak: Penyakit tungro, yang disebabkan oleh infeksi Rice tungro bacilliform virus (RTBV) dan Rice tungro spherical virus (RTSV), masih merupakan salah satu penyakit penting pada tanaman padi di Indonesia. Selain itu, penyakit yang ditularkan oleh wereng hijau secara semipersisten ini masih menjadi salah satu faktor pembatas peningkatan produksi. Kerugian yang diakibatkan oleh penyakit ini pada stadia awal pertumbuhan padi mampu menyebabkan kehilangan hasil hingga 90%, dan tak jarang menyebabkan tanaman menjadi puso. Hingga saat ini penyakit tungro dilaporkan telah menyerang pertanaman padi di 27 propinsi dengan luas serangan penyakit selama tahun 2012 mencapai 6441 ha dan puso 151 ha. Penggunaan varietas tahan merupakan salah satu teknik pengendalian yang efektif. Namun kurangnya jumlah varietas tahan tungro spesifik lokasi yang sesuai dengan preferensi petani, menyebabkan aplikasi di lapangan agak sulit dilakukan. Selain itu, informasi keragaman genetika virus tungro, khususnya isolat Indonesia, masih sangat terbatas. Berdasarkan hal tersebut perlu dipelajari faktorfaktor yang memengaruhi keberadaan penyakit tungro di lapangan, dan informasi mengenai keragaman genetika virus tungro yang sangat penting dalam pengembangan strategi pengendalian virus tungro. Pengembangan teknik deteksi cepat dan akurat perlu dilakukan untuk memudahkan pengambilan keputusan pengendalian penyakit di lapangan. Survei yang dilakukan di beberapa lokasi pertanaman padi di Indonesia menunjukkan bahwa penyakit tungro masih menjadi penyakit penting. Penyakit tungro telah meluas terutama di sentra produksi padi. Penyebaran virus tungro sangat bergantung pada jenis varietas yang dibudidayakan, pola tanam, keberadaan serangga vektor dan sumber inokulum, serta pengelolaan budidaya tanaman padi. Hasil survei menunjukkan spesies gulma yang ditemukan di sekitar persawahan di beberapa lokasi di Jawa Barat, Bali, Nusa Tenggara Barat, Sulawesi Selatan, Sulawesi Barat, Sulawesi Utara, dan Sumatera Selatan berperan menjadi inang alternatif virus tungro. Infeksi RTBV berhasil dideteksi dari enam spesies gulma (F miliacea, C. iria, M vagina/is, L. octovalvis, S. zeylanica, D. sanguinalis, dan E. crusgalli), dan infeksi RTSV berhasil dideteksi dari tiga spesies gulma (F miliacea, L. octovalvis, dan D. sanguinalis). Sanitasi gulma sebelum bertanam padi dinilai sebagai tindakan yang diperlukan dalam pengendalian penyakit tungro., Tungro disease, caused by double infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV), is still considered as an important rice disease in Indonesia. Rice production is affected by this disease, yield loss caused by infection of this viruses in the early stages ofrice growth may even reach 90%. Disease spread is dependent on its insect vector, green leafhopper, by semipersistent manner. Distribution of this disease in Indonesia is reported from 27 provinces with affected area of 6441 ha and 151 hapuso in 2012. The use of resistant varieties is one of the effective management techniques. However, the number of site-specific tungro resistant varieties that suitable with the farmer preferences still limited, so applications in the field is rather difficult to do. In addition, knowledge on genetic variability of tungro virus in Indonesia is very limited. Therefore, it becomes necessary to study all factors influencing the incidence of tungro virus in the field, and information on genetic variability of tungro virus in order to develop disease management strategy. Improvement on detection method of tungro virus also required to assist controlling the disease. Tungro disease
Keyword: Full length genome, LAMP PCR, Rice tungro virus, Strategy of management, Weeds, Rice Production, Disease Management, Tungro virus, virus detection, Serelogical Methods, Weed Species, Virus Inoculum

Judul: Diversity of coat protein gene of rice tungro bacilliform tungrovirus (RTBV) and rice grassy stunt tenuivirus (RGSV) isolates from several districts in Java Island
Abstrak: Indonesia is the largest consumer of rice in the world. International Rice Research Institute (IRRI) estimated that Indonesia may require an increase in rice production for the next 25 years. Among many constrains in rice production increement is plant diseases including tungro and grassy stunt diseases. Tungro disease is caused by infection of two viruses, Rice tungro bacilliform tungrovirus (RTBV) and Rice tungro spherical waikavirus (RTSV). These viruses are transmitted by the rice leaf hopper vectors which mainly is green leafhoppers (Nephotettix virescens). RTBV is a determinant of the disease symptoms eventhough it could not infect rice without the presence of RTSV. Infected plants showed typical tungro symptoms involving stunting, yellow or orange-yellow discoloration of the leaves, reduced number of tillers and rust-colored spots on the leaves. In 2006 a new symptoms was found in paddy crop in Indonesia, i.e. yellow-orange discoloration of the leaves, reduced number of tillers without any reduction in plant height. It was reported that the disease is caused by infection of Rice grassy stunt tenuivirus (RGSV) the cause of grassy stunt disease. Symptoms similarity of tungro and RGSV infection may cause difficulty in disease diagnosis and cause confusion in determining diseases control strategies. Therefore research on symptoms and genetic diversity of RTBV and RGSV is necessary to determine the appropriate control strategy. The genetic diversity of RTBV isolates from South Asia and Southeast Asia as well as from some tungro endemic area in Indonesia based on the symptoms variation and diversity of coat protein gene have been reported. The genetic diversity of the isolates RGSV from two areas in Taiwan and Philippines based on symptoms variation have also been reported. Genetic and symptoms diversity of RTBV and RGSV could be analysed through the diversity of coat protein gene. Coat protein gene is known as a determinant factor of infection, virulence, and symptoms induction. The research is conducted to study the diversity of symptoms and coat protein gene of RTBV and RGSV from several districts in Java. The areas in Bogor, Subang, Pandeglang, Klaten, Batang, Sleman, Jember and Banyuwangi were selected as disease survey location because these regions were reported as endemic areas for tungro disease and brown leafhopper. The study includes three main activities, i.e. observation of symptoms in the field and sampling of infected plants, detection of RTBV and RGSV, and analysis of diversity of coat protein gene of RTBV and RGSV. Most infected plants in the fields showed tungro-like symptoms. Two variations of symptoms can be classified by the number of tillers and plant height. These symptoms variations can be caused by RTBV or RGSV infection or mix infection of RTBV and RGSV as indicated by detection results using PCR. Identification of total 64 samples showed infection of RTBV in 13 samples, RGSV in 36 samples and mix of RTBV and RGSV in 2 samples. The results showed that tungro-like symptoms were positive from infection of RGSV. Therefore identification of diseases based only on symptoms are not sufficient. The whole coat protein gene of RTBV was amplified using DA-F and DA-R primers with the amplicon
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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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