Judul: Deteksi Virus Yang Menginfeksi Allium dan Beberapa Tanaman Hias Herba
Abstrak: Kelompok Allium (bawang putih, bawang merah, bawang bombai, bawang daun) dan tanaman hias herba merupakan komoditas hortikultura yang penting secara ekonomi dalam perdagangan internasional. Perdagangan komoditas ini sering kali dilakukan melalui umbi yang memiliki potensi besar terhadap munculnya penyakit baru di suatu negara, termasuk Indonesia. Potyvirus dan Carlavirus dilaporkan sebagai virus utama yang menginfeksi bawang. Tujuan dari penelitian ini adalah mendeteksi dan mengidentifikasi Carlavirus dan Potyvirus yang menginfeksi bawang dan tanaman hias herba yang berasal dari sampel lapangan dan umbi impor. Sampel bawang merah,bawang daun, dan tanaman hias herba diambil secara purposive sampling di beberapa lokasi. Sampel bawang putih merupakan umbi impor yang diperoleh dari Balai Besar Karantina Hewan, Ikan, dan Tumbuhan DKI Jakarta dan ditumbuhkan di laboratorium. Deteksi virus dilakukan dengan metode one-step reverse transcription polymerase chain reaction (RT-PCR) menggunakan primer universal, yaitu AlcarF/Poty1 untuk Carlavirus dan U341/Poty1 untuk Potyvirus. Hasil deteksi menunjukkan bahwa Carlavirus yaitu Shallot latent virus (SLV) ditemukan pada bawang merah, bawang putih, dan bawang daun serta Nerine latent virus (NeLV) pada Hippeastrum sp dan Hymenocallis speciosa. Onion yellow dwarf virus (OYDV), Shallot yellow stripe virus (SYSV), dan Amazon lily mosaic virus (ALiMV) anggota Potyvirus yang masing-masing ditemukan pada bawang merah, bawang putih, dan Hippeastrum sp. Deteksi NeLV dan ALiMV yang menginfeksi tanaman hias pada studi ini merupakan laporan pertama di Indonesia. Hasil dari penelitian ini dapat menjadi basis data bagi Badan Karantina Indonesia dalam melakukan upaya pencegahan masuk dan tersebarnya Organisme Pengganggu Tumbuhan Karantina., Alliums (garlic, onion, shallot) and herbaceous ornamental plants are economically important horticultural commodities in international trade. The trade of these commodities often through vegetative propagation that has big potential on new emerging diseases in a country, including Indonesia. Potyvirus and carlavirus are reported as the main viruses infecting allium. This research aims to detect and identify Carlavirus and Potyvirus infecting alliums and herbaceous ornamental plants. Garlic bulb samples were obtained from Indonesian Plant Quarantine Agency (BBKHIT DKI Jakarta) which were then grown in the laboratory. Samples of shallots, leeks, and ornamental plants were taken purposively in several locations. Virus detection was done by one step reverse transcription polymerase chain reaction (RT-PCR) method using universal primers, namely AlcarF/Poty1 for Carlavirus and U341/Poty1 for Potyvirus. Detection results showed that Carlavirus those are Shallot latent virus (SLV) was found in shallot, garlic, and leek, and Nerine latent virus (NeLV) in Hippeastrum sp. and Hymenocallis speciosa. Onion yellow dwarf virus (OYDV), Shallot yellow stripe virus (SYSV) and Amazon lily mosaic virus (ALiMV) are members of Potyvirus each found in shallot, garlic and Hippeastrum sp. The results of this study can be a basis data for Indonesian Plant Quarantine Agency to prevent the new emerging disease. For our knowledge, this is the first report of NeLV and AliMV infecting ornamental plants in Indonesia.
Keyword: ALiMV, Carlavirus, NeLV, Potyvirus, primer universal, Amaryllidaceae

Judul: Deteksi dan Distribusi Virus Bawang Putih pada Umbi Benih dan Konsumsi
Abstrak: Garlic is a horticultural commodity with high economic value. High consumption of garlic and low production of local garlic resulted in a lot of imported garlic in domestic market. One constraint in garlic production is virus infection which can be carried through vegetative propagation material (bulbs). The research was conducted to detect Garlic common latent virus (GCLV), Shallot latent virus (SLV), Onion yellow dwarf virus (OYDV), and Leek yellow stripe virus (LYSV) in local garlic bulbs used as seed bulbs and imported garlic bulbs used for consumption. Samples of local seed bulbs were collected from seed breeders in several garlic growing areas in Indonesia; while imported bulbs were collected from several local markets in Bogor. Morphological observations of each garlic bulb include skin color, neck hardness, and diameter size. The bulb samples were then grown in the laboratory, and the leaves were collected to be used as virus-detection material. Virus detection was conducted by RT-PCR (reverse transcription polymerase chain reaction) method using specific primers for each virus, namely GCLV-F/GCLV-R, GS-RT1/GS-RT2, OG-RT1/OG-RT2, and P-RT3/P-RT4, respectively for GCLV, SLV, OYDV, and LYSV. Seed and consumption bulbs have differences in their morphological characteristics, especially in the type of neck hardness and size of bulb diameter. OYDV and LYSV infections were successfully detected in seed and consumption bulbs; while SLV was only found in consumption bulbs and GCLV was only found in seed bulbs. Nucleotide sequence analysis showed that SLV from consumption bulbs formed one group, GCLV from seed bulbs formed one group, while OYDV and LYSV from seed and consumption bulbs were in different groups, indicating that the viruses came from different strains. Further research is needed to anticipate the spread of new garlic virus strains in Indonesia., Bawang putih merupakan komoditas hortikultura bernilai ekonomi tinggi. Konsumsi bawang putih yang tinggi dan rendahnya produksi bawang putih lokal mengakibatkan banyak bawang putih impor yang beredar di pasaran. Salah satu faktor kendala dalam produksi bawang putih adalah infeksi virus yang terbawa melalui bahan perbanyakan vegetatif (benih umbi). Penelitian dilakukan untuk mendeteksi Garlic common latent virus (GCLV), Shallot latent virus (SLV), Onion yellow dwarf virus (OYDV), dan Leek yellow stripe virus (LYSV) pada umbi bawang putih lokal yang digunakan sebagai umbi benih serta umbi bawang putih impor yang digunakan untuk konsumsi. Sampel umbi benih lokal dikumpulkan dari penangkar benih di beberapa sentra penanaman bawang putih di Indonesia; sementara umbi impor dikumpulkan dari beberapa pasar lokal di Bogor. Pengamatan morfologi dari masing-masing umbi bawang putih meliputi warna kulit umbi, kekerasan leher, dan ukuran diameter umbi. Sampel umbi kemudian ditumbuhkan di laboratorium, daun dikumpulkan untuk digunakan sebagai bahan deteksi virus. Deteksi virus dengan metode RT-PCR (reverse transcription polymerase chain reaction) menggunakan primer spesifik masing-masing virus, yaitu GCLV-F/GCLV-R, GS-RT1/GS-RT2, OG-RT1/OG-RT2 dan P-RT3/P-RT4, berturut-turut untuk GCLV, SLV, OYDV dan LYSV. Umbi benih dan umbi konsumsi memiliki perbedaan pada karakteristik morfologinya, terutama pada jenis kekerasan leher dan ukuran diamater umbi. Infeksi OYDV dan LYSV berhasil dideteksi dari umbi benih dan umbi konsumsi; sedangkan SLV hanya ditemukan pada umbi konsumsi dan GCLV hanya ditemukan pada umbi benih. Analisis sekuen nukleotida menunjukkan SLV dari umbi
Keyword: morphological characteristics, RT-PCR, sequence analysis, specific primers

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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