Judul: Genotypes Response and Resistance Induction of Phalaenopsis against Soft-Rot Pathogen (Dickeya dadantii)
Abstrak: Phalaenopsis merupakan salah satu genus anggrek yang terkenal dengan keragaman warna, bentuk, dan ukuran bunga yang tinggi. Hibridisasi Phalaenopsis telah dikembangkan secara intensif, menghasilkan > 100.000 varietas secara global. Tanaman dari genus ini digunakan sebagai tanaman hias pot karena keragaman varietas dan umur bunga yang panjang. Salah satu masalah paling kritis dalam budidaya Phalaenopsis adalah penyakit busuk lunak (SRD). Infeksi SRD muncul pada daun berupa bercak kecoklatan, busuk, dan tembus cahaya. SRD mungkin disebabkan oleh patogen dari genus Enterobacter. Identifikasi spesies yang dapat menjadi sumber ketahanan terhadap SRD dan pemahaman mekanisme yang terlibat merupakan langkah penting untuk efisiensi dalam pemuliaan Phalaenopsis. Penelitian ini bertujuan untuk mengidentifikasi spesies Phalaenopsis yang mungkin menunjukkan ketahanan terhadap patogen SRD dan mekanisme ketahanannya. Spesies yang tahan dapat digunakan lebih lanjut untuk tetua dalam persilangan Phalaenopsis. Pemahaman tentang mekanisme ketahanan di tingkat biokimia dan molekuler akan memberikan informasi dasar dalam pengembangan ketahanan tanaman terhadap SRD. Penelitian ini terdiri dari dua bagian. Pertama, karakterisasi molekuler patogen SRD dengan sekuensing gen marker 16S rRNA, karakterisasi fisik dan anatomi beberapa karakter daun spesies Phalaenopsis, dan pengujian respon ketahanan delapan spesies Phalaenopsis terhadap patogen busuk lunak. Isolat bakteri yang digunakan dalam percobaan ini dipastikan adalah Dickeya dadantii dengan 98.37% identitasnya sesuai dengan Erwinia spp. di NCBI. Hasil pengamatan karakteristik daun menunjukan ketebalan daun dan kadar air tidak berbeda, tetapi kerapatan stomata berbeda nyata diantara spesies yang diuji. P. bellina menunjukkan kepadatan stomata tertinggi di antara spesies yang diamati. Pengujian respon ketahanan spesies Phalaenopsis terhadap D. dadantii menggunakan metode detached leaf. Diameter gejala busuk lunak diamati pada jam 6, 12, dan 18 jam pasca inokulasi (JSI). Keparahan penyakit (KP) dan progres perkembangan penyakit (AUDPC) dihitung dari diameter gejala SRD. Populasi bakteri (CFU) dihitung menggunakan sampel daun di sekitar gejala busuk lunak pada 18 JSI. Hasil penelitian menunjukkan bahwa spesies yang paling tahan adalah P. amboinensis pada 18 JSI dengan KP sebesar 28% dibandingkan spesies lain yang menunjukkan KP ≥50%. Jenis yang paling rentan adalah P. amabilis, P. fimbriata, dan P. cornu-cervi. Jumlah CFU dan AUPDC pada P. amboinensis lebih rendah (5x104 CFUmg-1) dibandingkan pada spesies lain (≥3x105 CFUmg-1). Aktifitas pathogen-related enzymes meliputi Fenilalanin amonia-lyase (PAL) dan peroksidase (PRX) diamati pada dua waktu yang berbeda. Pengamatan pada 12 JSI menunjukkan bahwa P. pantherina dan P. amboinensis memiliki PAL (masing-masing 0.95 dan 1.20 u min-1mg protein-1 x 104) dan PRX (masing-masing 0.77 dan 0.21 u min-1mg protein-1 x 104). Aktivitas PAL (masing-masing 13.75 dan 13.41 u min-1mg protein-1 x 104) dan PRX (masing-masing 7.25 dan 8.73 u min-1mg protein-1 x 104) lebih rendah pada P. schilleriana dan P. amabilis. Tren serupa juga ditemukan pada 16 JSI. Analisis asam salisilat (SA) menunjukkan akumulasi SA yang lebih rendah pada spesies yang paling tahan (P. amboinensis) dibandingkan dengan spesies yang paling rentan (P. amabilis). Hasil saat ini menunjukkan bahwa mekanisme ketahanan P. amboinensis mungkin tidak bergantung pada jalur PAL, PRX dan SA. Namun, penelitian lebih lanjut diperlukan untuk mengkonfirmasi temuan ini. Bagian kedua penelitian ini bertujuan untuk mengevaluasi respon ketahanan genotipe Phalaenopsis terhadap D. dadantii setelah perlakuan SA sebagai penginduksi ketahanan potensial. Bagian ini terdiri dari tiga percobaan.
Keyword: colony-forming unit, disease severity, peroxidase, phenylalanine ammonia-lyase, salicylic acid

Judul: Biochemical and Transcriptomic Analyses in Phalaenopsis Response to Soft-Rot Disease Pathogen (Dickeya dadantii)
Abstrak: Phalaenopsis orchid is one of the orchid genera with high ornamental and economic value. Soft-rot disease (SRD) is a devastating disease in Phalaenopsis orchid caused by the necrotrophic pathogens, Dickeya dadantii. Evaluations of several Phalaenopsis species for their response to D. dadantii infection reveal that P. amboinensis is the most resistant, while P. amabilis is a very susceptible species. Resistant species information related to biochemical and molecular response under pathogen infection is essential in providing resistant parents to conduct conventional and molecular breeding programs of Phalaenopsis. Resistant species can be used as the parent in cross-breeding, while the biochemical and molecular mechanism of plant resistance can be used to develop biochemical and molecular markers for selecting resistant progenies. The main purpose of the research is to identify the intraspecies variation response of P. amboinensis and P. amabilis to SRD pathogens and analyze the possible resistance mechanism through a biochemical and transcriptomic approach. The research is provided on three topics. The first topic aims to evaluate intraspecies resistant variation in the P. amboinensis and P. amabilis wild populations and identify the plants that show resistance or susceptible responses to D. dadantii consistently to be used as breeding materials and resistant mechanism study in further experiments. The second topic was aimed to study the possible role of Phenylalanine ammonia-lyase (PAL), Peroxidase (POD), salicylic acid (SA) and jasmonic acid (JA) in the susceptible or resistance response of P. amboinensis and P. amboinensis to D. dadantii infection and its potential for biochemical markers for resistance to SRD. In the third topic, transcriptomic analyses based on the RNA sequencing approach were performed in P. amboinensis as a prospective resistant parent to predict the molecular plant response to D. dadantii infection and the potential genes and molecular mechanism involved in resistant species. The research results show the intraspecies variation of P. amboinensis and P. amabilis wild populations in their response to D. dadantii infection. The responses of 47 P. amboinensis and 29 P. amabilis individuals were tested against D. dadantii using the detached leaf inoculation method. Soft-rot symptom diameter was measured at 6 to 42 hours post-inoculation (HPI) for disease assessment, including disease symptom diameter, disease severity, and resistance level to D. dadantii. Of 47 plants of P. amboinensis, 2.13% are very susceptible, 2.12% are susceptible, 4.25% are moderate resistant, and 91.49% are resistant, while in P. amabilis, 20.69% are very susceptible, 3.45% are susceptible, 13.78% are moderate susceptible, and 62.08% are resistant. SRD-resistance trait in P. amboinensis is more stable compared to the P. amabilis. The selected resistant plants of P. amboinensis and very susceptible plants of P. amabilis were used for the second and third topics of the dissertation. The second topic of the research was predicting the biochemical defense (defense-related enzymes, PAL and POD, and signal transduction hormones (SA and JA) that may be involved in Phalaenopsis resistance mechanisms to SRD pathogen. The endogenous PAL, POD, SA and JA were measured under mock and D. dadantii inoculation on P. amboinensis and P. amabilis. The results showed that PAL and POD activities were higher in P.
Keyword: orchid, resistance mechanisms, RNA sequencing, species

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.
Keyword: