Judul: Functional Analysis of Mutated Genes in Hawara Bunar Mutant Rice through DNA Sequences Comparison, Protein Structure Prediction, and Gene Expression under Drought Stress Conditions
Abstrak: Perbedaan sekuen pada genom termutasi mempengaruhi regulasi gen dan tingkat toleransi tumbuhan terhadap cekaman kekeringan. Perbedaan sensitifitas diduga karena gen mengalami mutasi pada daerah fungsional dari genomnya. Penelitian ini bertujuan (1) mengidentifikasi kandidat gen-gen toleransi cekaman kekeringan melalui kombinasi identifikasi domain fungsional protein dan profil ekspresi transkriptom terkait kekeringan, (2) memvalidasi kandidat gen-gen terpilih melalui prediksi perubahan struktur protein dan analisis ekspresi gen melalui teknik qRT-PCR. Sekuen gen yang termutasi diintegrasikan dengan daftar gen umum yang mengalami perubahan ekspresi pada kondisi kekeringan melalui hasil meta-analisis transkriptom dan divalidasi dengan teknik qRT-PCR. Hasil penelitian menunjukan kandidat gen termutasi tidak terjadi perubahan fungsi protein meskipun terjadi perubahan beberapa asam amino. Gen Os01t0692100 mengalami peningkatan ekspresi, sedangkan gen Os01t0695700 dan Os10t0502400 mengalami penurunan ekspresi pada tanaman padi mutan sensitif cekaman kekeringan ketika mendapat cekaman kekeringan. Hasil penelitian ini dapat digunakan sebagai acuan dalam perakitan varietas tanaman padi toleran cekaman kekeringan., Sequence differences in the mutated genome affect gene regulation and plant tolerance levels to drought stress. This study aims (1) to identify candidate drought stress tolerance genes through a combination of identification of protein functional domains and drought-related transcriptome expression profiles and (2) to validate selected candidate genes by predicting changes in protein structure and analyzing gene expression through qRT-PCR techniques. The mutated gene sequences were integrated with a list of common genes that experienced changes in expression under drought conditions through transcriptome meta-analysis and validated by the qRT-PCR technique. The results showed that the mutated candidate gene did not change the protein function even though there was a change in several amino acids. The Os01t0692100 gene experienced an increase in expression, while the Os01t0695700 and Os10t0502400 genes experienced a decreased expression in drought-sensitive mutant rice plant under drought stress. The results of this study can be used as a reference of drought stress-tolerant rice varieties.
Keyword: gene regulation, Hawara Bunar, meta-analysis, mutation, qRT-PCR

Judul: Analisis Molekuler dan Fenotipe Galur Padi Transgenik IR64 Generasi T3 yang Mengandung Penanda Aktivasi untuk Toleransi Kekeringan
Abstrak: Activation tagging transgenic rice cv. IR64 had been developed by introducing a construct of activation tagging transposon Ac/Ds. Phenotipic character associated with drought stress tolerance of the transgenic rice lines have not been analyzed. This study aimed to evaluate T3 generation of activation tagging transgenic rice lines cv. IR64 to drought stress treatment. The methodology of study consisted of several steps including germination of samples seeds, screening the seedling with drought strees treatment, molecular analysis of the rice lines identify hpt and bar genes, and observation of agronomic character. Results of study showed that there were 34 out of 84 plants that tolerant to drought stress. A total of 23 plants of tolerant plants were detected carrying only bar gene after PCR analysis and indicated that the plants were stable mutants. Generaly, compared to the non-transgenic plants, there were changes in several agronomic parameters of transgenic rice plants cv. IR64 T3 generation. A total of nine plants increased of its height, six plants had a faster harvesting time, and 21 plants had higher weight of 100 seeds compared by non-transgenic plants.
Keyword: Bogor Agricultural University (IPB), drought stress tolerance, activation tagged, Rice (Oryza sativa L.)

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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