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: Functional Analysis of Mutant Genes in Hawara Bunar Rice through Sequence Comparison, Prediction of Protein Structure, and Gene Expression in Aluminum Stress
Abstrak: Mutasi gen pada padi mutan Hawara Bunar yang sensitif cekaman aluminium (Al) dapat memengaruhi stabilitas struktur dan fungsi protein, serta ekspresi gen responsif cekaman Al. Penelitian ini bertujuan menganalisis efek mutasi pada kandidat gen responsif cekaman Al terhadap stabilitas struktur dan fungsi protein, serta memvalidasi kandidat gen melalui analisis ekspresi gen menggunakan qRT-PCR. Identifikasi kandidat gen dilakukan dengan membandingkan sekuen DNA mutan Hawara Bunar dengan data transkriptom. Hasil penelitian menunjukan bahwa mutasi pada gen Os01g0699500, Os01g0699600, Os02g0807800, dan Os10g016284 dapat menurunkan stabilitas struktur protein. Seluruh gen, kecuali Os01g0699500, mengalami peningkatan ekspresi pada tanaman mutan yang diinduksi oleh cekaman Al dengan tingkat ekspresi relatif paling tinggi pada gen Os10g0162844. Hasil penelitian ini dapat mendukung penemuan gen-gen toleran Al untuk pengembangan varietas padi toleran cekaman Al., Gene mutation in Hawara Bunar mutant rice that is sensitive to aluminum (Al) can affect protein structure stability, protein function, and expression of Al-responsive gene candidates. The research aimed to analyze the effect of mutations on Al-tolerance gene candidates on the and structural stability and functional of the protein, and to validate the gene candidates by gene expression analysis using the qRT-PCR. Identification of Al-tolerance gene candidates was carried out by comparing DNA sequences of Hawara Bunar mutant with transcriptome data. The results showed that mutations in the sequence of Os01g0699500, Os01g0699600, Os02g0807800, and Os10g016284 genes could decrease protein structure stability. All genes, except Os01g0699500, increased their expression in the mutant after induced by Al stress with the highest relative expression level occured in Os10g0162844. The research can support the discovery of Al-tolerance genes that potential to develop Al-tolerant rice varieties
Keyword: aluminum, gene expression, Hawara Bunar, mutation, qRT-PCR

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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