Judul: Amplifikasi dan Karakterisasi In Silico Daerah Pengapit Ujung 5’ Gen APETALA1 Kakao (Theobroma cacao L.)
Abstrak: Cacao is one of important export comodities in Indonesia but its productivity is still in low category. The long juvenile phase is one of the cause of low productivity of cacao plantations. The effort to increase productivity drives on cacao studies of molecular flowering gene. In Arabidopsis, APETALA1 functions in earlier developmental stages in determination of the floral meristem identity and one of flowering identity genes that determines the formation of sepal and petal tissues. The purposes of the research are to amplify 5’-flanking regions APETALA1 gene from cacao (Theobroma cacao L.) and analyse its promoter characteristic. Amplification of 5’-flanking regions APETALA1 gene using Thermal Asymmetric Interlaced-PCR (TAIL-PCR) technique shows that spesific primer and arbitrary primer pairs can amplify the flanking region. Futhermore this fragment were transformed at competent cell E. Coli XL-1 Blue by using pGEMT Easy vector. The result of bioinformatic analysis using online promoter analysis software softberry shows undiscovered TATA box/enhancer on the amplified sequence and it contains 11 motifs of plant functional promoter element. Further analysis indicated that the amplified sequence belong to TATA-less promoter group with core motif microsatellite (CG)
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Judul: Isolasi dan Karakterisasi Promoter Gen AGAMOUS (TcAG) dari Kakao (Theobroma cacao L.)
Abstrak: Cocoa is one of the plantation commodities that is important to the national economy. Various efforts have been made to increase cocoa production. One such efforts in the field of genetic engineering discovery for the promoter of gene that has important role in flowering and fruiting. The aim of this research to isolate the promoter of reproductive gene AGAMOUS from Theobroma cacao L. (TcAG) using Thermal Asymmetric Interlaced Polymerase Chain Reaction (TAIL PCR) method and obtain the characteristics of the promoter using a computer program online Softberry. Technique of TAIL PCR using the reverse genespecific primers TcAG position +202 (TcAG+202) (5'- GGCCACGGCTAGAGAAGACAA-3') and position +67 (TcAG+67) (5’- ATCTCGATCTTTCCCCTTCCC-3'). Forward primer AP140 provided the best results are fragment genomic size of 1200 bp. Analysis of Transcription Start Site Prediction (TSSP) of softberry program from the 5' of the fragment has proven that it has three promoter regions. The regions which are nucleotide in position 126 (TATA box at position 93), nucleotide at position 735 (TATA box at position 702) and nucleotide at position 807 (TATA box at position 774). TATA box at position 774 is predicted to be the functional binding sites of RNA polymerase because it is in the position closest to the transcription start site.
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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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