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: Isolasi Promotor Gen LFY pada Tanaman Theobroma cacao L. dengan Teknik Genome WalkingTM
Abstrak: Cacao is one of the main agricultural commodities in Indonesia. Unfortunately, there are many obstacles faced by Indonesian cacao farmers, which results in the low cacao productivity. A major obstacle is the cherelle wilt disease. This disease is affected by the central flowering gene (gene LFY), whose expression level is regulated by its promoter. The objective of this research is to isolate the promoter of gene LFY, to then be cloned into its cloning and expression vectors. The promoter isolation was done from a young cacao leaf. The DNA in the leaf was extracted first, and then the promoter was isolated using Genome WalkingTM technique. Subsequently, the sequencing method and Softberry software were utilized to determine the promoter’s nucleotides. The result, which was then confirmed by TATA box, proved the existence of gene LFY promoter fragment. A fragment of 1650 bp size was then cloned into cloning and expression vectors: pGEM-T Easy and pCambia 1303. Next, the plasmid of the recombinant DNA was transformed into Agrobacterium tumefaciens using the AGLO strain. The conclusion of this research is that the gene LFY promoter of Theobroma cacao L. can be isolated using the Genome WalkingTM method, enabling more information on the occurence of cherelle wilt on cacao plants.
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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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