Judul: Utilization of enhanced random amplified polymorphic DNA (E-RAPD) for geneticc variability analysis on plantlets of smooth cayenne pineapple, Ananas comosus L. Merr.
Abstrak: Recently, RAPD markers have been widely used in speeding up and assisting practical plant breeding, crop improvement or plant characterization. RAPD is known as in-expensive and simple technique with a number of advantages: (1) universal set of oligonucleotide primers can be used for all plant species, (2) a large number of samples may be easily and rapidly characterized, (3) automatically process. However, RAPD those commonly use 10-base oligonucleotides of primers amplify target DNA sequences randomly and have low reproducibility. In this research, 11-base oligonucleotides of primers have been utilized as enhanced-RAPD (e-RAPD). Utilization of this e-RAPD has been evaluated on Smooth Cayenne pineapple plantlets obtained from tissue culture as target DNA materials. The e-RAPD has been expected increase specificity of DNA amplified products than RAPD's, result in easier to analyze and more reproducible. Beside of those, it has been expected amplifiable on this DNA genome of Smooth Cayenne pineapple plantlets and can be used to evaluate genetic variability among the plantlets. The DNA sample materials from plantlets of 20 combination treatments were isolated base on CTAB methods with some of modifications, and precipitated by phenol chloroform isoamyl alcohol. Primer 11-mers as enhancer of RAPD markers were selected on four single primers (SOB-1, SOB-2, SOB-3, and SOB-4) and its six combinations. Total volume of each amplification reaction was 25 μl which consisted of buffer 2.5 µl, MgCl 2 ul, dNTP 1 ul, primer 2 ul, DNA sample 1.5 ul. Taq polymerase 0.2 µl, and sterilized deionized water 15.8 µl. The PCR selected profile programmed pre-denaturation at 94 °C; 1.5", 45 cyles with each denaturation 94 °C; 0.5", annnealing 37 °C; 1', and elongation 72°C; 2", then final elongation at 72°C; 4. In evaluating the e-RAPD's products, the data of DNA amplified products on five treatment samples obtained from RAPD reaction of primer 10-mers (OPE-7) has been compared in analysis process. The e-RAPD results using four selected primers (SOB-1, SOB-1-2, SOB-2-3, SOB-3-4) has successfully amplified DNA genome of Smooth Cayenne pineapple plantlets. However it is not optimal yet. The best results of e-RAPD's Cabe obtained by precisely optimization of PCR program and the optimal concentration of all reaction reagents, such as optimization on the annealing temperature, the amount of DNA samples, and concentrations of dNTP, MgCl2, and Tag polymerase. The e-RAPD produced 57 total fragments which all 100% showed as polymorphic DNA. The dendogram clustering perform the high variability among all treatments. Treatment of BA 13.32 µM combined with NAA 2 µM show the shortest genetic distance to control treatment without exogenous hormones. This variability which refers to somaclonal variations may occur after tissue culturing. It can be caused of some posible factors, such as the using of exogenous hormones, subculture frequency, explant type, micropropagation system, and other technical defects.
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Judul: Genetic diversity analisis on pineapple (Ananas comosus (L.) Merr.) by random amplified polymrphic dna (RAPD)
Abstrak: Pineapple is belong to the Bromeliaceae, a large family of American tropics (only one species originated from Africa) which has 45 genera and 2 000 species. Out of six species of pineapple, Ananas comosus (L.) Merr. is the only species grown commercially for its fruit (Nakasone and Paull, 1998). To date, world cultivation just based on six cultivars, i.e., Cayenne, Queen, Singapore Spanish, Red Spanish, Abacaxi and Perolera, while the first three have been the genetic base of distribution from the original area. In Indonesia, cultivars that recommended by Department of Agriculture are only Queen (Bogor pineapple and Palembang pineapple) for fresh fruit and Cayenne (Smooth or Lisse) for processing uses and assumed to have low genetic variability. In this study, 17 accessions of pineapple (Ananas comosus (L.) Merr.) were evaluated for their morphological performance and subjected to analysis of Random Amplified Polymorphic DNA (RAPD). Eight morphological characters of the accessions were measured to examine their morphological relationship. For RAPD analysis, thirteen primers of 10-mers were used to amplify the genomic DNA of the pineapple accessions. Out of them, three random primers yielded monomorphic products while the remaining amplified a total of 20 (87%) fragments, all of which were polymorphic, with an average of 1.77 fragments per primer. A dendogram based on UPGMA-link method and principal component analysis (PCA) plots were examined the clustering pattern and distribution of the accessions, both for morphological characters and amplification products. As the result, RAPD analysis showed higher coefficient of similarity between pineapple accessions tested rather than morphological's, which may indicate the high environmental influence on the morphological performance. This study was demonstrated that RAPD analysis was able to detect genetic similarity among accessions in one species, eventhough among all primers used, there was no single primer could distinguish between Queen and Smooth Cayenne group of pineapple tested. ...
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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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