Judul: Primer Design and Optimisation of Pongo pygmaeus CFTR Gene: Eight High Mutation Exon (Range No. 1-11)
Abstrak: Orangutans are known to have respiratory diseases similar to cystic fibrosis symptoms in humans. Cystic fibrosis is a respiratory disease caused by mutations in the cystic fibrosis transmembrane regulator gene (CFTR). Research on the CFTR gene in Bornean orangutans is still rarely done. Therefore, this study will detect the CFTR gene mutation of the Bornean orangutan samples from the BOSF rehabilitation centre. This study aimed to design specific primers for the CFTR gene in several predefined gene exons with the densest mutation and to obtain the optimal annealing temperature for each primer. We used UGENE version 40.1 for manual primers design. Optimisation of PCR amplification program and primer annealing temperature was determined with pre-denaturation at 94 °C, denaturation at 95 °C, different annealing temperatures for each primer, and final extension at 72 °C. The optimum condition for annealing temperatures of designed specific primers for exons 3, 4, 6, 8, and 11 of the orangutan CFTR gene was at 51-58 °C. Primer can amplify the exon and intron regions flanking the target exon.
Keyword: Bornean orangutan, cystic fibrosis, PCR, primer design

Judul: Desain dan Optimasi Primer Gen CFTR Pongo pygmaeus: Lima Ekson dengan Mutasi Tertinggi (Rentang 12−27)
Abstrak: Respiratory disease is one of the leading causes of captive orangutan mortality. Some symptoms resemble cystic fibrosis caused by mutations in the CFTR gene. One study identified mutations that may cause cystic fibrosis-like disease in orangutans. Only several pieces of research focused on respiratory diseases in orangutans involve genetic analysis. Therefore, this study aims to design an effective primer for the Bornean orangutan CFTR gene amplification. This study tested reference primers for six exons with the densest mutation using UCSC PCR in-silico. Primers with no result in PCR in silico were re-designed manually using UGENE and measured via OligoAnalyzer™ Tool. Primer optimisation was conducted using Bornean orangutan DNA blood samples. The sequence result was further analysed using the BLAST-N program to confirm the effectiveness of the primers. Seven sets of primers for exons 12, 14, 17, 20, and 23 of the Bornean orangutan CFTR gene were designed with decent parameter quality. The primers amplified the intended exon along with several bases of the flanking intron.
Keyword: Bornean orangutan, captivity, cystic fibrosis, respiratory disease

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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