Judul: EGFR and KRAS Genes Mutation Analysis Based on PCR-HRM (High Resolution Melting) and RFLP (Restriction Fragment Length Polymorphisme) of Pleural Liquid from Lung Cancer Patients that Collected at Filter Paper
Abstrak: Lung cancer is the most frequent cause of cancer-related mortality worldwide, including in Indonesia. Today, a medical treatment for lung cancer patient, such as targeted therapies, has been developed to decrease the mortality. The methods need a rapid and a robust molecular characterisation technique to diagnose any gene mutations such as the KRAS and the EGFR. We developed a PCR-HRM and a PCR-RFLP for screening the EGFR and the KRAS mutations in pleural effusion of lung cancer patients. Sensitivity studies using the dilution assay revealed that the PCR-HRM was able to detect KRAS and EGFR mutations as little as 12.5% of mutant DNA in wild type DNA, while the PCR-RPLF was able to detect as little as 3.125 % of DNA mutant in wild type DNA. We analysed 63 of pleural effusion from lung cancer patient that were collected in filter paper. From our sample, we found that 1.6% (1/63) of them had the KRAS mutation; meanwhile 15.9 % (10/63) of them had the EGFR mutations. We also found that the EGFR mutation was more prevalent in men 21.43% (6/28) compared to women 15.3% (4/26). These results showed that the HRM and the RFLP are useful methods to detect the KRAS and the EGFR mutations in the clinical samples of lung cancer. The filter paper was also very potential material to be used in molecular analysis of lung cancer, especially for collecting and transferring the pleural effusion samples.
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Judul: Virtual screening of Ligands with Epidermal Growth Factor Receptor Protein as Candidate Targeted Therapy for Lung Cancer
Abstrak: Salah satu cara pengobatan kanker paru-paru yaitu melalui metode terapi target dengan mekanisme pemberian obat ke molekul spesifik yaitu sel kanker. Penelitian ini dimaksudkan untuk menemukan kandidat obat terapi kanker paru- paru melalui metode komputasi dengan melihat nilai energi afinitas dan pengujian toksisitasnya. Sebanyak 250 struktur EGFR (tipe wildtype dan mutasi) sebagai protein target akan dilakukan virtual screening dan penambatan molekul dengan ligan dari database zinc20 sejumlah 131.328 ligan. Hasil dari virtual screening tersebut didapatkan delapan belas struktur ligan terbaik yaitu tujuh ligan yang berinteraksi dengan struktur EGFR tipe wildtype dengan nilai energi afinitasnya sebesar -9,76 kcal/mol hingga -9,32 kcal/mol. Sebanyak sebelas ligan yang berinteraksi dengan struktur mutasi dengan nilai energi afinitas -9,11 kcal/mol hingga -8,08 kcal/mol. Terdapat lima ligan yang berinteraksi dengan baik di struktur wildtype dan mutasi yaitu ligan dengan rumus kimia C24H16F2N2O4, C20H13F2N5O4,C23H27N5O4,C19H21N5O4S2, dan C22H26ClN5O2. Struktur reseptor dari protein EGFR yang paling banyak berikatan dengan ligan terbaik adalah struktur dengan kode 3W33,3W2S, dan 4LI5. Jenis asam amino yang sama pada struktur wildtype dan mutasi yang muncul yaitu pada ikatan hidrofobik adalah Asp855 dan pada ikatan hidrogen adalah Val726 dan Leu718., One of the treatments for lung cancer is through targeted therapy, which involves the administration of drugs to specific molecules, namely cancer cells. This research aims to discover potential lung cancer therapy candidates through computational methods by examining the affinity energy values and conducting toxicity testing. A total of 250 EGFR structures (wildtype and mutations) as target proteins will undergo virtual screening and molecular docking with ligands from the zinc20 database, consisting of 131.328 ligands. The results of the virtual screening identified eighteen top ligand structures, including seven ligands that interacted with the wildtype EGFR structure with affinity energy values ranging from -9,76 kcal/mol to -9,32 kcal/mol. Eleven ligands interacted with the mutation structure with affinity energy values from -9,11 kcal/mol to -8,08 kcal/mol. Five ligands showed good interaction with both wildtype and mutation structures, namely C24H16F2N2O4,C20H13F2N5O4,C23H27N5O4, C19H21N5O4S2, and C22H26ClN5O. As for the receptor structure of the EGFR protein that bound most to the top ligands, the structures with the codes 3W33, 3W2S, and 4LI5 were predominant. The same amino acids that appeared in both wildtype and mutation structures in hydrophobic bonds were Asp855, and in hydrogen bonds is Val726 and Leu718.
Keyword: kanker paru-paru, EGFR, docking, energi afinitas, interaksi ligan-protein

Judul: Bifurkasi Hopf pada siklus bisnis IS-LM tanpa dan dengan waktu tunda
Abstrak: One of business cycle models in dynamical economics is the IS-LM business cycle model with time delay, where the time delay lies in stock capital variables. It is a time delay between the existence of stock capital and the time to get ready to invest. In a model without time delay, changing the parameter of investment rate on income could affect the system stability. On the other hand, in a model with time delay, there exists critical time delay changing the system stability. This shows limit cycle, which can be concluded that Hopf bifurcation occurs
Keyword: Bogor Agricultural University (IPB), time delay, Hopf bifurcation, business cycle model