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Abstrak :
Kanker payudara masih menjadi masalah kesehatan global. Modalitas terapi yang digunakan untuk pasien kanker payudara diataranya agen kemoterapi doksorubisin (DOX). DOX digunakan untuk pengobatan kanker dengan mekanisme interkalasi DNA dan penghambatan topoisomerase II, serta penggunaannya mengalami resistensi. Bahan alam berpotensi digunakan untuk terapi kombinasi mengatasi resistensi doksorubisin. Bahan alam yang digunakan diantaranya dari jahe merah yang mengandung 6-shogaol. Senyawa 6-Shogaol sebagai agen kemoterapi yang meregulasi ekspresi gen yang berhubungan dengan proses proliferasi sel. Pada penelitian ini dilakukan analisis ekspresi gen pada basis data Gene Expression Omnibus (GEO) terkait pengobatan doksorubisin (GSE124597) dan pemberian 6-shogaol (GSE36973) dengan tujuan mengetahui perbandingan pola ekspresi gen yang dipengaruhi keduanya terhadap sel kanker payudara MCF7. Dilakukan juga anotasi fungsi gen yang diekspresikan menggunakan Gen Ontologi (GO) dan KEGG, jejaring farmakologi menggunakan basis data STITCH, serta simulasi penambatan molekuler untuk mengetahui mekanisme kerja antikanker. Sifat antikanker doksorubisin, 6-shogaol, dan ekstrak jahe merah kemudian  dikonfirmasi secara invitro meggunakan metode MTT. Hasil analisis Diffrential Expression Genes (DEG) menghasilkan 227 DEG yang sama (DEG bersama) akibat pemberian doksorubisin dan 6-shogaol. Hasil anotasi fungsi gen dengan GO menunjukkan dari 227 DEG terkait dengan proliferasi sel melalui jalur TP53.Demikian juga terkait hasil analisis jejaring farmakologi menunjukkan doksorubisin dan 6-shogaol terhubung dengan protein TP53. Hasil analisis interaksi protein-protein (PPi) menunjukkan jalur persinyalan TP53 terhubung dengan protein CDKN1A, GADD45A, DDIT3 dan CXCL12. Penambatan molekuler senyawa doksorubisin dan 6-shogaol pada protein TP53 menghasilkan energi ikatan berturut-turut -7.97 kcal/mol dan -6.05 kcal/mol. Nilai IC50 senyawa doksorubisin, 6-shogaol, dan ekstrak jahe pada sel MCF-7 berturut-turut adalah: 15.45 µg/ml, 61.24 µg/ml dan 144.99 µg/ml. Hal ini menunjukkan 6-shogaol dapat digunakan sebagai kandidat komplementer antikanker pada sel MCF-7. ......Breast cancer is still a global health problem. Therapeutic modalities used for breast cancer patients include the chemotherapeutic agent doxorubicin (DOX). DOX is used for the treatment of cancer with DNA intercalation mechanisms and topoisomerase II inhibition, and its use has experienced resistance, so a combination therapy of natural ingredients is needed. The natural ingredients used include red ginger which contains 6-shogaol. 6-Shogaol compound as a chemotherapeutic agent that regulates gene expression related to cell proliferation processes. In this study, gene expression analysis was carried out on the Gene Expression Omnibus (GEO) database related to doxorubicin treatment (GSE124597) and 6-shogaol administration (GSE36973) with the aim of knowing a comparison of gene expression patterns affected by both of them on MCF7 breast cancer cells. Functional annotations of expressed genes were also performed using Gene Ontology (GO) and KEGG, pharmacological networks using the STITCH database, as well as molecular docking simulations to determine the mechanism of anticancer action. The anticancer properties of doxorubicin, 6-shogaol, and red ginger extract were then confirmed in vitro using the MTT method. The results of the Differential Expression Genes (DEG) analysis yielded the same 227 DEGs as a result of doxorubicin and 6-shogaol administration. The results of gene function annotations with GO showed that 227 DEGs were related to cell proliferation through the TP53 pathway. Likewise, the results of pharmacological network analysis showed that doxorubicin and 6-shogaol were linked to the TP53 protein. The results of protein-protein interaction (PPi) analysis showed that the TP53 signaling pathway was connected to the CDKN1A, GADD45A, DDIT3 and CXCL12 proteins. Molecular docking of the compounds doxorubicin and 6-shogaol to the TP53 protein produces a binding energy of -7.97 kcal/mol and -6.05 kcal/mol, respectively. The IC50 values ​​of doxorubicin, 6-shogaol, and ginger extract in MCF-7 cells were: 15.45 µg/ml, 61.24 µg/ml and 144.99 µg/ml, respectively. This shows that 6-shogaol can be used as a complementary anticancer candidate in MCF-7 cells.

Abstrak :
Human Immunodeficiency Virus (HIV) merupakan salah satu virus paling mematikan yang merusak sistem imun manusia melalui interaksi antar protein (PPI). Oleh karena itu, diperlukan suatu metode prediksi yang dapat melihat secara luas interaksi antar protein. Integrasi dari berbagai jenis data yang berbeda merupakan salah satu pendekatan untuk melihat interaksi protein secara luas. Dalam penelitian ini dibangun metode untuk prediksi PPI dengan mengintegrasikan gene expression dan ontology menggunakan Bayesian Network. Langkah pertama pada proses integrasi ini yaitu mencari nilai likelihood ratio berdasarkan evidence berupa nilai probabilistik PPI pada masing-masing dataset. Dimana likelihood ratio diperoleh dari kombinasi evidence menggunakan Bayesian Network. Kemudian hasil prediksi yang diperoleh diverifikasi menggunakan database NIAID sebagai Gold-Standard. Dari hasil keseluruhan eksperimen, model yang dibangun ini dievaluasi menggunakan Positive Predictive Value (PPV) dan memperoleh presisi mencapai 85.07%. .......Human Immunodeficiency Virus (HIV) is one of the most deadly virus that could damage the human immune system through protein interaction (PPI). Therefore, the extremely prediction method that determine interactions between proteins extensively is required. The integration of different data is one of the approaches to look at the proteins interactions. In this research, a prediction model of PPI by integrating gene expression and gene ontology using Bayesian Networks will be developed. The first step in the integration process is to find the value of likelihood ratio based on evidence from each dataset. Furthermore the likelihood ratio is obtained from a combination of evidence using Bayesian Networks. Finally, the prediction results will be verified using a database of NIAID as Gold-Standard. Overall, we use PPV as an evaluation method which achieve precision around 85.07%.

Abstrak :
Gen CSF3syn adalah gen sintetik yang menyandi protein G-CSF. Protein G-CSF dapat diproduksi secara rekombinan. Sel inang alternatif yang dapat digunakan yaitu Pichia pastoris. Penelitian bertujuan untuk menyeleksi P. pastoris transforman yang stabil, mendapatkan P. pastoris transforman yang terintegrasi dengan gen CSF3syn, dan menganalisis ekspresi protein G-CSF pada P. pastoris transforman dengan promotor konstitutif GAP. Sebanyak 47 transforman berhasil diseleksi pada konsentrasi zeosin 1000 µg/ml. Analisis PCR menunjukkan gen CSF3syn sebesar 567 pb berhasil terintegrasi dalam genom P. pastoris. Analisis SDS PAGE, slot blot, dan western blot menunjukkan protein G-CSF berhasil diekspresikan. Analisis western blot menunjukkan G-CSF terglikosilasi ~20 kDa dan tidak terglikosilasi ~18 kDa. Selain itu, terdapat protein dengan berat molekul lebih dari protein target yaitu protein fusi terglikosilasi ~40--60 kDa. ...... CSF3syn gene is a synthetic gene that encodes G-CSF protein. G-CSF protein can be produced by recombinant technique. Pichia pastoris can be used as an alternative host. The objectives of this study were to select stability of the P. pastoris transformant, to obtain P. pastoris transformants which were integrated with CSF3syn gene, and expressed G-CSF recombinant in P. pastoris using the constitutive GAP promoter. A total of 47 transformants were selected in YEPD medium with 1000 µg/ml zeocin. Analyses by PCR confirmed the inserted CSF3syn gene in P. pastoris genome of 567 bp. Analyses of SDS PAGE, western blot, and slot blot showed that the G-CSF protein was expressed successfully. Western blot analyses showed that the bands of ~20 kDa as glycosylated G-CSF and ~18 kDa as non glycosylated G-CSF. The result also showed that the band with higher molecular mass ~40--60 kDa which was probably glycosylated fusion protein.