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Abstrak :
Latar belakang: Karsinoma nasofaring (KNF) adalah tumor ganas yang jarang terjadi pada anak-anak. KNF pada anak prevalensinya kurang dari 1%, tetapi mewakili 20-50% tumor ganas pada anak yang berasal dari nasofaring. Pada orang dewasa Penelitian telah menemukan bahwa latent membrane protein -1  (LMP1) yang diekspresikan oleh virus Epstein-Barr (EBV) mendorong terjadinya perkembangan dan metastasis karsinoma nasofaring (KNF) dan berhubungan dengan sifat agresif dan invasive, namun pada anak belum ada penelitian yang meneliti bagaiamana ekspresi dan peranan LMP-1 tersebut. Metode penelitian: Penelitian ini menggunakan desain potong lintang pada 30 blok paraffin dari subjek KNF anak di Rumah Sakit Cipto Mangunkusumo Jakarta. Blok Parafin kemudian dilakukan ekstraksi dan pemeriksaan PCR LMP-1, kemudian dibandingkan dengan respons terapi. Hasil penelitian: Hasil LMP-1 positif sebanyak 28 subjek dan negatif sebanyak 2 subjek, dari 30 subjek hanya 27 subjek yang dapat dianalisis karena 2 subjek meninggal saat sebelum menyelesaikan terapi dan 1 subjek belum melakukan evaluasi pasca terapi. LMP-1 positif  sebanyak 17 subjek menunjukkan respons (16 respons komplit dan 1 respons parsial), sedangkan 8 subjek menunjukkan tidak ada respons (2 respons stabil 6 respons progresif). Terdapat 2 subjek dengan hasil LMP-1 negatif, seluruhnya memiliki respons terapi (p=1,000). Kesimpulan: Tidak terdapat hubungan antara ekspresi LMP-1 dan respons terapi. ......Background: Nasopharyngeal carcinoma (NPC) is a rare malignant tumor in children. KNF in children has a prevalence of less than 1%, but represents 20-50% of malignant tumors in children originating from the nasopharynx. In adults, studies have found that latent membrane protein -1 (LMP1) expressed by Epstein-Barr virus (EBV) promotes the occurrence, progression, and metastasis of nasopharyngeal carcinoma (NPC) and is associated with aggressive and invasive properties, but in children, no studies have examined the expression and role of LMP-1. Method: This study used a cross-sectional design on 30 paraffin blocks from pediatric NPC subjects at Cipto Mangunkusumo Hospital Jakarta. Paraffin blocks were then DNA extracted and PCR examination of LMP-1 was performed, then compared with the response to therapy. Result: LMP-1 positive was 28 subjects and negative was 2 subjects, and from 30 subjects, only 27 subjects can be analyzed because 2 subjects died before completing therapy and 1 subject has not conducted a post-therapy evaluation. LMP-1 positive as many as 17 subjects showed a response (16 complete responses and 1 partial response), while 8 subjects showed no response (2 stable responses 6 progressive responses). There were 2 subjects with negative LMP-1 results, all of whom responsded to therapy (p = 1.000). Conclusion: There was no association between LMP-1 expression and therapeutic response.

Abstrak :
With the aim of providing a deeper insight into possible mechanisms of biological self-organization, this thesis presents new approaches to describe the process of self-assembly and the impact of spatial organization on the function of membrane proteins, from a statistical physics point of view. It focuses on three important scenarios: the assembly of membrane proteins, the collective response of mechanosensitive channels and the function of the twin arginine translocation (Tat) system. Using methods from equilibrium and non-equilibrium statistical mechanics, general conclusions were drawn that demonstrate the importance of the protein-protein interactions. Namely, in the first part a general aggregation dynamics model is formulated, and used to show that fragmentation crucially affects the efficiency of the self-assembly process of proteins. In the second part, by mapping the membrane-mediated forces into a simplified many-body system, the dynamic and equilibrium behaviour of interacting mechanosensitive channels is derived, showing that protein agglomeration strongly impacts its desired function. The final part develops a model that incorporates both the agglomeration and transport function of the Tat system, thereby providing a comprehensive description of this self-organizing process.

Abstrak :
Latar belakang: Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) merupakan salah satu periodontopatogen yang sangat banyak ditemukan pada periodontitis agresif di mana kerusakan tulang sangat cepat terjadi. Periodontitis tidak akan terjadi tanpa diinisasi melalui invasi bakteri ke dalam sel target untuk berproliferasi di dalamnya. Bakteri A. actinomycetemcomitans memiliki faktor virulensi Omp29 yang memediasi proses invasi tersebut ke dalam sel epitel gingiva. Tujuan: Menganalisis interaksi bakteri A. actinomycetemcomitans dengan sel bone marrow macrophage, preosteoklas dan osteoklas berdasarkan ekspresi gen Omp29 sebagai faktor virulensi bakteri. Metode: Studi in vitro diawali dengan menginfeksikan bakteri A. actinomycetemcomitans ke sel prekursor osteoklas (bone marrow macrophage (BMM) dan preosteoklas) dan osteoklas selama 30 menit dengan multiplicity of infection (MOI) 1:1 dan 1:5. Setelah diinfeksikan, terdapat sebagian sel yang langsung dilakukan lisis dengan TRIzol sedangkan sebagiannya lagi diinkubasi kembali selama 16,5 jam sebelum dilisis oleh TRIzol. Analisis ekspresi relatif gen Omp29 bakteri pada medium pasca infeksi dilakukan pada mesin qPCR dengan menggunakan gen 16SrRNA sebagai housekeeping gene. Hasil: Terdapat penurunan ekspresi relatif gen Omp29 pada bakteri A. actinomycetemcomitans 18 jam pasca infeksi sel BMM, preosteoklas dan osteoklas terhadap kontrol yaitu bakteri 1,5 jam pasca infeksi sel-sel yang sama. Penurunan ekspresi relatif yang sama ditemukan pada perbandingan antara bakteri 18 jam pasca infeksi sel preosteoklas dengan MOI 1:5 terhadap bakteri 18 jam pasca infeksi sel preosteoklas dengan MOI 1:1. Kesimpulan: Interaksi direk antara bakteri A. actinomycetemcomitans dengan sel BMM, preosteoklas dan osteoklas menyebabkan kerusakan atau berkurangnya faktor virulensi Omp29 pada bakteri di mana mekanismenya belum diketahui secara pasti. ......Background: Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is one of the periodontopathogen involved in periodontitis and it is found in abundance in aggressive periodontitis where rapid bone destruction occur. Periodontitis will not happen if it is not initiated by the invasion of bacteria into the targeted cells so that bacteria can proliferate inside them. A. actinomycetemcomitans has a virulence factor named Omp29 which plays a role in gingival epithelium cell invasion. Objective: To analyze the interaction of A. actinomycetemcomitans and osteoclast precursor (bone marrow macrophage (BMM) and preosteoclast) as well as osteoclast itself through the expression of Omp29 gene as a virulence factor. Methods: In vitro study by infecting A. actinomycetemcomitans to osteoclast precursor and osteoclast that is obtained from mice for 30 minutes in two different multiplicity of infection (MOI) which are 1:1 and 1:5. After that, some of the infected cells are immediately lysed using TRIzol and some are incubated again for about 16,5 hours before being lysed. Relative expression of the Omp29 gene from the post-infection medium is obtained using real-time PCR with 16SrRNA as a housekeeping gene. Results: There is downregulation of the relative expression of Omp29 in A. actinomycetemcomitans 18 hpi of BMM, preosteoclast and osteoclast compared to the control which is A. actinomycetemcomitans 1,5 hpi of the same cells in both MOI 1:1 and 1:5. The same is observed when comparing the relative expression of Omp29 in A. actinomycetemcomitans 18 hpi of preosteoclast in MOI 1:1 with MOI 1:5. Conclusion: Direct interaction of A. actinomycetemcomitans and osteoclast cause destruction or decrease of Omp29 which mechanism is still not known and need further study.

Abstrak :
HIV-1 adalah virus yang menginfeksi serta menghancurkan atau mengganggu fungsi sel-sel sistem kekebalan tubuh manusia. HIV-1 memiliki enzim yang penting dan dibutuhkan dalam perakitan dan pematangan virion yaitu protease HIV-1. Protease HIV-1 telah diketahui selama beberapa dekade sebagai target yang potensial sebagai struktur dasar desain obat. Teknologi komputasi dapat digunakan dalam mengembangkan obat baru yang menggunakan metode penapisan virtual. Pada penelitian ini, proses validasi untuk penapisan virtual protease HIV-1 dilakukan dengan program Autodock dan Vina yang terdapat pada program PyRx menggunakan basis data dari A Directory of Useful Decoys (DUD). Parameter penapisan virtual yang divariasikan untuk validasi adalah ukuran Grid Box dan Maximum Number of Evaluation. Parameter validasi yang digunakan untuk menentukan penapisan virtual yang optimum yaitu EF 1%, 10%, dan 20% dan AUC ROC. Penapisan virtual menggunakan program AutoDock yang optimum adalah pada parameter Grid Box 50 x 50 x 50 dan Maximum Number of Energy Evaluations 1.000.000. Penapisan virtual meggunakan program Vina yang optimum adalah parameter Grid Box 22,5 x 22,5 x 22,5 untuk protease HIV-1 menggunakan air. ......HIV-1 is a virus that infects and destroys or interferes the function of cell of human immune system. HIV-1 has essential enzymes and needed for virion assembly and maturation such as HIV-1 protease. HIV-1 protease has been known for decades as a potential target of drug design as the basic structure. Computation technology that could be used for developing a new drug is virtual screening method. In this research, the validation process on the virtual screening of HIV-1 protease was done with AutoDock and Vina program contained in the PyRx program using database from A Directory of Useful decoys (DUD). Varied virtual screening parameters used for validation were Grid Box's size and Maximum Number of Evaluation. Validation parameters that were used to determine virtual screening optimum parameters are EF 1%, 10%, and 20% and AUC ROC. The optimum virtual screening parameter using AutoDock program was Grid Box 50 x 50 x 50 and the Maximum Number of Energy Evaluations 1,000,000 on HIV-1 protease using water. The optimum virtual screening parameter using Vina program was Grid Box 22.5 x 22.5 x 22.5 in HIV-1 protease using water.

Abstrak :
Caveolae are 50-100 nm flask-shaped invaginations of the plasma membrane that are primarily composed of cholesterol and sphingolipids. Using modern electron microscopy techniques, caveolae can be observed as omega-shaped invaginations of the plasma membrane, fully-invaginated caveolae, grape-like clusters of interconnected caveolae (caveosome), or as transcellular channels as a consequence of the fusion of individual caveolae. The caveolin gene family consists of three distinct members, namely Cav-1, Cav-2 and Cav-3. Cav-1 and Cav-2 proteins are usually co-expressed and particularly abundant in epithelial, endothelial, and smooth muscle cells as well as adipocytes and fibroblasts. On the other hand, the Cav-3 protein appears to be muscle-specific and is therefore only expressed in smooth, skeletal and cardiac muscles. Caveolin proteins form high molecular weight homo- and/or hetero-oligomers and assume an unusual topology with both their N- and C-terminal domains facing the cytoplasm.