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KAJIAN NUTRIGENOMIK: PENGHAMBATAN Igf-1 PADA ADIPOGENESIS JARINGAN LEMAK VISERAL TIKUS DENGAN EKSTRAK KULIT RAMBUTAN Nurdiansyah, Rizky; Lestari, Sri Rahayu; Fatchiyah, Fatchiyah
Biotropika Vol 1, No 6 (2013): Biotropika
Publisher : Jurusan Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam

Show Abstract | Download Original | Original Source | Check in Google Scholar

Tujuan penelitian adalah untuk mengetahui dan menjelaskan pengaruh dari ektrak kulit buah rambutan terhadap adipogenesis jaringan lemak viserall tikus dengan melihat ekspresi igf-1. Tahapan penelitian yang dilakukan adalah ekstraksi kulit buah rambutan, perlakuan pada tikus, isolasi protein lemak viserall, separasi protein dan western blot. Tikus strain wistar jantan dibagi menjadi tikus berat badan normal dan obesitas. Perlakuan yang dilakukan antara lain kontrol, asam elagat, placebo, dan perlakuan ekstrak dengan dosis 5, 10, 15, dan 20 mg/kg berat badan. Hasil menunjukkan bahwa tren penurunan berat badan terjadi pada grup tikus obesitas dengan asupan pakan yang tidak berbeda signifikan (P>0,05). Dosis efektif terlihat pada perlakuan 10 mg/kg dan pada dosis 20mg/kg justru terjadi kenaikan berat badan untuk kedua jenis grup tikus. Profil protein antara tikus normal dan obesitas menunjukkan pola yang hampir sama dengan perbedaan intensitas tiap pita. Ekspresi igf-1 terpaut dengan ekspresi igfbp-1 pada 36,7 kDa dan terjadi pada seluruh perlakuan dengan perbedaan nyata pada kedua grup. Ekstrak kulit buah rambutan dengan dosis efektif 10mg/kg memiliki efek anti-obesitas pada tikus obesitas. Menariknya, ekspresi igf-1 menurun pada perlakuan 20mg/kg berat badan dibandingkan dengan kelompok lain. Hal ini diduga penghambatan obesitas tidak melewati jalur tyrosin kinase pada IR family.

3D AND 2D RNA STRUCTURE PREDICTION OF THE BRCA2 GENE AND ITS SILENCING RNA IN THE BREAST CANCER Wijaya, Ryan; Parikesit, Arli Aditya; Nurdiansyah, Rizky
Walisongo Journal of Chemistry Vol 3, No 1 (2020): Walisongo Journal of Chemistry
Publisher : Department of Chemistry Faculty of Science and Technology Walisongo

Breast cancer is one of the most threatening diseases for women. It is found that BRCA2 gene plays a significant role in breast cancer, provided that mutations occurred. The objective of this study is to determine whether the bioinformatics approach could provide the gene networking, molecular simulation, and computational metabolomics information to shed the relation between BRCA2 gene mutation with breast cancer progression. The methods are utilizing molecular simulation tools to comprehend the biochemical interaction of BRCA2 gene with other oncogenic genes. Lastly, the molecular docking tool is devised to provide the molecular interactions information. It could be implied that the Computer-Aided Drug Design (CADD)-based in silico transcriptomics tools could provide the fine-grained information on the exact role of BRCA2 gene in the progression of breast cancer. The clinical impact of this study could only be measured after the wet laboratory experiment is conducted to validate the computational approach results

Drug Repurposing Option for COVID-19 with Structural Bioinformatics of Chemical Interactions Approach Parikesit, Arli Aditya; Nurdiansyah, Rizky
Cermin Dunia Kedokteran Vol 47, No 3 (2020): Dermatologi
Publisher : PT. Kalbe Farma Tbk.

The SARS-CoV-2 virus is the pathogenic agent that caused the COVID-19 disease. The epicenter of this disease is the city of Wuhan, China. It is already categorized as â€œpandemicâ€ by WHO, as many countries already affected with the infections, including recently Indonesia. Although the standard RT-PCR and DNA sequencing protocols has already developed for diagnostic, no drugs are available to cure this disease until today. The anti-malaria drug of chloroquine phosphate was repurposed, as well as other anti-viral drugs. In this regard, a structural bioinformatics pipeline was utilized to validate the claim in the computational realm. Within the sphere of the online molecular docking method, it was found that all the tested repurposed drugs attached accordingly with the SARS-CoV-2 protease enzyme that plays a role in viral replication. The repurposed drugs could be proposed as drug candidates for COVID-19, after clinical trials or further laboratory testing.Virus SARS-CoV-2 adalah patogen penyebab penyakit COVID-19. Episentrum penyakit ini adalah kota Wuhan, Tiongkok. WHO mengeluarkan peringatan â€˜pandemiâ€™ karena banyak negara sudah terkena infeksi, termasuk Indonesia. Meskipun protokol RT-PCR dan sekuensing DNA standar telah dikembangkan untuk tujuan diagnostik, hingga saat ini tidak ada obat untuk menyembuhkan penyakit ini. Obat anti-malaria chloroquine phosphate dicoba, bersama dengan beberapa obat anti-virus. Alur analisis bioinformatika struktural digunakan untuk validasi di ranah komputasi. Dalam lingkup metode molecular docking secara daring, ditemukan bahwa obat tersebut tertambat dengan enzim protease SARS-CoV-2 yang berperan dalam replikasi virus. Obat ini dapat diusulkan sebagai kandidat obat untuk COVID-19, setelah pengujian laboratorium dan uji klinis lebih lanjut.

The Structural Annotations of The Mir-122 Non-Coding RNA from The Tilapia Fish (Oreochromis niloticus) Arli Aditya Parikesit; Imron Imron; Rizky Nurdiansyah; David Agustriawan
HAYATI Journal of Biosciences Vol. 29 No. 2 (2022): March 2022
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.29.2.171-181

Tilapia (Oreochromis niloticus) is an important fisheries commodity. Scientific efforts have been done to increase its quality. One of them is staging a premium diet such as a fat-enriched diet. The transcriptomics approach is able to provide the signatures of the diet outcomes by observing the micro(mi)RNA signature in transcriptional regulation. Hence, it was found that the availability of mir-122 is essential in the regulation of a high-fat diet in tilapia. However, this transcriptomics signature is lacking structural annotations and the complete interaction annotations with its silencing(si)RNA. RNAcentral website was navigated for the latest annotation of mir-122 from tilapia and other species as a comparison. MEGA X was employed to comprehend the miRNA evolutionary repertoire. The RNA secondary structure prediction tools from the Vienna RNA package and the RNA tertiary structure prediction tools from simRNA and modeRNA are secured with default parameters. The HNADOCK tools were leveraged to observe the interaction between mir-122 and its siRNA. The post-processing was conducted with the Chimera visualization tool. The secondary and tertiary structure of the mir-122 and its siRNA could be elucidated, docked, and visualized. In this end, further effort to develop a comprehensive molecular breeding tool could be secured with the structural annotation information.

KAJIAN NUTRIGENOMIK: PENGHAMBATAN Igf-1 PADA ADIPOGENESIS JARINGAN LEMAK VISERAL TIKUS DENGAN EKSTRAK KULIT RAMBUTAN Rizky Nurdiansyah; Sri Rahayu Lestari; Fatchiyah Fatchiyah
Biotropika: Journal of Tropical Biology Vol 1, No 6 (2013)
Publisher : University of Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar

Tujuan penelitian adalah untuk mengetahui dan menjelaskan pengaruh dari ektrak kulit buah rambutan terhadap adipogenesis jaringan lemak viserall tikus dengan melihat ekspresi igf-1. Tahapan penelitian yang dilakukan adalah ekstraksi kulit buah rambutan, perlakuan pada tikus, isolasi protein lemak viserall, separasi protein dan western blot. Tikus strain wistar jantan dibagi menjadi tikus berat badan normal dan obesitas. Perlakuan yang dilakukan antara lain kontrol, asam elagat, placebo, dan perlakuan ekstrak dengan dosis 5, 10, 15, dan 20 mg/kg berat badan. Hasil menunjukkan bahwa tren penurunan berat badan terjadi pada grup tikus obesitas dengan asupan pakan yang tidak berbeda signifikan (P>0,05). Dosis efektif terlihat pada perlakuan 10 mg/kg dan pada dosis 20mg/kg justru terjadi kenaikan berat badan untuk kedua jenis grup tikus. Profil protein antara tikus normal dan obesitas menunjukkan pola yang hampir sama dengan perbedaan intensitas tiap pita. Ekspresi igf-1 terpaut dengan ekspresi igfbp-1 pada 36,7 kDa dan terjadi pada seluruh perlakuan dengan perbedaan nyata pada kedua grup. Ekstrak kulit buah rambutan dengan dosis efektif 10mg/kg memiliki efek anti-obesitas pada tikus obesitas. Menariknya, ekspresi igf-1 menurun pada perlakuan 20mg/kg berat badan dibandingkan dengan kelompok lain. Hal ini diduga penghambatan obesitas tidak melewati jalur tyrosin kinase pada IR family.

Computational modeling of AGO-mediated molecular inhibition of ARF6 by miR-145 Jeremias Ivan; Rizky Nurdiansyah; Arli Aditya Parikesit
Indonesian Journal of Biotechnology Vol 25, No 2 (2020)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.55631

Inhibition of ADP-ribosylation factor 6 messenger RNA (ARF6 mRNA) by microRNA-145 (miR-145), mediated by Argonaute (AGO) protein, has been found to play essential roles in several types of cancer and cellular processes. This study aimed to model the molecular interaction between miR-145 and ARF6 mRNA with AGO protein. The sequences of miR-145 and the 3’ untranslated region (UTR) of ARF6 mRNA were retrieved from miRTarBase, followed by miRNA target-site and structure predictions were done using RNAhybrid, RNAfold, and simRNAweb, respectively. The interaction between the miRNA-mRNA duplex and AGO was further assessed via molecular docking, interaction analysis, and dynamics, using PatchDock Server, PLIP, and VMD/NAMD, respectively. The models between miR-145, predicted target site of ARF6 mRNA, and AGO protein returned stable thermodynamic variables with negative free energy. Specifically, the RNA duplex had an energy of -19.80 kcal/mol, while the docking had -84.58 atomic contact energy supported by 70 hydrogen bonds and 14 hydrophobic interactions. However, the stability of the RMSD plot was still unclear due to limited computational resources. Nevertheless, these results computationally confirm favorable interaction of the three molecules, which can be utilized for further transcriptomics-based drugs or treatments.

THE PREDICTED STRUCTURE FOR THE ANTI-SENSE SIRNA OF THE RNA POLYMERASE ENZYME (RDRP) GENE OF THE SARS-COV-2 Arli Aditya Parikesit; Rizky Nurdiansyah
BERITA BIOLOGI Vol 19, No 1 (2020)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/beritabiologi.v19i1.3849

The SARS-CoV-2 or COVID-19 pandemic has reached a new height with an unprecedented infection rate and mortality post-world war II history. However, there is no particular designed drug for COVID-19 up to this point. Thus, there exist three strategies for COVID-19 drug design; drug repurposing option, herbal medicine development, and transcriptomics-based drug lead. As the most underutilized option, transcriptomics-based drug lead could be leveraged to deal with SARS-CoV-2 infection. One of the main methods to block the SARS-CoV-2 infection is to inhibit the RNA polymerase enzyme that is responsible to the viral replication. In this regard, the objective of the strategy is to design the anti-sense siRNA drug and lead to inhibit the mRNA of the RNA Polymerase Enzyme (RdRp) gene that encodes the viral RNA Polymerase of the SARS-CoV-2. The Computer-Aided Drug Design (CADD)-based method was leveraged with sequence retrieval of 24 RdRp gene sequences, multiple sequence alignment, phylogenetic tree reconstruction, 2D/3D RNA structure predictions, and RNA-RNA docking. Both the RNAalifold conserved structure from the RdRp genes and the RNAfold structure of the siRNA for blocking the conserved structure are negative or less than 0 kcal/mol. The predicted RNA docking occurred with the best RMSD score of 22.53 Å, which is beyond the accepted threshold of 10-20 Å. Based on the findings, the 2D/3D structures of both the siRNA and mRNA could be elucidated, and the docking between them is feasible. However, this finding should be elucidated in the wet laboratory setting for the final lead validation.

Computational design of ancestral and consensus sequence of apical membrane antigen 1 (AMA1) of Plasmodium spp Rizky Nurdiansyah; Rahmat Azhari Kemal
Acta Biochimica Indonesiana Vol. 2 No. 2 (2019): Acta Biochimica Indonesiana
Publisher : Indonesian Society for Biochemistry and Molecular Biology

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.32889/actabioina.v2i2.40

Background: It is important to design a malaria vaccine targeting all human malaria parasites as well as non-human primate parasites to eradicate malaria and prevent zoonotic malaria. Apical membrane antigen 1 (AMA1) protein is shared by human-infecting Plasmodium species. Ancestral sequence reconstruction (ASR) and consensus sequence construction on AMA1 might be able to overcome the antigenic distinction between those species. Objective: We aimed to computationally design the ancestral and consensus sequence of Plasmodium AMA1 protein and analyze the sequences for its putative immunogenicity. Methods: We utilized bioinformatics software to computationally design ancestral and consensus sequences of AMA1 protein. AMA1 protein sequences of human-infecting Plasmodium and non-human primate Plasmodium were retrieved from PlasmoDB. ASR was designed using MEGA X while consensus was inferred using UGENE. Phylogenetic tree consisting of existing Plasmodium sequences and the ancestral sequence was constructed using IQTREE webserver and visualized with FigTree. Results: Phylogenetic analysis showed that Plasmodium spp. were divided into 2 major groups, P. falciparum (Clade F) and non-falciparum (Clade NF) thus three ancestral and consensus sequences were designed based on each clade and both clades at once. Reconstructed ancestral sequences were located as sister branch for naturally occurring strains. On the contrary, consensus sequences are located within the branch of corresponding naturally occurring strains. Sequence analysis showed the presence of CD8+ T cell epitope in all computationally-designed sequences. Conclusion: Ancestral and consensus AMA1 sequences are potential for further studies as a malaria vaccine candidate.

PELATIHAN BERSERI TEKNOLOGI INFORMASI DAN KOMUNIKASI DI SEKOLAH DASAR MEKARSARI JAKARTA [A WORKSHOP SERIES OF INFORMATION COMMUNICATION AND TECHNOLOGY AT MEKARSARI ELEMENTARY SCHOOL JAKARTA] David Agustriawan; Arli Aditya Parikesit; Rizky Nurdiansyah
Jurnal Sinergitas PKM & CSR Vol 4, No 1 (2019): October
Publisher : Universitas Pelita Harapan

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Industry 4.0 era needs to introduce current information communication and technology (ICT) to the society starting from the elementary school. However, Mekarsari Elementary school does not have the facility nor curriculum to prepare the students to face the era. This corporate social responsibility (CSR) aimed to introduce the kids with the current development of hardware and software. The participants for the series of the workshop are the 15 4th and 5th grade students and two teachers from Mekarsari Elementary school. The intervention was devised by providing user-friendly teaching-learning materials with hands-on activities related to the current development of ICT. The type of study is the “direct philanthropic giving” because it aims at providing knowledge for free. As the result, the students are familiar with: the type of computer’s hardware and software; python programming; budgeting for their daily allowance using Microsoft Excel; and creating a short story and presentation in Microsoft Word and PowerPoint. Based on the survey, the students could comprehend and enthusiastic to complete the hands-on activities. This CSR suggests that each elementary school should have a curriculum and computer laboratory to prepare the youth to compete in industry 4.0 era.

3D And 2D RNA Structure Prediction Of The BRCA2 Gene And Its Silencing RNA In The Breast Cancer Ryan Wijaya; Arli Aditya Parikesit; Rizky Nurdiansyah
Walisongo Journal of Chemistry Vol 3, No 1 (2020): Walisongo Journal of Chemistry
Publisher : Department of Chemistry Faculty of Science and Technology Walisongo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21580/wjc.v3i1.6019

Breast cancer is one of the most threatening diseases for women. It is found that BRCA2 gene plays a significant role in breast cancer, provided that mutations occurred. The objective of this study is to determine whether the bioinformatics approach could provide the gene networking, molecular simulation, and computational metabolomics information to shed the relation between BRCA2 gene mutation with breast cancer progression. The methods are utilizing molecular simulation tools to comprehend the biochemical interaction of BRCA2 gene with other oncogenic genes. Lastly, the molecular docking tool is devised to provide the molecular interactions information. It could be implied that the Computer-Aided Drug Design (CADD)-based in silico transcriptomics tools could provide the fine-grained information on the exact role of BRCA2 gene in the progression of breast cancer. The clinical impact of this study could only be measured after the wet laboratory experiment is conducted to validate the computational approach results

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