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PREDIKSI STRUKTUR 2-DIMENSI NON-CODING RNA DARI BIOMARKER KANKER PAYUDARA TRIPLE-NEGATIVE DENGAN VIENNA RNA PACKAGE Parikesit, Arli Aditya; Anurogo, Dito
Chimica et Natura Acta Vol 4, No 1 (2016)
Publisher : Departemen Kimia

Berdasarkan data WHO, kanker adalah penyakit yang paling berbahaya. Dewasa ini para peneliti sedang berusaha memahami mekanisme molekular kanker. Berdasarkan dogma sentral, hanya protein coding gene yang diketahui fungsinya, sementara non-coding gene belum dapat dijelaskan. Kemudian, diketahui bahwa non-coding RNA (ncRNA) berperan dominan dalam regulasi molekular sel, sehingga berpengaruh secara langsung kepada proliferasi kanker. Dalam hal ini, instrumen RNA-seq maupun Tiling Array sudah mengumpulkan banyak data biologis dan mendeposisikannya kepada database genom. Diketahui bahwa, ncRNA tidak hanya dapat berperan sebagai biomarker untuk diagnostik kanker, namun juga akan dapat dikembangkan sebagai agen terapeutik. Kanker payudara memiliki empat subtipe molekular, yaitu luminal A, luminal B, Her-2 dan triple negative/basal-like. Kanker Payudara Triple-negative (TNBC) merupakan penyakit yang sangat berbahaya dan belum ditemukan pengobatan yang efektif. Memahami mekanisme dan struktur ncRNA pada Biomarker TNBC merupakan langkah awal untuk menentukan agen terapeutik dan propilaksis terbaik. Diketahui bahwa jalur ekspresi lincRNA-RoR/miR-145/ARF6 berperan dalam proliferasi TNBC. Berdasarkan pencarian di GenBank, ditemukanÂ lema-lema ncRNA untuk jalur tersebut. Hasil pencarian diolah dengan software Vienna RNA Package, untuk ditentukan struktur 2 dimensi (2-D) yang solid. Kedepannya, diharapkan dengan mencegah terbentuknya struktur 2-D tersebut, maka semua gen tersebut akan menjadi tidak aktif dan menghentikan proliferasi kanker.

Protein Domain Annotation of Plasmodium spp. Circumsporozoite Protein (CSP) Using Hidden Markov Model-based Tools Parikesit, Arli Aditya; Utomo, Didik Huswo; Karimah, Nihayatul
JURNAL BIOLOGI INDONESIA Vol 14, No 2 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

ABSTRACTPlasmodium sp. Circumsporozoite Protein (CSP) has a crucial role in sporozoite function and hepatocyte invasion. The basic understanding of this protein can reveal the mechanism of action. Protein domain annotation could determine the functional region of the specific protein. This study aimed is to identify the conserved and functional region of circumsporozoite protein using Hidden Markov Model approach. Three samples of CSP was retrieved from UniProt database; Circumsporozoite protein from Plasmodium vivax (P08677), Circumsporozoite protein from Plasmodium malariae (P13815), and Circumsporozoite protein from Plasmodium knowlesi (P02894). All sequenced was reviewed and could be used for further analysis. Multiple Sequences alignment (MSA) was used for analyzing the conserved region. CLUSTAL X software employed to run the MSA of circumsporozoite protein. Protein homology was clustered using MEGA 7.0, and domain annotation was done by the SUPERFAMILY hidden Markov models. The result showed that Circumsporozoite Protein has two specific conserved regions among species. This conserved region indicates the similar function and takes a vital role in their life cycle. Plasmodium knowlesi and Plasmodium vivax had more similar sequence than Plasmodium malariae. The clustering result based on Circumsporozoite Protein indicates that Plasmodium malariae may have distinct infection mode to the host. The CSP was identified has one domain in C-terminus. Domain family of CSP was TSP-1 type 1 repeat with high reliability. It can be concluded that conserved domain of Circumsporozoite Protein could reveal its critical role in Malaria Disease. To this end, CSP could be a potential candidate for vaccine development. Keywords: Circumsporozoite, conserved domain, Plasmodium spp, TSP-1 type 1 repeat.

KECEMASAN TERHADAP MATA AJAR ILMU PENGETAHUAN ALAM (IPA) PADA SISWA SEKOLAH DASAR DAN MENENGAH Parikesit, Arli Aditya
Manajemen Pendidikan Vol. 14, No. 2, Tahun 2019
Publisher : Universitas Muhammadiyah Surakarta

Ilmu Pengetahuan Alam (IPA) merupakan mata ajar wajib yang diajarkan di sekolah dasar dan menegah. Permasalahan yang terjadi pada pembelajaran IPA adalah terjadinya kecemasan pada siswa. Kecemasan pada IPA terjadi di berbagai spektrum populasi siswa, mulai dari kelompok minoritas, sampai pada kebangsaan dan gender tertentu. Di Indonesia, kecemasan IPA juga telah terjadi, dan menjadi masalah serius. Saat ini beberapa solusi untuk mengatasi kecemasan IPA sudah dapat dilakukan, diantaranya melalui pembelajaran tematik, pengembangan sekolah anak berbakat, pendekatan psikoterapi, pendekatan spiritualisme, kondisi kelas yang positif, Problem Based Learning, dan teknologi informasi. Namun, keberhasilan semua pendekatan tersebut baru dapat terjamin jika guru dapat menjalankan peran sebagai motivator bagi siswa.

PROTEIN DOMAIN ANNOTATION OF PLASMODIUM SPP. CIRCUMSPOROZOITE PROTEIN (CSP) USING HIDDEN MARKOV MODEL-BASED TOOLS Parikesit, Arli Aditya; Utomo, Didik Huswo; Karimah, Nihayatul
JURNAL BIOLOGI INDONESIA Vol 14, No 2 (2018): JURNAL BIOLOGI INDONESIA
Publisher : Perhimpunan Biologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/jbi.v14i2.3737

ABSTRACTPlasmodium sp. Circumsporozoite Protein (CSP) has a crucial role in sporozoite function and hepatocyte invasion. The basic understanding of this protein can reveal the mechanism of action. Protein domain annotation could determine the functional region of the specific protein. This study aimed is to identify the conserved and functional region of circumsporozoite protein using Hidden Markov Model approach. Three samples of CSP was retrieved from UniProt database; Circumsporozoite protein from Plasmodium vivax (P08677), Circumsporozoite protein from Plasmodium malariae (P13815), and Circumsporozoite protein from Plasmodium knowlesi (P02894). All sequenced was reviewed and could be used for further analysis. Multiple Sequences alignment (MSA) was used for analyzing the conserved region. CLUSTAL X software employed to run the MSA of circumsporozoite protein. Protein homology was clustered using MEGA 7.0, and domain annotation was done by the SUPERFAMILY hidden Markov models. The result showed that Circumsporozoite Protein has two specific conserved regions among species. This conserved region indicates the similar function and takes a vital role in their life cycle. Plasmodium knowlesi and Plasmodium vivax had more similar sequence than Plasmodium malariae. The clustering result based on Circumsporozoite Protein indicates that Plasmodium malariae may have distinct infection mode to the host. The CSP was identified has one domain in C-terminus. Domain family of CSP was TSP-1 type 1 repeat with high reliability. It can be concluded that conserved domain of Circumsporozoite Protein could reveal its critical role in Malaria Disease. To this end, CSP could be a potential candidate for vaccine development. Keywords: Circumsporozoite, conserved domain, Plasmodium spp, TSP-1 type 1 repeat.

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

The Binding Prediction Model of The Iron-responsive Element Binding Protein and Iron-responsive Elements Parikesit, Arli Aditya; Ramanto, Kevin Nathanael
Bioinformatics and Biomedical Research Journal Vol. 2 No. 1 (2019): Volume 2 Issue 1
Publisher : Future Science

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

Iron is essential to fulfilling an indispensable role in the biological process in human physiology. Various proteins were known involved in iron metabolism. One of the proteins called iron-responsive element binding protein (IRP)which acts as master iron of cellular iron homeostasis. There are two IRP known to date, which is: IRP1 and IRP2. Previous studies showed IRP bind to iron-responsive elements (IRE) located in 5â€™-UTR of the transferrin receptor 1. The interaction of IRP/IRE is well studied through many years to find a better treatment for the cellular disorder in iron metabolism. However, the structural differences of both IRP and the binding prediction model of IRP/IRE remain unclear. This study provides a better understanding of the IRP structure and the IRP/IRE2 binding prediction model in a healthy condition. Several bioinformatic analyses were implemented in this study, such as molecular docking simulation, domain prediction, and structural similarity analysis. Structural analysis of IRP demonstrates a low root mean square deviation score that indicates both of IRP have high similarity in structure with different characteristics, such as binding site, and metabolic pathway. Interestingly, molecular docking simulation showed IRP has a preferably binding site when targeting specific IRE. Thus, this information could be beneficial in developing a drug for an iron-related disease.

Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Posa, Gabrielle Ann Villar; Rizky, Wahyu Choirur; Permana, Sofy; Parikesit, Arli Aditya
Jurnal Teknologi Laboratorium Vol 10 No 1 (2021): inpress
Publisher : POLTEKKES KEMENKES YOGYAKARTA

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29238/teknolabjournal.v10i1.274

Acquired immune deficiency syndrome (AIDS) has been identified from US patients since 1981. AIDS is caused by infection with the human immunodeficiency virus type 1 (HIV-1) which is a retrovirus. HIV-1 gp120 can be recognized by the immune system because it is located outside the virion. The conserved region is identified in gp120, and it is recognized by an immune cell which then initiates specific immune responses, viral mutation escape, and increase vaccine protection coverage, a benefit derived from the conserved region-based vaccine design. However, previous researchers have little knowledge on this conserved region as a target for vaccine design. This paper explains how the conserved region of gp120 HIV-1 is a major target for vaccine design through a bioinformatics approach. The conserved region from gp120 was explored as a vaccine design target with a bioinformatics tool that consists of B-cell epitope mapping, vaccine properties, molecular docking, and dynamic simulation. The peptide vaccine candidate of B5 with the gp120 HIV-1 conserved region was found to provoke B-cell activation through a direct pathway, produce specific antibody, and increase protection from multi-strain viral infection.

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 Role of Bioinformatics in Personalized Medicine: Your Future Medical Treatment Deidre Valeska, Margareta; Patricia Adisurja, Gabriella; Bernard, Stefanus; Maulani Wijaya, Renadya; Aldino Hafidzhah, Muhammad; Aditya Parikesit, Arli
Cermin Dunia Kedokteran Vol 46, No 12 (2019): Kardiovaskular
Publisher : PT. Kalbe Farma Tbk.

Bioinformatika berperan sangat penting dalam personalized medicine. Dua metode penting dalam kajian ini adalah randomized algorithm dan computer assisted drug design (CADD). Kajian ini membahas aplikasi, kekurangan, dan masa depan kedua metode tersebut. Saran-saran untuk meningkatkan efek riset bioinformatika dalam kajian personalized medicine juga akan ditelaah.Bioinformatics is beneficial in personalized medicine. Two methods stand out, the randomized algorithm and computer assisted drug design (CADD). This article will discuss the application, pitfalls, and eventual future of those two methods. Suggestion to improve the clarity of the bioinformatics research in the field of personalized medicine will also be reviewed.

Troubled Helix â€“ Tinjauan Multiperspektif Genetika dalam Bioetika Anurogo, Dito; Aditya Parikesit, Arli
Cermin Dunia Kedokteran Vol 48, No 3 (2021): Obstetri dan Ginekologi
Publisher : PT. Kalbe Farma Tbk.

Dalam review ini, dibahas tinjauan multiperspektif genetika dalam bioetika. Dikemukakan prinsip-prinsip etika mutakhir, seperti: reciprocity, mutuality, solidarity, citizenry, dan universality. Dibahas pula prinsip-prinsip etika dan pemeriksaan genetika, seperti: otonomi, privasi, kebaikan, nonmaleficence, keadilan. Didiskusikan pula perspektif etnokultural dalam layanan genetika, milestones guideline etika dan regulasi riset biomedis internasional, prinsip-prinsip etika menurut Universal Declaration on Bioethics and Human Rights 2005, hak asasi manusia dan etika profesional: apresiasi translasional, perspektif utilitarianisme, perspektif deontologi, â€œsimalakamaâ€ pemeriksaan genetika, globalisasi bioetika, etika bioinformatika, dan riset eugenik.In this review, a multiperspective review of genetics in bioethics is discussed. The latest ethical principles are mentioned, such as: reciprocity, mutuality, solidarity, citizenry, and universality. The principles of ethics and genetic inquiry, such as: autonomy, privacy, kindness, nonmaleficence, justice was also discussed. Also discussed are multiperspective, ethnocultural perspectives in genetic services, milestones of ethical guidelines and international biomedical research regulations, ethical principles according to the Universal Declaration on Bioethics and Human Rights 2005, human rights and professional ethics: translational appreciation, utilitarianism perspective, deontological perspective, the â€œsimulacraâ€ of genetic examination, bioethics globalization, bioinformatics ethics, and eugenic research.

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