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All Journal Narra J Indonesian Journal of Life Sciences
Parikesit, Arli A.
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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Bioinformatics tools to Predict N-myristoylation Site a Comparison Study Arifin, Muhammad Zainul; Parikesit, Arli A.
Indonesian Journal of Life Sciences 2019: IJLS Vol 01 No .01
Publisher : Indonesia International Institute for Life Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (510.153 KB) | DOI: 10.54250/ijls.v1i1.10

Abstract

Protein N-myristoylation is the covalent attachment of myrstate, via an amide bond, to the N-terminal glycine residue of a nascent polypeptide assisted by myristol-CoA protein: N-myristoltransferases (NMT). PROSITE motif describes 5 amino acid after glycine site that would give rise to myristoylation site. However, applied to whole database extract, this motif give too many false postive results. Therefore 2 new tools were developed for N-myristoylation prediction.Taking physical properties into consideration inceases prediction scores greatly. However, these algorithms still cannot predict myristoylated site correctly 100% of the time due to limited understanding of the real mechanims underlying N-myristoylation
Application of CRISPR-Cas9 genome editing technology in various fields: A review Ansori, Arif NM.; Antonius, Yulanda; Susilo, Raden JK.; Hayaza, Suhaila; Kharisma, Viol D.; Parikesit, Arli A.; Zainul, Rahadian; Jakhmola, Vikash; Saklani, Taru; Rebezov, Maksim; Ullah, Md. Emdad; Maksimiuk, Nikolai; Derkho, Marina; Burkov, Pavel
Narra J Vol. 3 No. 2 (2023): August 2023
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v3i2.184

Abstract

CRISPR-Cas9 has emerged as a revolutionary tool that enables precise and efficient modifications of the genetic material. This review provides a comprehensive overview of CRISPR-Cas9 technology and its applications in genome editing. We begin by describing the fundamental principles of CRISPR-Cas9 technology, explaining how the system utilizes a single guide RNA (sgRNA) to direct the Cas9 nuclease to specific DNA sequences in the genome, resulting in targeted double-stranded breaks. In this review, we provide in-depth explorations of CRISPR-Cas9 technology and its applications in agriculture, medicine, environmental sciences, fisheries, nanotechnology, bioinformatics, and biotechnology. We also highlight its potential, ongoing research, and the ethical considerations and controversies surrounding its use. This review might contribute to the understanding of CRISPR-Cas9 technology and its implications in various fields, paving the way for future developments and responsible applications of this transformative technology.
Designing hybrid CRISPR-Cas12 and LAMP detection systems for treatment-resistant Plasmodium falciparum with in silico method Parikesit, Arli A.; Hermantara, Rio; kevin, Gregorius; Sidhartha, Elizabeth
Narra J Vol. 3 No. 3 (2023): December 2023
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v3i3.301

Abstract

Genes associated with drug resistance of first line drugs for Plasmodium falciparum have been identified and characterized of which three genes most commonly associated with drug resistance are P. falciparum chloroquine resistance transporter gene (PfCRT), P. falciparum multidrug drug resistance gene 1 (PfMDR1), and P. falciparum Kelch protein K13 gene (PfKelch13). Polymorphism in these genes could be used as molecular markers for identifying drug resistant strains. Nucleic acid amplification test (NAAT) along with DNA sequencing is a powerful diagnostic tool that could identify these polymorphisms. However, current NAAT and DNA sequencing technologies require specific instruments which might limit its application in rural areas. More recently, a combination of isothermal amplification and CRISPR detection system showed promising results in detecting mutations at a nucleic acid level. Moreover, the Loop-mediated isothermal amplification (LAMP)-CRISPR systems offer robust and straightforward detection, enabling it to be deployed in rural and remote areas. The aim of this study was to develop a novel diagnostic method, based on LAMP of targeted genes, that would enable the identification of drug-resistant P. falciparum strains. The methods were centered on sequence analysis of P. falciparum genome, LAMP primers design, and CRISPR target prediction. Our designed primers are satisfactory for identifying polymorphism associated with drug resistant in PfCRT, PfMDR1, and PfKelch13. Overall, the developed system is promising to be used as a detection method for P. falciparum treatment-resistant strains. However, optimization and further validation the developed CRISPR-LAMP assay are needed to ensure its accuracy, reliability, and feasibility
Co-Authors Ansori, Arif NM. Antonius, Yulanda Burkov, Pavel Derkho, Marina Hayaza, Suhaila Jakhmola, Vikash Kevin, Gregorius Kharisma, Viol D. Maksimiuk, Nikolai Muhammad Zainul Arifin Rahadian Zainul Rebezov, Maksim Rio Hermantara Saklani, Taru Sidhartha, Elizabeth Susilo, Raden JK. Ullah, Md. Emdad