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All Journal MPI (Media Pharmaceutica Indonesiana) Journal of Tropical Biodiversity and Biotechnology Bioinformatics and Biomedical Research Journal Jurnal Bioteknologi & Biosains Indonesia (JBBI)
PERMATASARI, Galuh Wening
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Education Engineering Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology

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The Role of Phytochelatin Synthase in Phytoremediation Agent: Structural Conservation of Phytochelatin (PC) Synthase to Maintain Its Activity as Heavy Metal Detoxification in Plant Vidayanti, Viky; Permatasari, Galuh Wening
Bioinformatics and Biomedical Research Journal Vol. 3 No. 2 (2020): Volume 3 issue 2
Publisher : Future Science

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Abstract

Phytochelatin (PC) Enzyme has crucial role in heavy metal detoxification and homeostasis in plants. This study aimed to evaluate the genetic variation of PC synthase related to its activity based on structural comparison. We evaluated PC genes and protein sequences from 6 plants namely, Brassica sp., Amaranthus sp., Noccaea sp., Arabidopsis sp., Nicotiana sp., and Pteris sp. All sequences were aligned based on CLUSTALW matrix for DN sequences and MUSCLE algorithm for protein sequences. Data were clustered using MEGA Software for similarity clustering. Selected data were further modeled using SWISSMODEL to evaluate the 3D-structural analysis based on homology modeling. Thus, all protein models were superimposed and evaluated the structure comparison based on RMSD data. The result showed that genetic variation of PC gene is high among species. But it is clustered for the same species has similar sequence. In addition, protein sequences also showed the high diversity among species and it is still clustered based on their genus. RMSD data showed that PC synthase from 6 plant has similar structure and tend to conserved even there is genetic variation or amino acid modification. We concluded that structural of PC gene is more conserved than its sequences. It is important to keep its function among species.
Sequence-Structure Comparative and Network-Based Prediction of Drought Gene Candidate Regulator in Elaeis guineensis Permatasari, Galuh Wening; Putranto, Riza Arief; Mardhika, Larasati Dena; Aksa, Annisa Aulia; Setiawati, Yuli; Minarsih, Hayati; Riyadi, Imron; Ernayunita, Ernayunita
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 3 (2024): September
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.90808

Abstract

Drought poses a significant threat to global food security, particularly impacting crops like oil palm. Selecting genes for genome editing to enhance drought tolerance presents formidable challenges. To ensure that the target gene is chosen correctly and results in the desired character, a pilot study is necessary to determine the target gene for knockout. Two genes drought-related, AtBRL3 and AtOST2, were scrutinized in this context. Aligned with the Elaeis guineensis genome, their neighbouring proteins and gene ontology were analysed to identify potential targets for genome editing. AtBRL3, identified as BRL1 (XP_010913986.1) in E. guineensis, exhibited 58.48% identity and 100% coverage. It interacts with 12 nodes, including BIR1, BRI1, and AT2G20050, crucial for signalling pathways and cellular responses. Molecular function analysis revealed kinase activity. AtOST2 showed high similarity to plasma membrane ATPase/HA1 (XP_010913679.1) in E. guineensis, with 87.46% identity and 100% query cover. It correlated with 14 genes associated with ABA stimulus, stomatal movement, and hormone response. EgBRL1 and EgHA1, resembling AtBRL3 and AtOST2, respectively, emerge as promising targets for developing drought-tolerant oil palm cultivars through gene editing. Nonetheless, further validation through in vitro gRNA target selection and in vivo conversion of OST2/BRL3-containing plasmids in oil palm calluses is indispensable to demonstrate their efficacy in conferring novel drought resistance traits. 
Active compounds of fingerroot (Boesenbergia pandurata) for obesity treatment: in silico approaches Yuniarto, Ari; Aji, Abdul; Ramadhani, Anggia Noor; Permatasari, Galuh Wening
MPI (Media Pharmaceutica Indonesiana) Vol. 4 No. 1 (2022): JUNE
Publisher : Fakultas Farmasi, Universitas Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24123/mpi.v4i1.4807

Abstract

Obesity has become increasingly prevalent worldwide each year. Several studies have proven that herbs are effective in preventing obesity. The research delved into the active compounds of Boesenbergia pandurata to reveal their mechanisms of action by utilizing bioinformatics approaches. The research methods included active compounds selection, QSAR analysis, networking analysis, molecular docking, and ADME prediction. The QSAR analysis predicted that the active compounds were correlated with some theoretical activities with more than 0.5 probability, namely vasoprotective, anti-hypercholesterolemic, anti-inflammatory, free radical scavenging, and as a lipid metabolism regulator and TNF expression inhibitor. Furthermore, the results of the networking analysis showed that five compounds (pinocembrin, cardamonin, flavokawain B, flavokawain C, and tectochrysin) had direct interactions with RPS6KB1. Pinocembrin exhibited the highest binding affinityof -7.26 kcal/mol, although not as strong as that of the control ligand (FS9). The ADME prediction indicated that the five compounds were non-toxic and had excellent absorption. It can be concluded that the active compounds of B. pandurata have the ability to improve metabolic syndrome, especially obesity, in silico through several mechanisms, such as suppression of pro-inflammatory cytokine, regulation of lipid metabolism, and those associated with antioxidants.
IDENTIFICATION OF KEY NITROGEN USE EFFICIENCY-RELATED GENES IN OIL PALM USING BIOINFORMATICS APPROACHES Permatasari, Galuh Wening; Setiowati, Retno Diah; Wening, Sri
Jurnal Bioteknologi dan Biosains Indonesia Vol. 12 No. 1 (2025)
Publisher : BRIN - Badan Riset dan Inovasi Nasional

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Abstract

Efficient nitrogen use is crucial for maximizing oil palm yield while reducing environmental impact. Poor nitrogen utilization causes excessive growth and nutrient loss. This study uses bioinformatics to identify key genes linked to nitrogen use efficiency, providing insights for genetic improvement and sustainable cultivation.Protein-protein interaction (PPI) networks, functional enrichment, and structural modeling were employed to uncover candidate genes regulating nitrogen uptake and metabolism. Sixty-two nitrogen use efficiency associated genes from rice (Oryza sativa) were analyzed via BLASTp against the E. guineensis genome (NCBI), selecting those with >80% similarity. PPI networks were constructed using STRING-db and analyzed in Cytoscape v3.7.1. Functional enrichment (Gene Ontology) and structural analysis (AlphaFold, PyMol v2.5.4) were performed. Twelve nitrogen use efficiency related genes were identified, with CESA4, CESA7, and CESA9 emerging as key regulators based on high degree and betweenness values in PPI analysis. These genes are linked to plant cell wall biosynthesis. Structural analysis showed high similarity to rice homologs, with RMSD values of 0.338 Å (CESA4) and 0.396 Å (CESA9), indicating strong conservation area. Their structural relevance suggests they are promising targets for molecular breeding marker to enhance nitrogen utilization and sustainability in oil palm.
Co-Authors Aji, Abdul Aksa, Annisa Aulia Ernayunita, Ernayunita Hayati Minarsih Imron Riyadi Mardhika, Larasati Dena PUTRANTO, Riza Arief Ramadhani, Anggia Noor Setiowati, Retno Diah Sri Wening Vidayanti, Viky Yuli Setiawati, Yuli Yuniarto, Ari