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All Journal Journal of Tropical Biodiversity and Biotechnology Jurnal Biologi Tropis Biota INDONESIAN JOURNAL OF MEDICAL LABORATORY SCIENCE AND TECHNOLOGY Jurnal Riset Biologi dan Aplikasinya Bioeksperimen
Kinasih, Anggiresti
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Education Environmental Science Health Professions Immunology & microbiology Medicine & Pharmacology Social Sciences

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In Silico Approach for DNA Barcoding using Phylogenetic Analysis of Coelogyne spp. based on the matK, rpoC1, rbcL and nrDNA Markers Pratiwi, Apriliana; Kinasih, Anggiresti; Meidianing, Maura Indria; Kurniawan, Febri Yuda; Semiarti, Endang
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 3 (2023): December
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.73130

Abstract

In silico biology is considered as an effective and applicable approach to initiate various research, such as biodiversity taxonomical conservation. Phylogenetic analysis using in silico taxonomy method for orchid species can provide data on genetic diversity and evolutionary relationships. One particular method that can be used to evaluate specific targets of gene loci in the taxonomic study is DNA barcoding. This research was conducted to determine the specific target locus gene using matK, rbcL, rpoC1, and nrDNA markers for DNA barcoding of the Coelogyne genus with in silico approach using phylogenetic analysis. All marker sequences were collected from the NCBI website and analysed using several softwares and methods, namely Clustal X for sample sequence alignment and MEGA 11 for phylogenetic tree construction and analysis. The results showed that the gene locus in Coelogyne recommended was the nrDNA gene locus. Phylogenetic analysis revealed that the use of the nrDNA gene locus was able to separate 17 Coelogyne species with two outgroup species, namely Cymbidium and Vanilla, then followed with ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) while the other gene loci, namely maturase K (matK) and polymerase beta' subunit (rpoC1) provided a visual phylogenetic tree in which the two outgroup species entered into the same clade as the Coelogyne species. Thus, the results of this study can be used as a reference to support the Coelogyne breeding and conservation program. 
In Silico Study of Secondary Metabolites in Dendrobium spp. as SARS-CoV-2 Antivirus on Main Protease (Mpro) Kinasih, Anggiresti; El Hakim, Alim; Arum, Dyah Ayu Puspita; Ramadhani, Aulia Noor; Semiarti, Endang
Jurnal Riset Biologi dan Aplikasinya Vol. 4 No. 1 (2022)
Publisher : Universitas Negeri Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.26740/jrba.v4n1.p19-25

Abstract

Infection and deaths cases by SARS-CoV-2 still increase and have not decreased significantly. Main protease (Mpro) is playing an important role in the replication of SARS-CoV-2 life cycle and causes of rapid transmission. Natural compounds are potential to be antiviral candidates with high bioavailability and low cytotoxicity. Orchids of Dendrobium genus have high diversity in Indonesia. Dendrobium has been used as traditional Chinese medicine and contains a group of secondary metabolites with antiviral activity. This study aimed to determine the potential of secondary metabolites of Dendrobium orchids as antiviral candidates against Mpro SARS-CoV-2 with in silico molecular docking. Secondary metabolites obtained from the KNApSAck and PubChem act as ligands. N3 inhibitors as native ligands were obtained from the RCSB. Mpro SARS-CoV-2 (6LU7) as a target macromolecule. Molecular docking was carried out using the online Covid-19 Docking Server using AutoDock Vina device. The most negative binding affinity value for each ligand compared to the native ligand binding affinity. Visualization with Discovery Studio software has been used to observe the protein amino acid residues contact for each ligand. The binding affinity of the native ligand inhibitor N3 is -7.5 kcal/mol. Based on the results of Mpro docking, three phytochemicals from Dendrobium spp., i.e., dendrocandin B, denthyrsinone, and denthyrsinol compounds have binding affinities of -7.7 kcal/mol, -7.9 kcal/mol, and -8.1 kcal/mol, respectively. It can be concluded that in Dendrobium orchid, denthyrsinol has the highest chance of binding so it has the potential to inhibit the Mpro SARS-CoV-2 activity.
Review: Perspective of Biotic and Abiotic Factors for Tropical Orchid Acclimatization and Ex-situ Conservation Kinasih, Anggiresti; Rafli, Muhamad; Nugrahening, Eria Rosanti; Oktaweni, Fiola; Budiastuti, Novi Saptariani; Hidayah, Nurul
Jurnal Biologi Tropis Vol. 25 No. 3 (2025): Juli-September
Publisher : Biology Education Study Program, Faculty of Teacher Training and Education, University of Mataram, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/jbt.v25i3.9718

Abstract

Acclimatization represents a critical transition phase in ex-situ conservation of tropical orchids, marking the shift from sterile in vitro conditions to more variable external environments. This literature review aims to synthesize recent experimental findings on the influence of abiotic and biotic factors on seedling viability and to propose an effective acclimatization protocol. A systematic analysis was conducted on over 30 peer-reviewed articles published between 2014 and 2024, covering media formulation, substrate selection, environmental controls, and microbial inoculation. The results highlight that optimized substrates such as moss, coconut fiber, and carbonized rice husk significantly improve root aeration and water retention. Supplementation with organic additives (e.g., peptone, coconut water, banana pulp) enhances early seedling vigor when applied to modified Murashige and Skoog (MS) media. Environmental parameters especially light intensity, diurnal temperature fluctuation (DIF), humidity, and photoperiod directly affect physiological responses. Moreover, inoculation with plant growth-promoting bacteria (PGPB) and mycorrhizal fungi contributes to phosphate solubilization, nitrogen fixation, siderophore production, and stress tolerance. In conclusion, the integration of species-specific abiotic and biotic strategies enhances survival and growth, offering scalable potential for orchid conservation and commercial propagation. It is recommended that future research focus on long-term physiological assessments and standardized inoculant formulations to improve protocol consistency across diverse orchid taxa.
Phylogenetic relationship of plastid large single copy genome and potential of ginsenoside compounds from Panax in Alzheimer disease Kinasih, Anggiresti; Ahmar, Rasyidah Fauzia; Fatmawati, Dwi Retno; Rivaldi, Muhammad; Suhaemi, Emi; Saputra, Novanda Eka; Haniyyah, Hernanda Afra
Biota Vol 18 No 1 (2025)
Publisher : Universitas Islam Negeri Mataram

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

Abstract

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the most prevalent cause of dementia, marked by cognitive decline and memory loss. Current treatments are largely symptomatic and do not halt disease progression, underscoring the urgent need for novel therapeutics. Natural products, such as Panax notoginseng, offer promising alternatives due to their structural diversity and multi-target potential. This study investigates the therapeutic potential of 125 terpenoid compounds identified from P. notoginseng, focusing on their relevance to AD. Eight ginsenosides demonstrated notable neuroprotective effects, including improvements in memory and cognitive function. Among them, Ginsenoside Rb1 and Notoginsenoside R1 exhibited low predicted toxicity via oral and intraperitoneal routes, indicating favorable safety profiles. Target prediction and molecular docking suggest these compounds interact with G protein-coupled receptors implicated in cognition and neuroprotection, such as dopaminergic, serotonergic, muscarinic, and adrenergic receptors. However, their deviation from Lipinski’s Rule of Five may limit oral bioavailability. To address this, nanotechnology-based delivery systems are proposed to enhance solubility, permeability, and drug-likeness. These findings support the continued exploration of P. notoginseng ginsenosides as potential anti-dementia agents and highlight nanotechnology's role in overcoming pharmacokinetic limitations
Integrating field inventory and in silico phylogenetic analysis of pteridophytes at Gandul Mount, Indonesia Candra, Sri Devi Galuh; Kinasih, Anggiresti; Khotimperwati, Lilih
Bioeksperimen: Jurnal Penelitian Biologi March 2026
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/bioeksperimen.v12i1.15947

Abstract

Pteridophytes are vascular plants that are considered the most primitive plants because they only use spores to reproduce. Several major fern families exhibit distinctive morphological and ecological characteristics that support their taxonomic recognition. Pteridophytes represent an important component of tropical biodiversity, yet their diversity and evolutionary relationships in karst ecosystems remain poorly documented. This study aimed to integrate field inventory and in silico phylogenetic analysis to assess pteridophyte diversity in Gandul Mount, Wonogiri, Central Java. Field data were collected using the cruise method, followed by morphological identification and habitat characterization. Phylogenetic relationships were inferred using matK gene sequences retrieved from the NCBI database and analyzed with the Maximum Likelihood method. The inventory recorded 17 species belonging to eight families, with Pteridaceae as the most dominant. Most species were lithophytic, indicating strong adaptation to rocky substrates. Two species were categorized as Least Concern, while the remaining species have not been evaluated by the IUCN. Eleven species showed ethnobotanical potential as medicinal plants, ornamentals, and phytoremediation agents. Phylogenetic analysis revealed clustering patterns consistent with taxonomic classification. These results demonstrate that Gandul Mount harbors considerable pteridophyte diversity and confirm that combining field-based inventory with in silico phylogenetic analysis provides a robust approach for biodiversity assessment and evolutionary interpretation.
Computational Modeling of a Novel CTX-M β-Lactamase Escherichia coli Isolated from Yogyakarta, Indonesia Using I-TASSER Kinasih, Anggiresti; Retnaningrum, Endah
JURNAL INDONESIA DARI ILMU LABORATORIUM MEDIS DAN TEKNOLOGI Vol 8 No 1 (2026): Integration of Molecular Approaches in Addressing Drug Resistance and Changing Gl
Publisher : Universitas Nahdlatul Ulama Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33086/ijmlst.v8i1.7267

Abstract

Extended-spectrum β-lactamases (ESBLs), especially those of the CTX-M family, significantly contribute to antibiotic resistance in Escherichia coli. While CTX-M variants are well-characterized in clinical settings, their structural features in foodborne E. coli remain underexplored, particularly in countries like Indonesia. This study aimed to predict and validate the three-dimensional (3D) structure of a novel CTX-M β-lactamase protein from an E. coli isolate (D4DU2-ESBL-EC) culture collection at Laboratory of Microbiology, Universitas Gadjah Mada (UGM). This study reports a novel CTX-M variant from E. coli D4DU2, a locally strain originated from raw chicken meat in Yogyakarta traditional market that has been shown to adapt and thrive in Sleman Regency, Indonesia. Based on phylogenetic and structural analyses, E. coli D4DU2 evolutionary link to Indian CTX-M-15, with distinct mutations at W253L, P254A amino acid near the active site. The 3D structure of D4DU2 CTX-M β-lactamase was predicted using I-TASSER and validated using PROCHECK. Ramachandran analysis showed 78.4% of residues in the most favored regions, 20.5% in allowed regions, and only 1.2% in disallowed regions, confirming high stereochemical quality. These findings highlight potential local adaptation and emergence of a unique ESBL-producing E. coli strain. This study provides a reliable model for CTX-M β-lactamase from foodborne E. coli in Indonesia, supporting One Health-based surveillance and intervention strategies. Overall, this study demonstrates that I-TASSER, complemented by PROCHECK validation, offers a valuable in silico approach for the structural characterization of ESBL proteins from foodborne bacterial isolates in resource-limited contexts
Co-Authors Ahmar, Rasyidah Fauzia Arum, Dyah Ayu Puspita Budiastuti, Novi Saptariani Candra, Sri Devi Galuh El Hakim, Alim Endang Semiarti Fatmawati, Dwi Retno Haniyyah, Hernanda Afra Khotimperwati, Lilih Kurniawan, Febri Yuda Meidianing, Maura Indria Nugrahening, Eria Rosanti NURUL HIDAYAH Oktaweni, Fiola Pratiwi, Apriliana Rafli, Muhamad Ramadhani, Aulia Noor Retnaningrum, Endah Rivaldi, Muhammad Saputra, Novanda Eka Suhaemi, Emi