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All Journal Journal of Tropical Biodiversity and Biotechnology Jurnal Biologi Tropis Jurnal Riset Biologi dan Aplikasinya
Kinasih, Anggiresti
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Immunology & microbiology Medicine & Pharmacology

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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.
Co-Authors Arum, Dyah Ayu Puspita Budiastuti, Novi Saptariani El Hakim, Alim Endang Semiarti Kurniawan, Febri Yuda Meidianing, Maura Indria Nugrahening, Eria Rosanti NURUL HIDAYAH Oktaweni, Fiola Pratiwi, Apriliana Rafli, Muhamad Ramadhani, Aulia Noor