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All Journal HAYATI Journal of Biosciences Jurnal Pendidikan Matematika dan IPA Journal of Tropical Biodiversity and Biotechnology Indonesian Journal of Jamu
Kurniawan, Febri Yuda
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Earth & Planetary Sciences Education Environmental Science Health Professions Immunology & microbiology Mathematics Medicine & Pharmacology Physics

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MORPHOLOGICAL AND CHROMOSOMAL CHARACTERIZATION OF ORCHID Peristylus goodyeroides Lindl. FROM CURUG SETAWING, KULONPROGO Kurniawan, Febri Yuda; Riyadi, Anindita Della Rosa
Jurnal Pendidikan Matematika dan IPA Vol 12, No 2 (2021): July 2021
Publisher : Universitas Tanjungpura

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (571.851 KB) | DOI: 10.26418/jpmipa.v12i2.41811

Abstract

Peristylus goodyeroides is a terestrial orchid that scattered around Southeast Asia. Morphological characters of P. goodyeroides can vary, depending on the ecological factors and habitat. Cytological characters in the form of chromosome configurations can be used as a taxonomic tool for the process of identifying and understanding variations in taxa. The purpose of this study was to determine the morphological characters and chromosome configuration of the P. goodyeroides from Curug Setawing, Kulonprogo. The method used was morphological characterization and plant chromosome preparation by squash method with the main steps of fixation, maceration, staining and observation. Data were analyzed with the help of Image raster 3, Corel Draw X7, and Microsoft Excel 2013. P. goodyeroides from Curug Setawing has the morphological characters of root tubers, cylindrical stems, ovate leaf shape, convolutive leaf arrangement and creamy white flowers. The orchid has a number of chromosomes 2n = 10 with a karyotype formula of 2n = 2x = 8m + 2t. Metacentric chromosomes are found on chromosomes 1-8 and telocentric chromosomes 9-10. The absolute arm length of the chromosomes has a range of 2.03-3.44 μm, the relative arm length of the chromosomes is 2.21-3.32 μm, the length of the p arm is 1.13-1.58 μm and the q arm is 1.23-2.12 μm.
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 Analysis of Phalaenopsis Orchid Homeobox1 (POH1) Functional Gene for Shoot Development in Phalaenopsis Orchid Rasjid, Nuzlan; Kurniawan, Febri Yuda; Putri, Saifa Usni; Linggabuwana, Aviesta; Prasojo, Ireneus Seno; 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.83934

Abstract

The most favorite ornamental crop in Indonesia is orchid which benefited as floriculture. Therefore, the quality of this crop must be improved.  Biotechnology is appropriate to be used to improve the quality and quantity of orchid plants. To conduct this method, researchers must know what genes function in plant development. In Phalaenopsis orchids, the gene has been identified as homeobox genes called Phalaenopsis Orchid Homeobox1 (POH1). This research aims to conduct in silico analysis of the gene. The materials were retrieved from mRNA and amino acid databases. Then, the materials are aligned, visualized, motif location analysis, motif function discovery, phylogenetic construction, and protein 3D structural modelling. Based on mRNA and amino acid alignment, there are 4 domain regions that are conserved in POH1 and other homologous genes, such as KNOX1, KNOX2, ELK Domain, and Homeobox KN Domain, which roles as a transcription factor involved in plant development. SWISS-MODEL and ColabFold were used in protein modelling of the protein. By ColabbFold modelling, the modelling prediction uses 325 residues, higher than SWISS-MODEL in 59 residues. ColabFold validation by Ramachandra Plot depicts having the most favourite regions is 68.6%, while SWISS-MODEL is 92.3%. Another validation parameter is overall quality factor and QMEAN Score. Protein modelling by ColabFold has overall quality factor 89.252 and QMEAN Score 0.41 ± 0.05. However, SWISS-MODEL 3D prediction has overall quality factor 98.039 and QMEAN score of 0.71 ± 0.11. 
Isolation and Characterization of Chalcone Synthase (CHS) Gene in Variegated-Flower of Dendrobium 'Enobi' and Phalaenopsis Hybrid Orchids Linggabuwana, Aviesta; Putri, Saifa Usni; Kurniawan, Febri Yuda; Semiarti, Endang
HAYATI Journal of Biosciences Vol. 31 No. 2 (2024): March 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.2.382-391

Abstract

Variegated flowers, characterized by the presence of different colors in flowers, have high economic and aesthetic values. The main pigment in the orchid's purple flowers is anthocyanin, while the chalcone synthase (CHS) gene is the key to anthocyanin biosynthesis. Analysis of the CHS gene can reveal some changes, including mutations, in the process of color patterning in flowers. This study aims to determine the structure of the CHS gene related to color patterning in Dendrobium 'Enobi' and Phalaenopsis hybrid with variegated flowers. The methods applied in this study are floral morphology observation, DNA isolation, CHS gene amplification, anthocyanin measurement, and bioinformatic analysis. Morphologically, the variegated pattern has appeared since the flowers were still in the bud on both orchids. Based on the anthocyanin content analysis, the difference in the genus is not directly related to the differences in the flower's anthocyanin content. In addition, the purple zone in the D. 'Enobi' and Phalaenopsis hybrid has a longer fragment of CHS than the white zone. Our analysis suggested several mutations in the white zone and differences in the type and location of several conserved domain proteins. Mutations at the CHS gene fragment might cause decreased anthocyanin pigment formation in the white region.
Jamu Kunir Asem: Ethnomedicine Overview by Javanese Herbal Medicine Formers in Yogyakarta Kurniawan, Febri Yuda; Jalil, Muhamad; Purwantoro, Aziz; Daryono, Budi Setiadi; Purnomo
Jurnal Jamu Indonesia Vol. 6 No. 1 (2021): Jurnal Jamu Indonesia
Publisher : Tropical Biopharmaca Research Center, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jji.v6i1.211

Abstract

Kunir asem is one of the traditional drinks that still survive in Javanese society. The young generation needs to be introduced to the heritage of traditional herbal medicine, so that its existence is maintained. Some people judge that herbal medicine is an ancient traditional drink and does not keep up with the times. The objectives of this study are: (1) Explain the study of etnobotany which make up turmeric acid; (2) Explain how the principle of the benefits of kunir asem is based on the understanding of the seller of herbs in the Province of Yogyakarta. This study uses a qualitative method. The research data was taken with documentation, interviews, and documentation. The research data were analyzed by qualitative descriptive. The conclusion of this study is that biopharmaca plants in kunir asem are turmeric and tamarind, and some are added spices in the form of brown sugar, lemongrass, cardamom, cloves, kedawung, lime, and cinnamon. Herb sellers reveal that kunir asem can promote haids, facilitate digestion, reduce stomach acid, as an antibiotic, fresh body, and eliminate acne.
Co-Authors Aziz Purwantoro BUDI SETIADI DARYONO Endang Semiarti Jalil, Muhamad Kinasih, Anggiresti Linggabuwana, Aviesta Meidianing, Maura Indria Prasojo, Ireneus Seno Pratiwi, Apriliana Purnomo Putri, Saifa Usni Rasjid, Nuzlan Riyadi, Anindita Della Rosa