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KARAKTERISTIK ISOLAT Rhizoctonia sp. PATOGENIK DAN Rhizoctonia MIKORIZA PADA TANAMAN ANGGREK TANAH (Spathoglottis plicata) S. Soelistijono; Christanti Sumardiyono; Achmadi Priyatmojo; Endang Semiarti
JURNAL ILMIAH AGRINECA Vol. 12 No. 1 (2012): JURNAL AGRINECA
Publisher : Fakultas Pertanian, Universitas Tunas Pembangunan Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36728/afp.v12i1.497

Abstract

Mycorrhizal Rhizoctonia is a fungus that capable to associate with terrestrial orchids. Apart from being mycorrhizal, there are isolates of Rhizoctonia sp. that are pathogenic and caused root rot disease on Spathoglottis plicata. This study aimed to know the differences between pathogenic Rhizoctonia sp. and mycorrhizal Rhizoctonia in morphology and molecular structure using RAPD technique. The results showed that colony colour,  cell lenght and nucleus number a several isolates of pathogenic Rhizoctonia sp. and of mycorrhizal Rhizoctonia on S. plicata had no differences, but had differences on cell thickness and isolate grouping based on hyphal anastomosis test. RAPD molecular technique showed that each isolate of pathogenic Rhizoctonia sp. and mycorrhizal Rhizoctonia had differences on DNA structure.
PENGARUH PEPTON TERHADAP PERTUMBUHAN EMBRIO ANGGREK Vanda tricolor Lindley var. Suasiv ASAL MERAPI SECARA IN VITRO Rizka Riliant Puspasari; Ikhsanudin Nur Rosyidi; Eka Fitriana Candra Ningrum; Endang Semiarti
Scripta Biologica Vol 5, No 1 (2018)
Publisher : Fakultas Biologi | Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (944.029 KB) | DOI: 10.20884/1.sb.2018.5.1.762

Abstract

Orchidaceae is a valuable ornamental plant in Indonesia’s export commodities. The growth of orchid in nature is prolonged due to its microscopic size of the seed and has no endosperm. In the mass-production, an inducer is required to accelerate the growth in an in-vitro culture, one of which is peptone. The embryos used in this study is Merapi endemic orchid, the Vanda tricolor Lindley var. Suavis. This study aimed to determine the effect of peptone on the growth of eight weeks old of Vanda tricolor Lindley var. Suavis embryos and to determine the optimal peptone concentration to induce the growth of the orchid embryo. This experiment was conducted in the Biotechnology Laboratory of the Faculty of Biology Universitas Gadjah Mada from September to October 2016. The treatments applied in this study was a variety of peptone concentrations (0–3 g/L) in growth media to induce eight weeks old protocorm subcultures. The study measured the morphological development of protocorm to determine the effect. The results showed a positive effect of peptone on the growth of orchid embryos at the NP1 treatment concentration of 1 g/L. The growth reached the phase 6 with the rate measured about 6.85±0.001% in the fourth week. This value was higher than the protocorm growth rate when it reached the phase 6 in the fourth week on the NP0 medium measured at 5.22±0.003%, on the medium NP2 at 1.15±0.002%, and on the medium NP3 at 1.02±0.001%. This result showed the effect of peptone concentration to induce the growth of Vanda tricolor Lindley var. Suavis embryo, but the excess concentration of peptone inhibited the growth of protocorm.
Morphological And Biochemical Responses Of Saccharum Spontaneum L. Accessions To Drought Stress Aminatun Munawarti; Taryono Taryono; Endang Semiarti; Sismindari Sismindari
Journal of Tropical Life Science Vol. 4 No. 1 (2014)
Publisher : Journal of Tropical Life Science

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

Abstract

Glagah (Saccharum spontaneum L.) has potential value as a crop species and may also be used in sugarcane breeding programs; however, this germplasm has not been extensively used in breeding programs, primarily in relation to improve drought tolerance. The objectives of this experiment were to evaluate the effect of drought stress initiated at vegetative growth stage on growth, leaf proline content and protein pattern of seven glagah accessions (BOT-53, BOT-54, BOT-60, BOT-77, BOT-78, BOT-84, and BOT-88). The plants were propagated from single node stalk segments in polybag in the field under non-stress condition for two months. The two month-old plants were then subjected to drought stress by withholding watering for eight weeks. Untreated control plants were watered every two days. Results indicated that drought stress reduced plant height, stalk diameter and green leaf number. On the other hand, there was a little difference between drought-stressed and control plants in terms of proline content. The protein pattern showed that drought stress caused a change in gene expression in the form of induction or repression of protein expression. A specific protein with a low range of molecular weight (Rf value about 0.647) showed constitutively expressed in accession BOT-53 but drought-inducible expressed in BOT-54. Keywords: Drought stress, glagah, proline, protein pattern, Saccharum spontaneum
Biodiversitas dan Kekerabatan Fenetik Spesies Anggrek Alam di Kawasan Ekowisata Ayunan Langit, Kulonprogo Evilili Usmanti; Febri Yuda Kurniawan; Maura Indria Meidianing; Amru Rizal Basri; Endang Semiarti
Al-Kauniyah: Jurnal Biologi Vol 15, No 2 (2022): AL-KAUNIYAH JURNAL BIOLOGI
Publisher : Department of Biology, Faculty of Science and Technology, Syarif Hidayatullah State Islami

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/kauniyah.v15i2.19801

Abstract

AbstrakEkowisata Ayunan Langit memiliki kondisi geografis yang mendukung bagi pertumbuhan anggrek, sehingga daerah tersebut memiliki diversitas anggrek alam yang tinggi sebagai salah satu daya tarik wisata. Beberapa spesies anggrek dapat memiliki kemiripan secara morfologi meskipun tidak berkerabat dekat. Dalam rangka pengembangan Kawasan Wisata Terpadu Ayunan Langit diperlukan data keragaman spesies-spesies anggrek di kawasan ini. Penelitian ini bertujuan untuk melakukan inventarisasi, identifikasi, dan melihat hubungan kekerabatan antar spesies anggrek alam di Kawasan Ayunan Langit. Metode yang digunakan dalam penelitian ini adalah koleksi spesimen, identifikasi, dan karakterisasi morfologi organ vegetatif spesimen, serta analisis hubungan kekerabatan. Analisis kekerabatan menggunakan software Ms Excel dan MVSP. Terdapat 14 spesies anggrek alam yang ditemukan di Kawasan Ayunan Langit. Anggrek alam di kawasan tersebut didominasi dari anggota Subfamili Epidendroideae dan anggrek epifit. Semua spesies masuk dalam kategori Appendix II CITES. Berdasarkan analisis kekerabatan fenetik, dendogram terbagi dalam dua kluster berdasarkan karakter morfologi organ vegetatifnya. Spesies anggrek yang berasal dari genus yang sama belum tentu dapat mengelompok pada klaster yang sama, misalnya pada Dendrobium. Karakter morfologi organ vegetatif belum dapat digunakan untuk melihat hubungan kekerabatan fenetik secara akurat pada anggrek. Karakter organ generatif berperan penting dalam memberikan hasil visualisasi kekerabatan antar spesies anggrek yang lebih akurat.AbstractAyunan Langit ecotourism has favorable geographical conditions for orchid growth, hence the area has a high diversity of wild orchids as a tourist attraction. Several orchid species can be morphologically similar even though they are not closely related. For Ayunan Langit integrated tourism area development, orchid diversity data are required. This study aimed to conduct an inventory, identification, and relationship analysis between wild orchid species in Ayunan Langit ecotourism. Specimen collection, identification, and morphological characterization were conducted on specimen's vegetative organs. Relationship analysis was conducted with Ms Excel and MVSP. There are 14 wild orchid species found in the Ayunan Langit, dominated by Epidendroideae members and epiphytic orchids. All species are included in the CITES Appendix II category. Based on the phenetic relationship analysis, the dendrogram was divided into two clusters based on the morphological characters of the vegetative organs. Orchid species belongs to the same genus may not necessarily be grouped in the same cluster, for example in Dendrobium. Morphological characters of vegetative organs cannot be used to visualize the phenetic relationship accurately in orchids. Generative organ characters play an important role in providing a more accurate visualization of the relationship between orchid species. 
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. 
Characterization of Flower’s Color based on CHS Gene Structure in Phalaenopsis ‘OX Queen’ and Dendrobium ‘Cheddi Jagan’ Orchids Hanifa, Yumna Rahmadias; Gildantia, Elke; Kasi, Pauline Destinugrainy; Purwantoro, Aziz; Semiarti, Endang
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.91511

Abstract

Orchids (Orchidaceae) are ornamental plants known for their high aesthetic value attributed to the shapes, colours, and fragrances of their flowers. Two types of hybrid orchids with attractive flowers, namely the Phalaenopsis 'OX Queen' orchid and the Dendrobium 'Cheddi Jagan' boast attractive flowers were used in this research, because of the beauty of its flower colour. The objective of this research is to characterise the morphology of flower colour and CHS (Chalcone Synthase) gene content that induces flower colour. The method used in this research analyzing the flower’s colour by using the RHS (Royal Horticultural Society) colour chart and molecular analysis by DNA genomic isolation and PCR amplification of gDNA for CHS gene specific primers. The results showed that purple colour is observed through the RHS, with P. 'OX Queen' coded as Deep Purple Pink (N73A) and D. 'Cheddi Jagan' coded as Strong Reddish Purple (N72C). The CHS gene can be amplified in P. ’OX Queen’ 1,287 bp and D. ’Cheddi jagan’ 3,731 bp. In both orchids, the results of amplification showed CHS motifs with conserved domains PLN03172 and PLN03170. The research results show that there is a significant difference in the morphology of the flowers of orchids. Purple colour is observed through the RHS, with P. 'OX Queen' coded as N73A and D. 'Cheddi Jagan' coded as N73C. The results showed that gDNA can be isolated by using CTAB method according to Murray and Thomson, and the CHS gene can be amplified by using CHS primers, resulting 1200 bp of P. 'OX Queen' and 2500 bp for D. 'Cheddi Jagan'. Through this study, preliminary data is expected to be obtained for future research, which is the formation of variegated flowers through editing the CRISPR/Cas9 genome in the CHS gene. This research is intended to support further studies on the formation of variegated flower patterns in P. 'OX Queen' and D. 'Cheddi Jagan’, focusing on the CHS gene using CRISPR/Cas9 technique. 
In silico study of RKD4 gene function in Coffea arabica L. and various cultivated plants related to embryo formation initiation Arimarsetiowati, Rina; Semiarti, Endang; Daryono, Budi Setiadi; Astuti, Yohana Theresia Maria; Prastowo, Erwin
Pelita Perkebunan (a Coffee and Cocoa Research Journal) Vol. 40 No. 2 (2024)
Publisher : Indonesian Coffee and Cocoa Research Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iccri.jur.pelitaperkebunan.v40i2.600

Abstract

Arabica coffee supplies 60% of world coffee production because has a unique taste as superior quality beverage. Arabica coffee micropropagation can be conducted by somatic embryogenesis technique which produce clonal, fast dan uniform plant. The somatic embryogenesis (SE) process describes the integration of endogenous signals and gene reprogramming, which releases signals to initiate embryogenic processes. The use of endogenous auxin, either alone or in combination with other PGRs or stress, induces differential gene expression, which modifies the genetic program of somatic cells and regulates the transition to each stage during SE development. The RKD4 gene (RWP-RK DOMAIN-4) is a gene that plays a role in early initiation embryo formation and development. The characterization of RKD4 genes in C. arabica is still limited and under explored. The objective of this research is to explore the characteristics of RKD4 gene by comparing the difference and similarity of RKD4 gene in C. arabica and other cultivated plants. The method was initiate by identifying nucleotide sequences from the National Center for Biotechnology Information (NCBI) database. Furthermore, consists of analysis of nucletide alignment, alignment of amino acid sequences, protein analysis, protein motif functions discovery, analysis of phylogenetic tree, protein 2D and 3D-modelling and physiochemical properties. According to the analysis, there were 100 polymorphism points with a total number of mutations of 211 points. The phylogenetic tree show C. arabica L. has a very close relationship with grapes (Vitis vinivera) based on the RKD4 protein, gene structures and protein motifs. There are nine highly conserved motifs found in the protein alignment. C. arabica L. had more methyl jasmonate element responses than A. thaliana. The findings are useful to understand the intitiation of embryo formation mechanisms of C. arabica L and other cultivate plants during propagation through somatic embryogenesis in the long run.
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.
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.
Co-Authors , Surifah A.A. Ketut Agung Cahyawan W Achmadi Priyatmojo Aditya Nur Subchan Agus Slamet Ahmad Suyoko Alisa Julia Nurulita Alydarafa, Hafshah Aminatun Munawarti Aminatun Munawarti, Aminatun Amru Rizal Basri Anami Riastri Andani Kesuma, Amarilis Annisa, RR Rifka Ari Indrianto Ari Indrianto Ari Indrianto Ari Indrianto Ari Indrianto Ari Indrianto Ari Indrianto Aries Bagus Sasongko Arimarsetiowati, Rina Arum, Dyah Ayu Puspita Asri Fajar Milasari Azis Purwantoro Azis Purwantoro Aziz Purwantoro Bekti Sulistya Utami Binti Tsulsiyah Brilliant Kharisma Apritadila BUDI SETIADI DARYONO Cahya Lembayung Sutra Catharina Tri Widyastuti Christanti Sumardiyono Christanti Sumardiyono Della Rosiana Ningtias Devi Bunga Pagalla Dewi Tika Sari Dewi Yuliana Rizqi Dika Sundari Eka Fitriana Candra Ningrum El Hakim, Alim Erwin Prastowo Evilili Usmanti Exsyupransia Mursyanti Exsyupransia Mursyanti Exsyupransia Mursyanti Faiza Senja Widya Perdana Falah Nur Alifianto Febri Yuda Kurniawan Fhea Putri Cristy Fitriana Puspitasari Frisca Damayanti Gde Cahyadi Wirajagat Gildantia, Elke Hanifa, Yumna Rahmadias Ikhsanudin Nur Rosyidi Ixora Sartika Mercuriani JAKA WIDADA Jose Gutierrez-Marcos Jose Gutierrez-Marcos Kana Ninomiya Kinasih, Anggiresti Kurniawan, Febri Yuda Linggabuwana, Aviesta Maryani Maryani Matsumoto, Shogo Maura Indria Meidianing Meidianing, Maura Indria Melati, Chrisnanda Ayu Muhammad Dylan Lawrie Muhammad Dylan Lawrie Muhammad Dylan Lawrie Muhammad Dylan Lawrie Naufal Ghozi Aditya Perdana Ni Luh Putu Kayika Febryanti Nintya Setiari Nintya Setiari Nopitasari, Sri Oedjijono Oedjijono, Oedjijono Oktaviana Herawati Pauline Destinugrainy Kasi Prasojo, Ireneus Seno Pratiwi, Apriliana Putra, Rinaldi Rizal Putri, Saifa Usni R Soelistijono Rahayu Sulistianingsih Ramadhani, Aulia Noor Rasjid, Nuzlan Rinaldi Rizal Putra, Rinaldi Rizal Rindang Dwiyani Rizka Riliant Puspasari Rumiyati Rumiyati Rumiyati, Rumiyati Seonghoe Jang Setiaji, Arkan Shogo Matsumoto Sismindari . Sismindari Sismindari Sismindari Sismindari Sitarina Widyarani Soenghoe Jang Sri Nopitasari Sri Wahyuningsih Stalis Norma Ethica Sukarti Moeljopawiro Sukarti Moeljopawiro Sukarti Moeljopawiro Sukarti Moeljopawiro Sukarti Moeljopawiro Sukarti Moeljopawiro Sukarti Moeljopawiro Sulastri Isminingsih Taryono, Taryono Thoyibatul Farida Tri Joko Raharjo Triono Bagus Saputro, Triono Bagus Umi Kulsum Nur Qomariah Windi Mose Windi Mose Woerjono Mangoendidjojo Woro Anindito Sri Tunjung Yasushi Yoshioka Yohana Theresia Maria Astuti, Yohana Theresia Maria Yoshioka, Yasushi Yuli Setiawati Yuuki Asano Zulfa Layina