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Sofyantoro F, Septriani NI, Yudha DS, Wicaksono EA, Priyono DS, Putri WA, Primahesa A, Raharjeng ARP, Purwestri YA, Nuringtyas TR. Zebrafish as Versatile Model for Assessing Animal Venoms and Toxins: Current Applications and Future Prospects. Zebrafish 2024. [PMID: 38608228 DOI: 10.1089/zeb.2023.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Animal venoms and toxins hold promise as sources of novel drug candidates, therapeutic agents, and biomolecules. To fully harness their potential, it is crucial to develop reliable testing methods that provide a comprehensive understanding of their effects and mechanisms of action. However, traditional rodent assays encounter difficulties in mimicking venom-induced effects in human due to the impractical venom dosage levels. The search for reliable testing methods has led to the emergence of zebrafish (Danio rerio) as a versatile model organism for evaluating animal venoms and toxins. Zebrafish possess genetic similarities to humans, rapid development, transparency, and amenability to high-throughput assays, making it ideal for assessing the effects of animal venoms and toxins. This review highlights unique attributes of zebrafish and explores their applications in studying venom- and toxin-induced effects from various species, including snakes, jellyfish, cuttlefish, anemones, spiders, and cone snails. Through zebrafish-based research, intricate physiological responses, developmental alterations, and potential therapeutic interventions induced by venoms are revealed. Novel techniques such as CRISPR/Cas9 gene editing, optogenetics, and high-throughput screening hold great promise for advancing venom research. As zebrafish-based insights converge with findings from other models, the comprehensive understanding of venom-induced effects continues to expand, guiding the development of targeted interventions and promoting both scientific knowledge and practical applications.
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Affiliation(s)
- Fajar Sofyantoro
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | | | - Ega Adhi Wicaksono
- Faculties of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Sendi Priyono
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Alfian Primahesa
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Anita Restu Puji Raharjeng
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Science and Technology, Universitas Islam Negeri Raden Fatah Palembang, South Sumatera, Indonesia
| | - Yekti Asih Purwestri
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Rini Nuringtyas
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Omadhika WA, Solikhah S, Adrianto AA, Purwestri YA, Paramita DK. M2 Macrophage Prominently Distributed in the Rat's Colon of DMH-Induced Inflammation Associated Colorectal Cancer. Asian Pac J Cancer Prev 2024; 25:1357-1362. [PMID: 38679997 DOI: 10.31557/apjcp.2024.25.4.1357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Indexed: 05/01/2024] Open
Abstract
OBJECTIVE The aim of this study is to examine the M1 and M2 macrophages distribution in the rat's colon of DMH-induced inflammation associated colorectal cancer. METHODS Colon tissue of three groups of 4 rats that induced using 1,2 dimethylhydrazine (DMH) at 30 mg/kg bw every week for 9, 11, and 13 weeks were used. The M1 and M2 distribution was examined by using antibody anti iNOS for M1 and anti-CD163 for M2 with immunohistochemistry method. The data was presents in figure and table in the form of percentage. RESULT M1 macrophage was found in all groups in the low distribution level (25% - 50%), while M2 macrophage was observed in all groups with 100% distribution. In the longer period of DMH induction, M2 macrophages was distributed more abundant. CONCLUSION All of the rat's colon showing chronic inflammation that led to the tumorigenesis.
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Affiliation(s)
| | | | - Albertus Ari Adrianto
- Digestive Surgery Department of Medical Faculty Universitas Diponegoro, Semarang, Indonesia
| | - Yekti Asih Purwestri
- Laboratory of Biochemistry, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Study Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dewi Kartikawati Paramita
- Study Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Histology and Cell Biology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Integrated Research Laboratory, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Kusuma WA, Fadli A, Fatriani R, Sofyantoro F, Yudha DS, Lischer K, Nuringtyas TR, Putri WA, Purwestri YA, Swasono RT. Prediction of the interaction between Calloselasma rhodostoma venom-derived peptides and cancer-associated hub proteins: A computational study. Heliyon 2023; 9:e21149. [PMID: 37954374 PMCID: PMC10637925 DOI: 10.1016/j.heliyon.2023.e21149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/04/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
The use of peptide drugs to treat cancer is gaining popularity because of their efficacy, fewer side effects, and several advantages over other properties. Identifying the peptides that interact with cancer proteins is crucial in drug discovery. Several approaches related to predicting peptide-protein interactions have been conducted. However, problems arise due to the high costs of resources and time and the smaller number of studies. This study predicts peptide-protein interactions using Random Forest, XGBoost, and SAE-DNN. Feature extraction is also performed on proteins and peptides using intrinsic disorder, amino acid sequences, physicochemical properties, position-specific assessment matrices, amino acid composition, and dipeptide composition. Results show that all algorithms perform equally well in predicting interactions between peptides derived from venoms and target proteins associated with cancer. However, XGBoost produces the best results with accuracy, precision, and area under the receiver operating characteristic curve of 0.859, 0.663, and 0.697, respectively. The enrichment analysis revealed that peptides from the Calloselasma rhodostoma venom targeted several proteins (ESR1, GOPC, and BRD4) related to cancer.
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Affiliation(s)
- Wisnu Ananta Kusuma
- Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia
- Tropical Biopharmaca Research Center, IPB University, Bogor, 16128, Indonesia
| | - Aulia Fadli
- Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia
| | - Rizka Fatriani
- Tropical Biopharmaca Research Center, IPB University, Bogor, 16128, Indonesia
| | - Fajar Sofyantoro
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Donan Satria Yudha
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Kenny Lischer
- Faculty of Engineering, University of Indonesia, Jakarta, 16424, Indonesia
| | - Tri Rini Nuringtyas
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | | | - Yekti Asih Purwestri
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Respati Tri Swasono
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
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Purwestri YA, Nurbaiti S, Putri SPM, Wahyuni IM, Yulyani SR, Sebastian A, Nuringtyas TR, Yamaguchi N. Seed Halopriming: A Promising Strategy to Induce Salt Tolerance in Indonesian Pigmented Rice. Plants (Basel) 2023; 12:2879. [PMID: 37571030 PMCID: PMC10420915 DOI: 10.3390/plants12152879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023]
Abstract
Unfavorable environmental conditions and climate change impose stress on plants, causing yield losses worldwide. The Indonesian pigmented rice (Oryza sativa L.) cultivars Cempo Ireng Pendek (black rice) and Merah Kalimantan Selatan (red rice) are becoming popular functional foods due to their high anthocyanin contents and have great potential for widespread cultivation. However, their ability to grow on marginal, high-salinity lands is limited. In this study, we investigated whether seed halopriming enhances salt tolerance in the two pigmented rice cultivars. The non-pigmented cultivars IR64, a salt-stress-sensitive cultivar, and INPARI 35, a salt tolerant, were used as control. We pre-treated seeds with a halopriming solution before germination and then exposed the plants to a salt stress of 150 mM NaCl at 21 days after germination using a hydroponic system in a greenhouse. Halopriming was able to mitigate the negative effects of salinity on plant growth, including suppressing reactive oxygen species accumulation, increasing the membrane stability index (up to two-fold), and maintaining photosynthetic pigment contents. Halopriming had different effects on the accumulation of proline, in different rice varieties: the proline content increased in IR64 and Cempo Ireng Pendek but decreased in INPARI 35 and Merah Kalimantan Selatan. Halopriming also had disparate effects in the expression of stress-related genes: OsMYB91 expression was positively correlated with salt treatment, whereas OsWRKY42 and OsWRKY70 expression was negatively correlated with this treatment. These findings highlighted the potential benefits of halopriming in salt-affected agro-ecosystems.
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Affiliation(s)
- Yekti Asih Purwestri
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.N.); (T.R.N.)
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Siti Nurbaiti
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.N.); (T.R.N.)
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Sekar Pelangi Manik Putri
- Biotechnology Master Program, The Graduate School, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.P.M.P.); (I.M.W.); (S.R.Y.)
| | - Ignasia Margi Wahyuni
- Biotechnology Master Program, The Graduate School, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.P.M.P.); (I.M.W.); (S.R.Y.)
| | - Siti Roswiyah Yulyani
- Biotechnology Master Program, The Graduate School, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.P.M.P.); (I.M.W.); (S.R.Y.)
| | - Alfino Sebastian
- Institute of Plant Science and Resources, Okayama University, Okayama 710-0046, Japan;
| | - Tri Rini Nuringtyas
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia; (S.N.); (T.R.N.)
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Nobutoshi Yamaguchi
- Plant Stem Cell Regulation and Floral Patterning Laboratory, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0101, Japan;
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Salsinha YCF, Rini DS, Indradewa D, Rachmawati D, Alam T, Purwestri YA. Exogenously applied Casuarina equisetifolia leaf extracts act as an osmoprotectant on proline accumulation under drought stress in local rice from Indonesia. Front Plant Sci 2023; 14:1210241. [PMID: 37600188 PMCID: PMC10437820 DOI: 10.3389/fpls.2023.1210241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/07/2023] [Indexed: 08/22/2023]
Abstract
The effects of exogenously supplied osmoprotectants in crops have not yet been extensively studied. In this study, an osmoprotectant containing a high concentration of proline (2.5 g mol-1 FW) was obtained from a Casuarina equisetifolia leaf extract. The effect of the extract was evaluated in local Indonesian rice cultivars Boawae Seratus Malam (BSM), Gogo Jak (GJ), Situ Bagendit (SB) (drought-tolerant), Kisol Manggarai (KM) and Ciherang (drought-susceptible) cultivars under drought at the morphological, physiological, and genetic levels. Under drought, the KM showed an increased level of OsWRKY, OsNAC, OsDREB1A, and OsDREB2A expression after application of the osmoprotectant, leading to the activation of proline synthesis genes including OsP5CS1, OsP5CR, and OsProDH, while the tolerant cultivars (BSM, GJ, and SB) showed no difference. The content of chlorophyll, carotenoids, anthocyanins, ascorbate peroxidase, catalase, and superoxide dismutase activities also increased in GJ and KM, during drought stress and applied osmoprotectants, but remained low in the BSM. We conclude that the foliar application of osmoprotectants derived from C.equisetifolia caused an accumulation of proline in susceptible plants. The existence of these extracts stabilizes leaf cells and supports photosynthetic compartments and carbon assimilation in plants, leading to growth.
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Affiliation(s)
- Yustina Carolina Febrianti Salsinha
- Research Center for Genetic Engineering, National Research and Innovation Agency, Bogor, West Java, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Setyo Rini
- Research Center for Genetic Engineering, National Research and Innovation Agency, Bogor, West Java, Indonesia
| | - Didik Indradewa
- Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Diah Rachmawati
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Taufan Alam
- Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yekti Asih Purwestri
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Suputri NPAEO, Prasojo IS, Prabowo LAT, Purwestri YA, Semiarti E. Identification of early flowering mutant gene in Phalaenopsis amabilis (L.) Blume for sgRNA construction in CRISPR/Cas9 genome editing system. BRAZ J BIOL 2023; 84:e268133. [PMID: 37283391 DOI: 10.1590/1519-6984.268133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/12/2023] [Indexed: 06/08/2023] Open
Abstract
Phalaenopsis amabilis (L.) Blume commonly called Moth Orchid (Orchidaceae) is a natural orchid species designated as the National Flower of Indonesia for its beautiful flower shape and long-lasting flowering period. Basically, P. amabilis has a long vegetative phase that cause late flowering, about 2 to 3 years for flowering, hence a method to shorten vegetative period is desired. The latest technological approach that can be used to accelerate flowering of P. amabilis is the CRISPR/Cas9 genome editing method to inactivate the GAI (Gibberellic Acid Insensitive) gene as a mutant gene that can accelerate the regulation of FLOWERING TIME (FT) genes flowering biosynthesis pathway. The approach that needs to be taken is to silence the GAI gene with a knockout system which begins with identifying and characterizing the GAI target gene in the P. amabilis which will be used as a single guide RNA. CRISPR/Cas9 mediated knockout efficiency is highly dependent on the properties of the sgRNA used. SgRNA consists of a target sequence, determining its specificity performance. We executed phylogenetic clustering for the PaGAI protein with closely related orchid species such as Dendrobium capra, Dendrobium cultivars and Cymbidium sinensis. SWISS-Model as tool webserver for protein structure homology modeling. Results show that P. amabilis has a specific domain with the occurrence of point mutations in the two conservative domains. Therefore, a single guide RNA reconstruction needs to be implemented.
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Affiliation(s)
- N P A E O Suputri
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
| | - I S Prasojo
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
| | - L A T Prabowo
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
| | - Y A Purwestri
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
| | - E Semiarti
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
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Purwestri YA, Lee YS, Meehan C, Mose W, Susanto FA, Wijayanti P, Fauzia AN, Nuringtyas TR, Hussain N, Putra HL, Gutierrez-Marcos J. RWP-RK Domain 3 (OsRKD3) induces somatic embryogenesis in black rice. BMC Plant Biol 2023; 23:202. [PMID: 37076789 PMCID: PMC10114336 DOI: 10.1186/s12870-023-04220-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Plants have the unique capability to form embryos from both gametes and somatic cells, with the latter process known as somatic embryogenesis. Somatic embryogenesis (SE) can be induced by exposing plant tissues to exogenous growth regulators or by the ectopic activation of embryogenic transcription factors. Recent studies have revealed that a discrete group of RWP-RK DOMAIN-CONTAINING PROTEIN (RKD) transcription factors act as key regulators of germ cell differentiation and embryo development in land plants. The ectopic overexpression of reproductive RKDs is associated with increased cellular proliferation and the formation of somatic embryo-like structures that bypass the need for exogenous growth regulators. However, the precise molecular mechanisms implicated in the induction of somatic embryogenesis by RKD transcription factors remains unknown. RESULTS In silico analyses have identified a rice RWP-RK transcription factor, named Oryza sativa RKD3 (OsRKD3), which is closely related to Arabidopsis thaliana RKD4 (AtRKD4) and Marchantia polymorpha RKD (MpRKD) proteins. Our study demonstrates that the ectopic overexpression of OsRKD3, which is expressed preferentially in reproductive tissues, can trigger the formation of somatic embryos in an Indonesian black rice landrace (Cempo Ireng) that is normally resistant to somatic embryogenesis. By analyzing the transcriptome of induced tissue, we identified 5,991 genes that exhibit differential expression in response to OsRKD3 induction. Among these genes, 50% were up-regulated while the other half were down-regulated. Notably, approximately 37.5% of the up-regulated genes contained a sequence motif in their promoter region, which was also observed in RKD targets from Arabidopsis. Furthermore, OsRKD3 was shown to mediate the transcriptional activation of a discrete gene network, which includes several transcription factors such as APETALA 2-like (AP2-like)/ETHYLENE RESPONSE FACTOR (ERF), MYB and CONSTANS-like (COL), and chromatin remodeling factors associated with hormone signal transduction, stress responses and post-embryonic pathways. CONCLUSIONS Our data show that OsRKD3 modulates an extensive gene network and its activation is associated with the initiation of a somatic embryonic program that facilitates genetic transformation in black rice. These findings hold substantial promise for improving crop productivity and advancing agricultural practices in black rice.
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Affiliation(s)
- Yekti Asih Purwestri
- Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281.
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia, 55281.
| | - Yang-Seok Lee
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Cathal Meehan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Windi Mose
- Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia, 55281
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Febri Adi Susanto
- Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281
| | - Putri Wijayanti
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia, 55281
| | - Anisa Nazera Fauzia
- Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281
| | - Tri Rini Nuringtyas
- Research Center for Biotechnology, Universitas Gadjah Mada Jl. Teknika Utara, Depok, Sleman, Yogyakarta, Indonesia, 55281
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada Jl. Teknika Selatan, Sekip Utara, Yogyakarta, Indonesia, 55281
| | - Nosheen Hussain
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Hadi Lanang Putra
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Dewatisari WF, Nugroho LH, Retnaningrum E, Purwestri YA. Inhibition of protease activity and anti‐quorum sensing of the potential fraction of ethanolic extract from Sansevieria trifasciata Prain leaves against Pseudomonas aeruginosa. Indones J Biotechnol 2023. [DOI: 10.22146/ijbiotech.73649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Sansevieria trifasciata is a plant that is commonly utilized in traditional medicine. The leaves of S. trifasciata show antibacterial properties against Pseudomonas aeruginosa. This bacterium is an opportunistic pathogen that can cause serious illness in humans and produce a variety of virulence factors responsible for bacterial pathogenesis with quorum sensing (QS) systems that mediate intracellular communication. Bacteria produce protease through a QS mechanism in which they express signaling molecules to become pathogens. Proteases are extracellular enzymes required for successful infection that mediate biofilm spread through QS and regulate a variety of cellular and physiological functions. This research aimed to evaluate the protease, and anti‐QS activities of the ethanolic extract from S. trifasciata leaves against P. aeruginosa and the expression of QS genes. An azocasein test was used to determine the protease activity in qualitative and quantitative methods. Using real‐time quantitative polymerase chain reaction, a study was conducted to investigate the effect of ethanolic extract from S. trifasciata leaves on selected QS‐regulatory genes at the transcriptional level. The results showed that the potential ethanolic extract from S. trifasciata leaves inhibited the protease enzyme activity by as much as 77.1%. The potential ethanolic extract from S. trifasciata leaves decreased the expressions of lasA, lasB, lasI, lasR, rhlI, and rhlR with 2‐ΔΔCt values of 0.81, 0.93, 0.76, 0.97, 0.90, and 0.55 respectively.
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Susila H, Purwestri YA. PEBP Signaling Network in Tubers and Tuberous Root Crops. Plants (Basel) 2023; 12:264. [PMID: 36678976 PMCID: PMC9865765 DOI: 10.3390/plants12020264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Tubers and tuberous root crops are essential carbohydrate sources and staple foods for humans, second only to cereals. The developmental phase transition, including floral initiation and underground storage organ formation, is controlled by complex signaling processes involving the integration of environmental and endogenous cues. FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1/CENTRORADIALIS (TFL1/CEN), members of the phosphatidylethanolamine-binding protein (PEBP) gene family, play a central role in this developmental phase transition process. FT and FT-like proteins have a function to promote developmental phase transition, while TFL1/CEN act oppositely. The balance between FT and TFL1/CEN is critical to ensure a successful plant life cycle. Here, we present a summarized review of the role and signaling network of PEBP in floral initiation and underground storage organ formation, specifically in tubers and tuberous root crops. Lastly, we point out several questions that need to be answered in order to have a more complete understanding of the PEBP signaling network, which is crucial for the agronomical improvement of tubers and tuberous crops.
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Affiliation(s)
- Hendry Susila
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Yekti Asih Purwestri
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
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Hidayah A, Nisak RR, Susanto FA, Nuringtyas TR, Yamaguchi N, Purwestri YA. Seed Halopriming Improves Salinity Tolerance of Some Rice Cultivars During Seedling Stage. Bot Stud 2022; 63:24. [PMID: 35877013 PMCID: PMC9314496 DOI: 10.1186/s40529-022-00354-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Saline land in coastal areas has great potential for crop cultivation. Improving salt tolerance in rice is a key to expanding the available area for its growth and thus improving global food security. Seed priming with salt (halopriming) can enhance plant growth and decrease saline intolerance under salt stress conditions during the subsequent seedling stage. However, there is little known about rice defense mechanisms against salinity at seedling stages after seed halopriming treatment. This study focused on the effect of seed halopriming treatment on salinity tolerance in a susceptible cultivar, IR 64, a resistant cultivar, Pokkali, and two pigmented rice cultivars, Merah Kalimantan Selatan (Merah Kalsel) and Cempo Ireng Pendek (CI Pendek). We grew these cultivars in hydroponic culture, with and without halopriming at the seed stage, under either non-salt or salt stress conditions during the seedling stage. RESULTS The SES scoring assessment showed that the level of salinity tolerance in susceptible cultivar, IR 64, and moderate cultivar, Merah Kalsel, improved after seed halopriming treatment. Furthermore, seed halopriming improved the growth performance of IR 64 and Merah Kalsel rice seedlings. Quantitative PCR revealed that seed halopriming induced expression of the OsNHX1 and OsHKT1 genes in susceptible rice cultivar, IR 64 and Merah Kalsel thereby increasing the level of resistance to salinity. The expression levels of OsSOS1 and OsHKT1 genes in resistant cultivar, Pokkali, also increased but there was no affect on the level of salinity tolerance. On the contrary, seed halopriming decreased the expression level of OsSOS1 genes in pigmented rice cultivar, CI Pendek, but did not affect the level of salinity tolerance. The transporter gene expression induction significantly improved salinity tolerance in salinity-susceptible rice, IR 64, and moderately tolerant rice cultivar, Merah Kalsel. Induction of expression of the OsNHX1 and OsHKT1 genes in susceptible rice, IR 64, after halopriming seed treatment balances the osmotic pressure and prevents the accumulation of toxic concentrations of Na+, resulting in tolerance to salinity stress. CONCLUSION These results suggest that seed halopriming can improve salinity tolerance of salinity-susceptible and moderately tolerant rice cultivars.
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Affiliation(s)
- Anik Hidayah
- Biotechnology Study Program, The Graduate School, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281, Indonesia
- Agricultural Environmental Division, Indonesian Agency For Agricultural Research and Development, Jl. Raya Jakenan-Jaken Km. 5, Central Java, 59182, Pati, Indonesia
| | - Rizka Rohmatin Nisak
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Febri Adi Susanto
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281, Indonesia
| | - Tri Rini Nuringtyas
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281, Indonesia
| | - Nobutoshi Yamaguchi
- Plant Stem Cell Regulation and Floral Patterning Laboratory, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yekti Asih Purwestri
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia.
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281, Indonesia.
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Sebastian A, Nugroho IC, Putra HSD, Susanto FA, Wijayanti P, Yamaguchi N, Nuringtyas TR, Purwestri YA. Identification and characterization of drought-tolerant local pigmented rice from Indonesia. Physiol Mol Biol Plants 2022; 28:1061-1075. [PMID: 35722514 PMCID: PMC9203631 DOI: 10.1007/s12298-022-01185-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 05/03/2023]
Abstract
Water is essential to support life. Because limited water availability may affect their life cycles, plants have developed multiple responses to drought stress. Plant physiological and metabolic changes during drought may reflect changes that occur at the level of gene expression. In this study, we investigated the variation in drought-mitigating strategies employed by pigmented rice (Oryza sativa) varieties and the genes involved in their possible drought tolerance. We screened 21 local pigmented rice cultivars from Indonesia for increased drought tolerance using the fraction transpirable soil water method to exert precise control of the drought stress imposed on plants. We then determined the expression of OsDREB1A, OsNAC6, OsNHX1, OsCuZnSOD2, OsOSCAT2, and OsCAT3 in plants grown under well-watered conditions and under moderate or severe drought stress. Among the pigmented rice cultivars, Merah Pari Eja had the greatest drought tolerance, while the red rice Inpari 24 had the highest mortality rate (60%). We also included the white rice cultivar Putih Payo, which is fully sensitive to drought (with 100% mortality under the conditions used) as a negative control. Gene expression profiling revealed a general upregulation of drought-related genes in Merah Pari Eja and a downregulation of such genes in the other two cultivars. Measurements of antioxidant enzyme activity, leaf damage, free radicals, chlorophyll, and anthocyanin contents provided further evidence that Merah Pari Eja is more drought tolerant than the other two cultivars. We conclude that OsDREB1A, OsNAC6, OsNHX1, OsCuZnSOD2, OsOSCAT2 and OsCAT3 expression patterns can reveal plants that have increased drought tolerance.
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Affiliation(s)
- Alfino Sebastian
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281 Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281 Indonesia
| | - Ilham Cahyo Nugroho
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281 Indonesia
| | - Herdin Surya Dwi Putra
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281 Indonesia
| | - Febri Adi Susanto
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281 Indonesia
| | - Putri Wijayanti
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281 Indonesia
| | - Nobutoshi Yamaguchi
- Plant Stem Cell Regulation and Floral Patterning Laboratory, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan
| | - Tri Rini Nuringtyas
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281 Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281 Indonesia
| | - Yekti Asih Purwestri
- Biochemistry Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281 Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Jl. Teknika Utara, Sleman, Yogyakarta, 55281 Indonesia
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Latifah E, Mulyani PD, Purwestri YA. Lignolytic Enzyme Activity of Isolated Bacteria from Termite (Coptotermes Sp.) and Milkfish (Chanos chanos Forsskal, 1775) Guts. J Bio Bio Edu 2021. [DOI: 10.15294/biosaintifika.v13i1.19333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria BSR 2, Pseudomonas alcaligenes (BSR 3), Brevibacillus parabrevis (BSR 8), Brevibacillus sp. (BSR 9), isolated from termite gut and Bacillus licheniformis (BSA B1) isolated from milkfish gut have been known to possess celluloytic activity. However, their lignolytic ability has not been known. This study aimed to determine the lignolytic ability of bacteria isolated from termit (Coptotermes sp.) and milkfish (Chanos chanos Forsskal, 1775) guts and their enzymes characterization. The qualitative test was done through the spot test method, while quantitative assay was performed spectrophotometrically at 335 nm to calculate vanillin concentration. The isolates were grown in Lignin Mineral Medium, then the optical density (OD620) were measured every 24 hours for 5 days using spectrophotometer to determine their growth profile and the best isolation time of the lignolytic enzyme. Based on results, the best lignolytic enzyme isolation time for strains Bacillus licheniformis (BSA B1) and BSR 2 were 5 days, yielding lignolytic enzyme activity of 0.961 ± 0.168 U/mg and 2.176 ± 0.088 U/mg respectively,  while strains Pseudomonas alcaligenes (BSR 3), Brevibacillus parabrevis (BSR 8), and Brevibacillus sp. (BSR 9) were 4 days, yielding of 1.206 ± 0.045 U/mg, 1.162 ± 0.191 U/mg, and 0.896 ± 0.108 U/mg, respectively. The strain BSR 2 showed the highest lignolytic activity compared to other strains. The optimum temperature for lignolytic enzyme activity of BSR 2 was 30 ℃ and the optimum pH was 7. The lignolytic enzyme activity showed that these bacterial isolates can be a chance to be used as new alternative lignolytic enzyme source in commercial bioconversion process.
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Hanifah N, Asih Purwestri Y. The Effect Of NaCl Salinity Stress To Phenolic Compound, Total Flavonoid And Antioxidant Activity Of Pegagan (Centella asiatica (L.) Urban) Leaves. BIO Web Conf 2021. [DOI: 10.1051/bioconf/20214106004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pegagan (Centella asiatica (L.) Urban) is a herbal plant that contain secondary metabolite compounds like phenol and flavonoid. NaCl salinity is one of abiotic stress that enhanced synthesis of some secondary metabolites in plants. This study was investigated the effect of NaCl salinity stress to phenolic compound, total flavonoid and antioxidant activity of pegagan leaves. Pegagan were treated with five different NaCl concentrations, 0 mM (1), 50 mM (2), 100 mM (3), 150 mM (4) and 200 mM (5) for a week. Morphological leaves were observed for the present of necrotic symptom. Phenolic compound and total flavonoid content were measured using spectrophotometer at wavelength 765 nm and 415 nm. Antioxidant activity was measured based on DPPH method. The result showed that increasing NaCl concentration cause increasing necrotic spot in leaves. Phenolic compound, total flavonoid and antioxidant activity are increased by increasing NaCl concentration. The result indicated that phenol and flavonoid have important role in plant defense mechanism against NaCl toxicity effects.
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Eskundari RD, Taryono T, Indradewa D, Purwestri YA. Protein Profile of Tissue Culture of TRI2025 Tea Clone. J Bio Bio Edu 2019. [DOI: 10.15294/biosaintifika.v11i1.17522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tea is well known as favourite healthy drink for almost all people over the world. Tea propagation using conventional and modern ways are now developing rapidly. However, information regarding the protein profile of tissue culture of tea plant has not been revealed yet. This study aimed to determine the difference of protein profile of tea’s tissue culture using SDS-PAGE. This study was conducted using embryonic axes of TRI2025 tea clone cultured on MS media supplemented with 2,4-D for inducing somatic embryogenesis and globular-like structure (GLS) regeneration, and MS media supplemented with BAP for inducing shoot via organogenesis. The results revealed that proteins in the size of 37.69; 54.89; 60.77; 71.35; 87.34; and 92.99 KDa might be involved at somatic embryogenesis, and about 38.69 KDa, 69.27 KDa, and 55.76 KDa respectively for GLS, initiation of shoot, and initiation of GLS derived leaf. Predicted key protein for leaf initiation both directly or through GLS was about 31-33 KDa, while for callusing were about 27.56 and 52.73 KDa, and constitutive protein was about 22.75 KDa. This study provides the first report of protein profile of tea’s tissue culture. The information obtained can be beneficial as a marker for explant for somatic embryogenesis, GLS, or organogenesis pathway and as a scientific information for further biotechnology development.
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de Fretes CE, Suryani R, Asih Purwestri Y, Nuringtyas TR, Widianto D. Diversity of Endophytic Bacteria in Sweet Sorghum (Sorghum bicolor (L.) Moench) and Their Potential for Promoting Plant Growth. ACTA ACUST UNITED AC 2018. [DOI: 10.17485/ijst/2018/v11i11/120283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Abstract
Background: There are many local black rice cultivars in Indonesia, yet only a few of these are formally described in the literature. It has been reported that black rice has many phytochemical variants which may contribute to its use as a functional food, including nutraceuticals and secondary metabolites such as anthocyanin, oryzanol, and more. The purpose of this article was to review literature describing black rice cultivars from Indonesia, with a particular focus on its potential use as a functional food. Our literature search revealed several articles that describe black rice in relation to its nutraceutical properties and its role in reducing non-communicable diseases. Other studies describe the diversity of local pigmented rice and its potential for lowering the risk of hyperlipidemia, hyperglycemia, and for cancer prevention. Black rice has been described as a functional food in several countries; however, there is great diversity among cultivars and further research on Indonesian varieties will determine whether local variants are candidates as well for the development of functional foods. Keywords: black rice cultivar, functional food, non-communicable diseases, nutraceutical, phytochemical
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Purwestri YA, Ogaki Y, Tamaki S, Tsuji H, Shimamoto K. The 14-3-3 Protein GF14c Acts as a Negative Regulator of Flowering in Rice by Interacting with the Florigen Hd3a. ACTA ACUST UNITED AC 2009; 50:429-38. [DOI: 10.1093/pcp/pcp012] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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