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Jafari M, Daneshvar MH. Machine learning-mediated Passiflora caerulea callogenesis optimization. PLoS One 2024; 19:e0292359. [PMID: 38266002 PMCID: PMC10807783 DOI: 10.1371/journal.pone.0292359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/19/2023] [Indexed: 01/26/2024] Open
Abstract
Callogenesis is one of the most powerful biotechnological approaches for in vitro secondary metabolite production and indirect organogenesis in Passiflora caerulea. Comprehensive knowledge of callogenesis and optimized protocol can be obtained by the application of a combination of machine learning (ML) and optimization algorithms. In the present investigation, the callogenesis responses (i.e., callogenesis rate and callus fresh weight) of P. caerulea were predicted based on different types and concentrations of plant growth regulators (PGRs) (i.e., 2,4-dichlorophenoxyacetic acid (2,4-D), 6-benzylaminopurine (BAP), 1-naphthaleneacetic acid (NAA), and indole-3-Butyric Acid (IBA)) as well as explant types (i.e., leaf, node, and internode) using multilayer perceptron (MLP). Moreover, the developed models were integrated into the genetic algorithm (GA) to optimize the concentration of PGRs and explant types for maximizing callogenesis responses. Furthermore, sensitivity analysis was conducted to assess the importance of each input variable on the callogenesis responses. The results showed that MLP had high predictive accuracy (R2 > 0.81) in both training and testing sets for modeling all studied parameters. Based on the results of the optimization process, the highest callogenesis rate (100%) would be obtained from the leaf explant cultured in the medium supplemented with 0.52 mg/L IBA plus 0.43 mg/L NAA plus 1.4 mg/L 2,4-D plus 0.2 mg/L BAP. The results of the sensitivity analysis showed the explant-dependent impact of the exogenous application of PGRs on callogenesis. Generally, the results showed that a combination of MLP and GA can display a forward-thinking aid to optimize and predict in vitro culture systems and consequentially cope with several challenges faced currently in Passiflora tissue culture.
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Affiliation(s)
- Marziyeh Jafari
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz, Iran
- Department of Horticultural Sciences, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
| | - Mohammad Hosein Daneshvar
- Department of Horticultural Sciences, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran
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Mazurek M, Siekierzyńska A, Piechowiak T, Spinardi A, Litwińczuk W. Comprehensive Analysis of Highbush Blueberry Plants Propagated In Vitro and Conventionally. Int J Mol Sci 2023; 25:544. [PMID: 38203713 PMCID: PMC10779370 DOI: 10.3390/ijms25010544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
In vitro culture allows the production of numerous plants with both desirable and undesirable traits. To investigate the impact of the propagation method on highbush blueberry plants, an analysis was performed on four groups of differentially propagated plants: in vitro with axillary (TC-Ax) or adventitious shoots (TC-Ad), conventionally (SC) and using a mixed method (TC/SC). The analysis included plant features (shoot length and branching, chlorophyll and fluorescence and DNA methylation) and fruit properties (antioxidant compounds). The data obtained indicated significant differences between plants propagated conventionally and in vitro, as well as variations among plants derived from in vitro cultures with different types of explants. SC plants generally exhibited the lowest values of morphological and physiological parameters but produced fruits richest in antioxidant compounds. TC/SC plants were dominant in length, branching and fluorescence. Conversely, TC-Ax plants produced fruits with the lowest levels of antioxidant compounds. The methylation-sensitive amplified polymorphism (MSAP) technique was employed to detect molecular differences. TC-Ad plants showed the highest methylation level, whereas SC plants had the lowest. The overall methylation level varied among differentially propagated plants. It can be speculated that the differences among the analysed plants may be attributed to variations in DNA methylation.
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Affiliation(s)
- Marzena Mazurek
- Department of Physiology and Plant Biotechnology, Institute of Agricultural Sciences, Environment Management and Protection University of Rzeszow, Ćwiklińskiej 2, 35-601 Rzeszow, Poland; (A.S.)
| | - Aleksandra Siekierzyńska
- Department of Physiology and Plant Biotechnology, Institute of Agricultural Sciences, Environment Management and Protection University of Rzeszow, Ćwiklińskiej 2, 35-601 Rzeszow, Poland; (A.S.)
| | - Tomasz Piechowiak
- Department of Chemistry and Food Toxicology, Institute of Food Technology and Nutrition, University of Rzeszow, St. Cwiklinskiej 1a, 35-601 Rzeszow, Poland;
| | - Anna Spinardi
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, Università degli Studi di Milano, 20133 Milan, Italy
| | - Wojciech Litwińczuk
- Department of Physiology and Plant Biotechnology, Institute of Agricultural Sciences, Environment Management and Protection University of Rzeszow, Ćwiklińskiej 2, 35-601 Rzeszow, Poland; (A.S.)
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Mantovska DI, Zhiponova MK, Petrova D, Alipieva K, Bonchev G, Boycheva I, Evstatieva Y, Nikolova D, Tsacheva I, Simova S, Yordanova ZP. Exploring the Phytochemical Composition and Biological Potential of Balkan Endemic Species Stachys scardica Griseb. PLANTS (BASEL, SWITZERLAND) 2023; 13:30. [PMID: 38202340 PMCID: PMC10780532 DOI: 10.3390/plants13010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024]
Abstract
Stachys scardica Griseb. is a Balkan endemic species listed in The Red Data Book of Bulgaria with the conservation status "endangered". Successful micropropagation was achieved on MS medium supplemented with 1.5 mg/L benzyladenine (BA), followed by a subsequent ex vitro adaptation in an experimental field resulting in 92% regenerated plants. Using nuclear magnetic resonance (NMR), phenylethanoid glycosides (verbascoside, leucosceptoside A), phenolic acids (chlorogenic acid), iridoids (allobetonicoside and 8-OAc-harpagide), and alkaloids (trigonelline) were identified, characteristic of plants belonging to the genus Stachys. High antioxidant and radical scavenging activities were observed in both in situ and ex vitro acclimated S. scardica plants, correlating with the reported high concentrations of total phenols and flavonoids in these variants. Ex vitro adapted plants also exhibited a well-defined anti-inflammatory potential, demonstrating high inhibitory activity against the complement system. Employing a disk diffusion method, a 100% inhibition effect was achieved compared to positive antibiotic controls against Staphylococcus epidermidis and Propionibacterium acnes, with moderate activity against Bacillus cereus. The induced in vitro and ex vitro model systems can enable the conservation of S. scardica in nature and offer future opportunities for the targeted biosynthesis of valuable secondary metabolites, with potential applications in the pharmaceutical and cosmetic industries.
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Affiliation(s)
- Desislava I. Mantovska
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria (M.K.Z.); (D.P.)
| | - Miroslava K. Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria (M.K.Z.); (D.P.)
| | - Detelina Petrova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria (M.K.Z.); (D.P.)
| | - Kalina Alipieva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, bl. 9 Acad. Georgi Bonchev Str., 1113 Sofia, Bulgaria; (K.A.); (S.S.)
| | - Georgi Bonchev
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria; (G.B.); (I.B.)
| | - Irina Boycheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria; (G.B.); (I.B.)
| | - Yana Evstatieva
- Department of Biotechnology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria; (Y.E.); (D.N.)
| | - Dilyana Nikolova
- Department of Biotechnology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria; (Y.E.); (D.N.)
| | - Ivanka Tsacheva
- Department of Biochemistry, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria;
| | - Svetlana Simova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, bl. 9 Acad. Georgi Bonchev Str., 1113 Sofia, Bulgaria; (K.A.); (S.S.)
| | - Zhenya P. Yordanova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria (M.K.Z.); (D.P.)
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Jafari M, Daneshvar MH. Prediction and optimization of indirect shoot regeneration of Passiflora caerulea using machine learning and optimization algorithms. BMC Biotechnol 2023; 23:27. [PMID: 37528396 PMCID: PMC10394921 DOI: 10.1186/s12896-023-00796-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/21/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Optimization of indirect shoot regeneration protocols is one of the key prerequisites for the development of Agrobacterium-mediated genetic transformation and/or genome editing in Passiflora caerulea. Comprehensive knowledge of indirect shoot regeneration and optimized protocol can be obtained by the application of a combination of machine learning (ML) and optimization algorithms. MATERIALS AND METHODS In the present investigation, the indirect shoot regeneration responses (i.e., de novo shoot regeneration rate, the number of de novo shoots, and length of de novo shoots) of P. caerulea were predicted based on different types and concentrations of PGRs (i.e., TDZ, BAP, PUT, KIN, and IBA) as well as callus types (i.e., callus derived from different explants including leaf, node, and internode) using generalized regression neural network (GRNN) and random forest (RF). Moreover, the developed models were integrated into the genetic algorithm (GA) to optimize the concentration of PGRs and callus types for maximizing indirect shoot regeneration responses. Moreover, sensitivity analysis was conducted to assess the importance of each input variable on the studied parameters. RESULTS The results showed that both algorithms (RF and GRNN) had high predictive accuracy (R2 > 0.86) in both training and testing sets for modeling all studied parameters. Based on the results of optimization process, the highest de novo shoot regeneration rate (100%) would be obtained from callus derived from nodal segments cultured in the medium supplemented with 0.77 mg/L BAP plus 2.41 mg/L PUT plus 0.06 mg/L IBA. The results of the sensitivity analysis showed the explant-dependent impact of exogenous application of PGRs on indirect de novo shoot regeneration. CONCLUSIONS A combination of ML (GRNN and RF) and GA can display a forward-thinking aid to optimize and predict in vitro culture systems and consequentially cope with several challenges faced currently in Passiflora tissue culture.
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Affiliation(s)
- Marziyeh Jafari
- Department of Horticultural Science, College of Agriculture, Shiraz University, Shiraz, 7144113131, Iran.
- Department of Horticultural Sciences, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, 6341773637, Iran.
| | - Mohammad Hosein Daneshvar
- Department of Horticultural Sciences, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, 6341773637, Iran
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Sykłowska-Baranek K, Gaweł M, Kuźma Ł, Wileńska B, Kawka M, Jeziorek M, Graikou K, Chinou I, Szyszko E, Stępień P, Zakrzewski P, Pietrosiuk A. Rindera graeca (A. DC.) Boiss. & Heldr. (Boraginaceae) In Vitro Cultures Targeting Lithospermic Acid B and Rosmarinic Acid Production. Molecules 2023; 28:4880. [PMID: 37375435 DOI: 10.3390/molecules28124880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The in vitro cultures of Rindera graeca, a rare endemic plant, were developed as a sustainable source of phenolic acids. Various shoot and root cultures were established and scaled up in a sprinkle bioreactor. A multiplication rate of 7.2 shoots per explant was achieved. HPLC-PDA-ESI-HRMS analysis revealed the presence of rosmarinic acid (RA) and lithospermic acid B (LAB) as the main secondary metabolites in both the shoot and root cultures. The maximum RA (30.0 ± 3.2 mg/g DW) and LAB (49.3 ± 15.5 mg/g DW) yields were determined in root-regenerated shoots. The strongest free radical scavenging activity (87.4 ± 1.1%), according to 2,2-diphenyl-1-picrylhydrazyl-hydrate assay, was noted for roots cultivated in a DCR medium. The highest reducing power (2.3 µM ± 0.4 TE/g DW), determined by the ferric-reducing antioxidant power assay, was noted for shoots cultivated on an SH medium containing 0.5 mg/L 6-benzylaminopurine. A genetic analysis performed using random amplified polymorphic DNA and start codon targeted markers revealed genetic variation of 62.8% to 96.5% among the investigated shoots and roots. This variability reflects the capacity of cultivated shoots and roots to produce phenolic compounds.
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Affiliation(s)
- Katarzyna Sykłowska-Baranek
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Małgorzata Gaweł
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Łukasz Kuźma
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Łódź, 1 Muszyńskiego, 90-151 Łódź, Poland
| | - Beata Wileńska
- Faculty of Chemistry, University of Warsaw, 1 Pasteura St., 02-093 Warsaw, Poland
- Biological and Chemical Research Centre, 101 Żwirki i Wigury St., 02-097 Warsaw, Poland
| | - Mateusz Kawka
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Małgorzata Jeziorek
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Konstantia Graikou
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece
| | - Ioanna Chinou
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771 Athens, Greece
| | - Ewa Szyszko
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Piotr Stępień
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Patryk Zakrzewski
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
| | - Agnieszka Pietrosiuk
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha St., 02-097 Warsaw, Poland
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Effect of Explant Source on Phenotypic Changes of In Vitro Grown Cannabis Plantlets over Multiple Subcultures. BIOLOGY 2023; 12:biology12030443. [PMID: 36979133 PMCID: PMC10044989 DOI: 10.3390/biology12030443] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/06/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023]
Abstract
Drug-type cannabis is often multiplied using micropropagation methods to produce genetically uniform and disease/insect-free crops. However, micropropagated plantlets often exhibit phenotypic variation, leading to culture decline over time. In cannabis, the source of these changes remains unknown, though several factors (e.g., explant’s sources and prolonged in vitro culture) can result in such phenotypical variations. The study presented herein evaluates the effects of explant sources (i.e., nodal segments derived from the basal, near-basal, middle, and apical parts of the greenhouse-grown mother plant) over multiple subcultures (4 subcultures during 235 days) on multiplication parameters and leaf morphological traits of in vitro cannabis plantlets. While initial in vitro responses were similar among explants sourced from different regions of the plant, there were significant differences in performance over the course of multiple subcultures. Specifically, explant source and/or the number of subcultures significantly impacted plantlet height, number of nodes, and canopy surface area. The explants derived from the basal and near-basal parts of the plant resulted in the tallest shoots with the greatest number of nodes, while the explants derived from the middle and apical regions led to shorter shoots with fewer nodes. Moreover, the basal-derived explants produced cannabis plantlets with shorter but wider leaves which demonstrated the potential of such explants for in vitro rejuvenation practices with minimal culture decline. This study provides new evidence into the long-term impacts of explant source in cannabis micropropagation.
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