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Türkoğlu A, Haliloğlu K, Demirel F, Aydin M, Çiçek S, Yiğider E, Demirel S, Piekutowska M, Szulc P, Niedbała G. Machine Learning Analysis of the Impact of Silver Nitrate and Silver Nanoparticles on Wheat ( Triticum aestivum L.): Callus Induction, Plant Regeneration, and DNA Methylation. PLANTS (BASEL, SWITZERLAND) 2023; 12:4151. [PMID: 38140479 PMCID: PMC10747064 DOI: 10.3390/plants12244151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023]
Abstract
The objective of this study was to comprehend the efficiency of wheat regeneration, callus induction, and DNA methylation through the application of mathematical frameworks and artificial intelligence (AI)-based models. This research aimed to explore the impact of treatments with AgNO3 and Ag-NPs on various parameters. The study specifically concentrated on analyzing RAPD profiles and modeling regeneration parameters. The treatments and molecular findings served as input variables in the modeling process. It included the use of AgNO3 and Ag-NPs at different concentrations (0, 2, 4, 6, and 8 mg L-1). The in vitro and epigenetic characteristics were analyzed using several machine learning (ML) methods, including support vector machine (SVM), random forest (RF), extreme gradient boosting (XGBoost), k-nearest neighbor classifier (KNN), and Gaussian processes classifier (GP) methods. This study's results revealed that the highest values for callus induction (CI%) and embryogenic callus induction (EC%) occurred at a concentration of 2 mg L-1 of Ag-NPs. Additionally, the regeneration efficiency (RE) parameter reached its peak at a concentration of 8 mg L-1 of AgNO3. Taking an epigenetic approach, AgNO3 at a concentration of 2 mg L-1 demonstrated the highest levels of genomic template stability (GTS), at 79.3%. There was a positive correlation seen between increased levels of AgNO3 and DNA hypermethylation. Conversely, elevated levels of Ag-NPs were associated with DNA hypomethylation. The models were used to estimate the relationships between the input elements, including treatments, concentration, GTS rates, and Msp I and Hpa II polymorphism, and the in vitro output parameters. The findings suggested that the XGBoost model exhibited superior performance scores for callus induction (CI), as evidenced by an R2 score of 51.5%, which explained the variances. Additionally, the RF model explained 71.9% of the total variance and showed superior efficacy in terms of EC%. Furthermore, the GP model, which provided the most robust statistics for RE, yielded an R2 value of 52.5%, signifying its ability to account for a substantial portion of the total variance present in the data. This study exemplifies the application of various machine learning models in the cultivation of mature wheat embryos under the influence of treatments and concentrations involving AgNO3 and Ag-NPs.
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Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye;
| | - Fatih Demirel
- Department of Agricultural Biotechnology, Faculty of Agriculture, Igdır University, Igdir 76000, Türkiye;
| | - Murat Aydin
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Semra Çiçek
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Esma Yiğider
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye; (M.A.); (S.Ç.); (E.Y.)
| | - Serap Demirel
- Department of Molecular Biology and Genetics, Faculty of Science, Van Yüzüncü Yıl University, Van 65080, Türkiye;
| | - Magdalena Piekutowska
- Department of Geoecology and Geoinformation, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, 27 Partyzantów St., 76-200 Słupsk, Poland;
| | - Piotr Szulc
- Department of Agronomy, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Gniewko Niedbała
- Department of Biosystems Engineering, Faculty of Environmental and Mechanical Engineering, Poznań University of Life Sciences, Wojska Polskiego 50, 60-627 Poznań, Poland
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Sharma A, Pandey H, Nampoothiri Devadas VAS, Kartha BD, Jha R. Production of, Factors Affecting, Gene Regulations, and Challenges in Tissue Cultured Plant through Soilless Culture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5804-5811. [PMID: 36995942 DOI: 10.1021/acs.jafc.2c08162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Soilless culture also known as water based culture and substrate based culture has immense potential to grow tissue cultured plants in a closed and controlled environment system. This review analyzes the various factors that affect the vegetative growth, reproductive growth, metabolic processes, and gene regulatory functions of tissue cultured plants and the suitability of soilless culture for tissue culture plants. Experiments show that morphological and reproductive abnormalities are mitigated in tissue cultured plants by gene regulation in a closed and controlled environment system. Various factors of a soilless culture influence gene regulation and enhance cellular, molecular, and biochemical processes and compensate constraints in tissue cultured plants in closed and controlled environment conditions. The soilless culture can be utilized to harden and grow tissue culture plants. The tissue cultured plants counter water logging problems and are supplied with nutrients at 7 day intervals in the water based culture. It is necessary to analyze the involvement of regulatory genes in detail in combating challenges of tissue cultured plants in soilless cultures under closed systems. Detailed studies are also required to determine anatomy, genesis, and function of microtuber cells in tissue cultured plants.
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Affiliation(s)
- Avinash Sharma
- Faculty of Agricultural Sciences, Arunachal University of Studies, Namsai, Arunachal Pradesh 792103, India
| | - Himanshu Pandey
- Division of Plant Physiology and Biochemistry, Indian Institute of Sugarcane Research, Lucknow, Uttar Pradesh 226005, India
| | | | - Bhagya D Kartha
- Department of Fruit Crops, College of Agriculture, Kerala Agricultural University, Thrissur, Kerala 680656, India
| | - Rani Jha
- Faculty of Chemistry, Arunachal University of Studies, Namsai, Arunachal Pradesh 792103, India
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The calcium signaling module CaM-IQM destabilizes IAA-ARF interaction to regulate callus and lateral root formation. Proc Natl Acad Sci U S A 2022; 119:e2202669119. [PMID: 35763576 PMCID: PMC9271181 DOI: 10.1073/pnas.2202669119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Induction of a pluripotent cell mass, called callus, from detached organs is an initial step in in vitro plant regeneration, during which phytohormone auxin-induced ectopic activation of a root developmental program has been shown to be required for subsequent de novo regeneration of shoots and roots. However, whether other signals are involved in governing callus formation, and thus plant regeneration capability, remains largely unclear. Here, we report that the Arabidopsis calcium (Ca2+) signaling module CALMODULIN IQ-MOTIF CONTAINING PROTEIN (CaM-IQM) interacts with auxin signaling to regulate callus and lateral root formation. We show that disruption of IQMs or CaMs retards auxin-induced callus and lateral root formation by dampening auxin responsiveness, and that CaM-IQM complexes physically interact with the auxin signaling repressors INDOLE-3-ACETIC ACID INDUCIBLE (IAA) proteins in a Ca2+-dependent manner. We further provide evidence that the physical interaction of CaM6 with IAA19 destabilizes the repressive interaction of IAA19 with AUXIN RESPONSE FACTOR 7 (ARF7), and thus regulates auxin-induced callus formation. These findings not only define a critical role of CaM-IQM-mediated Ca2+ signaling in callus and lateral root formation, but also provide insight into the interplay of Ca2+ signaling and auxin actions during plant regeneration and development.
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Mujib A, Bansal Y, Malik MQ, Syeed R, Mamgain J, Ejaz B. Internal and External Regulatory Elements Controlling Somatic Embryogenesis in Catharanthus: A Model Medicinal Plant. Methods Mol Biol 2022; 2527:11-27. [PMID: 35951180 DOI: 10.1007/978-1-0716-2485-2_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Somatic or in vitro embryogenesis is a unique embryo producing process from vegetative cells observed in plants since 1958. Even over 60 years of research, the transition of somatic cells into embryonic fate is still not elucidated fully. Various networks and signaling elements have been noted to play important role in this "vegetative to reproductive" transition process. The networks include genotypes, explant types, the sugar/carbohydrate sources, cultural/environmental conditions like light quality and intensity, dissolved oxygen (DO) level, cell density, plant growth regulator (PGR) (auxin and cytokinin) signaling, PGR-gene interplay, stresses are important and cause new cellular reprogramming during embryonic acquisition. A wide array of genes, specific to zygotic embryogenesis, also express during somatic embryogenesis. A few embryogenesis-specific genes such as SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE, LEAFY COTYLEDON, AGAMOUS-LIKE 15, and BABY BOOM are crucial and have been discussed. The chapter focuses the importance of these gene products, e.g., proteins, enzymes, and transcription factors in regulating embryogenesis. Many of these encoded proteins act as potential somatic embryogenesis markers. Besides, important elements such as genotype, herbaceous/woody plants' response in culture in inducing embryos have been discussed. All these elements are connected and form network in complex fashion thus difficult to unfold fully; some of the current progress and developments have been presented in this chapter.
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Affiliation(s)
- A Mujib
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India.
| | - Yashika Bansal
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Moien Qadir Malik
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Rukaya Syeed
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Jyoti Mamgain
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Bushra Ejaz
- Cellular Differentiation and Molecular Genetics Section, Department of Botany, Jamia Hamdard, New Delhi, India
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Genes, proteins and other networks regulating somatic embryogenesis in plants. J Genet Eng Biotechnol 2020; 18:31. [PMID: 32661633 PMCID: PMC7359197 DOI: 10.1186/s43141-020-00047-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/01/2020] [Indexed: 11/21/2022]
Abstract
Background Somatic embryogenesis (SE) is an intricate molecular and biochemical process principally based on cellular totipotency and a model in studying plant development. In this unique embryo-forming process, the vegetative cells acquire embryogenic competence under cellular stress conditions. The stress caused by plant growth regulators (PGRs), nutrient, oxygenic, or other signaling elements makes cellular reprogramming and transforms vegetative cells into embryos through activation/deactivation of a myriad of genes and transcriptional networks. Hundreds of genes have been directly linked to zygotic and somatic embryogeneses; some of them like SOMATIC EMBRYOGENESIS LIKE RECEPTOR KINASE (SERK), LEAFY COTYLEDON (LEC), BABYBOOM (BBM), and AGAMOUS-LIKE 15 (AGL15) are very important and are part of molecular network. Main text (observation) This article reviews various genes/orthologs isolated from different plants; encoded proteins and their possible role in regulating somatic embryogenesis of plants have been discussed. The role of SERK in regulating embryogenesis is also summarized. Different SE-related proteins identified through LC–MS at various stages of embryogenesis are also described; a few proteins like 14-3-3, chitinase, and LEA are used as potential SE markers. These networks are interconnected in a complicated manner, posing challenges for their complete elucidation. Conclusions The various gene networks and factors controlling somatic embryogenesis have been discussed and presented. The roles of stress, PGRs, and other signaling elements have been discussed. In the last two-to-three decades’ progress, the challenges ahead and its future applications in various fields of research have been highlighted. The review also presents the need of high throughput, innovative techniques, and sensitive instruments in unraveling the mystery of SE.
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Song Y, Chen S, Wang X, Zhang R, Tu L, Hu T, Liu X, Zhang Y, Huang L, Gao W. A novel strategy to enhance terpenoids production using cambial meristematic cells of Tripterygium wilfordii Hook. f. PLANT METHODS 2019; 15:129. [PMID: 31719835 PMCID: PMC6836502 DOI: 10.1186/s13007-019-0513-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Tripterygium wilfordii Hook. f. (T. wilfordii) is an important medicinal plant with anti-inflammatory, immunosuppressive and anti-tumor activities. The main bioactive ingredients are diterpenoids and triterpenoids, such as triptolide, triptophenolide and celastrol. However, the production of terpenoids from original plants, hairy roots and dedifferentiated cells (DDCs) are not satisfactory for clinical applications. To find a new way to further improve the production of terpenoids, we established a new culture system of cambial meristematic cells (CMCs) with stem cell-like properties, which had strong vigor and high efficiency to produce large amounts of terpenoids of T. wilfordii. RESULTS CMCs of T. wilfordii were isolated and cultured for the first time. CMCs were characterized consistent with stem cell identities based on their physiological and molecular analysis, including morphology of CMCs, hypersensitivity to zeocin, thin cell wall and orthogonal partial least square-discriminant analysis, combination of transcriptional data analysis. After induction with methyl jasmonate (MJ), the maximal production of triptolide, celastrol and triptophenolide in CMCs was 312%, 400% and 327% higher than that of control group, respectively. As for medium, MJ-induced CMCs secreted 231% triptolide and 130% triptophenolide at the maximum level into medium higher than that of control group. Maximal celastrol production of induced CMCs medium was 48% lower than that of control group. Long-term induction significantly enhanced the production of terpenoids both in cells and medium. The reason for increasing the yield of terpenoids was that expression levels of 1-deoxy-d-xylulose-5-phosphate synthase (DXS), 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) and hydroxymethylglutaryl-CoA synthase (HMGS) were upregulated in CMCs after induction. CONCLUSIONS For the first time, CMCs of T. wilfordii were isolated, cultured, characterized and applied. Considering the significant enrichment of terpenoids in CMCs of T. wilfordii, CMCs could provide an efficient and controllable platform for sustainable production of terpenoids, which can be a better choice than DDCs.
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Affiliation(s)
- Yadi Song
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
| | - Shang Chen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
| | - Xiujuan Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
| | - Rui Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
| | - Tianyuan Hu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
| | - Xihong Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
| | - Yifeng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069 China
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, 100069 China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069 China
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Abstract
Abstract
Umbilical cord is a waste material, and therefore does not raise ethical concerns related to its use for research and medicine. Stem cells from umbilical cord have a significant advantage over cells from other sources. First, the umbilical cord is an infinite source of stem cells, because it can be taken theoretically during each delivery. Secondly, acquisition of umbilical cord is a non-invasive, safe procedure for mother and child. Thirdly, the transplantation of umbilical cord stem cells is associated with a lower risk of infection and a less-frequent “graft versus host” reaction. In this work, the authors present a historical background of research on the cell from its discovery to modern times characterized by highly advanced methods of obtaining stem cells from umbilical cord and from other sources.
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Jiang P, Gao Y, Chen X, Ke Q, Jin X, Huang C. Poly(butylene terephthalate) Fiber Assembly with Controllable Pore Size and Gradient Wettability: Potential in Simplifying Cell Culture Procedure. ACS Macro Lett 2018; 7:1192-1197. [PMID: 35651271 DOI: 10.1021/acsmacrolett.8b00545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This study reports the scalable fabrication of a poly(butylene terephthalate) fiber assembly featured with controllable pore size and gradient wettability. Pore size is controlled via adjusting the throughput of melt blown process, while gradient wettability is achieved through single-sided plasma exposure and subsequent chitosan coating. When used in cell culture, the fiber assembly takes much less time in reaching a high cell collecting/releasing rate up to ≥99.5%, which is similar to that of the conventional centrifugal method. Other advantages of the fiber assembly, such as improved cell viability, reduced risk of contamination, and excellent reusability are also proved, leading us to believe its great potential in making the current cell culture procedure simpler and faster.
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Affiliation(s)
- Peilin Jiang
- Department of Nonwoven Materials and Engineering, College of Textiles, Donghua University, Shanghai 201620, China
| | - Yingjun Gao
- Department of Nonwoven Materials and Engineering, College of Textiles, Donghua University, Shanghai 201620, China
| | - Xin Chen
- Department of Nonwoven Materials and Engineering, College of Textiles, Donghua University, Shanghai 201620, China
| | - Qinfei Ke
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiangyu Jin
- Department of Nonwoven Materials and Engineering, College of Textiles, Donghua University, Shanghai 201620, China
| | - Chen Huang
- Department of Nonwoven Materials and Engineering, College of Textiles, Donghua University, Shanghai 201620, China
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Ethnomedicinal, Phytochemical and Pharmacological Profile of Anthriscus sylvestris as an Alternative Source for Anticancer Lignans. Molecules 2015; 20:15003-22. [PMID: 26287153 PMCID: PMC6331990 DOI: 10.3390/molecules200815003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/06/2015] [Accepted: 08/11/2015] [Indexed: 11/17/2022] Open
Abstract
Anthriscus sylvestris (L.) Hoffm. is a wild herbaceous plant common in most temperate regions. It has been used traditionally to treat headaches, as a tonic, as antitussive, antipyretic, analgesic and diuretic. The plant contains deoxypodophyllotoxin, which is proven to have antitumor and anti-proliferative effects, anti-platelet aggregation, antiviral, anti-inflammatory and insecticidal activity. Deoxypodophyllotoxin is considered to be the plant’s most important constituent, because of its pharmacological properties and because it can be converted into epipodophyllotoxin, the main raw material for the semisynthesis of the cytostatic agents etoposide and teniposide. This work summarizes for the first time the results related to the botanical description, distribution and habitat, phytochemical and pharmacological properties and emphasizes the aspects for future biotechnological research to establish its utility in the therapeutic arsenal.
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Iwase A, Mita K, Nonaka S, Ikeuchi M, Koizuka C, Ohnuma M, Ezura H, Imamura J, Sugimoto K. WIND1-based acquisition of regeneration competency in Arabidopsis and rapeseed. JOURNAL OF PLANT RESEARCH 2015; 128:389-97. [PMID: 25810222 DOI: 10.1007/s10265-015-0714-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/17/2015] [Indexed: 05/20/2023]
Abstract
Callus formation and de novo organogenesis often occur in the wounded tissues of plants. Although this regenerative capacity of plant cells has been utilized for many years, molecular basis for the wound-induced acquisition of regeneration competency is yet to be elucidated. Here we find that wounding treatment is essential for shoot regeneration from roots in the conventional tissue culture of Arabidopsis thaliana. Furthermore, we show that an AP2/ERF transcription factor WOUND INDUCED DEDIFFERENTIATION1 (WIND1) plays a pivotal role for the acquisition of regeneration competency in the culture system. Ectopic expression of WIND1 can bypass both wounding and auxin pre-treatment and increase de novo shoot regeneration from root explants cultured on shoot-regeneration promoting media. In Brassica napus, activation of Arabidopsis WIND1 also greatly enhances de novo shoot regeneration, further corroborating the role of WIND1 in conferring cellular regenerative capacity. Our data also show that sequential activation of WIND1 and an embryonic regulator LEAFY COTYLEDON2 enhances generation of embryonic callus, suggesting that combining WIND1 with other transcription factors promote efficient and organ-specific regeneration. Our findings in the model plant and crop plant point to a possible way to efficiently induce callus formation and regeneration by utilizing transcription factors as a molecular switch.
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Affiliation(s)
- Akira Iwase
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan,
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Tyler SEB. The Work Surfaces of Morphogenesis: The Role of the Morphogenetic Field. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s13752-014-0177-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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