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Hairy root culture technology: applications, constraints and prospect. Appl Microbiol Biotechnol 2020; 105:35-53. [PMID: 33226470 DOI: 10.1007/s00253-020-11017-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022]
Abstract
Hairy root (HR) culture, a successful biotechnology combining in vitro tissue culture with recombinant DNA machinery, is intended for the genetic improvement of plants. This technology has been put to use since the last three decades for genetic advancement of medicinal and aromatic plants and also to harvest the economical products in the form of secondary metabolites that are significantly important for their ethnobotanical and pharmacological properties. It also provides an efficient way out for the quicker extraction and quantification of the valuable phytochemicals. The current review provides an account of the in vitro HR culture technology and its wide-scale applications in the field of research as well as in pharmaceutical industries. Different facets of HR with respect to the culture establishment, phytochemical production as well as research investigations concerning the areas of gene manipulation, biotransformation of the secondary metabolites, phytoremediation, their industrial utilisations and different problems encountered during the application of this technology have been covered in this appraisal. Eventually, an idea has been provided on HR about the recent trends on the progress of this technology that may open up newer prospects in near future and calls for further research and explorations in this field. KEY POINTS: • Genetic engineering-based HR culture aims towards enhanced secondary metabolite production. • This review explores an insight in the HR technology and its multi-faceted approaches. • Up-to-date ground-breaking research applications and constraints of HR culture are discussed.
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Hesami M, Alizadeh M, Naderi R, Tohidfar M. Forecasting and optimizing Agrobacterium-mediated genetic transformation via ensemble model- fruit fly optimization algorithm: A data mining approach using chrysanthemum databases. PLoS One 2020; 15:e0239901. [PMID: 32997694 PMCID: PMC7526930 DOI: 10.1371/journal.pone.0239901] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/15/2020] [Indexed: 12/21/2022] Open
Abstract
Optimizing the gene transformation factors can be considered as the first and foremost step in successful genetic engineering and genome editing studies. However, it is usually difficult to achieve an optimized gene transformation protocol due to the cost and time-consuming as well as the complexity of this process. Therefore, it is necessary to use a novel computational approach such as machine learning models for analyzing gene transformation data. In the current study, three individual machine learning models including Multi-Layer Perceptron (MLP), Adaptive Neuro-Fuzzy Inference System (ANFIS), and Radial Basis Function (RBF) were developed for forecasting Agrobacterium-mediated gene transformation in chrysanthemum based on eleven input variables including Agrobacterium strain, optical density (OD), co-culture period (CCP), and different antibiotics including kanamycin (K), vancomycin (VA), cefotaxime (CF), hygromycin (H), carbenicillin (CA), geneticin (G), ticarcillin (TI), and paromomycin (P). Consequently, best-obtained results were used in the fusion process by bagging method. Results showed that ensemble model with the highest R2 (0.83) had superb performance in comparison with all other individual models (MLP:063, RBF:0.69, and ANFIS: 0.74) in the validation set. Also, ensemble model was linked to Fruit fly optimization algorithm (FOA) for optimizing gene transformation, and the results showed that the maximum gene transformation efficiency (37.54%) can be achieved from EHA105 strain with 0.9 OD600, for 3.8 days CCP, 46.43 mg/l P, 9.54 mg/l K, 18.62 mg/l H, and 4.79 mg/l G as selection antibiotics and 109.74 μg/ml VA, 287.63 μg/ml CF, 334.07 μg/ml CA and 87.36 μg/ml TI as antibiotics in the selection medium. Moreover, sensitivity analysis demonstrated that input variables have a different degree of importance in gene transformation system in the order of Agrobacterium strain > CCP > K > CF > VA > P > OD > CA > H > TI > G. Generally, the developed hybrid model in this study (ensemble model-FOA) can be employed as an accurate and reliable approach in future genetic engineering and genome editing studies.
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Affiliation(s)
- Mohsen Hesami
- Department of Plant Agriculture, Gosling Research Institute for Plant Preservation, University of Guelph, Guelph, ON, Canada
| | - Milad Alizadeh
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran
- * E-mail:
| | - Masoud Tohidfar
- Department of Plant Biotechnology, Faculty of Sciences & Biotechnology, Shahid Beheshti University, G.C., Tehran, Iran
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Hesami M, Jones AMP. Application of artificial intelligence models and optimization algorithms in plant cell and tissue culture. Appl Microbiol Biotechnol 2020; 104:9449-9485. [PMID: 32984921 DOI: 10.1007/s00253-020-10888-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 12/28/2022]
Abstract
Artificial intelligence (AI) models and optimization algorithms (OA) are broadly employed in different fields of technology and science and have recently been applied to improve different stages of plant tissue culture. The usefulness of the application of AI-OA has been demonstrated in the prediction and optimization of length and number of microshoots or roots, biomass in plant cell cultures or hairy root culture, and optimization of environmental conditions to achieve maximum productivity and efficiency, as well as classification of microshoots and somatic embryos. Despite its potential, the use of AI and OA in this field has been limited due to complex definition terms and computational algorithms. Therefore, a systematic review to unravel modeling and optimizing methods is important for plant researchers and has been acknowledged in this study. First, the main steps for AI-OA development (from data selection to evaluation of prediction and classification models), as well as several AI models such as artificial neural networks (ANNs), neurofuzzy logic, support vector machines (SVMs), decision trees, random forest (FR), and genetic algorithms (GA), have been represented. Then, the application of AI-OA models in different steps of plant tissue culture has been discussed and highlighted. This review also points out limitations in the application of AI-OA in different plant tissue culture processes and provides a new view for future study objectives. KEY POINTS: • Artificial intelligence models and optimization algorithms can be considered a novel and reliable computational method in plant tissue culture. • This review provides the main steps and concepts for model development. • The application of machine learning algorithms in different steps of plant tissue culture has been discussed and highlighted.
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Affiliation(s)
- Mohsen Hesami
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Andrew Maxwell Phineas Jones
- Gosling Research Institute for Plant Preservation, Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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Hesami M, Naderi R, Tohidfar M, Yoosefzadeh-Najafabadi M. Development of support vector machine-based model and comparative analysis with artificial neural network for modeling the plant tissue culture procedures: effect of plant growth regulators on somatic embryogenesis of chrysanthemum, as a case study. PLANT METHODS 2020; 16:112. [PMID: 32817755 PMCID: PMC7424974 DOI: 10.1186/s13007-020-00655-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/08/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Optimizing the somatic embryogenesis protocol can be considered as the first and foremost step in successful gene transformation studies. However, it is usually difficult to achieve an optimized embryogenesis protocol due to the cost and time-consuming as well as the complexity of this process. Therefore, it is necessary to use a novel computational approach, such as machine learning algorithms for this aim. In the present study, two machine learning algorithms, including Multilayer Perceptron (MLP) as an artificial neural network (ANN) and support vector regression (SVR), were employed to model somatic embryogenesis of chrysanthemum, as a case study, and compare their prediction accuracy. RESULTS The results showed that SVR (R2 > 0.92) had better performance accuracy than MLP (R2 > 0.82). Moreover, the Non-dominated Sorting Genetic Algorithm-II (NSGA-II) was also applied for the optimization of the somatic embryogenesis and the results showed that the highest embryogenesis rate (99.09%) and the maximum number of somatic embryos per explant (56.24) can be obtained from a medium containing 9.10 μM 2,4-dichlorophenoxyacetic acid (2,4-D), 4.70 μM kinetin (KIN), and 18.73 μM sodium nitroprusside (SNP). According to our results, SVR-NSGA-II was able to optimize the chrysanthemum's somatic embryogenesis accurately. CONCLUSIONS SVR-NSGA-II can be employed as a reliable and applicable computational methodology in future plant tissue culture studies.
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Affiliation(s)
- Mohsen Hesami
- Department of Plant Agriculture, University of Guelph, Guelph, ON Canada
| | - Roohangiz Naderi
- Department of Horticultural Science, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Masoud Tohidfar
- Department of Plant Biotechnology, Faculty of Science and Biotechnology, Shahid Beheshti University, G.C., Tehran, Iran
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Application of Artificial Neural Network for Modeling and Studying In Vitro Genotype-Independent Shoot Regeneration in Wheat. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10155370] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Optimizing in vitro shoot regeneration conditions in wheat is one of the important steps in successful micropropagation and gene transformation. Various factors such as genotypes, explants, and phytohormones affect in vitro regeneration of wheat, hindering the ability to tailor genotype-independent protocols. Novel computational approaches such as artificial neural networks (ANNs) can facilitate modeling and predicting outcomes of tissue culture experiments and thereby reduce large experimental treatments and combinations. In this study, generalized regression neural network (GRNN) were used to model and forecast in vitro shoot regeneration outcomes of wheat on the basis of 10 factors including genotypes, explants, and different concentrations of 6-benzylaminopurine (BAP), kinetin (Kin), 2,4-dichlorophenoxyacetic acid (2,4-D), indole-3-acetic acid (IAA), indole-3-butyric acid (IBA), 1-naphthaleneacetic acid (NAA), zeatin, and CuSO4. In addition, GRNN was linked to a genetic algorithm (GA) to identify an optimized solution for maximum shoot regeneration. Results indicated that GRNN could accurately predict the shoot regeneration frequency in the validation set with a coefficient determination of 0.78. Sensitivity analysis demonstrated that shoot regeneration frequency was more sensitive to variables in the order of 2,4-D > explant > genotype < zeatin < NAA. Results of this study suggest that GRNN-GA can be used as a tool, besides experimental approaches, to develop and optimize in vitro genotype-independent regeneration protocols.
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Yi TG, Park Y, Park JE, Park NI. Enhancement of Phenolic Compounds and Antioxidative Activities by the Combination of Culture Medium and Methyl Jasmonate Elicitation in Hairy Root Cultures of Lactuca indica L. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19861867] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lactuca indica L. has been traditionally used as a wild vegetable and as a medicinal plant for centuries. The various compounds present in it and their biological activities have been extensively reported. Hairy-root culture combined with agrobacterium-meditated metabolic engineering is a useful technique to achieve stable production of biologically active plant compounds. Here, we evaluated the enhancement of secondary metabolites in L. indica L. and their bioactivities by testing culture media composition and the use of an elicitor. Hairy roots were induced and cultured in MS or SH liquid media for 2 weeks prior to treatment with various concentrations of MeJa, for different periods. The resulting phenolic contents and physiological activities were analyzed. Higher total phenolic, flavonoid, and hydroxycinnamic acids contents were attained by elicitation with MeJa. Metabolite accumulation, especially in SH media and in the presence of MeJa, was time dependent. Particularly, accumulation of chicoric acid increased markedly with time. Similarly, we observed time dependent positive and negative responses of antioxidant activity in DPPH and ABTS assays, respectively. As in previous studies, the highest correlation was found between total phenolic content and total flavonoid content. Further, 3,5-DCQA showed the highest correlation with total phenolic content, total flavonoid content, and antioxidant activities in hydroxycinnamic acids. Our data effectively identified optimal culture conditions to increase the accumulation of secondary metabolites and antioxidant activity in hairy roots cultures of L. indica L.
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Affiliation(s)
- Tae Gyu Yi
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Yeri Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Jai-Eok Park
- Smart Farm Research Center, KIST Gangneung Institute of National Products, Gangneung, South Korea
| | - Nam Il Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
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Arab MM, Yadollahi A, Eftekhari M, Ahmadi H, Akbari M, Khorami SS. Modeling and Optimizing a New Culture Medium for In Vitro Rooting of G×N15 Prunus Rootstock using Artificial Neural Network-Genetic Algorithm. Sci Rep 2018; 8:9977. [PMID: 29967468 PMCID: PMC6028477 DOI: 10.1038/s41598-018-27858-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/12/2018] [Indexed: 11/17/2022] Open
Abstract
The main aim of the present investigation is modeling and optimization of a new culture medium for in vitro rooting of G×N15 rootstock using an artificial neural network-genetic algorithm (ANN-GA). Six experiments for assessing different media culture, various concentrations of Indole - 3- butyric acid, different concentrations of Thiamine and Fe-EDDHA were designed. The effects of five ionic macronutrients (NH4+, NO3-, Ca2+, K+ and Cl-) on five growth parameters [root number (RN), root length (RL), root percentage (R%), fresh (FW) and dry weight (DW)] were evaluated using the ANN-GA method. The R2 correlation values of 0.88, 0.88, 0.98, 0.94 and 0.87 between observed and predicted values were acquired for all five growth parameters, respectively. The ANN-GA results indicated that among the input variables, K+ (7.6) and NH4+ (4.4), K+ (7.7) and Ca2+ (2.8), K+ (36.7) and NH4+ (4.3), K+ (14.7) and NH4+ (4.4) and K+ (7.6) and NH4+ (4.3) had the highest values of variable sensitivity ratio (VSR) in the data set, for RN, RL, R%, FW and DW, respectively. ANN-GA optimized LS medium for G×N15 rooting contained optimized amounts of 1 mg L-1 IBA, 100, 150, or 200 mg L-1 Fe-EDDHA and 1.6 mg L-1 Thiamine. The efficiency of the optimized culture media was compared to other standard media for Prunus rooting and the results indicated that the optimized medium is more efficient than the others.
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Affiliation(s)
- Mohammad Mehdi Arab
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
- Department of Horticulture, College of Aburaihan, University of Tehran (UT), Tehran, Iran
| | - Abbas Yadollahi
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran.
| | - Maliheh Eftekhari
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Hamed Ahmadi
- Bioscience and Agriculture Modeling Research Unit, College of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Akbari
- Department of Horticultural Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Saadat Sarikhani Khorami
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
- Department of Horticulture, College of Aburaihan, University of Tehran (UT), Tehran, Iran
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Yeon Kwon D, Hoon Kim H, Seok Park J, Un Park S, Il Park N. Production of Bacalin, Bacalein and Wogonin in Hairy Root Culture of American Skullcap (Scutellaria lateriflora)by Auxin Treatment. ACTA ACUST UNITED AC 2017. [DOI: 10.13005/bbra/2493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
ABSTRACT: The hairy root culture of American Skullcap (Scutellaria lateriflora) was studied to investigate the biomass and flavonoids content (baicalin, baicalein and wogonin) in response of various auxin concentrations.The growth rates of the hairy roots varied significantly only at IBA 0.1 mg/L and for all other auxin treatments did not vary significantly. The biomass of hairy roots was 8% higher when treated with IBA 0.1 mg/L and biomass was almost similar and slightly lower levels when treated with various IAA concentration and NAA, respectively. However, the auxins treatments responsed positively to increase flavone production in American Skullcaphairy root culture. The auxin indole-3-butyric acid (IBA) at 1 mg/L performed the best for the accumulation of baicalin and wogonin. The auxin IBA at 1 mg/L accumulated 1.64 and 2.92 times higher baicalin and wogonin, respectively compared to control treatment. Meanwhile, the highest levels of baicalein were observed for hair root cultures in the presence of 1-naphthaleneacetic acid (NAA) at 0.1 mg/L achieving 2.38 times higher than that of accumulated in the control. These findings indicate that hairy root cultures of S. lateriflorausing liquid 1/2MS medium supplemented with auxin could be a valuable alternative approach for flavonoid production.
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Affiliation(s)
- Do Yeon Kwon
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Haeng Hoon Kim
- Department of Well-being Resources, Sunchon National University, Suncheon, Jeollanam-do, 540-742, Korea
| | - Jong Seok Park
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Sang Un Park
- Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Nam Il Park
- Deptartment of Plant Science, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si, Gangwon-do 25457, Korea
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Prasad A, Prakash O, Mehrotra S, Khan F, Mathur AK, Mathur A. Artificial neural network-based model for the prediction of optimal growth and culture conditions for maximum biomass accumulation in multiple shoot cultures of Centella asiatica. PROTOPLASMA 2017; 254:335-341. [PMID: 27068291 DOI: 10.1007/s00709-016-0953-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 02/03/2016] [Indexed: 06/05/2023]
Abstract
An artificial neural network (ANN)-based modelling approach is used to determine the synergistic effect of five major components of growth medium (Mg, Cu, Zn, nitrate and sucrose) on improved in vitro biomass yield in multiple shoot cultures of Centella asiatica. The back propagation neural network (BPNN) was employed to predict optimal biomass accumulation in terms of growth index over a defined culture duration of 35 days. The four variable concentrations of five media components, i.e. MgSO4 (0, 0.75, 1.5, 3.0 mM), ZnSO4 (0, 15, 30, 60 μM), CuSO4 (0, 0.05, 0.1, 0.2 μM), NO3 (20, 30, 40, 60 mM) and sucrose (1, 3, 5, 7 %, w/v) were taken as inputs for the ANN model. The designed model was evaluated by performing three different sets of validation experiments that indicated a greater similarity between the target and predicted dataset. The results of the modelling experiment suggested that 1.5 mM Mg, 30 μM Zn, 0.1 μM Cu, 40 mM NO3 and 6 % (w/v) sucrose were the respective optimal concentrations of the tested medium components for achieving maximum growth index of 1654.46 with high centelloside yield (62.37 mg DW/culture) in the cultured multiple shoots. This study can facilitate the generation of higher biomass of uniform, clean, good quality C. asiatica herb that can efficiently be utilized by pharmaceutical industries.
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Affiliation(s)
- Archana Prasad
- Division of Plant Biotechnology, CSIR-Central Institute of Medicinal & Aromatic Plants (CSIR-CIMAP); PO CIMAP, Lucknow, 226015, India
| | - Om Prakash
- Division of Molecular and Structural Biology, CSIR-Central Institute of Medicinal & Aromatic Plants (CSIR-CIMAP); PO CIMAP, Lucknow, 226015, India
| | - Shakti Mehrotra
- Division of Plant Biotechnology, CSIR-Central Institute of Medicinal & Aromatic Plants (CSIR-CIMAP); PO CIMAP, Lucknow, 226015, India
| | - Feroz Khan
- Division of Molecular and Structural Biology, CSIR-Central Institute of Medicinal & Aromatic Plants (CSIR-CIMAP); PO CIMAP, Lucknow, 226015, India
| | - Ajay Kumar Mathur
- Division of Plant Biotechnology, CSIR-Central Institute of Medicinal & Aromatic Plants (CSIR-CIMAP); PO CIMAP, Lucknow, 226015, India
| | - Archana Mathur
- Division of Plant Biotechnology, CSIR-Central Institute of Medicinal & Aromatic Plants (CSIR-CIMAP); PO CIMAP, Lucknow, 226015, India.
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Arab MM, Yadollahi A, Shojaeiyan A, Ahmadi H. Artificial Neural Network Genetic Algorithm As Powerful Tool to Predict and Optimize In vitro Proliferation Mineral Medium for G × N15 Rootstock. FRONTIERS IN PLANT SCIENCE 2016; 7:1526. [PMID: 27807436 PMCID: PMC5069296 DOI: 10.3389/fpls.2016.01526] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/29/2016] [Indexed: 05/23/2023]
Abstract
One of the major obstacles to the micropropagation of Prunus rootstocks has, up until now, been the lack of a suitable tissue culture medium. Therefore, reformulation of culture media or modification of the mineral content might be a breakthrough to improve in vitro multiplication of G × N15 (garnem). We found artificial neural network in combination of genetic algorithm (ANN-GA) as a very precise and powerful modeling system for optimizing the culture medium, So that modeling the effects of MS mineral salts ([Formula: see text], [Formula: see text], [Formula: see text], Ca2+, K+, [Formula: see text], Mg2+, and Cl-) on in vitro multiplication parameters (the number of microshoots per explant, average length of microshoots, weight of calluses derived from the base of stem explants, and quality index of plantlets) of G × N15. Showed high R2 correlation values of 87, 91, 87, and 74 between observed and predicted values were found for these four growth parameters, respectively. According to the ANN-GA results, among the input variables, [Formula: see text] and [Formula: see text] had the highest values of VSR in data set for the parameters studied. The ANN-GA showed that the best proliferation rate was obtained from medium containing (mM) 27.5 [Formula: see text], 14 [Formula: see text], 5 Ca2+, 25.9 K+, 0.7 Mg2+, 1.1 [Formula: see text], 4.7 [Formula: see text], and 0.96 Cl-. The performance of the medium optimized by ANN-GA, denoted as YAS (Yadollahi, Arab and Shojaeiyan), was compared to that of standard growth media for all Prunus rootstock, including the Murashige and Skoog (MS) medium, (specific media) EM, Quoirin and Lepoivre (QL) medium, and woody plant medium (WPM) Prunus. With respect to shoot length, shoot number per cultured explant and productivity (number of microshoots × length of microshoots), YAS was found to be superior to other media for in vitro multiplication of G × N15 rootstocks. In addition, our results indicated that by using ANN-GA, we were able to determine a suitable culture medium formulation to achieve the best in vitro productivity.
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Affiliation(s)
- Mohammad M. Arab
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares UniversityTehran, Iran
- Department of Horticultural Sciences, College of Abooraihan, University of TehranTehran, Iran
| | - Abbas Yadollahi
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares UniversityTehran, Iran
| | - Abdolali Shojaeiyan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares UniversityTehran, Iran
| | - Hamed Ahmadi
- Department of Poultry Sciences, Faculty of Agriculture, Tarbiat Modares UniversityTehran, Iran
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Mansouri A, Fadavi A, Mortazavian SMM. An artificial intelligence approach for modeling volume and fresh weight of callus – A case study of cumin (Cuminum cyminum L.). J Theor Biol 2016; 397:199-205. [DOI: 10.1016/j.jtbi.2016.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 02/19/2016] [Accepted: 03/06/2016] [Indexed: 10/22/2022]
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Verma P, Anjum S, Khan SA, Roy S, Odstrcilik J, Mathur AK. Envisaging the Regulation of Alkaloid Biosynthesis and Associated Growth Kinetics in Hairy Roots of Vinca minor Through the Function of Artificial Neural Network. Appl Biochem Biotechnol 2015; 178:1154-66. [DOI: 10.1007/s12010-015-1935-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/22/2015] [Indexed: 11/28/2022]
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Pathak L, Singh V, Niwas R, Osama K, Khan S, Haque S, Tripathi CKM, Mishra BN. Artificial Intelligence versus Statistical Modeling and Optimization of Cholesterol Oxidase Production by using Streptomyces Sp. PLoS One 2015; 10:e0137268. [PMID: 26368924 PMCID: PMC4569268 DOI: 10.1371/journal.pone.0137268] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 08/16/2015] [Indexed: 12/05/2022] Open
Abstract
Cholesterol oxidase (COD) is a bi-functional FAD-containing oxidoreductase which catalyzes the oxidation of cholesterol into 4-cholesten-3-one. The wider biological functions and clinical applications of COD have urged the screening, isolation and characterization of newer microbes from diverse habitats as a source of COD and optimization and over-production of COD for various uses. The practicability of statistical/ artificial intelligence techniques, such as response surface methodology (RSM), artificial neural network (ANN) and genetic algorithm (GA) have been tested to optimize the medium composition for the production of COD from novel strain Streptomyces sp. NCIM 5500. All experiments were performed according to the five factor central composite design (CCD) and the generated data was analysed using RSM and ANN. GA was employed to optimize the models generated by RSM and ANN. Based upon the predicted COD concentration, the model developed with ANN was found to be superior to the model developed with RSM. The RSM-GA approach predicted maximum of 6.283 U/mL COD production, whereas the ANN-GA approach predicted a maximum of 9.93 U/mL COD concentration. The optimum concentrations of the medium variables predicted through ANN-GA approach were: 1.431 g/50 mL soybean, 1.389 g/50 mL maltose, 0.029 g/50 mL MgSO4, 0.45 g/50 mL NaCl and 2.235 ml/50 mL glycerol. The experimental COD concentration was concurrent with the GA predicted yield and led to 9.75 U/mL COD production, which was nearly two times higher than the yield (4.2 U/mL) obtained with the un-optimized medium. This is the very first time we are reporting the statistical versus artificial intelligence based modeling and optimization of COD production by Streptomyces sp. NCIM 5500.
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Affiliation(s)
- Lakshmi Pathak
- Department of Biotechnology, Institute of Engineering and Technology (Uttar Pradesh Technical University), Lucknow, 226021, India
| | - Vineeta Singh
- Microbiology Division, CSIR-Central Drug Research Institute, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Ram Niwas
- Microbiology Division, CSIR-Central Drug Research Institute, Sitapur Road, Lucknow, 226031, Uttar Pradesh, India
| | - Khwaja Osama
- Department of Biotechnology, Institute of Engineering and Technology (Uttar Pradesh Technical University), Lucknow, 226021, India
| | - Saif Khan
- Deratment of Clinical Nutrition, College of Applied Medical Sciences, Ha’il University, Ha’il, Saudi Arabia
| | - Shafiul Haque
- Centre for Drug Research, Faculty of Pharmacy, Viikki Biocenter-2, University of Helsinki, Helsinki, FIN-00014, Finland
- Research and Scientific Studies Unit, College of Nursing & Applied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - C. K. M. Tripathi
- Fermentation Technology Division, CSIR-Central Drug Research Institute, Sitapur Road, Lucknow-226031, Uttar Pradesh, India
| | - B. N. Mishra
- Department of Biotechnology, Institute of Engineering and Technology (Uttar Pradesh Technical University), Lucknow, 226021, India
- * E-mail:
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Mehrotra S, Srivastava V, Ur Rahman L, Kukreja AK. Hairy root biotechnology--indicative timeline to understand missing links and future outlook. PROTOPLASMA 2015; 252:1189-201. [PMID: 25626898 DOI: 10.1007/s00709-015-0761-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/12/2015] [Indexed: 05/13/2023]
Abstract
Agrobacterium rhizogenes-mediated hairy roots (HR) were developed in the laboratory to mimic the natural phenomenon of bacterial gene transfer and occurrence of disease syndrome. The timeline analysis revealed that during 90 s, the research expanded to the hairy root-based secondary metabolite production and different yield enhancement strategies like media optimization, up-scaling, metabolic engineering etc. An outlook indicates that much emphasis has been given to the strategies that are helpful in making this technology more practical in terms of high productivity at low cost. However, a sequential analysis of literature shows that this technique is upgraded to a biotechnology platform where different intra- and interdisciplinary work areas were established, progressed, and diverged to provide scientific benefits of various hairy root-based applications like phytoremediation, molecular farming, biotransformation, etc. In the present scenario, this biotechnology research platform includes (a) elemental research like hairy root-mediated secondary metabolite production coupled with productivity enhancement strategies and (b) HR-based functional research. The latter comprised of hairy root-based applied aspects such as generation of agro-economical traits in plants, production of high value as well as less hazardous molecules through biotransformation/farming and remediation, respectively. This review presents an indicative timeline portrayal of hairy root research reflected by a chronology of research outputs. The timeline also reveals a progressive trend in the state-of-art global advances in hairy root biotechnology. Furthermore, the review also discusses ideas to explore missing links and to deal with the challenges in future progression and prospects of research in all related fields of this important area of plant biotechnology.
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Affiliation(s)
- Shakti Mehrotra
- Plant Biotechnology Division, Central Institute of Medicinal & Aromatic Plants, PO: CIMAP, Picnic Spot Road, Lucknow, 226015, India,
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Mehrotra S, Goel MK, Srivastava V, Rahman LU. Hairy root biotechnology of Rauwolfia serpentina: a potent approach for the production of pharmaceutically important terpenoid indole alkaloids. Biotechnol Lett 2014; 37:253-63. [DOI: 10.1007/s10529-014-1695-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 10/03/2014] [Indexed: 12/19/2022]
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Modeling the effects of light and sucrose on in vitro propagated plants: a multiscale system analysis using artificial intelligence technology. PLoS One 2014; 9:e85989. [PMID: 24465829 PMCID: PMC3896442 DOI: 10.1371/journal.pone.0085989] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 12/03/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plant acclimation is a highly complex process, which cannot be fully understood by analysis at any one specific level (i.e. subcellular, cellular or whole plant scale). Various soft-computing techniques, such as neural networks or fuzzy logic, were designed to analyze complex multivariate data sets and might be used to model large such multiscale data sets in plant biology. METHODOLOGY AND PRINCIPAL FINDINGS In this study we assessed the effectiveness of applying neuro-fuzzy logic to modeling the effects of light intensities and sucrose content/concentration in the in vitro culture of kiwifruit on plant acclimation, by modeling multivariate data from 14 parameters at different biological scales of organization. The model provides insights through application of 14 sets of straightforward rules and indicates that plants with lower stomatal aperture areas and higher photoinhibition and photoprotective status score best for acclimation. The model suggests the best condition for obtaining higher quality acclimatized plantlets is the combination of 2.3% sucrose and photonflux of 122-130 µmol m(-2) s(-1). CONCLUSIONS Our results demonstrate that artificial intelligence models are not only successful in identifying complex non-linear interactions among variables, by integrating large-scale data sets from different levels of biological organization in a holistic plant systems-biology approach, but can also be used successfully for inferring new results without further experimental work.
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