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  1. Article ; Online: Enhancing petunia tissue culture efficiency with machine learning

    Hamed Rezaei / Asghar Mirzaie-Asl / Mohammad Reza Abdollahi / Masoud Tohidfar

    PLoS ONE, Vol 18, Iss 11, p e

    A pathway to improved callogenesis.

    2023  Volume 0293754

    Abstract: The important feature of petunia in tissue culture is its unpredictable and genotype-dependent callogenesis, posing challenges for efficient regeneration and biotechnology applications. To address this issue, machine learning (ML) can be considered a ... ...

    Abstract The important feature of petunia in tissue culture is its unpredictable and genotype-dependent callogenesis, posing challenges for efficient regeneration and biotechnology applications. To address this issue, machine learning (ML) can be considered a powerful tool to analyze callogenesis data, extract key parameters, and predict optimal conditions for petunia callogenesis, facilitating more controlled and productive tissue culture processes. The study aimed to develop a predictive model for callogenesis in petunia using ML algorithms and to optimize the concentrations of phytohormones to enhance callus formation rate (CFR) and callus fresh weight (CFW). The inputs for the model were BAP, KIN, IBA, and NAA, while the outputs were CFR and CFW. Three ML algorithms, namely MLP, RBF, and GRNN, were compared, and the results revealed that GRNN (R2≥83) outperformed MLP and RBF in terms of accuracy. Furthermore, a sensitivity analysis was conducted to determine the relative importance of the four phytohormones. IBA exhibited the highest importance, followed by NAA, BAP, and KIN. Leveraging the superior performance of the GRNN model, a genetic algorithm (GA) was integrated to optimize the concentration of phytohormones for maximizing CFR and CFW. The genetic algorithm identified an optimized combination of phytohormones consisting of 1.31 mg/L BAP, 1.02 mg/L KIN, 1.44 mg/L NAA, and 1.70 mg/L IBA, resulting in 95.83% CFR. To validate the reliability of the predicted results, optimized combinations of phytohormones were tested in a laboratory experiment. The results of the validation experiment indicated no significant difference between the experimental and optimized results obtained through the GA. This study presents a novel approach combining ML, sensitivity analysis, and GA for modeling and predicting callogenesis in petunia. The findings offer valuable insights into the optimization of phytohormone concentrations, facilitating improved callus formation and potential applications in plant tissue culture and genetic ...
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Comparative analysis of different artificial neural networks for predicting and optimizing in vitro seed germination and sterilization of petunia.

    Hamed Rezaei / Asghar Mirzaie-Asl / Mohammad Reza Abdollahi / Masoud Tohidfar

    PLoS ONE, Vol 18, Iss 5, p e

    2023  Volume 0285657

    Abstract: The process of optimizing in vitro seed sterilization and germination is a complicated task since this process is influenced by interactions of many factors (e.g., genotype, disinfectants, pH of the media, temperature, light, immersion time). This study ... ...

    Abstract The process of optimizing in vitro seed sterilization and germination is a complicated task since this process is influenced by interactions of many factors (e.g., genotype, disinfectants, pH of the media, temperature, light, immersion time). This study investigated the role of various types and concentrations of disinfectants (i.e., NaOCl, Ca(ClO)2, HgCl2, H2O2, NWCN-Fe, MWCNT) as well as immersion time in successful in vitro seed sterilization and germination of petunia. Also, the utility of three artificial neural networks (ANNs) (e.g., multilayer perceptron (MLP), radial basis function (RBF), and generalized regression neural network (GRNN)) as modeling tools were evaluated to analyze the effect of disinfectants and immersion time on in vitro seed sterilization and germination. Moreover, non‑dominated sorting genetic algorithm‑II (NSGA‑II) was employed for optimizing the selected prediction model. The GRNN algorithm displayed superior predictive accuracy in comparison to MLP and RBF models. Also, the results showed that NSGA‑II can be considered as a reliable multi-objective optimization algorithm for finding the optimal level of disinfectants and immersion time to simultaneously minimize contamination rate and maximize germination percentage. Generally, GRNN-NSGA-II as an up-to-date and reliable computational tool can be applied in future plant in vitro culture studies.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Resistance mechanisms of the two-spotted spider mite, Tetranychus urticae (Acari

    Mohammad Khanjani / Fatemeh Saberfar / Asghar Mirzaie-Asl / Aziz Sheikhi Garjan

    Journal of Crop Protection, Vol 9, Iss 2, Pp 337-

    Tetranychidae) populations to fenpyroximate

    2020  Volume 345

    Abstract: The two-spotted spider mite, Tetranychus urticae (Acari: Tetranychidae) is one of the most important pests of field crops, orchard trees and ornamentals around the world. The short life cycle, high reproductive potential, accompanied by frequent ... ...

    Abstract The two-spotted spider mite, Tetranychus urticae (Acari: Tetranychidae) is one of the most important pests of field crops, orchard trees and ornamentals around the world. The short life cycle, high reproductive potential, accompanied by frequent acaricide applications have caused resistance development to wide range of acaricides. In this study the susceptibility of two populations, collected from Karaj and Mahllat, was investigated against fenpyroximate. The bioassay test was carried out by using the leaf-dip method. The results showed that the LC50 values for Karaj and Mahallat population were 2.1 and 92 (mg/ml), respectively. The resistance ratio was 43.8. The enzyme assay results revealed that the activity ratios of esterase in Mahallat to Karaj populations were 2.5 and 1.2 when α-NA and β-NA were used as a substrate, respectively. The activity of cytochrome P450 in Mahallat population was 1.37 times higher than the Karaj population. There was no significant difference in glutathion S-transferase activity between the two populations. The gene expression (qRT-PCR) results showed that the expression level of CYP392A11 in Mahallat population was 3.52 times higher than Karaj population. These results suggested that esterase and cytochrome P450 monoxygenase are probably involved in resistance of T. urticae to fenpyroximate.
    Keywords biochemical assay ; cytochrome p450 ; detoxification enzymes ; glutathion s-transferase ; qrt-pcr ; Agriculture ; S
    Subject code 580
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher University of Tarbiat Modares
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Identification and tissue-specific expression of rutin biosynthetic pathway genes in Capparis spinosa elicited with salicylic acid and methyl jasmonate

    Farzad Kianersi / Mohammad Reza Abdollahi / Asghar Mirzaie-asl / Dara Dastan / Faiza Rasheed

    Scientific Reports, Vol 10, Iss 1, Pp 1-

    2020  Volume 15

    Abstract: Abstract Capparis spinosa is an edible medicinal plant which is considered as an excellent source of rutin. Rutin is a glycoside of the flavonoid quercetin that has been reported to have a beneficial role in controlling various diseases such as ... ...

    Abstract Abstract Capparis spinosa is an edible medicinal plant which is considered as an excellent source of rutin. Rutin is a glycoside of the flavonoid quercetin that has been reported to have a beneficial role in controlling various diseases such as hypertension, arteriosclerosis, diabetes, and obesity. In this study, the partial cDNA of four genes involved in the rutin biosynthetic pathway including 4-coumaroyl CoA ligase (4CL), flavonoid 3′-hydroxylase (F3′H), flavonol synthase (FLS) and flavonol-3-O-glucoside L-rhamnosyltransferase (RT) were identified in C.spinosa plants for the first time. The protein sequences of these genes shared high similarity with the same proteins in other plant species. Subsequently, the expression patterns of these genes as well as rutin accumulation in C.spinosa leaves treated with different concentrations of salicylic acid (SA) and methyl jasmonate (MeJA) and also in different tissues of Caper plants treated with 100 mgL−1 SA and 150 μM MeJA were evaluated. The expression of all four genes was clearly up-regulated and rutin contents increased in response to MeJA and SA treatments after 24 h. The highest rutin contents (5.30 mgg−1 DW and 13.27 mgg−1 DW), as well as the highest expression levels of all four genes, were obtained using 100 mgL−1 SA and 150 μM MeJA, respectively. Among the different tissues, the highest rutin content was observed in young leaves treated with 150 μM MeJA, which corresponded to the expression of related genes, especially RT, as a key gene in the rutin biosynthetic pathway. These results suggest that rutin content in various tissues of C. spinosa can be enhanced to a significant extent by MeJA and SA treatments and the gene expression patterns of rutin-biosynthesis-related genes are regulated by these elicitors.
    Keywords Medicine ; R ; Science ; Q
    Subject code 580
    Language English
    Publishing date 2020-06-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Identification and expression profiling of rosmarinic acid biosynthetic genes from Satureja khuzistanica under carbon nanotubes and methyl jasmonate elicitation

    Fatemi, Farzaneh / Mohammad Reza Abdollahi / Asghar Mirzaie-asl / Dara Dastan / Constantine Garagounis / Kalliope Papadopoulou

    Plant cell, tissue, and organ culture. 2019 Mar., v. 136, no. 3

    2019  

    Abstract: Satureja khuzistanica is a medicinal herb endemic to Iran which can serve as a source of rosmarinic acid (RA). In the present study, the effect of different concentrations of methyl jasmonate (MeJA) and multi-walled carbon nanotubes (MWCNTs) on the ... ...

    Abstract Satureja khuzistanica is a medicinal herb endemic to Iran which can serve as a source of rosmarinic acid (RA). In the present study, the effect of different concentrations of methyl jasmonate (MeJA) and multi-walled carbon nanotubes (MWCNTs) on the rosmarinic acid accumulation and the expression of genes involved in its biosynthetic pathway was evaluated in nodal segment cultures of S. khuzistanica. The concentration of RA varied in plant extracts derived from the field, plants obtained under in vitro solid media, calli, suspension cultures and nodal segment cultures in liquid medium, with the highest amount recorded in nodal segment cultures. Phenylalanine ammonia-lyase (PAL), tyrosine aminotransferase (TAT), 4-hydroxyphenylpyruvate reductase (HPPR) and RA synthase (RAS) cDNA clones as key biosynthetic genes of RA production were identified and expression patterns were assayed in response to MeJA and MWCNTs, exogenously applied at a range of 0, 50, 100, 250 mg L⁻¹. The expression levels of HPPR, PAL and TAT were up-regulated at 100 mg L⁻¹ MWCNTs, whereas down-regulated levels were observed at 250 mg L⁻¹. RAS was up-regulated in all MWCNTs treatments. HPPR, PAL and TAT expression increased sharply at 250 mg L⁻¹ MeJA. The highest levels of RAS transcripts were observed at 100 mg L⁻¹ MeJA. The highest HPPR, PAL and TAT expression levels were observed at 250 mg L⁻¹ MeJA. In accordance, HPLC analysis showed a high amount of RA under MeJA and MWCNT elicitors. Our results provide helpful information on the expression profiles of biosynthetic genes in connection with RA accumulation.
    Keywords Satureja ; biochemical pathways ; biosynthesis ; callus ; carbon nanotubes ; clones ; complementary DNA ; elicitors ; gene expression ; genes ; high performance liquid chromatography ; liquids ; medicinal plants ; methyl jasmonate ; phenylalanine ammonia-lyase ; plant extracts ; rosmarinic acid ; tyrosine transaminase ; Iran
    Language English
    Dates of publication 2019-03
    Size p. 561-573.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 406394-6
    ISSN 1573-5044 ; 0167-6857
    ISSN (online) 1573-5044
    ISSN 0167-6857
    DOI 10.1007/s11240-018-01537-8
    Database NAL-Catalogue (AGRICOLA)

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