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A computational study is employed to provide an insight view of the behaviour and function of the complexing agents for environmental friendly silver electroplating. The electronic properties of th...

One of the strategies to reduce the off-target mutations in CRISPR/Cas9 system is to use the temperature-independent gene transformation method. Mesoporous silica nanoparticles (MSNs)-gene delivery system is temperature-independent; thus, it can transfer the interesting plasmid (pDNA) to the target plant at different temperatures, including 37 °C. Due to the high activity of SpCas9 at 37 °C compared to lower temperatures, on-target mutagenesis increases at 37 °C. Therefore, we describe the synthesis of the functionalized MSNs with the particle size of less than 40 nm, binding pDNA to the MSNs, and transferring of the pDNA-MSNs into the target plants.

The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.

The retarding of metal corrosion due to the effect on economic and safety matters is a challenging research area. The theoretical study could be helpful to understand the mechanism of inhibition and design some new inhibitors. The electronic properties of some pyrimidine derivatives in the gas and aqueous phase were investigated using the m062x/6-311G(3df,3pd) level of theory and the plane wave pseudopotential method and PBE functional were used in the analysis on the Fe(111) surface. The volume and HLG gave the better results for isolated molecule study. Different groups substituted or replaced in thion 2-mercapto pyrimidine (S=Py) structure to enhance its inhibition efficiency. The replacement of Se instead of S revealed the best results in all parameters. The study of inhibitor interaction with the metal surface provides better correlation with the experimental inhibition efficiency and better insight. Keto tautomers represented more efficiency in both gas and solid phase. We predicted that halogenate compounds obey different mechanism to prevent corrosion. Bader analysis indicated that the charge flow occurs from Fe atoms toward inhibitor molecules. As thermodynamic studies confirm that Se=Py is a good inhibitor, the kinetic study of dehydrogenation by CI-NEB method showed lower activation energy for it. So it may be introduced as a new inhibition candidate.

Benzo (α) pyrene (Bap) is one of the well-known compounds which forming covalent DNA and leads to carcinogenic activity. The [2 + 2] cycloaddition reaction of the benzopyrene epoxide (BaPe) with fu...

Due to their biodegradability and biocompatibility, mesoporous silica nanoparticles (MSNs) are employed as DNA nanocarriers in the following novel transient gene expression approach in tomato. The synthesized MSNs were analyzed in size, shape and charge, using FE-SEM, TEM, and Zetasizer, respectively. The tomato plants were then transformed with the MSNs containing pPZP122:35S:GUS (pDNA-MSNs) via three innovative methods including spray and injection the solution into the abaxial surface of leaves and injection into the shoot. The RT-PCR expression of GUS in combination with the histochemical GUS assay results show that pDNA-MSNs entered the cells and undergo the processes of transcription and translation. Subsequently, to investigate the efficiency of the newly developed methods, cryIAb gene through pPZP122:35S:cryIAb-MSNs was transferred into the tomatoes to control Tuta absoluta. The related molecular and bioassay analysis confirmed the transcription and translation of cryIAb in association with an enhanced resistance against Tuta in the tomatoes. Accordingly, for the first time, MSN-mediated gene transient transformation was successfully performed under in vivo condition, and the pDNA-MSN injection into the lower surface of leaves was recognized as the best approach. Since this system is biocompatible and saves time and energy consumption; it could be utilized as a new and more efficient technique in crop genetic engineering.

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

In this study, a novel and stable gene transformation system was developed under control of Maize Proteinase Inhibitor (MPI) as an inducible promoter using the Mesoporous Silica Nanoparticles (MSNs). The functionalized MSNs with a proper particle size were synthesized and attached to a recombinant construct (pDNA) containing cryIAb gene under the control of MPI promoter (pPZP122:MPI:cryIAb:MSN [pDNA: MSN]) following transformation of tomato plants through injection of the pDNA: MSN complex into tomato red fruit at early ripening stage and then, putative transgenic seeds were collected. As an initial selection, gentamicin-resistant seedlings of T1 (24.24%) and T2 (61.37%) plants were identified. The transgene integration and expression were confirmed through the PCR, RT-PCR, and western blot approaches in the selected seedlings. PCR analysis showed that transformation frequency was equal to 10.71% in T1 plants. Semi-quantitative RT-PCR analysis confirmed the transcript expression of cryIAb in all the T1 and T2 PCR-positive plants. Western blot analysis confirmed the existence of CryIAb protein in the leaves of T2 putative transgenic plants. Accordingly, the results demonstrated that the transgene has more likely integrated into the tomato genome through homologous recombination. Bioassay was carried out for further assessment of the plant responses to Tuta absoluta resulting in an enhanced tolerance of the plant. In conclusion, the MSN-mediated stable transformation system under the MPI as an inducible promoter can be used as a suitable alternative for conventional genetic transformation methods due to its biodegradability, biocompatibility, cost and time-effectiveness, and positive effect on the plant defense against pathogens and pests.

Understanding the interaction of organic molecule on metal surfaces is essential for a wide range of technological applications. Adsorption of nitrobenzene (NB) on Pd (1 1 1) surface in different positions was investigated with the periodic density functional theory (DFT) calculation. The most favorable adsorption configuration energetically was a parallel configuration that nitrogen located on top of Pd atom with −0.303 eV. In these weakly adsorption, choice of proper exchange-correlation is critical. VdW-C09 functional with −2.46 eV had the most adsorption energy. Some bimetallic surfaces like V/Pd (1 1 1), Fe/Pd (1 1 1), Ni/Pd (1 1 1), Pt/Pd (1 1 1) and Zn/Pd (1 1 1) were investigated in magnetic property and d-band model as well as geometry and energy to find the appropriate surface. The position of d-band center in the vicinity of Fermi energy represented more active bimetallic surfaces. PDOS, work function and charge transfer of the system were studied before and after adsorption of NB on the most appropriate surface (Fe/Pd (1 1 1)). Adsorption of nitrobenzene causes a decrease in work function of the surface and an increment of charge in the interface region.

In this study, a novel and stable gene transformation system was developed under control of Maize Proteinase Inhibitor (MPI) as an inducible promoter using the Mesoporous Silica Nanoparticles (MSNs). The functionalized MSNs with a proper particle size were synthesized and attached to a recombinant construct (pDNA) containing cryIAb gene under the control of MPI promoter (pPZP122:MPI:cryIAb:MSN [pDNA: MSN]) following transformation of tomato plants through injection of the pDNA: MSN complex into tomato red fruit at early ripening stage and then, putative transgenic seeds were collected. As an initial selection, gentamicin-resistant seedlings of T(1) (24.24%) and T(2) (61.37%) plants were identified. The transgene integration and expression were confirmed through the PCR, RT-PCR, and western blot approaches in the selected seedlings. PCR analysis showed that transformation frequency was equal to 10.71% in T(1) plants. Semi-quantitative RT-PCR analysis confirmed the transcript expression of cryIAb in all the T(1) and T(2) PCR-positive plants. Western blot analysis confirmed the existence of CryIAb protein in the leaves of T(2) putative transgenic plants. Accordingly, the results demonstrated that the transgene has more likely integrated into the tomato genome through homologous recombination. Bioassay was carried out for further assessment of the plant responses to Tuta absoluta resulting in an enhanced tolerance of the plant. In conclusion, the MSN-mediated stable transformation system under the MPI as an inducible promoter can be used as a suitable alternative for conventional genetic transformation methods due to its biodegradability, biocompatibility, cost and time-effectiveness, and positive effect on the plant defense against pathogens and pests. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-020-02359-2) contains supplementary material, which is available to authorized users.

The CRISPR/Cas9 system (clustered regularly interspaced short palindromic repeat-associated protein 9) is a powerful genome-editing tool in animals, plants, and humans. This system has some advantages, such as a high on-target mutation rate (targeting efficiency), less cost, simplicity, and high-efficiency multiplex loci editing, over conventional genome editing tools, including meganucleases, transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs). One of the crucial shortcomings of this system is unwanted mutations at off-target sites. We summarize and discuss different approaches, such as dCas9 and Cas9 paired nickase, to decrease the off-target effects in plants. According to studies, the most effective method to reduce unintended mutations is the use of ligand-dependent ribozymes called aptazymes. The single guide RNA (sgRNA)/ligand-dependent aptazyme strategy has helped researchers avoid unwanted mutations in human cells and can be used in plants as an alternative method to dramatically decrease the frequency of off-target mutations. We hope our concept provides a new, simple, and fast gene transformation and genome-editing approach, with advantages including reduced time and energy consumption, the avoidance of unwanted mutations, increased frequency of on-target changes, and no need for external forces or expensive equipment.

In the present study, genetic diversity of 48 individual plants from four Iranian cultivated populations of alfalfa (Medicago sativa L.) was evaluated using sequence-related amplified polymorphism (SRAP) markers. Fourteen SRAP primer combinations produced 193 fragments of which 95 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 3 to 10 bands with an average of 6.78 bands. Average polymorphic information content (PIC) was 0.343 for all primer combinations. Although the AMOVA (analysis of molecular variance) results showed a significant difference in the genetic diversity among the populations (P < 0.0001), the genetic variation mainly caused by the variation of intra population accounted for 93.17% of the total genetic variation. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data clearly separated the populations of subtropical (Yazdi) and semi-cold (Hamadani and Nikshahri) as well as Kodi, an improved population. It can be concluded that SRAP markers are useful for studying diversity and relationships among and within alfalfa populations.

Chloroplast DNA has been used extensively to analyze plant phylogenies at different taxonomic levels because of its size, organization and sequence conservation. In the present research, two chloroplastic regions, petA–psaJ, trnC–trnD and four DNA barcodes (trnH–psbA, ITS, rbcL, matK), were used to introduce suitable regions for the assessment of genetic diversity among P. granatum L. genotypes. Analysis of psbE–petL in petA–psaJ region revealed 1,300 nucleotides with 4.29 % genetic diversity among genotypes, while trnC–petN in trnC–trnD region showed 1.8 % genetic diversity. Therefore, despite the results obtained from the study of other plants, the trnC–trnD region had a low potential for the evaluation of diversity among pomegranate genotypes. Analysis of DNA barcodes in pomegranate showed that trnH–psbA (genetic diversity 2.91 %) provides the highest intra-species variation, followed by ITS (genetic diversity 0.44 %). Eighteen genotypes from different geographical origins of Iran were used to investigate psbE–petL and trnH–psbA potential as novel barcodes to determine genetic polymorphism and characterize pomegranate genotypes. The results suggested that two regions, psbE–petL and trnH–psbA, were more suitable for determining intra-species relationships of pomegranate.