مجله فنآوری زیستی در کشاورزی
سال هجدهم شماره 1 (بهار و تابستان 1398)

Nowadays, antibody engineering is an important approach to design and generate of therapeutic and diagnostic antibodies. The study of the interactions between antibodies and antigens is a critical step in the design of antibodies with desired properties, In silico docking analyzes is a useful tool for structural characterization of bimolecular interactions. Docking is the process of predicting bound conformations and binding enthalpy of antibody–antigen complexes. In this study, the three-dimensional structures of FMV nucleocapsid protein as an antigen as well as monoclonal antibody in form of scFv which was selected against the antigen by Phage display technique were built by I-TASSER software and then the binding complexes and molecular dynamics (MD) simulations were done by Hex software. By analyzing of the FMVNp-scFv complexes, important amino acids involved in antigen–antibody interactions were identified which all of them were belong to the CDRs. In conclusion, results obtained from this bioinformatics study could be helpful to design and development of the new antibodies with high affinities for FMV diagnosis.

Citrus belongs to rutaceae family, which has great importance both from industrial and agricultural aspects. This studywas conducted to assess genetic diversity in Citrus commercial cultivars and unknown genotypes resistant to droughtstress using ISSR molecular markers that 28 citrus genotypes were evaluated using 10 ISSR markers. The Clusteranalysis was performed according to the Simple Matching similarity coefficient and UPGMA algorithm and finally, thestudied genotypes were divided into five groups at similarity coefficient of 0.64. Results indicated that the lowestsimilarity (0.43) was observed between two unrecognized genotype G5 and G1, as well as between Alemow (G21) andChangsha (G4) genotypes. However, the highest similarity (0.91) was observed between Lisbon lemon (G28) andSweet lime (G26) genotypes. Likewise, it was observed high levels of polymorphism with ISSR markers in the presentstudy. The value of Polymorphism Information Content (PIC) ranged from 0.275 to 0.359 and the average ofpolymorphic percentage was 88.82% per primer. These results showed that ISSR markers are a suitable moleculartechnique for genetic diversity analysis of the studied genotypes.

Plant can be produced through the production of a wide range of antimicrobial compounds, including oxidizing enzymes such as Polyphenol Oxidase (PPO) and Peroxidase (POX) protect against phytopatogenic agents. In order to identify the role of these enzymes in maize resistance to fungus F. verticillioides, the experiment was conducted with three corn genotypes with different phenotypes for tolerant to fusarium ear rot consist of C7 (resistant line), B73 (semi resistant line) and MO17 (susceptible line) in three replications. Inoculating corn silk and kernel with Fusarium suspension and they were sampled at 12, 24, 48, 72 and 96 hours after inoculation. Uninfected ears were considered as controls. After evaluating the expression of PPO and POX genes using the Real Time PCR method, it was found that the expression of these two genes increased after maize Fusarium inoculation, but the expression of the gene in the resistant line during the first hours of inoculation was observed higher than the sensitive and semi-resistant lines. In the early hours of inoculation, the resistant line of PPO and POX gene expression in the silk sample was more than the sensitive line, in contrast, the sensitive line of PPO and POX gene expression in the kernel sample was more than the resistant line. However the resistant line showed a higher ability to respond to the disease and immediately after inoculation, the expression of PPO and POX genes was shown. It can be said that probably the importance of PPO and POX genes in the first hours of inoculation that causes the plant's resistance to pathogen entry.

The Oat (Avena sativa L.), is a plant of the Poaceae family and is one of the important crops in the world. Despite the high nutritional value, there is no annotated reference genome and there is no report of microRNA identification for this plant. In the present study, 733 million short reads was used to identify the conserved miRNAs and to investigate the expression of their target genes in the drought and salt-stressed leaf transcriptome of oat. Out of a total of 73419 assembled unigenes, 1419 non-coding unigenes were identified and considered as miRNA precursor. Finally, among non-coding unigenes, eight miRNAs named asa-miR5181b, asa-miR5049a-3p, asa-miR169d-5p, asa-miR5181a, asa-miR2118b-5p, asa-miR5049-3p, asa-miR5049b-3p and asa-miR1130-5p with Minimal Free Energy Index (MFEI) of -1.29 kcal/mol belonging to five conserved families were identified. Identified miRNAs down-regulated under the drought stress compared to control and salt stress conditions. Although the response to different types of abiotic stresses in plants is very similar, however, the expression of identified miRNAs was different between drought and salinity stresses. This is probably related to differences in the type of tissue, the sensing mechanism, and the initial response of plants to various stresses. In general, considering the regulatory role of conserved miRNAs in the control of the gene regulatory network, the identified miRNAs in this study, especially asa-miR1130-5p, can be used to regulate the expression of stress-responsive genes, including members of MYB, bHLH, and ERF transcription factors gene families in oat.

The aim of this study is to evaluate and comprehensively quantify the molecular changes created in the expression of rice embryo axes proteins by two-dimensional electrophoresis method. The variability in the protein pattern of the embryonic axes was evaluated in two rice tolerant and salinity-sensitive cultivars (Hassani and Sangjoo, respectively) during three replications. As result of the analysis of two-dimensional electrophoresis gels in the rice embryo axes, 328 repeatable spots were observed, which 63 spots showed a significant difference at the level of 1%. Multivariate statistical methods, such as cluster analysis and diagnostic function analysis, were used to group the stains expressed in Sangjoo and Hassani cultivars. The significant difference between the two cultivar showed that the tolerable cultivar they had the characteristic of stress tolerance. Cluster analysis placed proteins -in terms of expression- in three main clusters, indicating the presence of proteins with similar expression in each cluster. This indicates the similar performance of the proteins in each cluster and the presence of all of them in a common biological pathway. Discriminant analysis confirmed the results of clustering analysis 100% approved and indicating that the protein data are consistent with the experimental conditions. Due to the higher number of expression stains in Hassani's tolerance to salinity stress, and the decrease in stain expression in sensitive Sangjoo cultivar, it is possible to suggest the identification of genes related to these proteins. Overall, the results showed that using statistical software and analysis, it is easy to evaluate significant expression changes due to differences in the cultivar fetal proteome levels and can to determine the index of changes.

Nowadays due to inefficiency of copper antibacterial activity, especially increasing resistance of bacteria towards copper, the use of copper particles in nano-scale is considered. According to the literature, limited studies have been performed on the applicability of these materials to control plant pathogenic bacteria. Aim of this study was to evaluate the antibacterial activity of copper nanoparticles (CuNPs) and copper-chitosan (Cu-Cs) nanocomposite on some important plant pathogenic bacteria. The nanoparticles were synthesized with sumac extract and their antibacterial activity in different concentrations was evaluated to determine their Minimum Inhibitory Concentration (MIC). The structure and physical properties of nanoparticles were characterized by Scanning Electron Microscope (SEM), Transmission Electron Microscopy (TEM), and UV-Visible spectroscopy. Results showed that the CuNPs and nanocomposite had quasi-spherical shape in a uniform distribution with the average size of 100 and 20nm respectively. Green biosynthesized CuNPs showed minimum inhibitory concentration against Xanthomonas perforans, Clavibacter michiganensis subsp. michiganensis, Erwinia amylovora and Pseudomonas syringae pv. syringae at concentrations 0.5 ppm, 0.5ppm, 1ppm and 1.5ppm respectively. Also, Cu-Cs nanocomposite had an effective antibacterial activity at higher concentrations than copper nanoparticles. The lowest inhibitory concentration of nanocomposite was for X. perforans in combination of 1ppm CuNP and 3.93ppm Chitosan. However, chitosan did not increase the antibacterial activity of copper nanoparticles and no synergistic effect was observed for this compound.