Iranian Journal of Biotechnology
Volume:20 Issue: 1, Winter 2022

Cymbidium mosaic virus (CymMV) is one of the most devastating viruses causing losses in the orchid industry, affecting economies worth millions of US dollars. CymMV significantly affects the orchid population and could be controlled through an integrated management strategy consisting of virus detection, good sanitation care of gardeners and their tools, and maintaining virus-free explants.

 This review was written based on research publications relevant to the CymMV infection in orchids. The literature cited were obtained from online literature databases such as web of Science, Scopus, and Google Scholar. The searched term used was “Cymbidium mosaic virus”. Related publications to the initial search were also examined.

This review describes the threat of CymMV to the orchid population by examining its history, genome organization, symptoms on individual orchids, detection, and management. Current research has been focusing on the prospect of transgenic orchids with viral resistance. This review also highlights the potential role of the symbiotic relationship between orchids and arbuscular mycorrhiza fungi that could be useful to improve the protection of orchids against virus infection. Overall, this review provides information on how CymMV infection impacts the orchid population.

Drought response in plants at molecular level, aiding them to overcome the adverse effects of drought, remarkably depends on the expression of a few regulator genes and signal transduction. For reducing the drought stress, nanoparticles show great promise compared to other commonly used methods, even though the underlying mechanisms are still unknown. This study was performed to investigate the expression analysis of genes involved in drought tolerance and the use of zinc oxide nanoparticles (ZnO NPs) to mitigate the undesirable effects of drought stress in wheat. A factorial experiment based on completely randomized design (CRD) was performed with three replicates. The experiment was carried out in the greenhouse of Mohaghegh Ardabili University, Ardabil, Iran in 2017. The factorial combination of stress levels of water supply (including 85%, 60%, and 35% fi eld capacity) and ZnO NPs (0, 0.5, and 1.0 g. L-1) were used on three wheat cultivars (Mihan, Heidari, and Gascogne). Three days after sprayingthe ZnO NPs in the three-leaf stage, drought stress was applied for ten days and physio-biochemical traits and gene expression of wheat cultivars were investigated. The expression of Wdhn13, DREB2, P5CS, and CAT1 genes in leaves were analyzed by real-time polymerase chain reaction (PCR). Generally, drought stress signifi cantly enhanced total protein and lysine, soluble sugars, chlorophyll, carotenoid contents, antioxidant enzymes activities, and proline accumulation in plants treated with ZnO NPs. Moreover, the ZnO NPs increased the expression of the genes involved in proline biosynthesis (i.e., P5CS), catalase activity (i.e., CAT1), and dehydration-responsive genes DREB2 and Wdhn13, which are known as drought-tolerance parameters. According to our results, ZnO NP-treated wheat induced drought-tolerance genes and effectively facilitated defi ciency tolerance. Therefore, under drought stress, we recommend spraying bread wheat with ZnO NPs (1 g. L-1) in the growing season, which can improve wheat grain yield under dry conditions.

Camelina sativa is one of the most important oilseeds that has a proportionate profile of essential unsaturated fatty acids that are suitable for human nutrition. In this regard, we can mention a high percentage and a reasonable ratio of omega 3 and omega 6. In the current study, the created variation of second-generation mutant (M2) camelina lines in terms of fatty acid profiles and ISSR molecular markers in C. sativa was evaluated. For this purpose, while producing the first-generation of mutant plants (M1), 200 M2 seeds with 0.1% and 0.5% ethyl methanesulfonate (EMS) mutations were treated in two replications for 8 and 16 hours based on a completely randomized design. The results of mean comparisons showed that there was no significant difference between treatments in terms of fatty acids of palmitic acid, stearic acid, linoleic acid, eicosadienoic acid, oleic acid and erucic acid. The cluster analysis revealed that all the treatments used with five replications were divided into eight groups. It was found that all replications of the treatment with a concentration of 0.1% and a time of 16 hours (C1T2) were in the second group with the lowest palmitic acid was present among other treatments. Therefore, C1T2 treatment is recommended as the best treatment to reduce palmitic acid. Examination of the information content of ISSR molecular markers also showed that markers 2, 5, and 6 were the best informative markers in the detection of camelina fatty acid profiles. A significant variation has been created in the fatty acids profile and it can be applied in future breeding programs depending on the intended purpose.

The most common polymers in the treatment of wounds are natural (e.g., polysaccharides, proteins, and peptides) and synthetic polymers (e.g., poly-glycolic acid, polyacrylic acid, polylactic acid, and polyvinyl alcohol) due to their biodegradability, biocompatibility, and their structural resemblance to the macromolecules known to the human body. The current study aimed to develop an electrospinning method using the nanofibers of polyvinyl alcohol (PVA)/carboxymethyl cellulose (CMC)/polyamide amine (PAMAM)/tetracycline (Tet) to cover the wound. The antibacterial effect of PAMAM was also tested against E. coli and S. aureus bacteria. The morphology of the composite nanofiber was studied by a field emission scanning electron microscope. Infrared spectroscopy (FTIR) was used to characterize the nano chemical structure. Nanofibers were evaluated based on the release of different amounts of the antibiotic tetracycline (1%, 3%, 5%, and 7% by weight) while preventing wound infection. The findings indicated that the highest-profile release of all nanofibers occurred early within 12 hours. It was found that nanofiber membranes loaded with 1%, 3%, and 5% tetracycline released drugs for over 28 days, while those containing 7% tetracycline released drugs for more than 14 days. According to the findings related to the drug release of PVA/CMC/15% PAMAM/Tet and surface morphology of the nanofibers, the optimal amount of Tet was 5%. The results of FTIR spectroscopy indicated that the tetracycline and polyamidoamine were successfully placed in nanofibers.

Bacillus subtilis can produce urease in the presence of urea as the main carbon source and induce mineralization in the presence of precipitable cations. The objective of our study was to demonstrate that Bacillus subtilis catabolizes glucose first in the presence of both glucose and urea carbon sources. Using its feature of catabolizing glucose first to delay the mineralization time, it proved its potential application in enhancing the recovery of heterogeneous reservoirs. The metabolic process of Bacillus subtilis was monitored by changing the glucose content in the bacterial medium by UV spectrophotometer and pH meter. Using a non-homogeneous physical model, experiments were conducted to improve reservoir recovery by microbial mineralization after polymer oil drive. The higher the glucose content in the medium, the longer the time for the pH of the bacterial solution to reach 7 and the longer the end of the logarithmic phase of growth. the glucose content of the 48 h medium was significantly correlated with the consumption of the bacteria and the quality of the precipitation. In the oil drive experiment: the permeability of the high permeability model was reduced from 1200 md to 136 md with a reduction rate of 88.6 %, and the permeability of the low permeability model was reduced by 22 md, and the crude oil recovery was increased by 7.9 %. It was demonstrated that the addition of glucose to the culture medium retarded the mineralization of bacteria. Only 0.2 times the pore volume of the bacterial solution and the cementing solution is required to form an effective seal, thus improving the recovery of crude oil.

Chromium is one of the most used toxic heavy metals. A large amount of chromium waste is discharged into the environment every year, causing serious environmental pollution, especially the pollution of soil and water by hexavalent chromium. Eliminating hexavalent chromium is the primary challenge to achieve a pollution-free environment. This study aims to understand the mechanism of Pichia guilliermondii’s reduction of hexavalent chromium through enzymatic characteristic, oxidative stress response, and reduction product. The strain Pichia guilliermondii ZJH-1 was isolated and stored in our laboratory. The hexavalent chromium uses 1,5-diphenyl carbazide method (DPC) to measure. The UV spectrophotometer was used to measure the intracellular antioxidant enzyme activity, and the kit was used to measure the activity of catalase and glutathione reductase. The reduction products were analyzed by ultraviolet full-wavelength scanning and FTIR. The reduction of hexavalent chromium by ZJH-1 is accompanied by an increase in active oxygen and antioxidant levels. Chromate reductase mainly exists in the extracellular fluid, and the carboxyl, amide, hydroxide and other groups of the cell wall are involved in the bioremediation of Cr(VI) by complexing with Cr(VI) and Cr(III). After ZJH-1 was treated with different concentrations of Cr(VI), the expression of proteins with molecular weights of 15 kDa, 18 kDa, 35 kDa, 62 kDa, and 115 kDa increased significantly. This strain is the most suitable for chromate reductase (CChR). The optimum temperature is 40℃ and the optimum pH is 7.0. Cu2+ can enhance the activity of chromate reductase. At the optimum temperature and pH, the chromate reductase Km of this strain is 0.40 μmol and Vmax is 14.47 μmoL.L-1·min-1. The bioremediation of Cr(VI) by Pichia guilliermondii ZJH-1 is attributable to the reduction product (Cr(III)) that can be removed in the precipitate and can be fixed on the cell surface and accumulated in the cell.

Glucose oxidase is an oxidoreductase that depletes oxygen in food processing and is used in biosensors, glucose diagnostic kits, food processing, cosmetics, and chemical industries. This enzyme is often isolated from fungi, such as Penicillium and Aspergillus Niger. The objective of this study was to clone and express a full-length GOX gene from soil thermophilic streptomyces for bioinformatic and enzyme activity evaluations. After collecting samples from the Gandom Beryan area of Kerman province, Iran, Streptomyces strains were identified with specific biochemical and molecular tests. Streptomyces strains with glucose oxidase gene were detected by PCR, and the amplified gene fragment was cloned into Escherichia coli host bacterium using TA cloning technique. The expression of the cloned GOX gene in the host bacterium was measured using real-time PCR, and the recombinant plasmids were sequenced. The enzymatic activity was measured in the extracts of E. coli cells carrying the plasmids. After screening the samples, 12 strains of Streptomyces were identified, 4 of which carried the GOX gene. The GOX open reading frame, obtained by PCR, was cloned into a vector and transformed into Escherichia coli origami to generate GOX-producing bacteria. Enzyme activity was confirmed and a phylogenetic tree showed the degree of kinship between Streptomyces species and other species, including Streptomyces SP MI02-7b. The expression levels of GOX genes mRNA were found to be approximately 4-fold higher in transformed E. coli than in soil thermophilic Streptomyces (P <0.001). This study showed that natural thermostable streptomyces producing glucose oxidase enzyme could be found in Iran. The enzyme gene was successfully transformed into Escherichia coli generating a recombinant host with high yield capability that can be a major step towards the production of this enzyme from indigenous strains. It should be emphasized that the GOX enzyme produced by these strains is profitable due to high production levels correlated to the optimum condition in cheap culture media, short fermentation cycles, high expression capability, and ease of growth.

One of the deadliest and most prevalent cancer is pancreatic ductal adenocarcinoma (PDAC). Microarray has become an important tool in the research of PDAC genes and target therapeutic drugs. This study intends to clarify the promising prognostic and biomarker targets in PDAC using GSE78229 and GSE62452 datasets, publicly accessible at the Gene Expression Omnibus database. Utilizing GEOquery, Bio base, gplots, and ggplot2 packages in the R program, this study detects 428 differentially expressed genes that are further applied to build a co-expression network by the weighted correlation network analysis (WGCNA). The turquoise module presented a higher correlation with PDAC progression. 79 candidate genes were selected based on the co-expression and protein-protein interaction (PPI) networks. In addition, the functional enrichment analysis was studied. Five significant KEGG pathways linked to PDAC were detected, in which the endoplasmic reticulum protein processing pathway was remarked to be vital. The resulting 19 hub genes as HSPA4, PABPC1, HSP90B1, PPP1CC, USP9X, EIF2S3, MSN, RAB10, BMPR2, P4HB, UBC, B2M, SLC25A5, MMP7, SPTBN1, RALB, DNAJB1, CENPE, and PDIA6 were identified by the Network Analyst web tool founded on PPI network by the STRING. These were identified as the most connected hub proteins. The quantification of the expression of levels and survival probabilities were analyzed overall survival (OS) of the real hub genes and were investigated by Kaplan–Meier (KM) plotter through The Cancer Genome Atlas Program (TCGA) database. The protein-protein interactions and KEGG pathway enrichment by DAVID indicated that some pathways were involved in PDAC, such as “pathways in cancer (hsa05200)”, “protein processing in the endoplasmic reticulum (hsa04141)”, “antigen processing and presentation (hsa04612)”, “dopaminergic synapse (hsa04728)”, and “measles (hsa05162)”; in which these pathways, the “protein processing in endoplasmic reticulum (hsa04141)”, was further studied because of its closely relationship with PDAC. The rest of the hub genes reviewed throughout the study might be promising targets for diagnosing and treating PDAC and relevant diseases.

Chinese liquorice (Glycyrrhiza uralensis), an important medicinal plant, contains various valuable secondary metabolites. Secondary metabolites biosynthesis is very tightly regulated; therefore, elucidation and manipulation of the biosynthetic pathways are of great interest. Recent studies have shown that lncRNAs play important regulatory roles in many biological processes, thus identification and modification of their expression is essential to metabolic pathways for biosynthesis of secondary metabolites. In this study we attempted to identify non-coding RNA transcripts (lncRNAs) that may act as important regulators of diverse biological processes, including stress responses and developmental programs in Glycyrrhiza uralensis. Identification of potential lncRNAs in Chinese liquorice was performed using a bioinformatics pipeline from the available EST dataset of G. uralensis. Bioinformatics analysis revealed that 1365 identical sequences in the range of 200 to 1286 base pair are putative lncRNAs. Only less than one percent of the predicted lncRNAs display sequence conservation with lncRNAs from other species. Moreover, 13 lncRNAs were detected as the potential precursors of 16 miRNAs. From this analysis, we also detected possible target genes of 16 known miRNA genes. The majority of the predicted miRNA target genes have important role in response to plant disease and a couple of them contribute to signalling and metabolic pathways. This study demonstrates the existence of lncRNAs in G. uralensis which has not been found before and provides valuable resources for further understanding and characterizing of lncRNAs and also a basis for additional investigation to reveal specific roles of lncRNAs in various biological processes and particularly in response to plant diseases.

Interleukin-6 (IL-6) has undeniable roles in inflammatory processes due to autoimmune diseases. In this regard, soluble receptors are considered a potential approach to mitigate its inflammatory effects and modulate its physiological effects by reducing the IL-6 binding to cell surface-specific receptors.

This study aimed to produce IL-6 receptor (IL-6R) in soluble form with enhanced affinity to IL-6 without signal transduction ability.

The 3D structure of IL-6R with the selective mutations for enhancing the IL-6 binding, with minimum ability to signal transduction (mIL-6R), was predicted using Modeller 9.19. This mutated form was docked to IL-6 and gp130 (a part of the native IL-6 receptor involved in signal transduction) by the HADDOCK2.2 web server. The expression of mIL-6R was performed in E. coli BL21 (DE3), using pTWIN-1 plasmid as its linkage to the Ssp Intein. IMPACT system manual was used to purify the protein at 25 °C overnight. Next, ELISA was performed to compare the affinity of mutated and native IL-6R to IL-6. Finally, A549 cells were used to compare the inhibition of cytotoxic effects of native and mutated IL-6R.

In the silico section, results established the stability of mutant’s structure with more and less affinity to IL-6 and gp130, respectively. The expression and purification results showed bands of about 50 and 23 kDa, representing the correct size of the Intein1-mIL-6R fusion protein and cleavaged mIL-6R in SDS-PAGE, respectively. Furthermore, a significant enhancement in the affinity of mutated IL-6R to IL-6 was observed compared to the native receptor. Finally, A549 cells showed more cytotoxic effects followed by treating with mutated IL-6R in comparison to cells treated with native soluble IL-6R.

The recombinant production of a mutated form of IL-6R with the potential ability to antagonize the IL-6 inflammatory effects confirmed with in silico studies was successfully performed for the first time to create a new drug candidate for suppressing the inflammatory effects of IL-6.