Dehydration response element binding factors (DREBs) are one of the principal plant transcription factor subfamilies that regulate the expression of many abiotic stress-inducible genes. This sub-family belongs to AP2 transcription factor family and plays a considerable role in improving abiotic stresses tolerance in plants. Therefore, it is of interest to identify critical cis-acting elements involved in abiotic stress responses. In this study, we survey promoter cis-elements for ATDREBs genes (Arabidopsis thaliana DREBs). Regulatory networks based on ATDREB candidate genes were also generated to find other genes that are functionally similar to DREBs. The study was conducted on all 20 Arabidopsis thaliana non redundant DREB genes stored in RefSeq database. Promoter analysis and regulatory network prediction was accomplished by use of Plant CARE program and GeneMANIA web tool, respectively. The results indicated that among all genes, DREB1A, DREB1C, DREB2C, DREB2G and DEAR3 have the most type of diverse motifs involved in abiotic stress responses. It is implied that co-operation of abscisic acid, ethylene, salicylic acid and methyl jasmonate signaling is crucial for the regulation of the expression of drought and cold responses through DREB transcription factors. Gene network analysis showed different co-expressed but functionally similar genes that had physical and functional interactions with candidate DREB genes.

The emergence of a rapidly spreading and highly infectious COVID-19 outbreak by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has caused a global pandemic with unprecedented, social and economic dimensions. Therefore, the development of effective strategies is urgent to control COVID-19 outbreak. According to the recent investigations, cell entry of coronaviruses relies on binding of the viral spike glycoprotein to the host cellular receptors. Therefore, in the present study aimed to predict immunogenic epitopes in silico by analyzed spike protein. In parallel, by screening the immunogenic SARS-CoV-2 spike derived epitopes provided in the literature, we chose a set of epitopes believed to induce immunogenic response. Next, we provided the selected epitopes from both approaches, we performed immunoinformatic analysis that map identically to antigen regions and have antigenic properties. Finally, by suggesting a screened set of epitopes, we designed a novel virus-like particle (VLP) vaccine, optimized to be produced in plants by using molecular farming biotechnology techniques. We anticipate our assay to be a starting point for guiding experimental efforts toward the development of a vaccine against SARS-CoV-2.

Background Virus-like particles are an interesting vector platform for vaccine development. Particularly, Hepatitis B virus core antigen has been used as a promising VLP platform. It is highly expressed in different recombinant expression systems, such as E. coli, and self-assembled in vitro. It effectively improves the immunogenicity of foreign antigenic epitopes on its surface. Various foreign antigens from bacteria, viruses, and protozoa can be genetically inserted into such nanoparticles. The effective immunogenicity due to VLP vaccines has been reported. However, no research has been performed on the SARS-CoV2 vaccine within this unique platform through genetic engineering. Considering the high yield of target proteins, low cost of production, and feasibility of scaling up, E. coli is an outstanding expression platform to develop such vaccines. Therefore, in this investigation, we planned to study and develop a unique HBc VLP-based vaccine against SARS-Cov2 utilizing the E. coli expression system due to its importance. Results Insertion of the selected epitope was done into the major immunodominant region (MIR) of truncated (149 residues) hepatitis B core capsid protein. The chimeric protein was constructed in PET28a+ and expressed through the bacterial E. coli BL21 expression system. However, the protein was expressed in inclusion body forms and extracted following urea denaturation from the insoluble phase. Following the extraction, the vaccine protein was purified using Ni2 + iminodiacetic acid (IDA) affinity chromatography. SDS-PAGE and western blotting were used to confirm the protein expression. Regarding the denaturation step, the unavoidable refolding process was carried out, so that the chimeric VLP reassembled in native conformation. Based on the transmission electron microscopy (TEM) analysis, the HBC VLP was successfully assembled. Confirming the assembled chimeric VLP, we explored the immunogenic effectivity of the vaccine through mice immunization with two-dose vaccination with and without adjuvant. The utilization of adjuvant was suggested to assess the effect of adjuvant on improving the immune elicitation of chimeric VLP-based vaccine. Immunization analysis based on anti-spike specific IgG antibody showed a significant increase in antibody production in harvested serum from immunized mice with HBc-VLP harboring antigenic epitope compared to HBc-VLP- and PBS-injected mice. Conclusions The results approved the successful production and the effectiveness of the vaccine in terms of humoral IgG antibody production. Therefore, this platform can be considered a promising strategy for developing safe and reasonable vaccines; however, more complementary immunological evaluations are needed.

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Catharanthus roseus is known as the only source for the low-abundance anticancer agents namely vinblastine and vincristine. Fine tuning of accumulation of such secondary metabolites is highly governed by the regulatory genes. Among these genes, Catharanthus roseus MYC1 (CrMYC1) is known as one of the key transcription factors regulating the biosynthesis of terpenoid indole alkaloid metabolites in C. roseus. In this study, CrMYC1 coding sequence (AF283506) was isolated and cloned in PBI121 plant binary vector. Then, CrMYC1 was transiently overexpressed in C. roseus leaves using agroinfiltration method. In addition to molecular analysis for confirming CrMYC1 overexpression, the profile of some chief terpenoid indole alkaloids in control and transgenic plants was evaluated by HPLC to elucidate the role of CrMYC1 in an increased in the anticancer components. The results indicated that overexpression of CrMYC1 transcription factor can increase most important terpenoid indole alkaloids including vinblastine, vincristine, and catharanthine in C. roseus. HPLC analysis of catharanthine and vinblastine contents showed about 3 and 2.5 fold increases, respectively, while the increase in vinecristine was not significant compared to that of the control. Therefore, CrMYC1 is introduced as an efficient candidate for manipulating TIA pathway in C. roseus and increasing at least the most valuable terpenoid indole alkaloids in this plant.

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Context and aims Due to the effect of seed priming on abiotic stress-induced tolerance in plants, this study has been performed to identify the key genes responding to the seed osmo-priming process in a sensitive barley variety under drought stress. Methods The microarray data regarding barley expression analysis under drought stress (expression profile of GSE56437) was used to determine differentially expressed probes in time-series data with the BETR package in R. 1388 differentially expressed probes were ranked by 10 attribute weighting approaches in RapidMiner. Also, decision tree models were applied to provide insight into the combination of important probes in a ranked structure. Key results Following attribute weighting approaches analysis, 328 differentially probes were identified by at least one attribute weighting approach. The top-ranked genes were HORVU6Hr1G089600 (sugar transporter), HORVU7Hr1G060130 (superoxide dismutase [CU-ZN] 2, Chloroplastic), HORVU4Hr1G076520 (non-specific serine/threonine protein kinase/threonine-specific protein kinase) and HORVU3Hr1G082260 (3-phosphoinositide dependent protein kinase-1). Conclusions According to the promoter analysis of key genes, important transcription factor binding sites related to developmental processes, biotic and abiotic stress responses were identified. The most frequent consensus binding sites were related to the vernalisation1 transcription factor. Enriched gene ontology term analysis pointed out processes with a distinguished role in drought tolerance like oxidation–reduction. Implications To our awareness, this is the first study for identifying genes involved in priming-induced tolerance via integrating time-series data analysis, various attribute weighting approaches and decision tree models.

Saccharomyces cerevisiae is known for its outstanding ability to produce ethanol in industry. Underlying the dynamics of gene expression in S. cerevisiae in response to fermentation could provide informative results, required for the establishment of any ethanol production improvement program. Thus, representing a new approach, this study was conducted to identify the discriminative genes between improved and repressed ethanol production as well as clarifying the molecular responses to this process through mining the transcriptomic data. The significant differential expression probe sets were extracted from available microarray datasets related to yeast fermentation performance. To identify the most effective probe sets contributing to discriminate ethanol content, 11 machine learning algorithms from RapidMiner were employed. Further analysis including pathway enrichment and regulatory analysis were performed on discriminative probe sets. Besides, the decision tree models were constructed, the performance of each model was evaluated and the roots were identified. Based on the results, 171 probe sets were identified by at least 5 attribute weighting algorithms (AWAs) and 17 roots were recognized with 100% performance Some of the top ranked presets were found to be involved in carbohydrate metabolism, oxidative phosphorylation, and ethanol fermentation. Principal component analysis (PCA) and heatmap clustering validated the top-ranked selective probe sets. In addition, the top-ranked genes were validated based on GSE78759 and GSE5185 dataset. From all discriminative probe sets, OLI1 and CYC3 were identified as the roots with the best performance, demonstrated by the most weighting algorithms and linked to top two significant enriched pathways including porphyrin biosynthesis and oxidative phosphorylation. ADH5 and PDA1 were also recognized as differential top-ranked genes that contribute to ethanol production. According to the regulatory clustering analysis, Tup1 has a significant effect on the top-ranked target genes CYC3 and ADH5 genes. This study provides a basic understanding of the S. cerevisiae cell molecular mechanism and responses to two different medium conditions (Mg2+ and Cu2+) during the fermentation process.