A new member of Tau-class glutathione S-transferase from barley leaves

Glutathione S-transferase is a family of multifunctional detoxification enzymes which are mainly cytosolic that detoxify natural and exogenous toxic compounds by conjugation with glutathione. Glutathione, an endogenous tripeptide, is important as either a reducing agent or a nucleophilic scavenger. This molecule alleviates the chemical toxicity in plants by reaction of glutathione S-transferase, and its conjugates can be transported to vacuole or apoplast. The plant soluble glutathione S-transferases grouped today into seven distinct Phi, Tau, Zeta, Theta, lambda, dehydroascorbate reductase, and tetrachlorohydroquinone dehalogenase classes. In this study, bioinformatics analysis of glutathione S-transferase gene in barley was carried out using Tau-class of barley glutathione S-transferase sequences in NCBI GenBank and isolated sequence. DNA extraction, primer design, PCR, electrophoresis, column purification, DNA sequencing and analysis by some software led to identify new sequences of Tauclass of glutathione S-transferase from barley, which is similar to Tau GST of the diploid wheat. Comparison of the deduced amino acid sequences of the three barley GST genes showed that they have 99 % identity with each other but only 45 % identity with the new GST. This sequence was submitted to NCBI GenBank with FI131240 accession number

Antibacterial and antibiofilm activities of Prangos acaulis Bornm. extract against Streptococcus mutans: an in silico and in vitro study

Introduction: Streptococcus mutans is a principal pathogenic agent in biofilm formation on the teeth surfaces and subsequently development of dental caries and plaque. Therefore, currently introducing novel anti-bacterial and anti-biofilm agents, especially plant based materials are highly regarded. This study was planned to investigate in silico and in vitro antibacterial activities of Prangos acaulis extracts against S. mutans in single and biofilm forms and their mutagenicity in Ames test. Methods: The anti-bacterial and anti-biofilm effects of methanol extracts from various parts of P. acaulis were evaluated using disk diffusion and microtiter assay. Moreover, the potential mutagenicity of the extracts was investigated using Ames test. In addition, dominant constitutes of P. acaulis that reported in previous studies were subjected to an in silico analysis. The ability of selected phytochemicals to inhibit the glucosyltransferase was evaluated using molecular docking method. Results: All tested extracts especially root extract had significant antibacterial activity against the single form of S. mutans and inhibited biofilm formation without any mutagenic activity. The results also confirmed that three compounds consisting of ar-curcumene, d-limonene and alpha-pinene had strong and appropriate interactions to glucosyltransferase. Conclusion: This study indicated that P. acaulis has potent antibacterial and biofilm inhibition activity against S. mutans and can be good candidate for in vitro and in vivo studies with the aim of introducing novel inhibitors of dental caries developmen

Metabolic engineering of Deinococcus radiodurans for pinene production from glycerol

Background: The objective of this work was to engineer Deinococcus radiodurans R1 as a microbial cell factory for the production of pinene, a monoterpene molecule prominently used for the production of fragrances, pharmaceutical products, and jet engine biofuels. Our objective was to produce pinene from glycerol, an abundant by-product of various industries. Results: To enable pinene production in D. radiodurans, we expressed the pinene synthase from Abies grandis, the geranyl pyrophosphate (GPP) synthase from Escherichia coli, and overexpressed the native 1-deoxy-d-xylulose 5-phosphate synthase. Further, we disrupted the deinoxanthin pathway competing for the substrate GPP by either inactivating the gene dr0862, encoding phytoene synthase, or substituting the native GPP synthase with that of E. coli. These manipulations resulted in a D. radiodurans strain capable of producing 3.2 \ub1 0.2\ua0mg/L pinene in a minimal medium supplemented with glycerol, with a yield of 0.13 \ub1 0.04\ua0mg/g glycerol in shake flask cultures. Additionally, our results indicated a higher tolerance of D. radiodurans towards pinene as compared to E. coli. Conclusions: In this study, we successfully engineered the extremophile bacterium D. radiodurans to produce pinene. This is the first study demonstrating the use of D. radiodurans as a cell factory for the production of terpenoid molecules. Besides, its high resistance to pinene makes D. radiodurans a suitable host for further engineering efforts to increase pinene titer as well as a candidate for the production of the other terpenoid molecules

Computer-aided design of nano-filter construction using DNA self-assembly

Computer-aided design plays a fundamental role in both top-down and bottom-up nano-system fabrication. This paper presents a bottom-up nano-filter patterning process based on DNA self-assembly. In this study we designed a new method to construct fully designed nano-filters with the pores between 5 nm and 9 nm in diameter. Our calculations illustrated that by constructing such a nano-filter we would be able to separate many molecules

Identification and Purification of a hemolysin from Bacillus group by Zymography method

Background and Aim: Hemolysin is an extracellular protein which is secreted by many pathogenic and non-pathogenic bacteria. This protein is mostly active on plasma membrane of red blood cells. The objective of this study was to extract hemolysin from bacillus strains producing it, measure the molecular weight, and identify the functional characteristics of this enzyme. Materials and Methods: At first, hemolysin-producing bacillus strains were identified and then the strongest one was isolated. The hemolysin produced by this bacterium was extracted using Zymography and the effect of lysing it on blood agar medium was studied. Finally, SDS-PAGE method was used to measure the molecular weight of hemolysin. A new method was applied for purification and analysis of properties of the produced hemolysin. Results: Among the 8 studied strains, M3, with the access number of KC577596.1, was the best and strongest strain degrading blood on blood agar medium. The hemolysin produced by this strain was extracted and its lysis properties were studied. SDS-PAGE method showed that this strain of bacillus is able to produce two types of hemolysin with molecular weights of 13 and 23 kDa. Conclusions: According to the results, the studied strain, which was firstly isolated at Microbiology laboratories of University of Isfahan, contains a strong type of hemolysin with a high lysis power. Given the high power of lysis of this hemolysin and as M3 strain of bacillus is non-pathogenic, various applications of this protein can be used in industrial and medical sectors

Computational Prediction for the Binding Affinity of Interleukins 3 and 5 and GM- CSF to Cell Surface Receptors on Human Eosinophils

Abstract. Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a 14.477 kD glycoprotein comprising 144 amino acids residues. The respective encoding gene is located on chromosome 5 in human. This protein stimulates proliferation and differentiation of macrophages. N-terminally seventeen amino acid residues are serving as a signal peptide while, the rest of 127 amino acids, known to have therapeutics application, is termed Molgramostim. Previous studies have revealed a high affinity of this protein for binding to a heterodimer receptor on surface of the cell. The respective receptor includes α and β chains which the β chain is similar to interleukins 3 and 5 receptors. Due to this similarity, interleukins 3 and 5 are capable to compete with GM-CSF in binding to the shared receptor. In the present study, to evaluate the binding affinity of interleukins 3 and 5 and GM-CSF to the same receptor, a computational prediction study carried out using Modeller, Hex and Molegro softwares. According to the results, interleukin 3 with -517.09 kJ/mole, interleukin 5 with -538.05 kJ/mole and GM-CSF with -606.17 kJ/mole energy could bind to the α and β chains of receptor. In the next step the two chains of the receptor were separated and the affinity of each protein to both chains was studied. Based on the results the binding affinity of all three considered proteins to α chain of the protein was weaker than the binding to β chain. The binding energy of interleukin 3, interleukin 5 and GM-CSF to β chain of receptors was -620.37 kJ/mole,-663.80 kJ/mole and -696.07 kJ/mole respectively. According to the results, interleukin 3 and interleukin 5 strongly compete with GM-CSF in binding to cell surface receptors on human eosinophils

Homology Modeling and Conformational Epitope Prediction of Envelope Protein of Alkhumra Haemorrhagic Fever Virus

Background: The aim of this study was to generate in silico 3D-structure of the envelope protein of AHFV using homology modeling method to further predict its conformational epitopes and help other studies to investigate its structural features using the model. Methods: A 3D-structure prediction was developed for the envelope protein of Alkhumra haemorrhagic fever virus (AHFV), an emerging tick-borne flavivirus, based on a homology modeling method using M4T and Modweb servers, as the 3D-structure of the protein is not available yet. Modeled proteins were validated using Modfold 4 server and their accuracies were calculated based on their RSMDs. Having the 3D predicted model with high quality, conformational epitopes were predicted using DiscoTope 2.0. Results: Model generated by M4T was more acceptable than the Modweb-generated model. The global score and Pvalue calculated by Modfold 4 ensured that a certifiable model was generated by M4T, since its global score was almost near 1 which is the score for a high resolution X-ray crystallography structure. Furthermore, itsthe P-value was much lower than 0.001 which means that the model is completely acceptable. Having 0.46 Å rmsd, this model was shown to be highly accurate. Results from DiscoTope 2.0 showed 26 residues as epitopes, forming conformational epitopes of the modeled protein. Conclusion: The predicted model and epitopes for envelope protein of AHFV can be used in several therapeutic and diagnostic approaches including peptide vaccine development, structure based drug design or diagnostic kit development in order to facilitate the time consuming experimental epitope mapping process