فهرست مطالب ali riahi-madvar

Codon usage and rare codons have mixed results on the protein structure and function. An increasing amount of data is shown that replacing the rare codons with frequently synonymous ones has diverse results as a decrease in a protein’s specific activity, changing the folding pathway, and reducing protein solubility. In this study, we investigated the situation of codon usage of the Lampyridae family luciferases using computational databases. For this, the codon feature of these luciferases was studied, bioinformatically. Also, in silico analyses of this enzyme were conducted by structural modeling on the I-TASSER web server. The status of these rare codons in these structural models was studied using SPDBV and PyMOL software. Finally, the binding site properties were studied using the AutoDock Vina. Using molecular modeling, two rare codons (Arg533 and Arg536) were analyzed that may have a critical role in the structure and function of these luciferases. AutoDock Vina was used in molecular docking that recognizes some residues that yield closely related to luciferyl-adenylate binding sites. These analyses created a new understanding of the sequence and structure of these luciferases, and our findings can be used in some fields of clinical and industrial biotechnology. This bioinformatics analysis plays an essential role in the design of new drugs.

Peroxidases are one of the most applicable enzyem in the fields of industry, medicine and biotechnology. In this study, comprehensive information on the advantages and disadvantages and also applications of plant peroxidases and nanozymes (with peroxidase-like properties), are provided in a categorized manner using of numerous articles. Peroxidase enzymes are belong to the oxidoreductases group which are found in all living organisms and are classified into different classes, one of the most applicable of which is plant peroxidases. However, applications of peroxidases limit by the some factors such as high cost of purification, low stability and degradation by proteases. Todays, in order to overcome these problems, non protein substances or compounds with peroxidase-like properties, such as nanozymes, have been considered. For industrial applications, peroxidases can be provided by purification from various sources, and also their catalytic activities and stabilities can be optimized using various methods such as environmental engineering and protein engineering, whilest these methods are costly and time consuming. Peroxidase-like nanozymes can be prepared from various materials which their catalytic activities and stabilities can be optimized throuth changing of their size, shape and combination with other materials that are usually easy, fast and cheape. At the same time, problems such as storage and degradation by proteases, which are a challenge for enzymes, are not associated with the nanozymes. Overall, it seems in industrial and medical applications, plant peroxidases can replace by nanozymes.

Entrance nanoparticles into the environment provides possibility of their entry into living organisms body. Their entry into the body can affect biological macromolecules and affect their life. Here, to investigate effect of copper oxide nanoparticle (nCuO) on recombinant Lepidium draba peroxidase, changes in enzyme activity and structure were analyzed in the presence of nCuO. Enzyme activity was measured in the presence of different concentrations of nCuO and repeated three times. Results were statistically analyzed using SPSS software at a significance level of 5%. Intrinsic fluorescence studies in the presence of nanoparticles were utilized to investigate structural changes of the enzyme. These studies were done at different temperatures to determine thermodynamic parameters such as the type of forces involved in the nanoparticle-enzyme interaction. Enzyme activity in the presence of nCuO significantly increased at the level of 5%. The most enzyme activity were attributed to the concentration ranges of 80-180 nM nanoparticles, which it increased more than 46% compared to the control. Intrinsic fluorescence intensity decreased in the manner nanoparticles concentrations increased in media. Decrease intrinsic fluorescence emission indicates changes in the enzyme structure in presence of nanoparticle. Thermodynamic parameters including entropy (∆S°) and enthalpy (∆H°) related to the interaction of enzyme with nanoparticle were calculated as 0.108 and 3.81 respectively. The positive sign of these parameters indicates the important role of hydrophobic interactions in this process. On the other hand, negativity of free energy (∆G°) changes indicates that this process is exergonic and proceeds spontaneously.

Codon usage and rare codons have mixed results on the protein structure and function. An increasing amount of data is shown that replacing the rare codons with frequently synonymous ones has diverse results as a decrease in a protein’s specific activity, changing the folding pathway, and reducing protein solubility. In this study, we investigated the situation of codon usage of the Lampyridae family luciferases using computational databases. For this, the codon feature of these luciferases was studied, bioinformatically. Also, in silico analyses of this enzyme were conducted by structural modeling on the I-TASSER web server. The status of these rare codons in these structural models was studied using SPDBV and PyMOL software. Finally, the binding site properties were studied using the AutoDock Vina. Using molecular modeling, two rare codons (Arg533 and Arg536) were analyzed that may have a critical role in the structure and function of these luciferases. AutoDock Vina was used in molecular docking that recognizes some residues that yield closely related to luciferyl-adenylate binding sites. These analyses created a new understanding of the sequence and structure of these luciferases, and our findings can be used in some fields of clinical and industrial biotechnology. This bioinformatics analysis plays an essential role in the design of new drugs.

Propolis is a resinous natural substance with various biological properties produced by honey bees. In this project, the ethanolic extracts of propolis samples collected from three regions of Kerman province (Lalehzar, Rayen and Sarasiab) have been studied. The total phenolic and flavonoid contents of the extracts were investigated by Folin-Ciocalteu and Aluminum Chloride methods, respectively, and their antioxidant and anticholinesterase activity were evaluated using DPPH and Ellman methods. The obtained results showed that the contents of total phenol (165.97 mg equivalent gallic acid per gram of extract) and flavonoid (72.26 mg equivalent quercetin per gram of extract) of Lalehzar sample are more than two-fold higher than that of Sarasiab and Rayen samples. The ability of Lalehzar propolis to inhibit DPPH free radical (IC50: 5.64 µg/ml) was also approximately seven times greater than that of the other two samples. Therefore, there is a direct relationship between antioxidant activity and total phenolic and flavonoid contents of the propolis samples. The data obtained from Ellman test indicated that the anticholinesterase activity of Lalehzar sample (IC50: 14.37 µg/ml) is 4.8 and 5.4-fold greater than that of Rayen and Sarasiab samples, respectively. Summing up the results, the Lalehzar propolis is a very good candidate for further studies.

Nanoparticles (NPs) have broad applications in various industries, that it can be expected them find a way to enter into the environment and affected the living organism with unexpected consequences. According to the broad applications of the Fe2O3 nanoparticles (nFe2O3) in different industries, in this study, its interaction with human serum albumen (HSA), as an abundant protein in blood, was investigated using intrinsic fluorescence at different temperature ranges, extrinsic fluorescence and circular dichroism (CD) methods. Results showed, with increasing NP concentration in media, intrinsic fluorescence intensity of the protein decreased in all temperatures. Based on the quenching rate constant (Kq), it revealed that interaction between HAS and nFe2O3 take place through static mechanism. Thermodynamic parameters indicate the sign of enthalpy and entropy are negative, which implies the role of hydrogen bands and Van der Waals forces in this interaction. The negative sign of free energy (∆G°), revealed this reaction is exergonic and spontaneously. On the other hand, ANS fluorescence intensity increased more for HSA in interaction with NP in contrast to the ANS. Furthermore, Far-UV CD spectra shows an alteration in the secondary structure of this protein in interaction with the NP. The results all together revealed changes in the structure of HSA upon exposed to this nanoparticle which can affected its performance.

Lepidium draba peroxidase (LDP) belonging to the class III plant peroxidases that its amino acid sequence shows over 90% similarity with horseradish peroxidase (HRP).

In this study, after expression and purification of LDP, its immobilization conditions were optimized on the Zinc metal-organic framework (Zn-MOF) using glutaraldehyde as a cross-linking agent for firm binding. Then physicochemical properties, kinetic parameters and stability of the immobilized enzyme were compared with the free one.

The best conditions for enzyme immobilization with 67% yield were optimized at concentration of 0.02 g of Zn-MOF, 0.75mg/ml and 1.2 dM of glutaraldehyde, after 3h incubation. The results showed that the specific activity of the immobilized enzyme increased more than doubled that of free enzyme and its Km was reduced by 49% compared to the free one for TMB substrate. Also its kinetic stability reduced against pH and temperature in compared to the free enzyme.

Sulforaphane is produced through a hydrolytic reaction catalyzed by myrosinase from  glucoraphanin. It has recently attracted researcher's interest due to its anticancer activities. The present study was conducted to evaluate the effects of various concentrations of yeast extract (YE) and silver ion (Ag+) on sulforaphane production level in Lepidium draba seedlings. Our results revealed that the sulforaphane content is increased in seedlings that treated with the both elicitors, but more significantly by Ag+. All elicitor influences are depend on the elicitor dose and time of elicitation and maximized with YE at 1 mg/mL for 8 hours and with Ag+ at 50 µM for 4 hours treatment. It seems that the promotion of sulforaphane content results in induction of glucoraphanin biosynthesis pathway which in turn is mediated by H2O2, as revealed by a significant increase in the activity of H2O2 scavenger enzymes.

Lepidium draba, a perennial plant belonging to the Brassicaceae family, contains high level of the glucosinolate glucoraphanin that  after enzymatic hydrolysis produce sulforaphane. In this study, sulforaphane content, morphological and biochemical properties were analyzed of the treated L. draba seedlings which grown for 7 days in the presence of different concentrations (0 (as control), 25, 50, 100, 250, 500 and 1000 mg/L) of nano zinc oxide (nZnO). Based on the results, seed germination rate was significantly reduced in the presence of concentrations more than 100 mg/L nanoparticle, so that it reduced about 30% in the presence of the highst doses of nZnO. Root and shoot lengths of the treated seedlings were also significantly decreased in compared to the control with the increase nanoparticles concentration in the medium, So that in the presence of the hightst concentration, length of the root and shoot were reduced about 70 and 60 % respectively. Moreover, it is also shown that chlorophyll, carotenoid and flavonoid contents were significantly decreased in treatment with all nanoparticle concentrations compared to the control. In contrast, the results shown that an increase in sulforaphane content in treated seedlings with the concentrations more than 100 mg/L nanoparticle compared to the control. Catalase activity was significantly increased in treated seedlings more than 100 mg/L nZnO concentration compared to the control, so that in the presence of the highst concentration, its activity increased more than 3 factors.  The positive effects of this particle were also seen on soluble protein concentration (in the presence of all nZnO concentrations) and anthocyanin content (up to 100 mg/L nZnO concentrations) in compared to the control sample. Furthermore, the amount of the abzorbed Zn ion in the root and shoot of the treated seedlings increase with the increase nanoparticle concentration in the medium. Overall, based on the increase sulforaphane and anthocyanin contents and activity of catalase, it seems that surface adsorption or accumulation of these particles, induced oxidative stress which resulted in decreasing of seedling growth. So, it is suggested for determining the exact mechanism effects of nZnO on this plant, others physiological, biochemical and genetics parameters must be analysed.

Glucoraphanine is an aliphatic glucosinolate, which largly found in Lepidium draba from Brassicaceae family. This glucosinolate convert to isothiocyanate, sulforaphane (SFN) in the presence of myrosinase which has different biological activities such as the antioxidant and anti bacterial properties, and also able to prevent proliferating of cancer cells.  CYP79F1 is the first enzyme in the biosynthesis pathway of glucoraphanine.

 In this study, L. draba seedlings wer grown for 7 days in the presence of different concentration of sucrose and chitosan (0, 25, 50, 100, 200 and 400 mg/L), in fully-random designs with three repetitions. After collection of the seedlings, SFN content in the arial parts of them were measured using HPLC apparatus. Furthermore, in the treated seedlings, the gene expression level of CYP79F1 were examined using the Real Time PCR technique.

 The results showed, that SFN content in the sucrose treated seedlings significantly increased compared to the control. While in the chitosan treated seedlings significant increase in SFN content was only seen at the 200 mg/L concentration. The results showed that the expression of CYP79 F1 was significantly increased in the treated seedlings with 50 mg/L sucrose and 50 and 100 mg/L chitosan compared to the control.

 According to the results, it concluded that the mentioned elicitor's concentrations can stimulate aliphatic glucosinolate biosynthesis through expression of CYP79F1 gene. Based on the role of SFN as a valuable medicinal metabolit and also the role of CYP79F1 enzyme in the glucoraphanin biosynthesis, it suggested that the effects of others concentrations and time of treatment of the mentioned elicitors were analyzed on this plant.

Salinity is one of the most important abiotic stresses that can affect the yield of wheat. It is important to study the mechanisms of tolerance to salinity in crops and their ancestors. The purpose of this project was to investigate the responsive protein spots to salt stress in tolerant population. In this research, five diploid wheat population of T. boeoticum (A1, A10, B3, B4, C5) were grown in greenhouse as factorial experiment in a completely randomized design with three replications. Salinity was applied at two levels of zero and 150 mM. Then, the traits of shoot and root height, fresh and dry shoot weights, chlorophyll a, b, total carotenoids and total protein content were measured. Total protein was extracted using TCA / acetone method. The proteins were separated in the first dimension by isoelectric point using IPGs pH 4-7 followed by SDS-PAGE as the second dimension using molecular weight. The results of physiological data analysis showed that for fresh and dry shoot weights and total protein content, the interaction effect of the population*salinity was significant. For the two traits of fresh weight and total protein, the population of B4 had the highest average. Two-dimensional electrophoresis gel analysis revealed 205 repetitive spots. Out of these, 7 spots showed upregulation and 7 spots downregulation. Identified proteins include proteins involved in the cell wall, photosynthesis, energy metabolism, chromatin-related proteins, chaperones, proteolytic, in the removal of reactive oxygen species, in repairing damaged proteins and in the transmission of the message. These results can be used to improve wheat cultivars.

IIce nucleation active (INA) bacteria are common epiphytic inhabitants that cause frost damage in many plants in the near-zero temperatures. Yet, no studies were found in ice nucleation bacteria associated with pistachio trees. In our earlier study some INA strains were identified and reported. These were assigned as Pseudomonas fragi, P. putida, P. moraviensis and Pantoea agglomerans. In current work, two new strains namely P. viridiflava and Entrobacter cloacea were identified. Their ice nucleation frequency were evaluated and compared with above-mentioned ice positive strains isolated from pistachio trees. Pseudomonas fragi raf3 was considered as the most ice nucleation active bacteria. This was followed by P. putida raf6, P. moraviensis raf1, P. moraviensis raf5, Pantoea agglomeranse raf7, P. viridiflava raf2, Entrobacter cloacea raf8 and Pseudomonas sp. raf4, respectively. To detect INA genes, two sets of degenerate primers were used and partial INA gene sequences were amplified. INA gene sequence) 425bp) for Pseudomonas putida raf6, Pantoea agglomerans raf7 and P. fragi raf3 were amplified with primer pair of 3308/3463. Whereas, a fragment of 194bp was detected in Pseudomonas sp. raf4, P. moraviensis raf5 and P. moraviensis raf1using forward and reverse primer pair of 3076/3463. Entrobacter cloacea raf8 has reported for the first time as epiphytic ice plus strain. The capability of the latter as a bacterial biocontrol agent against insect pests was reported.

Peroxidase enzymes are vastly applicable in industry and diagnosiss. Recently, we introduced a new kind of peroxidase gene from Lepidium draba (LDP). According to protein multiple sequence alignment results, LDP had 93% similarity and 88.96% identity with horseradish peroxidase C1A (HRP C1A). In the current study we employed in silico tools to determine, to which group of peroxidase enzymes LDP belongs. The tertiary structure of protein was built using homology modeling method and the overall quality of predicted model was evaluated. The physicochemical and spatial properties of protein were measured. The binding site of protein which made a motif, was determined. The predicted tertiary structure possesses acceptable quality, based on several criteria. The predicted motif was also in agreement with previous studies. The isoelectric point (pI) of LDP was calculated as 8.25. Due to neutral pI of LDP and high similarity between structure of LDP and HRP C1A, it is assumed that LDP belongs to the neutral or neutral-basic isoenzymes.

The rhizosphere is the area around the root of a plant occupied by a unique population of useful bacteria known as plant growth promoting rhizobacteria (PGPR). In this study, the isolation and identification of rhizobacteria from orange (Citrus sinensis) orchards using 16S rRNA gene, as well as biological and biochemical assays is reported. Analysis of 16S rRNA gene was confirmed bybiological and biochemical assays and showed that the isolated bacteria belong to the genera Bacilli,Enterobacter and Pseudomonas. Accordingly, Enterobacterkobei MR-R2, Pseudomonas putida MRR5, Bacillus cereus MR-R, Bacillus thuringiensis MR-R1 and Bacillus mycoides MR-R4 were identified and registered in GenBank. The results of phosphate solubilization testing revealed that the maximum rate of phosphate solubilization was observed for B. thuringiensis, and E. kobei; however, B. cereus, B. mycoides, and P. putida indicated the least activity. It can be concluded that the isolated strains (especially B. thuringiensis) are newly identified phosphate solubilizing bacterial strains, among which B. thuringiensis can be used for growth promotion of orange trees.

Sulforaphane (SFN) is an isothiocyanate which is produced through glucoraphanin hydrolysis via myrosinase activity. In the present study, SFN content and peroxidase activity has been assessed in treated Lepidium draba seedlings with different concentrations of iron and copper during 8 and 16 hours treatment. The results showed that the SFN content drastically elevated at treatment with 1 mg/L Fe2+ after 8 hours treatment which was around two-fold compared to the control. But its content decreased in treated seedlings with higher Fe2+ concentrations as well as treatment with all concentrations of Cu2+. Furthermore, promotion of peroxidase activity was seen in the treated seedlings with the both elicitors. The data revealed that not only the inhibitory effect of Cu2+ on SFN production was stronger than Fe2+, but its stimulatory effect on peroxidase activity was also remarkable especially after 16 hours treatment. It seems that the metals induce triggering of reactive oxygen species (ROS) which at low Fe2+ concentration leads to induce glucoraphanin biosynthesis pathway. While at higher Fe2+ concentrations as well as treatment seedlings with Cu2+, ROS lead to induce antioxidant enzyme system.

A. calamus that grows in province of Baluchistan and Kerman in Iran plays a major role in the revival of traditional medicine. Despite the useful role of this plant in many ailments, its anti-bacterial properties are not well understood. In this study, we investigated anti-bacterial activities of rhizomes ware of A. calamus against various strains of bacteria such as Staphylococcus aureus and Escherichia coli. The anti-microbial activity of extracts of A.calamus was assessed by disc diffusion method. Rhizomes extracted by ethanol, methanol solvents and essential oil were obtained by clevenger apparatus. Antibacterial effects of the extracts tested at concentrations (25, 100, 200, 250, 300, 400 mg/ml). The Minimal Inhibitory Concentration (MIC) of extracts ranged from 25-100 mg/ml against the susceptible bacteria. All the Minimal Bactericidal Concentrations (MBCs) were the same as the MICs. Our results revealed that ethanolic and methanolic extracts have an inhibitory effect on all gram positive and negative strains and it is comparable with kanamycin, an anti-bacterial reference drug. Amongst extracts of A.calamus, ethanolic extracts showed maximum inhibitory activity (16mm) against Staphylococcus epidermidis. So we can conclude that this plant has anti-bacterial properties on all gram positive and negative bacteria. The result can be related to the nature of the compounds found in this plant. The effective GC-MS method was performed for the determination of essential oil compounds of A.calamus. The Gas Chromatography and Mass Spectrometry (GC-MS) analysis revealed that the presence of phenyl propanoids, monoterpenes, sesquiterpenes and β-asarone in essential oil of the plant caused its antibacterial properties. Our result showed that the ethanolic and methanolic extracts of A. calamus could be useful for the development of effective treatment for the control of infectious diseases.

Rhizosphere bacteria assist growth of plants via dissolving phosphate, production of special compounds such as phytohormones and release of hydrolytic enzymes such as a-amylase and kitinase. This study aimed to isolate and to identify a a-amylase producing bacillus in rhizosphere of orange orchards and to investigate microbial activity to enzyme production in presence of different source of carbon ranges.
This study was conducted in order to isolation of a-amylase bacilli from rhizosphere of orange orchards located at Kerman province, Iran. After sample collection, bacteria were isolated by growing on starch agar. Several molecular (based on 16SrRNA) and biochemical methods were used to identify bacterial species. The starch rapid hydrolysis test was used to investigate amylase activity of the isolates. Additionally, the enzyme production level was studied in the presence of several carbon sources include glucose, fructose and starch ranges.
Molecular and biochemical analysis showed that isolated bacterium is a strain of Bacillus cereus named as Bacillus cereus MR-R3 and recorded in GeneBank under accession number of KC306945.1. Moreover, results showed that starch and glucose have the highest positive effects on alpha amylase production in the presence of 0.5 g/l and fructose have the highest effect in the presence of 0.25 g/l.
Isolation and identification of orange orchards rhizospher-derived bacillus species considering their ability to produce a-amylase and phosphate solvation showed that the presence of this species in this region is very important. Moreover, increase in production of the enzyme after treatment with different carbon sources can be related to their gene expression induction effects.