Modares Journal of Biotechnology

Abstract Aspergillus has many species that are important in medicine, agriculture, and various industries. The genus has 446 identified species, which are difficult to distinguish from each other with the use of morphological characteristics. Xylan 1,4-beta-xylosidase is an enzyme that catalyzes the hydrolysis process of xylose in xylooligosaccharides and is produced by different species of Aspergillus. This research was conducted with the aim of a bioinformatics study of the gene region related to this enzyme and to evaluate its similarities and differences in some Aspergillus species. The results showed that this gene region, due to the presence of conserved motifs, was able to distinguish some species studied in this research.

Abstract In this study, the wheat germ was fermented with industrial bakery yeast powder to produce FWGE with high 2,6-DMBQ content in a Bench-scale bioreactor by scale-up approach. The 2,6-DMBQ content of FWGE was increased by optimizing the three initial variables of pH, fermentation temperature, and agitation rate at two levels using the Taguchi method. The 2,6-DMBQ content of the samples was determined at 14, 16, and 18 hours of the fermentation process. Then, the results were analyzed by Qualitek software. The effect of centrifugation speed on turbidity and the yeast's number in the final supernatant was then investigated. Finally, the supernatant was dried by spray dryer with an inlet temperature of 120 °C and outlet temperature of 70°C, and the amount of active 2,6-DMBQ, pH, moisture, and ash was determined. Under optimal conditions: initial pH of 6, fermentation temperature of 32 °C, and agitation rate of 80 rpm, maximum 1.527 mg of 2,6-DMBQ per gram of FWGE obtained. The separation results showed that the centrifugation rate doesn't have a significant effect on the final turbidity and the number of yeasts left, and thus 3000 g was selected as the optimal speed. However, because of the high content of yeast in the supernatant, filtration was required after centrifugation. Due to the high speed of sample drying, the low moisture of the final product, and high efficiency on an industrial scale, the samples were dried using a spray dryer. Finally, the moisture, protein, ash, and pH of the final product were measured.

Abstract Fibrinogen is a major component of the coagulation cascade following tissue damage and rapidly forms an insoluble fibrin scaffold. Fibrin is a filamentous biopolymer that naturally forms from fibrinogen polymerization during blood clotting. After tissue damage and coagulation cascade initiation, soluble fibrinogen polymerization by thrombin enzymebegins and forms an insoluble fibrin network and blood clots with platelets. This fibrin network is crucial for the development of homeostasis after tissue damage. This biopolymer also plays a key role in the wound healing as a temporary scaffoldand due to its unique structural properties and physiological function; it is used in reconstructive medicine. Fibrin is able to absorb extracellular matrix proteins (ECM) such as fibronectin and growth factors. The main types of fibrin scaffolds like platelet-rich fibrin (PRF) and platelet-rich plasma (PRP) are being used as autologous biomaterials in reconstructive medicine, wound healing, orthopedics and skin reconstruction and cosmetic sciences. Fibrin derivatives and degradation products also play an important role in the process of wound healing by stimulating cell infiltration and tissue regeneration and they are being widely used in developing new products as a biological material for over a century.

Abstract Datura (Datura stramonium) is known as a rich source of tropane alkaloids, including scopolamine and hyoscyamine as parasympatholytics that competitively antagonize acetylcholine. Production of secondary metabolites often occurs in plants against the various elicitors or signal molecules. In this study, the effect of yeast extract as a biotic elicitor on tropane alkaloid production was evaluated. Surface-sterilized Datura seeds were cultured on 1/2 MS medium supplemented with different concentrations of yeast extract (0, 1.5, and 3g/L). One month after germination, alkaloid yield of Datura plantlets was measured by the use of High-Performance Liquid Chromatography (HPLC). Also, total protein content and antioxidative enzymes activity were determined by spectrophotometry method. According to the results, the fresh weight of root and shoot parts of Datura plantlets at 1.5g/L yeast extract was increased about 2 and 4 times, respectively. Yeast extract (1.5g/L) caused to 1.7 times increase of hyoscyamine amount of root and shoot parts and 2.5 folds scopolamine of Datura plantlets. Moreover, on yeast extract (1.5g/L)-treated plantlets, total protein content, and activity of catalase and guaiacol peroxidase were almost the same as the control group. Altogether, yeast extract (1.5g/L) can be used as a good candidate for enhancement production of tropane alkaloids especially hyoscyamine and scopolamine with high medicinal value.

Abstract Aims: Information of the protein structure is essential to understand the protein functions. Flexibility is one of the most important characteristics related to protein functions. Knowledge about flexibility of the protein structures can be helpful to improve protein structure prediction and comprehend their function. This study was conducted with the aim of investigating the flexibility prediction of protein structures, using support vector machine.
Materials and Methods: In this study, a balanced dataset containing 95 proteins was used. The features used in the present study for modeling amino acids formed a 33-dimensional vector. Some of them were obtained by crawling a window with the length of 17 focusing on the target amino acid on the protein chain, and some were only related to the target amino acid. To define the flexibility factor, the characteristics based on the information derived from the two-dimensional angular variations was used. The information was calculated for each amino acid by considering the position of each amino acid alone and for the adjacent amino acid pairs in a seventeenth window, and the support vector machine method was used for prediction.
Findings: The accuracy was 73.1%, F-measure was 71%, precision was 73%, and sensitivity was 73.2%. Acceptable superiority of the proposed method was confirmed in comparison with the current methods. The angular representation of each protein was able to accurately demonstrate the 3D characteristics and properties of the protein structure.
Conclusion: The accuracy is 73.1%, F-measure is 71%, precision is 73%, and sensitivity is 73.2% and angular aspect is the best descriptor for flexibility prediction. Angular representation of each protein can accurately reflect the 3D characteristics and properties of the protein structure.