Binding of divalent metal ions to calcium-free peroxidase: thermodynamic and kinetic studies

Thermodynamics of binding of divalent metal ions including Ca(2+) , Mg(2+) , Ba(2+) , and Cd(2+) to Ca-free horseradish peroxidase (HRP) enzyme was investigated using UV/VIS spectrophotometry and molecular-mechanic (MM) calculations. According to the obtained binding and thermodynamic parameters, trend of the relative binding affinities of these divalent metal cations was found to be: Ca(2+) >Cd(2+) >Mg(2+) >Ba(2+) . Binding analysis based on Scatchard and Hill models showed positive cooperativity effect between the two distal and proximal binding sites. Furthermore, kinetics of binding and reconstitution process was examined (using relaxation-time method) for binding of Ca(2+) (as the typical metal ion) to Ca-free HRP, which was found a second-order type having a two-step mechanism involving fast formation of Ca-free HRP/1?Ca(2+) as the kinetic intermediate in step 1. Finally, by means of MM calculations, the comparative stability energies were evaluated for binding of M(2+) metal cations to Ca-free HRP. Based on MM calculations, preferential binding of Ca(2+) ion was occurred on distal and proximal binding sites of Ca-free HRP associated with higher stability energies (E(total) ). Indeed, among the divalent metal ions, Ca(2+) with the highest binding affinity (maximum value of K(bin) and minimum value of ΔG$\rm{{_{bin}^{0}}}$), maximum value of exothermic binding enthalpy, and stability energies stabilizes the HRP structure along with an optimized catalytic activity.     

Homology Modeling and Functional Characterization of PR-1a Protein of Hordeum vulgare subsp. Vulgare

Pathogenesis-related protein 1a of Hordeum vulgare subsp. Vulgare (HvPR-1a) is induced by various pathogens and stress related factors. It plays important roles in plant defense system. Since the discovery of HvPR-1a a great deal of research has been focused on its isolation and characterization. However, three dimensional structure of HvPR-1a is still unknown. 3D structure can be used for determining protein function, and identifying novel protein folds and potential targets for regulation. The protein model was developed using MODELLER 9v10. Physicochemical characterization and functional annotation of the model carried out with Expasy''s ProtParam server and three different conserved domain finding programs including InterProScan, Proteins Families Database (Pfam), and NCBI Conserved Domains Database (NCBI-CDD). Applying validation programs revealed that the model has good quality and the RMSD value is 0.7. The predicted model submitted in Protein Model Database, PMDB for public use. This model will be used in wide range of studies for functional analysis and improvement activity of the protein.     

The stochastic nature of biochemical networks

Cell behaviour and the cellular environment are stochastic. Phenotypes vary across isogenic populations and in individual cells over time. Here we will argue that to understand the abilities of cells we need to understand their stochastic nature. New experimental techniques allow gene expression to be followed in single cells over time and reveal stochastic bursts of both mRNA and protein synthesis in many different types of organisms. Stochasticity has been shown to be exploited by bacteria and viruses to decide between different behaviours. In fluctuating environments, cells that respond stochastically can out-compete those that sense environmental changes, and stochasticity may even have contributed to chromosomal gene order. We will focus on advances in modelling stochasticity, in understanding its effects on evolution and cellular design, and on means by which it may be exploited in biotechnology and medicine.     

Field observations of the effect of Metarhizium anisopliae var. acridum on the saxaul locust,Dericorys albidula Serville (Orthoptera: Dericorythidae)

Dericorys albidula Serville (Orthoptera: Dericorythidae) is a major pest of Haloxylon ammodendron and other saxaul plant species in the Qom province, Iran. Using fungal insecticides can be an alternative method for chemical insecticides. Effect of insecticide fungi, Metarhizium anisopliae var. acridum, on the various nymphs of D. albidula was studied in the field through 2005 and 2006. Fixed concentrations of fungi (10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰ and 10¹³ spore mL^?1) were prepared as gasoline formulation and were sprayed on the locusts on H. ammodendron trees, and mortality percentage was recorded 15 days after treatment. The results showed that various concentrations significantly affected on the second, third, fourth and fifth nymphal instars of D. albidula compared to control in 2006, although this effect was lower in 2005 on nymphs. Mortality of the highest concentration (10¹³ spore mL^?1) was higher (17.6–24%) than other concentrations in all tests, but these values were not notable. The results of this study showed that using M. anisopliae var. acridum diluted in gasoline can be effective on nymphal instars of locust, D. albidula, in two continuous years.     

Effect of fungicidal essential oils against Botrytis cinerea and Rhizopus stolonifer rot fungus in vitro conditions

The development of natural crop protection products as alternatives to the use of synthetic fungicides is currently popular. The aim of this study is to evaluate the antifungal effects of several essential oils against the fungal pathogens, Botrytis cinerea and Rhizopus stolonifer, under in vitro condition. Four essential oils (fennel, black caraway, peppermint and thyme) were each tested at five concentrations (0, 200, 400, 600 or 800 μl l^?1). In vitro results showed that the essential oil of black caraway and fennel had the highest fungicidal effect against B. cinerea and R. stolonifer, respectively. The growth of B. cinerea was completely inhibited by the essential oil of black caraway at 400 μl l^?1. Fennel oil perfectly inhibited growth of R. stolonifer fungus colonies at concentration higher than 600 μl L^?1 in potato dextrose agar medium. Percentage of spores germination was the lowest in medium of Fennel and black caraway essential oils, and was the highest in Thyme ones. These results show that plant essential oils can have a strong effect on reducing post-harvest decay. These plant essential oils could provide an alternative to synthetic chemicals to control post-harvest phytopathogenic fungi on fruit.     

Molecular interactions of thymol with bovine serum albumin: Spectroscopic and molecular docking studies

Thymol is the main monoterpene phenol present in the essential oils which is used in the food industry as flavoring and preservative agent. In this study, the interaction of thymol with the concentration range of 1 to 6 μM and bovine serum albumin (BSA) at fixed concentration of 1 μM was investigated by fluorescence, UV‐vis, and molecular docking methods under physiological‐like condition. Fluorescence experiments were performed at 5 different temperatures, and the results showed that the fluorescence quenching of BSA by thymol was because of a static quenching mechanism. The obtained binding parameters, K, were in the order of 10⁴ M^?1, and the binding number, n, was approximately equal to unity indicating that there is 1 binding site for thymol on BSA. Calculated thermodynamic parameters for enthalpy (ΔH), entropy (ΔS), and Gibb's free energy (ΔG) showed that the reaction was spontaneous and hydrophobic interactions were the main forces in the binding of thymol to BSA. The results of UV‐vis spectroscopy and Arrhenius' theory showed the complex formation in the interaction of thymol and BSA. Negligible conformational changes in BSA by thymol were observed in fluorescence experiments, and the same results were also obtained from UV‐vis studies. Results of molecular docking indicated that the subdomain IA of BSA was the binding site for thymol.     

Penconazole alleviates salt-induced damage in safflower (Carthamus tinctorius L.) plants

It has been shown that penconazole (PEN) acts as an endogenous signal molecule responsible for inducing stress tolerance in plants. The effect of PEN (15?mg?l^–1) and sodium chloride (0, 100, and 200 mM NaCl) on some biochemical and molecular responses of safflower was studied. Results revealed that chlorophylls and total soluble protein contents decreased under salinity, however total carotenoid, anthocyanin, flavonoid, and carbohydrate contents increased as well as SOS1 and NHX1 genes expression. The exogenous PEN had a positive effect on chlorophylls, carotenoid, anthocyanin, flavonoid, soluble protein and carbohydrate contents. In addition, RT-qPCR analysis showed that the exogenous PEN induced expression of SOS1 and NHX1 genes in both salt-treated and untreated plants. Our data indicate that PEN helps safflower plants to better cope with salt stress. The results can provide new insights to better realizing the responsible mechanisms to regulate salinity resistance in safflower. PEN can be considered in order to ameliorate salinity effects, due to the low price and their availability.     

Nitric oxide production and absorption in trachea, bronchi, bronchioles, and respiratory bronchioles of humans

Different volumesof dead-space gas were collected and analyzed for nitric oxide (NO)content, either immediately after inspiration or after a period ofbreath holding on clean air or NO mixtures. This allowed calculation ofNO equilibrium, NO production, and NO absorption. In seven young,healthy, adult nonsmokers, the mean NO equilibrium values in parts perbillion (ppb) were 56 ± 11 (SE) in the trachea, 37 ± 6 in thebronchi, 21 ± 3 in the bronchioles, and 16 ± 2 in therespiratory bronchioles. At any given NO concentration, the NOabsorption rate (in nl/min) equaled the NO concentration (in ppb) timesA (the absorption coefficient inl/min). A values (in l/min) were 0.11 ± 0.01 in the trachea, 0.17 ± 0.04 in the bronchi, 0.66 ± 0.09 in the bronchioles, and 1.35 ± 0.32 in the respiratorybronchioles. NO equilibrium concentrations and production rates in one74-yr-old subject were three to five times as high as those found inthe young subjects. Mouth equilibrium NO concentrations were 3 and 6 parts per million in two subjects who had oral production rates of 6 and 23 nl/min, respectively. In conclusion, production and absorptionof NO occur throughout the first 450 ml of the airways.

     

A mosquito predator survey in Townsville, Australia, and an assessment of Diplonychus sp. and Anisops sp. predatorial capacity against Culex annulirostris mosquito immatures.

A twelve-month survey for mosquito predators was conducted in Townsville, Queensland, Australia, which is located in the arid tropics. The survey revealed the presence of five predaceous insects but only Anisops sp. (backswimmers) and Diplonychus sp. were common. Predatorial capacity and factors influencing this capacity were then assessed for adult Anisops sp. and adult and nymph stages of Diplonychus sp. against Culex annulirostris mosquito immatures under laboratory conditions. Predatorial capacity bioassays showed that adult Diplonychus sp. preyed upon both larval and pupal stages of Cx. annulirostris quite successfully. Nymphs of Diplonychus sp. proved to be more successful with smaller prey immatures, and Anisops sp adults did not prey successfully on any prey pupae. Increasing the foraging area and introducing aquatic vegetation significantly reduced the predatorial capacity of Diplonychus sp. nymphs, while only vegetation and not foraging area had a significant effect on adult Diplonychus sp. predation capacity. Overall, adult Diplonychus sp. proved to be a more efficient predator than Anisops sp., and field trials are now recommended to further assess the potential of Diplonychus sp. as a biocontrol agent.     

Enhanced chondrogenic differentiation of dental pulp-derived mesenchymal stem cells in 3D pellet culture system: effect of mimicking hypoxia

High incidence of articular cartilage defects resulting from age-related degeneration or trauma injuries is a major problem worldwide. Limited self-regeneration ability of cartilage often leads to inappropriate biochemistry and structure of healed tissue. Considering Impairments of traditional treatments, cell-based therapies are promising. The rapid ex vivo expansion and chondrogenic differentiation capability make dental pulp stem cells (DPSCs) a favorable cell type for therapeutic application, however strategies in order to efficient cartilage tissue-like production are imperative. In the present study the potential role of hypoxia mimicking agent, cobalt chloride (CoCl2), on chondrogenic differentiation of human DPSCs was surveyed. Cell viability assay used to obtain the optimum dose and exposure time of CoCl2. DPSCs were differentiated in pellet culture system after CoCl2 pretreatment. Chondrogenic differentiation efficiency was evaluated by histological and immunohistological analyses. The results showed that CoCl2 led to increased pellet size, integrity and matrix deposition with organizations more resembled typical cartilage lacuna structure. Furthermore, CoCl2 could improve differentiation by elevated chondrogenic markers, glycosaminoglycans (GAGs) and collagen II expression. CoCl2 pretreatment mitigated hypertrophy, as well, which was reflected in decreased collagen X expression. Alkaline phosphatase (ALP) specific activity did not change significantly by CoCl2 preconditioning. Based on current study hypoxia mimicking agent, CoCl2, could be suggested to promote DPSCs chondrogenic differentiation.