PVP-coated graphene oxide for selective determination of ochratoxin A via quenching fluorescence of free aptamer

In this paper, we developed a simple method to detect fungi toxin (ochratoxin A) produced by Aspergillus Ochraceus and Penicillium verrucosumm, utilizing graphene oxide as quencher which can quench the fluorescence of FAM (carboxyfluorescein) attached to toxin-specific aptamer. By optimizing the experimental conditions, we obtained the detection limit of our sensing platform based on bare graphene oxide to be 1.9 μM with a linear detection range from 2 μM to 35 μM. Selectivity of this sensing platform has been carefully investigated; the results showed that this sensor specifically responded to ochratoxin A without interference from other structure analogues (N-acetyl-l-phenylalanine and warfarin) and with only limited interference from ochratoxin B. Experimental data showed that ochratoxin A as well as other structure analogues could adsorb onto the graphene oxide. As compared to the non-protected graphene oxide based biosensor, PVP-protected graphene oxide reveals much lower detection limit (21.8 nM) by two orders of magnitude under the optimized ratio of graphene oxide to PVP concentration. This sensor has also been challenged by testing 1% red wine containing buffer solution spiked with a series of concentration of ochratoxin A.     

EUROCarbDB: An open-access platform for glycoinformatics

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.     

Estimation of a novel method to produce bio-oil from sewage sludge by microwave pyrolysis with the consideration of efficiency and safety

This paper presented a feasible method to produce bio-oil from sewage sludge by microwave pyrolysis. The results showed that oils derived under 400 W obtained an attractive yield (49.8 wt.%) with favorable characteristics such as high calorific value (35.0 MJ/kg), low density (929 kg/m3) and preferable chemical composition (29.5 wt.% of monoaromatics). A model to study the relationship between microwave power and mass balance of product fractions was developed, and the results indicated that the power range of the highest transforming efficiency for organics in sludge into oils was 400-600 W, the subsequent increase of power to the range of 600-800 W favored gases formation at the expense of oils, and increase of power to above 800 W led to the conversion of solids into gases, while oils remained unchanged. The analysis of sulfur and nitrogen compounds in oils showed that bio-oil should be extracted before being used as fuel.     

Biosorption of tetradecyl benzyl dimethyl ammonium chloride on activated sludge: kinetic, thermodynamic and reaction mechanisms

The biosorption of tetradecyl benzyl dimethyl ammonium chloride (C₁₄BDMA) onto activated sludge was examined in aqueous solution with respect to the contact time, temperature and particle size. Equilibrium reached in about 2 h contact time. An decrease in the temperature increases of biosorption capacity of C₁₄BDMA onto activated sludge, which also increases with decreasing particle size. The experimental data fit the pseudo-second-order kinetics model well. The Langmuir and Freundlich models were applied to describe equilibrium isotherms, and the equilibrium partitioning data was described well by both models. Thermodynamic data showed that C₁₄BDMA biosorption onto activated sludge was feasible, spontaneous and exothermic. The Fourier transform infrared (FT-IR) spectrophotometry results show that both physisorption and chemisorption were involved. The measured zeta potential values and the enhanced cation concentration indicate the presence of electrostatic interactions, hydrophobic interactions and ion exchange.     

Effects of pH and ORP on microbial ecology and kinetics for hydrogen production in continuously dark fermentation

The microbial structure and kinetic characteristics of the hydrogen producing strains in two fermentative continuous stirred-tank reactors (CSTRs) were studied by controlling pH and oxidation and reduction potential (ORP). The fluorescence in situ hybridization (FISH) tests were conducted to investigate the fermentative performance of Clostridium histolyticum (C. histolyticum), Clostridium lituseburense (C. lituseburense) and Enterobacteriaceae. The experimental results showed that in ethanol-type reactor 1#, the relative abundance of the strains was 48%, 30% and 22%. Comparatively, the relative abundance in butyric acid-type reactor 2# was 24%, 55% and 19% with butyric acids and hydrogen as the main products. The kinetic results indicated that the hydrogen yield coefficients Y_P/X in both reactors were 8.357 and 5.951 l-H₂/g, while the coefficients of the cellular yield were 0.0268 and 0.0350 g-Cell/g, respectively. At the same biomass, the hydrogen yield in ethanol-type reactors was more than that in butyric acid reactors. However, the cellular synthesis rate in ethanol-type reactors was low when the same carbon source was used.     

Neuronal dynamics underlying high- and low-frequency EEG oscillations contribute independently to the human BOLD signal

Work on animals indicates that BOLD is preferentially sensitive to local field potentials, and that it correlates most strongly with gamma band neuronal synchronization. Here we investigate how the BOLD signal in humans performing a cognitive task is related to neuronal synchronization across different frequency bands. We simultaneously recorded EEG and BOLD while subjects engaged in a visual attention task known to induce sustained changes in neuronal synchronization across a wide range of frequencies. Trial-by-trial BOLD fluctuations correlated positively with trial-by-trial fluctuations in high-EEG gamma power (60-80 Hz) and negatively with alpha and beta power. Gamma power on the one hand, and alpha and beta power on the other hand, independently contributed to explaining BOLD variance. These results indicate that the BOLD-gamma coupling observed in animals can be extrapolated to humans performing a task and that neuronal dynamics underlying high- and low-frequency synchronization contribute independently to the BOLD signal.     

Improvement of the production of a red pigment in Penicillium sp. HSD07B synthesized during co-culture with Candida tropicalis

Co-culture of Penicillium sp. HSD07B and Candida tropicalis resulted in the production of a red pigment consisting of six components as determined by TLC and HPLC. The pigment showed no acute toxicity in mice and was mot mutagenic in the Ames test. The pigment was stable between pH 2 and 10 and temperatures of 10-100 °C and exhibited good photo-stability and resistance to oxidization by hydrogen peroxide and reduction by Na₂SO₃. Glucose and ratio of C. tropicalis to strain HSD07B (w/w) in the inoculum were the important factors influencing production of the pigment. Under optimized conditions, a pigment yield of 2.75 and 7.7 g/l was obtained in a shake-flask and a 15 l bioreactor, respectively. Thus, co-culture of strain HSD07B and C. tropicalis is a promising way to produce a red pigment potentially useful for coloring applications.     

Linking microbial community structure to membrane biofouling associated with varying dissolved oxygen concentrations

In order to elucidate how dissolved oxygen (DO) concentration influenced the generation of extracellular polymeric substance (EPS) and soluble microbial products (SMP) in mixed liquor and biocake, 16S rDNA fingerprinting analyses were performed to investigate the variation of the microbial community in an aerobic membrane bioreactor (MBR). The function of microbial community structure was proved to be ultimately responsible for biofouling. Obvious microbial community succession from the subphylum of Betaproteobacteria to Deltaproteobacteria was observed in biocake. High concentration of EPS in biocake under the low DO concentration (0.5 mg L⁻¹) caused severe biofouling. The correlation coefficient of membrane fouling rate with EPS content in biocake (0.9941-0.9964) was much higher than that in mixed liquor (0.6689-0.8004).     

Virtual screening using molecular simulations

Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) surface area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin β, thrombin α, cyclin-dependent kinase (CDK), cAMP-dependent kinase (PKA), urokinase-type plasminogen activator, β-glucosidase A, and coagulation factor Xa. The effect of protein dielectric constant in the implicit-solvent model on the binding free energy calculation is shown to be important. The statistical correlations between the binding energy calculated from the implicit-solvent approach and experimental free energy are in the range of 0.56-0.79 across all the families. This performance is better than that of typical docking programs especially given that the latter is directly trained using known binding data whereas the molecular mechanics is based on general physical parameters. Estimation of entropic contribution remains the barrier to accurate free energy calculation. We show that the traditional rigid rotor harmonic oscillator approximation is unable to improve the binding free energy prediction. Inclusion of conformational restriction seems to be promising but requires further investigation. On the other hand, our preliminary study suggests that implicit-solvent based alchemical perturbation, which offers explicit sampling of configuration entropy, can be a viable approach to significantly improve the prediction of binding free energy. Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery.     

The activity of recombinant human neuroglobin as an antioxidant and free radical scavenger

Free radicals are by-products of metabolism and exist in a homeostasis between generation and scavenging in vivo. Excessive free radicals cause various diseases, including nervous system diseases. Neuroglobin (Ngb), a nervous system-specific oxygen-binding protein, has been suggested to be a potential free radical scavenger in the nervous system in vivo; however, its underlying mechanism remains unclear. In this study, we investigated the antioxidant potential and free radical scavenging properties of recombinant human Ngb (rhNgb) in vitro. Interestingly, we found that the rhNgb protein itself has a direct and distinct antioxidant capacity and can efficiently scavenge a variety of free radicals, including the [2,2'-azino-di-(3-ethyl-benzthiazoline-6-sulfonic acid)] (ABTS) cation, superoxide anion, hydrogen peroxide, and hydroxyl radical. The capacity of rhNgb to scavenge the superoxide anion and hydrogen peroxide was even comparable to that of vitamin C. In addition, rhNgb had Fe(2+) chelating activity but hemoglobin did not. In conclusion, our results indicated that the rhNgb protein itself has antioxidant and free radical scavenging activities, providing fundamental evidence for the neuroprotective function of Ngb. These data provide key information for the origin of the neuroprotective and physiological role of Ngb and will promote the treatment of reactive oxygen species (ROS)-related diseases using this novel oxygen-binding globin.