DFT modelling of hydrogen on Cu(110)- and (111)-type clusters

Density Functional Theory (DFT) calculations using gaussian 98 have been performed on hydrogen adsorbed on clusters representing the (110) and (111) surfaces of Cu. Clusters were constructed to model different adsorption sites, and at least two different size clusters were used for each site. On the (111) surface, hydrogen prefers to adsorb in a hollow site, though with the hcp variant being favoured by the adsorption energy, and the fcc alternative by the vibrational frequencies. On the (110) surface, the "fcc" site on a (1 2 2) reconstructed surface is preferred.     

Monte-Carlo Simulations of Centrifugal Gas Separation

The use of a Monte–Carlo formalism in a centrifugal gas process separation simulation provides an efficient predictor of dew-pointing as a function of the imposed radial pressure gradient. Previously, this was done by simply calculating radial pressure and then resorting to a separate equation of state routine for evaluating whether condensation will occur or not. In our model, we incorporate the potential energy associated with rotation of a gas element into the simulation along with molecular interaction terms. This enables us to predict when sufficient nucleation has occurred that condensed material forms—an important limit for stable operation of a gas centrifuge.     

The Stabilizing Effects of O-glycosylation on the Secondary Structural Integrity of the Designed α-loop-α motif by Molecular Dynamics Simulations

Abstract

In this study, various 400 ps molecular dynamics simulations were conducted to determine the stabilizing effect of O-glycosylation on the secondary structural integrity of the design α-loop-α motif, which has the optimal loop length of 7 Gly residues (denoted as N-A₁₆G₇A₁₆-C). In general, O-glycosylation stabilizes the structural integrity of the model peptide regardless of the length and position of glycosylation sites because it decreases the opportunity for water molecules to compete for the intramolecular hydrogen bonds. The designed peptide exhibits the highest helicity when residues 11 and 31 are replaced with Ser residues followed by O-linked with 3 galactose residues, representing the “face-to-face” glycosylation near the loop. In this case, the loop exhibits an extended conformation and several new hydrogen bonds are observed between the main chain of the loop and the galactose residues, resulting in decreasing the fluctuation and increasing the stability of the entire peptide. When the glycosylation are made close to the loop, the secondary structural integrity of the α-loop-α motif increases with the number of galactose residues. In addition, “face- to-face” glycosylation increases the structural integrity of this motif to a greater extent than “back-to-back” glycosylation. However, when the glycosylation are created away from the loop and near the N- and C-termini, no general rule is found for the stabilizing effect.     

Simultaneous biological removal of nitrogen–sulfur–carbon: Recent advances and challenges

Biological removal of carbon, nitrogen and sulfur is drawing increasing research interest in search for an efficient and cost-effective wastewater treatment. While extensive work on separate removal of nitrogen and sulfur is well documented, investigation on simultaneous denitrifying sulfide removal has only been reported recently. Most of the work on denitrifying sulfide removal has been focusing on bioreactor performance, loading and operating conditions. Nonetheless, underlying principles elucidating the biochemical reactions and the mechanisms of the microbial degradation are yet to be established. In addition, unstable denitrifying sulfide removal which is a major operating problem that hinders practical application of the process, is yet to be resolved. This paper provides a review on the state-of-the-art development of simultaneous biological removal of sulfur, nitrogen and carbon. Research on bioreactor operation and performance, reactor configurations, mechanisms and modeling work including the use of mass balance analysis and artificial neural networks is delineated. An in-depth discussion on the microbial community and functional consortium is also provided. Challenges and future work on simultaneous biological removal of nitrogen–sulfur–carbon are also outlined.     

Removal of Contaminating Metals from Soil by Sulfur-Based Bioleaching and Biogenic Sulfide-Based Precipitation

The potential of a hybrid process incorporating sulfur-based bioleaching and sulfide-based precipitation for treatment of metal-contaminated soil was examined in batch-type experiments. The sulfur-based soil bioleaching process with Acidithiobacillus sp. could be initiated at a wide range of initial pH from 4.0 to 6.3. After 15 days, 98% of Zn, 89% of Cu and 79% of Cd was bioleached. The gaseous sulfides recycling from Desulfovibrio sp.-mediated sulfate-reducing reactor via N₂ sparging efficiently treated metal-loaded soil leachate. With a sulfide/metal ratio of 3.0, 88% of Zn, 100% of Cu and 95% of Cd were precipitated, resulting in effluent metal concentrations of 3.5 mg Zn²⁺/L, 0.2 mg Cu²⁺/L and 0.03 mg Cd²⁺/L.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Formation of Covellite (CuS) Under Biological Sulfate-Reducing Conditions

Sulfate-reducing bacteria (SRB) play a major role in the precipitation of metal sulfides in the environment. In this work, biogenic copper sulfide formation was examined in cultures of SRB and compared to chemically initiated Cu sulfide precipitation as a reference system. Mixed cultures of SRB were incubated at 22, 45, and 60°C in nutrient solutions that contained copper sulfate. Abiotic reference samples were produced by reacting uninoculated liquid media with Na₂S solutions under otherwise identical conditions. Precipitates were collected anaerobically by centrifugation, frozen in liquid N₂, and freeze-dried, followed by analysis using X-ray diffraction (XRD), X-ray fluorescence, and scanning electron microscopy. Covellite (CuS) was the only mineral found in the precipitates. Covellite was less crystalline in the biogenic precipitates than in the abiotic samples based on XRD peak widths and peak to background ratios. Poor crystallinity may be the result of slower precipitation rates in bacterial cultures as compared to the abiotic reference systems. Furthermore, bacterial cells may inhibit the nucleation steps that lead to crystal formation. Incubation at elevated temperatures improved the crystallinity of the biotic specimens.     

Structural Basis for the Different Stability and Activity between the Cdk5 Complexes with p35 and p39 Activators

Cyclin-dependent kinase 5 (Cdk5) is a brain-specific membrane-bound protein kinase that is activated by binding to the p35 or p39 activator. Previous studies have focused on p35-Cdk5, and little is known regarding p39-Cdk5. The lack of functional understanding of p39-Cdk5 is due, in part, to the labile property of p39-Cdk5, which dissociates and loses kinase activity in nonionic detergent conditions. Here we investigated the structural basis for the instability of p39-Cdk5. p39 and p35 contain N-terminal p10 regions and C-terminal Cdk5 activation domains (AD). Although p35 and p39 show higher homology in the C-terminal AD than the N-terminal region, the difference in stability is derived from the C-terminal AD. Based on the crystal structures of the p25 (p35 C-terminal region including AD)-Cdk5 complex, we simulated the three-dimensional structure of the p39 AD-Cdk5 complex and found differences in the hydrogen bond network between Cdk5 and its activators. Three amino acids of p35, Asp-259, Asn-266, and Ser-270, which are involved in hydrogen bond formation with Cdk5, are changed to Gln, Gln, and Pro in p39. Because these three amino acids in p39 do not participate in hydrogen bond formation, we predicted that the number of hydrogen bonds between p39 and Cdk5 was reduced compared with p35 and Cdk5. Using substitution mutants, we experimentally validated that the difference in the hydrogen bond network contributes to the different properties between Cdk5 and its activators.     

A Method for Molecular Analysis of Catalase Gene Diversity in Seawater

Catalase plays an important role in the metabolism of marine bacteria and has potential impact on the marine environment. Four PCR primers were designed to amplify the catalase gene fragments in marine bacteria by applying metagenomic DNA from Yellow Sea surface water as the template. Of the four reproducible target PCR products, the longest one with 900 bp were chosen for catalase gene library construction by the T-vector and the white Escherichia coli colonies in the library was screened through restriction-digesting the reamplified insert fragments by the selected restriction endonuclease MboI, and then the bands of the resulting products were displayed in the agarose gel by electrophoresis. The unique restriction fragment length polymorphism (RFLP) pattern was selected and the corresponding catalase gene fragments were sequenced, which verified that every unique RFLP pattern represented one type of catalase. This PCR–RFLP method above was established to investigate the bacterial catalase diversity in seawater.     

Hydrogen sulfide protects SH-SY5Y neuronal cells against d-galactose induced cell injury by suppression of advanced glycation end products formation and oxidative stress

d-Galactose is widely used as an agent to cause aging effects in experimental animals. The present study aims to investigate the effects of hydrogen sulfide (H₂S) in human neuroblastoma SH-SY5Y cells exposed to d-galactose. Cells were pretreated with NaHS, an H₂S donor, and then exposed to d-galactose (25–400 mM for 48 h). We found that NaHS pretreatment significantly reversed the d-galactose-induced cell death and cellular senescence. MTT assay shows that NaHS significantly increased cell viability from 62.31 ± 1.29% to 72.34 ± 0.46% compared with d-galactose (200 mM) treatment group. The underlying mechanism appeared to involve a reduction by NaHS in the formation of advanced glycation end products (AGEs), which are known to contribute to the progression of age-related diseases. In addition, NaHS decreased the elevation of reactive oxygen species from 151.17 ± 2.07% to 124.8 ± 2.89% and malondialdehyde from 1.72 ± 0.07 to 1.10 ± 0.08 (nmol/mg protein) in SH-SY5Y cells after d-galactose exposure. NaHS also stimulated activities of superoxide dismutase from 0.42 ± 0.05 to 0.73 ± 0.04 (U/mg protein) and glutathione peroxidase from 3.98 ± 0.73 to 14.73 ± 0.77 (nmol/min/mg protein) and upregulated the gene expression levels of copper transport protein ATOX1, glutathione synthetase (GSS) and thioredoxin reductase 1 (TXNRD1) while down-regulated aldehyde oxidase 1 (AOX1). In summary, our data indicate that H₂S may have potentially anti-aging effects through the inhibition of AGEs formation and reduction of oxidative stress.     

Effect of Dimethyl Sulfides on the Induction of Apoptosis in Human Leukemia Jurkat Cells and HL-60 Cells

Organosulfur compounds have been established to possess anticancer effects. To provide a better understanding of the biological function of dimethyl sulfides, dimethyl monosulfide (Me₂S), dimethyl disulfide (Me₂S₂), dimethyl trisulfide (Me₂S₃) and dimethyl tetrasulfide (Me₂S₄) were used as experimental materials to investigate their effects on apoptosis induction in human leukemia Jurkat cells and HL-60 cells. Treatment with 20 μM dimethyl sulfides for 24 h decreased the viability of both cells. The cell viability-reducing effect of these sulfides was in the following order: Me₂S₄ ≈ Me₂S₃ > Me₂S₂ ≈ Me₂S for Jurkat cells and Me₂S₄ > Me₂S₃ > Me₂S₂ ≈ Me₂S for HL-60 cells. Me₂S₃ and Me₂S₄ significantly induced DNA fragmentation and caspase-3 activation. The addition of GSH or NAC completely suppressed the sulfide-induced apoptosis. Our results indicate that dimethyl sulfides with a larger number of sulfur atoms more strongly induced apoptosis in both human leukemia cells via ROS production and caspase-3 activation.