Molecular dynamics simulations of the orientation properties of cytochrome <Emphasis Type="Italic">c</Emphasis> on the surface of single-walled carbon nanotubes

Electron transfer between cytochrome c (Cytc) and electrodes can be influenced greatly by the orientation of protein on the surface of the electrodes. In the present study, different initial orientations of Cytc on the surface of five types of single-walled carbon nanotubes (SWNTs), with different diameters and chirality, were constructed. Properties of the orientations of proteins on the surface of these tubes were first investigated through molecular dynamics simulations. It was shown that variations in SWNT diameter do not significantly affect the orientation; however, the chirality of the SWNTs is crucial to the orientation of the heme embedded in Cytc, and the orientation of the protein can consequently be influenced by the heme orientation. A new electron pathway between Cytc and SWNT, which hopefully benefits electron transfer efficiency, has also been proposed. This study promises to provide theoretical guidance for the rational design of bio-sensors or bio-fuel cells by using Cytc-decorated carbon nanotube electrodes.     

The protonated 2-halogenated imidazolium cation as the noncovalent interaction donor: the σ-hole and π-hole interactions

The σ-hole and π-hole of the protonated 2-halogenated imidazolium cation (XC₃H₄N₂ ⁺; X = F, Cl, Br, I) were investigated and analyzed. The monomers of (CH₃)₃SiY(Y=F, Cl, Br, I), considered as the Lewis base, were combined with the σ-hole and π-hole of XC₃H₄N₂ ⁺ to form the σ-hole and π-hole interactions in the bimolecular complexes (CH₃)₃SiY?·?·?·?XC₃H₄N₂ ⁺ and (CH₃)₃SiY?·?·?·?C₃(X)H₄N₂ ⁺(X/Y=F, Cl, Br, I), respectively. For both the σ-hole and π-hole interactions, the equilibrium geometries of complexes show regular changes according to the sequence of heavy sequence of the noncovalent interaction acceptors and donors. The electrostatic energy is the main contribution in the formation of both kinds of interactions, it has linear relations with the V _S,max values of σ-hole and the V′ _S,max values of π-hole. Both the σ-hole and π-hole interactions belong to the closed-shell and noncovalent interactions. The π-hole interactions are stronger than the σ-hole interactions. For the π-hole interactions, the contribution percents of the dispersion energies are somewhat greater than those of the σ-hole interactions, while it is contrary for the polarization energy.

Open image in new window

Graphical Abstract The protonated 2-halogenated imidazolium cation as the noncovalent interaction donor: the σ-hole and π-hole interactions?

     

The p70S6K Specific Inhibitor PF-4708671 Impedes Non-Small Cell Lung Cancer Growth

Background

As a serine/threonine protein kinase, p70S6K plays an important role in tumor cells. Evidence has revealed overexpression of p70S6K and phosphorylated p70S6K (p-p70S6K) in various tumor tissues, with these proteins identified as independent prognostic markers in non-small cell lung cancer (NSCLC). In this study, we explored the role of the p70S6K specific inhibitor PF-4708671 in NSCLC.

Methods

Three NSCLC cell lines (A549, SK-MES-1, and NCI-H460) were treated with PF-4708671 at five different concentrations, including 0.1μM, 0.3μM, 1μM, 3μM and 10μM, and protein levels were determined by Western-blot. Then, PF-4708671’s effects were assessed both in vitro (cell proliferation, apoptosis, cell cycle distribution, and invasion) and in vivo.

Results

The expression levels of p-p70S6K and the downstream effector S6 were significantly reduced by PF-4708671. Diametrically opposite, the downstream protein levels of BAD, Caspase3 and ERK had increased after treatment with PF-4708671. In addition, PF-4708671 drastically inhibited cell proliferation and invasion ability in A549, SK-MES-1 and NCI-H460 cells in vitro, causing cell cycle arrest in G0-G1 phase. Limited effects of PF-4708671 were observed on apoptosis in the three NSCLC cell lines assessed. Importantly, PF-4708671 could inhibit tumorigenesis in nude mice in vivo.

Conclusion

These findings demonstrated that the p70S6K specific inhibitor PF-4708671 has inhibitory effects on NSCLC tumorigenesis in vitro and in vivo. Therefore, P70S6K should be considered a new potential therapeutic target, and PF-470867 may be used as targeted drug for cancer treatment.     

Plasmid and Host Strain Characteristics of Escherichia coli Resistant to Extended-Spectrum Cephalosporins in the Norwegian Broiler Production

Escherichia coli resistant to extended-spectrum cephalosporins have been detected in the Norwegian broiler production, despite the fact that antimicrobial agents are rarely used. The genetic mechanism responsible for cephalosporin resistance is mainly attributed to the presence of the bla_CMY-2 gene encoding a plasmid-mediated AmpC-beta-lactamase (pAmpC). The aim of this study was to characterize and compare bla_CMY-2 containing Escherichia coli isolated from the intestinal flora of broilers and retail chicken meat (fillets) to identify possible successful clones and/or resistance plasmids widespread in the Norwegian broiler production. Methods used included PCR based phylotyping, conjugation experiments, plasmid replicon typing, pulsed-field gel electrophoresis, multiple locus variable-number tandem-repeats analysis and whole genome sequencing. The nucleotide sequence of an IncK plasmid carrying bla_CMY-2 was determined. Intestinal isolates displayed a higher degree of genetic diversity than meat isolates. A cluster of genetically related isolates belonging to ST38, phylogroup D, carrying bla_CMY-2 containing IncK plasmids was identified. Furthermore, genes encoding plasmid stability systems (relBE/stbDE and pndAC) were identified on the IncK plasmid. Single nucleotide polymorphism (SNP) analysis of a subset of isolates confirmed a close genetic relationship within the two most prevalent STs. The IncK plasmids within these two STs also shared a high degree of similarity. Cephalosporin-resistant E. coli with the same genetic characteristics have been identified in the broiler production in other European countries, and the IncK plasmid characterized in this study showed close homology to a plasmid isolated from retail chicken meat in the Netherlands. The results indicate that both clonal expansion and horizontal transfer of bla_CMY-2 containing plasmids contribute to dissemination of cephalosporin resistant E. coli in the broiler production. The presence of plasmid stability systems may explain why the IncK plasmid containing bla_CMY-2 is maintained and disseminated in the Norwegian broiler production in absence of selection pressure from the use of antimicrobial agents.     

Gardnerella vaginalis Subgroups Defined by cpn60 Sequencing and Sialidase Activity in Isolates from Canada,Belgium and Kenya

Increased abundance of Gardnerella vaginalis and sialidase activity in vaginal fluid is associated with bacterial vaginosis (BV), a common but poorly understood clinical entity associated with poor reproductive health outcomes. Since most women are colonized with G. vaginalis, its status as a normal member of the vaginal microbiota or pathogen causing BV remains controversial, and numerous classification schemes have been described. Since 2005, sequencing of the chaperonin-60 universal target (cpn60 UT) has distinguished four subgroups in isolate collections, clone libraries and deep sequencing datasets. To clarify potential clinical and diagnostic significance of cpn60 subgroups, we undertook phenotypic and molecular characterization of 112 G. vaginalis isolates from three continents. A total of 36 subgroup A, 33 B, 35 C and 8 D isolates were identified through phylogenetic analysis of cpn60 sequences as corresponding to four “clades” identified in a recently published study, based on sequencing 473 genes across 17 isolates. cpn60 subgroups were compared with other previously described molecular methods for classification of Gardnerella subgroups, including amplified ribosomal DNA restriction analysis (ARDRA) and real-time PCR assays designed to quantify subgroups in vaginal samples. Although two ARDRA patterns were observed in isolates, each was observed in three cpn60 subgroups (A/B/D and B/C/D). Real-time PCR assays corroborated cpn60 subgroups overall, but 13 isolates from subgroups A, B and D were negative in all assays. A putative sialidase gene was detected in all subgroup B, C and D isolates, but only in a single subgroup A isolate. In contrast, sialidase activity was observed in all subgroup B isolates, 3 (9%) subgroup C isolates and no subgroup A or D isolates. These observations suggest distinct roles for G. vaginalis subgroups in BV pathogenesis. We conclude that cpn60 UT sequencing is a robust approach for defining G. vaginalis subgroups within the vaginal microbiome.     

Net land gain or loss for two Mississippi River diversions: Caernarvon and Davis Pond

Coastal wetland restoration can be complex and expensive, so knowing long‐term consequences makes it important to inform decisions about if, when, and where to conduct restoration. We determined temporal changes in land gain and loss in receiving basins and adjacent reference areas for two diversions of the Mississippi River in south Louisiana (Davis Pond and Caernarvon initiated in 1991 and 2002, respectively). Water from both diversions went into receiving basins with vegetated areas as did the adjoining reference areas. The results from two different types of satellite imagery analyses demonstrate a net land loss after diversions began. The results were confirmed for the Caernarvon diversion using a before–after/control–impact analysis of independently collected data over a larger area of the estuary. These results are consistent with an analysis of land gain and loss after a natural levee break on the Mississippi River in 1973. The positive influences of adding new sediments were apparently counter‐balanced by other factors, and consistent with the conclusion from other studies indicating that increased nutrient supply and flooding are, by themselves, negative influences on marsh health. Modeling the ecosystem effects of diversions can be calibrated and tested using landscape‐scale analyses like this to understand the chronic and delayed effects, including the unintended consequences. Basing the legitimacy of river diversion on ecosystem modeling will be premature without successfully reproducing empirical results like these in ecosystem models.