Vertical distribution of Fe, P and correlation with organic carbon in coastal sediments of Yellow Sea, Eastern China

The coastal zone is considered as a major carbon pool. Iron minerals and phosphates are vital factors affecting the amounts and occurrence of total organic carbon (TOC) in sediments. However, coupling mechanisms of iron (Fe) and phosphorous (P) in the source-sink transition of TOC in coastal sediments is poorly understood. This study characterized the distribution of Fe, P and TOC contents of three independent 170 cm sediment cores sampled from a coastal aquaculture area in the eastern Jiangsu Province, and quantified the correlations among Fe, P, median grain diameter (Dx(50)), and TOC. The results showed total phosphorus (TP) content ranges in a scope of 337.4-578.0 mg/kg, and many depths recorded moderate P eutrophication. Inorganic phosphorus (DA + IP) and biogenic apatite were the primary components of TP, accounting for 25.19–55.00 and 26.71–49.62%, respectively. The Fe contents varied from 987.9 mg/kg to 2900.7 mg/kg, in which oxidized iron (Feox) accounted for about 62.2–79.4%. In the vertical profile, the TOC was positively correlated with the contents of low-crystallinity Fe-bearing carbonates (Fecarb), high crystallinity pyrite (FePy), iron-bound phosphorus (PCDB), manganeses (Mn), and nitrogen (N), while it was negatively correlated with DA + IP, organic phosphorus (OP), and Dx(50). Based on the the partial least squares (PLS) model, we proposed that the higher FePy, Mn, magnetite (FeMag), Fecarb, PCDB, amorphous exchangeable Fe (Ex-Fe), and authigenic apatite phosphorus (Bio-P) in sediments represent the high capacity for TOC sink, whereas, higher DA + IP, and OP indicate a TOC conversion to the source. The non-siginificat indication of Feox on TOC source-sink is due to its surplus and strong reactivity relative to TOC content. These revealed correlations provide a theoretical reference for understanding and regulating the burial rate and storage of TOC by changing the input of Fe minerals and P components into coastal sediments

The application of inelastic neutron scattering to investigate the ‘dry’ reforming of methane over an alumina-supported nickel catalyst operating under conditions where filamentous carbon formation is prevalent

The use of CO2 in reforming methane to produce the industrial feedstock syngas is an economically and environmentally attractive reaction. An alumina-supported nickel catalyst active for this reaction additionally forms filamentous carbon. The catalyst is investigated by inelastic neutron scattering as well as elemental analysis, temperature-programmed oxidation, temperature-programmed hydrogenation, X-ray diffraction, transmission electron microscopy and Raman scattering. Isotopic substitution experiments, using 13CO2 for 12CO2, show the oxidant to contribute to the carbon retention evident with this sample. At steady-state operation, a carbon mass balance of 95 % is observed. A kinetic scheme is proposed to account for the trends observed

Loaded delta-hemolysin shapes the properties of Staphylococcus aureus membrane vesicles

BackgroundMembrane vesicles (MVs) are nanoscale vesicular structures produced by bacteria during their growth in vitro and in vivo. Some bacterial components can be loaded in bacterial MVs, but the roles of the loaded MV molecules are unclear.MethodsMVs of Staphylococcus aureus RN4220 and its derivatives were prepared. Dynamic light scattering analysis was used to evaluate the size distribution, and 4D-label-free liquid chromatography–tandem mass spectrometry analysis was performed to detect protein composition in the MVs. The site-mutation S. aureus RN4220-Δhld and agrA deletion mutant RN4220-ΔagrA were generated via allelic replacement strategies. A hemolysis assay was performed with rabbit red blood cells. CCK-8 and lactate dehydrogenase release assays were used to determine the cytotoxicity of S. aureus MVs against RAW264.7 macrophages. The serum levels of inflammatory factors such as IL-6, IL-1β, and TNFα in mice treated with S. aureus MVs were detected with an enzyme-linked immunosorbent assay kit.ResultsDelta-hemolysin (Hld) was identified as a major loaded factor in S. aureus MVs. Further study showed that Hld could promote the production of staphylococcal MVs with smaller sizes. Loaded Hld affected the diversity of loaded proteins in MVs of S. aureus RN4220. Hld resulted in decreased protein diversity in MVs of S. aureus. Site-mutation (RN4220-Δhld) and agrA deletion (RN4220-ΔagrA) mutants produced MVs (ΔhldMVs and ΔagrAMVs) with a greater number of bacterial proteins than those derived from wild-type RN4220 (wtMVs). Moreover, Hld contributed to the hemolytic activity of wtMVs. Hld-loaded wtMVs were cytotoxic to macrophage RAW264.7 cells and could stimulate the production of inflammatory factor IL-6 in vivo.ConclusionThis study presented that Hld was a major loaded factor in S. aureus MVs, and the loaded Hld played vital roles in the MV-property modification

Human Papillomavirus Type 18 E6 and E7 Genes Integrate into Human Hepatoma Derived Cell Line Hep G2

Background and Objectives: Human papillomaviruses have been linked causally to some human cancers such as cervical carcinoma, but there is very little research addressing the effect of HPV infection on human liver cells. We chose the human hepatoma derived cell line Hep G2 to investigate whether HPV gene integration took place in liver cells as well. Methods: We applied PCR to detect the possible integration of HPV genes in Hep G2 cells. We also investigated the expression of the integrated E6 and E7 genes by using RT-PCR and Western blotting. Then, we silenced E6 and E7 expression and checked the cell proliferation and apoptosis in Hep G2 cells. Furthermore, we analyzed the potential genes involved in cell cycle and apoptosis regulatory pathways. Finally, we used in situ hybridization to detect HPV 16/18 in hepatocellular carcinoma samples. Results: Hep G2 cell line contains integrated HPV 18 DNA, leading to the expression of the E6 and E7 oncogenic proteins. Knockdown of the E7 and E6 genes expression reduced cell proliferation, caused the cell cycle arrest at the S phase, and increased apoptosis. The human cell cycle and apoptosis real-time PCR arrays analysis demonstrated E6 and E7-mediated regulation of some genes such as Cyclin H, UBA1, E2F4, p53, p107, FASLG, NOL3 and CASP14. HPV16/18 was found in only 9% (9/100) of patients with hepatocellular carcinoma. Conclusion: Our investigations showed that HPV 18 E6 and E7 genes can be integrated into the Hep G2, and we observed a low prevalence of HPV 16/18 in hepatocellular carcinoma samples. However, the precise risk of HPV as causative agent of hepatocellular carcinoma needs further study

Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity

BACKGROUND: Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Shotgun sequencing method failed to complete the sequence of this genome. RESULTS: After persevering for 10 years and going over three generations of sequencing techniques, we successfully completed the sequence of the PaP1 genome with a length of 91,715 bp. Single-molecule real-time sequencing results revealed that this genome contains 51 N-6-methyladenines and 152 N-4-methylcytosines. Three significant modified sequence motifs were predicted, but not all of the sites found in the genome were methylated in these motifs. Further investigations revealed a novel immune mechanism of bacteria, in which host bacteria can recognise and repel modified bases containing inserts in a large scale. This mechanism could be accounted for the failure of the shotgun method in PaP1 genome sequencing. This problem was resolved using the nfi(-) mutant of Escherichia coli DH5α as a host bacterium to construct a shotgun library. CONCLUSIONS: This work provided insights into the hard-to-sequence phage PaP1 genome and discovered a new mechanism of bacterial immunity. The methylome of phage PaP1 is responsible for the failure of shotgun sequencing and for bacterial immunity mediated by enzyme Endo V activity; this methylome also provides a valuable resource for future studies on PaP1 genome replication and modification, as well as on gene regulation and host interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-803) contains supplementary material, which is available to authorized users

Virulence alterations in staphylococcus aureus upon treatment with the sub-inhibitory concentrations of antibiotics

Background: The treatment of patients with Staphylococcus aureus infections mainly relies on antistaphylococcal regimens that are established with effective antibiotics. In antibiotic therapy or while living in nature, pathogens often face the sub-inhibitory concentrations (sub-MICs) of antibiotics due to drug pharmacokinetics, diffusion barriers, waste emission, resistant organism formation, and farming application. Different categories of antibiotics at sub-MICs have diverse effects on the physiological and chemical properties of microorganisms. These effects can result in virulence alterations. However, the mechanisms underlying the actions of antibiotics at sub-MICs on S. aureus virulence are obscure. Aim of review: In this review, we focus on the effects of sub-MICs of antibiotics on S. aureus virulence from the aspects of cell morphological change, virulence factor expression, bacterial adherence and invasion, staphylococcal biofilm formation, and small-colony variant (SCV) production. The possible mechanisms of antibiotic-induced S. aureus virulence alterations are also addressed. Key scientific concepts of review: Five main aspects of bacterial virulence can be changed in S. aureus exposure to the sub-MIC levels of antibiotics, resulting in deformed bacterial cells to stimulate abnormal host immune responses, abnormally expressed virulence factors to alter disease development, changed bacterial adhesion and invasion abilities to affect colonization and diffusion, altered biofilm formation to potentate material-related infections, and increased SCV formation to achieve persistent infection and recurrence. These advanced findings expand our knowledge to rethink the molecular signaling roles of antibiotics beyond their actions as antimicrobial agents

Analysis and simulation of the "after-pulse" RF breakdown

During the high power experiment of a single-cell standing-wave accelerating structure, it was observed that many RF breakdowns happen when the field inside cavity is decaying after the input rf pulse is off. The distribution of breakdown timing shows a peak at the moment of RF power switches off. A series of simulation was performed to study the after-pulse breakdown effect in such a standing-wave structure. A method of calculating poynting vector over time is proposed in this article to study the modified poynting vector at critical points in the cavity. Field simulation and thermal calculation were also carried out to analyse possible reasons for the after-pulse breakdown effect

Silencing of Tumor Necrosis Factor Receptor 1 by siRNA in EC109 Cells Affects Cell Proliferation and Apoptosis

Tumor necrosis factor receptor 1 (TNFR1) is a membrane receptor able to bind TNF-α or TNF-β. TNFR1 can suppress apoptosis by activating the NF-κB or JNK/SAPK signal transduction pathway, or it can induce apoptosis through a series of caspase cascade reactions; the particular effect may depend on the cell line. In the present study, we first showed that TNFR1 is expressed at both the gene and protein levels in the esophageal carcinoma cell line EC109. Then, by applying a specific siRNA, we silenced the expression of TNFR1; this resulted in a significant time-dependent promotion of cell proliferation and downregulation of the apoptotic rate. These results suggest that TNFR1 is strongly expressed in the EC109 cell line and that it may play an apoptosis-mediating role, which may be suppressed by highly activated NF-κB

A tool orientation smoothing method for five-axis machining to avoid singularity problems

In numerically controlled grinding of aeroengine blades, a sharp change in a rotating shaft caused by a singular zone greatly reduces grinding precision and quality. This paper proposes an algorithm to optimize the tool-path that combines optimization of the C-axis rotation angle, a modification to the tool orientation and adjustments to the tool position by taking a four-array machine tool with two rotational axes (B-axis and C-axis) as an example. The algorithm was verified using VERICUT software, furthermore, in machining experiments, the rotation amplitudes of the rotary axis in singular areas was effectively reduced, which ensured grinding quality of blades