Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations

To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism

A Roughness Study of Ytterbium-Doped Potassium Yttrium Tungstate (YB: KYW) Thin-Disk Femtosecond Ablated Dentin

Introduction: The aim of this study was to evaluate the morphological changes and quantitatively assess the roughness of dentin after the ablation with a Ytterbium-Doped Potassium Yttrium Tungstate (YB: KYW) thin-disk femtosecond pulsed laser of different fluences, scanning speeds and scanning distances.Method: Twelve extracted human premolars were sectioned into crowns and roots along the cementum-enamel junction, and then the crowns were cut longitudinally into sheets about 1.5 mm thick with a cutting machine. The dentin samples were fixed on a stage at focus plane. The laser beam was irradiated onto the samples through a galvanometric scanning system, so rectangular movement could be achieved. After ablation, the samples were examined with a scanning electron microscope and laser three-dimensional profile measurement microscope for morphology and roughness study.With increasing laser fluence, dentin samples exhibited more melting and resolidification of dentin as well as debris-like structure and occluded parts of dentinal tubules.Results: When at the scanning speed of 2400mm/s and scanning distance of 24μm, the surface roughness of dentin ablated with femtosecond pulsed laser decreased significantly and varied between values of dentin surface roughness grinded with two kinds of diamond burs with different grits. When at the scanning speed of 1200mm/s and scanning distance of 12μm, the surface roughness decreased slightly, and the surface roughness of dentin ablated with femtosecond pulsed laser was almost equal to that grinded with a low grit diamond bur.Conclusion: This study showed that increased laser influence may lead to more collateral damage and lower dentin surface roughness, while scanning speed and scanning distance were also negatively correlated with surface roughness. Adequate parameters should be chosen to achieve therapeutic benefits, and different parameters can result in diverse ablation results

Insight into CO activation over Cu(100) under electrochemical conditions

The reduction of CO2 on copper electrodes has attracted great attentions in the last decades, since it provides a sustainable approach for energy restore. During the CO2 reduction process, the electron transfer to COads is experimentally suggested to be the crucial step. In this work, we examine two possible pathways in CO activation, i.e. to generate COHads and CHOads, respectively, by performing the state-of-the-art constrained ab initio molecular dynamics simulations on the charged Cu(100) electrode under aqueous conditions, which is close to the realistic electrochemical condition. The free energy profile in the formation of COHads via the coupled proton and electron transfer is plotted. Furthermore, by Bader charge analyses, a linear relationship between C-O bond distance and the negative charge in CO fragment is unveiled. The formation of CHOads is identified to be a surface catalytic reaction, which requires the adsorption of H atom on the surface first. By comparing these two pathways, we demonstrate that kinetically the formation of COHads is more favored than that of CHOads, while CHOads is thermodynamically more stable. This work reveals that CO activation via COHads intermediate is an important pathway in electrocatalysis, which could provide some insights into CO2 electroreduction over Cu electrodes

Insights into the mechanism of Nitrobenzene reduction to aniline over Pt catalyst and the significance of the adsorption of phenyl group on kinetics

Aniline (C6H5NH2) plays a significant role in both industry and daily life, and can be synthesized via catalytic hydrogenation of nitrobenzene (C6H5NO2) over transition metals; however fundamental investigations on reaction mechanisms in the heterogeneous catalysis are still lacking. In this work, the nitrobenzene reduction reaction over the Pt(111) model catalyst was studied using density functional theory (DFT) with the inclusion of van der Waals interaction, for fundamentally understanding the mechanisms at atomic and molecular levels. It was found that the double H-induced dissociation of N-O bond was the preferential path for the activation of nitro group, having a much lower reaction barrier than that of the direct dissociation and single H-induced dissociation paths. The overall mechanisms have been identified as: C6H5NO2* → C6H5NOOH* → C6H5N(OH)2* → C6H5NOH* → C6H5NHOH* → C6H5NH* → C6H5NH2*. The overall barrier of the nitro group reduction was calculated to be 0.75 eV, which is much lower than that of the benzene reduction (1.08 eV). Our DFT data elucidates clearly the reason why the major product of nitrobenzene reduction reaction was aniline. Furthermore, the adsorption/desorption of phenyl group was found to have significant impacts on kinetic barriers. Generally, in the hydrogenation process (N-H or O-H bond association), the phenyl group preferred to adsorb on the surface; but in the dissociation process (N-O bond dissociation) it preferred to desorb transiently at the transition state and to adsorb again when the dissociation was completed. This study also provides a solid theoretical insight into the selective catalysis of the large aromatic compounds

Field-scale bioremediation of soil contaminated with crude oil

Field-scale remediation of oil-contaminated soils from the Liaohe Oil Fields in China was examined using composting biopiles in windrow technology. Micronutrient-enriched chicken excrement and rice husk were applied as nutrition and a bulking agent. The lipase activities of indigenous micro-organisms were analyzed, and three indigenous fungi with high lipase activities was identified. An inoculum consisting of the three indigenous fungi and one introduced (exotic) fungus was applied to four different types of oil-contaminated soils. The results showed that the inoculum of indigenous fungi increased both the total colony-forming units (TCFU) and increased the rate of degradation of total petroleum hydrocarbons (TPH) in all contaminated soils but at different rates. In sharp contrast to other studies, the introduction of exotic micro-organisms did not improve the remediation, and suggests that inoculation of oil-contaminated sites with nonindigenous species is likely to fail. On the other hand, indigenous genera of microbes were found to be very effective in increasing the rate of degradation of TPH. The degradation of TPH was mainly controlled by the compositions of aromatic hydrocarbons and asphaltene and resin. Between 38 to 57% degradation of crude oils (with densities ranging from 25,800 to 77,200 mg/kg dry weight) in contaminated soils was achieved after 53 days of operation. The degradation patterns followed typical first-order reactions. We demonstrate that the construction and operation of field-scale composting biopiles in windrows with passive aeration is a cost-effective bioremediation technology.<br /

Prognostic Analysis of Duodenal Gastrointestinal Stromal Tumors

Aim. This study aims to analyze factors possibly related to the prognosis of duodenal gastrointestinal stromal tumors (DGISTs). Methods. We collected and retrospectively analyzed clinical and pathological data of 62 patients with primary DGISTs. All the patients were hospitalized and received complete surgical resection at Shanghai Ruijin Hospital from September 2003 to April 2015. We followed up the patients to determine survival outcomes. We also analyzed the effect of clinical and pathological factors on disease-free survival (DFS) and overall survival (OS) of the patients. Results. Kaplan-Meier univariate survival analysis demonstrated that tumor size, mitotic index, Ki-67 index, and pathological risk were correlated with the DFS and OS of the patients (DFS P=0.039, 0.001, <0.001, and 0.005, resp.; OS P=0.027, 0.007, <0.001, and 0.012, resp.). Cox multivariate regression analysis revealed that Ki-67 index was an independent prognostic factor affecting DFS and OS (P=0.007 and 0.028, resp.). Moreover, Kaplan-Meier survival analysis showed that imatinib treatment for patients with recurrence was correlated with prolonged OS (P=0.002). Conclusion. Prognosis for DGIST treated by R0 resection is favorable. High level of Ki-67 can be an independent risk factor of DGIST prognosis. Adjuvant imatinib therapy for patients with tumor recurrence could probably lead to prolonged survival