Eph/ephrin recognition and the role of Eph/ephrin clusters in signaling initiation

The Eph receptors and their ephrin ligands play crucial roles in a large number of cell–cell interaction events, including those associated with axon pathfinding, neuronal cell migration and vasculogenesis. They are also involved in the patterning of most tissues and overall cell positioning in the development of the vertebrate body plan. The Eph/ephrin signaling system manifests several unique features that differentiate it from other receptor tyrosine kinases, including initiation of bi-directional signaling cascades and the existence of ligand and receptor subclasses displaying promiscuous intra-subclass interactions, but very rare inter-subclass interactions. In this review we briefly discuss these features and focus on recent studies of the unique and expansive high-affinity Eph/ephrin assemblies that form at the sites of cell–cell contact and are required for Eph signaling initiation. This article is part of a Special Issue entitled: Emerging recognition and activation mechanisms of receptor tyrosine kinases.     

Display of heterologous protein on the surface of Lactobacillus plantarum by using the CspI anchor protein

The C-terminus of the putative cell surface protein CspI which contains one putative LPxTG motif region and a signal peptides fragment were amplified from L. plantarum CICC6024, and the green fluorescent protein gene gfp was amplified from the plasmid pACGFP. The three genes were ligated and the fusion gene was named SgfpL. The fusion gene SgfpL was then cloned into shuttle expression vector pMG36e and transformed into L. plantarum. SDS-PAGE identified that the fusion protein was expressed and the band of fusion protein was observed at the predicated molecular size. Fluorescence assay, western blot against GFP antibody, protease accessibility and SDS sensitivity assays were performed to determine that the GFP was successfully displayed on the surfaces of L. plantarum cells and the maximum display capacity of the GFP fusion protein was ca. 65 μg?ml^?1. The fermentation condition experiments determined that the amounts of GFP fusion protein were increased at a higher temperature and reached the peak at 2.5 h. Then, the β-galactosidase from Bifidobacterium bifidum was functionally displayed on the surface of L. plantarum cells via CspI to demonstrate the applicability of the CspI-mediated surface display system.     

Culture-independent analysis of Pseudomonas community structures in fertilized and unfertilized agricultural soils

Pseudomonas community structures were investigated by analyzing 16S rRNA clone libraries derived from fertilized and unfertilized soil plots under corn–alfalfa rotation in a long-term experiment. Amplified 16S rRNA fragments derived by polymerase chain reaction (PCR) were cloned and sequenced. A total of 729 clone sequences were analyzed, of which 51 were possible chimeras and discarded. The remaining clone sequences (678) belonged to γ-proteobacteria with 61.8 % (419) classified to the genus Pseudomonas. Unclassified Gammaproteobacteria accounted for 23.4 % of total clones sequences. Rarefaction analyses showed a more diverse community structure of both Gammaproteobacteria and Pseudomonas in unfertilized than fertilized field soils irrespective of plant types under cultivation. Bacterial or Pseudomonas community structures differed significantly between fertilized and unfertilized soil plots. Clone sequences that are affiliated to Pseudomonas putida and P. oryzihabitans were more prominent in libraries from fertilized plots, while those that clustered with Pseudomonas frederiksbergensis were more often retrieved from unfertilized soil plots. A strong influence of fertilizer applications on community structure was supported by principal component analysis. We conclude that long-term use of mineral fertilizers could influence Pseudomonas community structure.     

A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

Halogen bonding, a non-covalent interaction between the halogen σ-hole and Lewis bases, could not be properly characterized by majority of current scoring functions. In this study, a knowledge-based halogen bonding scoring function, termed XBPMF, was developed by an iterative method for predicting protein-ligand interactions. Three sets of pairwise potentials were derived from two training sets of protein-ligand complexes from the Protein Data Bank. It was found that two-dimensional pairwise potentials could characterize appropriately the distance and angle profiles of halogen bonding, which is superior to one-dimensional pairwise potentials. With comparison to six widely used scoring functions, XBPMF was evaluated to have moderate power for predicting protein-ligand interactions in terms of “docking power”, “ranking power” and “scoring power”. Especially, it has a rather satisfactory performance for the systems with typical halogen bonds. To the best of our knowledge, XBPMF is the first halogen bonding scoring function that is not dependent on any dummy atom, and is practical for high-throughput virtual screening. Therefore, this scoring function should be useful for the study and application of halogen bonding interactions like molecular docking and lead optimization.

Electrochemical Performance of Porous Carbon/Tin Composite Anodes for Sodium‐Ion and Lithium‐Ion Batteries

The electrochemical performance of mesoporous carbon (C)/tin (Sn) anodes in Na‐ion and Li‐ion batteries is systematically investigated. The mesoporous C/Sn anodes in a Na‐ion battery shows similar cycling stability but lower capacity and poorer rate capability than that in a Li‐ion battery. The desodiation potentials of Sn anodes are approximately 0.21 V lower than delithiation potentials. The low capacity and poor rate capability of C/Sn anode in Na‐ion batteries is mainly due to the large Na‐ion size, resulting in slow Na‐ion diffusion and large volume change of porous C/Sn composite anode during alloy/dealloy reactions. Understanding of the reaction mechanism between Sn and Na ions will provide insight towards exploring and designing new alloy‐based anode materials for Na‐ion batteries.     

At-line near-infrared spectroscopy for monitoring concentrations in temperature-triggered glutamate fermentation

Rapid development in the glutamate fermentation industry has dictated the need for effective fermentation monitoring by rapid and precise methods that provide real-time information for quality control of the end-product. In recent years, near-infrared (NIR) spectroscopy and multivariate calibration have been developed as fast, inexpensive, non-destructive and environmentally safe techniques for industrial applications. The purpose of this study was to develop models for monitoring glutamate, glucose, lactate and alanine concentrations in the temperature-triggered process of glutamate fermentation. NIR measurements of eight batches of samples were analyzed by partial least-squares regression with several spectral pre-processing methods. The coefficient of determination (R ²), model root-mean square error of calibration (RMSEC), root-mean square error of prediction (RMSEP) and residual predictive deviation (RPD) of the test calibration for the glutamate concentration were 0.997, 3.11 g/L, 2.56 g/L and 19.81, respectively. For the glucose concentration, R ², RMSEC, RMSEP and RPD were 0.989, 1.37 g/L, 1.29 g/L and 9.72, respectively. For the lactate concentration, R ², RMSEC, RMSEP and RPD were 0.975, 0.078 g/L, 0.062 g/L and 6.29, respectively. For the alanine concentration, R ², RMSEC, RMSEP and RPD were 0.964, 0.213 g/L, 0.243 g/L and 5.29, respectively. New batch fermentation as an external validation was used to check the models, and the results suggested that the predictive capacity of the models for the glutamate fermentation process was good.     

Systematic research on the pretreatment of peptides for quantitative proteomics using a C18 microcolumn

Reversed phase microcolumns have been widely used for peptide pretreatment to desalt and remove interferences before tandem LC–MS in proteomics studies. However, few studies have characterized the effects of experimental parameters as well as column characteristics on the composition of identified peptides. In this study, several parameters including the concentration of ACN in washing buffer, the microcolumn's purification effect, the peptide recovery rate, and the dynamic‐binding capacity were characterized in detail, based upon stable isotope labeling by amino acids in a cell culture quantitative approach. The results showed that peptide losses can be reduced with low ACN concentration in washing buffers resulting in a recovery rate of approximately 82%. Furthermore, the effects of ACN concentration and loading amount on the properties of identified peptides were also evaluated. We found that the dynamic‐binding capacity of the column was approximately 26 μg. With increased loading amounts, more hydrophilic peptides were replaced by hydrophobic peptides.