Cyclic sample pooling using two‐dimensional liquid chromatography system enhances coverage in shotgun proteomics

We report a cyclic sample pooling technique devised in two‐dimensional liquid chromatography–electrospray ionization mass spectrometry (LC‐ESI‐MS) shotgun proteomics that renders deeper proteome coverage; we combined low pH reversed‐phase (RP) LC in trifluoroacetic acid in the first dimension, followed by cyclic sample pooling of the eluate and low‐pH RP‐LC in formic acid in the second dimension. The new protocol has a significantly higher resolving power suitable for LC‐ESI‐MS/MS shotgun proteomics. Copyright © 2013 John Wiley & Sons, Ltd.     

Short Communication: Crystal Structure of a Molecular Complex from Native β-Cyclodextrin and Copper(II) Chloride

Reaction of β-cyclodextrin (β-CD) with CuCl₂ in neutral aqueous solutions gave a stable molecular complex without any side-arm support. The X-ray crystallographic analysis clarified that the copper ion was located at the bottom of the primary-hydroxy side as a CuCl₂(H₂O)₂ form. Hydrogen bonds were found between the Cl and H₂O ligands and β-CD hydroxy and ether groups. The copper ion is axially coordinated with a hydroxy group of a neighboring β-CD molecule, giving a one-dimensional β-CD/CuCl₂ array.     

Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation

Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.     

Exploiting Transient Radical Cations as Brønsted Acids for Allylic C–H Heteroarylation of Enol Silyl Ethers

Intermediary radical cations, generated through single-electron oxidation of enol silyl ethers by excited Ir-based photocatalysts, can be exploited as Brønsted acids for the activation of heteroarylcyanides. This strategy enables the direct allylic C−H heteroarylation of enol silyl ethers under visible-light irradiation.     

Neutron Halo Structure at the Limit of Stability Probed by Breakup Reactions

Atomic nuclei along the neutron drip line are investigated experimentally by breakup reactions of the rare isotope beams. Such exotic nuclei often show the neutron halo structure, which is the main focus of this paper. Characteristic features of the Coulomb and nuclear breakup at intermediate to high incident energies are described. Then, recent experimental results on halo nuclei, mainly on ³¹Ne, obtained at the new-generation RI-beam facility, RIBF (RI Beam factory) at RIKEN, are presented. Perspectives for the breakup experiments using the new facility SAMURAI at RIBF ara also discussed.     

Morphological studies of a hydrogen-bonded LC polymer obtained by photopolymerization in LC solvents

Anisotropic morphologies and the phase behaviour of a hydrogen-bonded LC polymer obtained by photopolymerization in two kinds of LC solvent are discussed. The hydrogen-bonded LC monomer, 4-(6-acryloyloxyhexyloxy) benzoic acid (A6OBA), was photopolymerized in 4-cyano-4′-hexyloxybiphenyl (6OCB) and in 4-cyano-4′-undecyloxybiphenyl (11OCB), which show a nematic phase and a smectic A phase, respectively. After photo-polymerization, the LC media were removed by extraction and the pure polymer was observed by scanning electron microscopy. SEM images showed that the polymer possessed fibrous morphology with a fibre diameter of a few micrometers, based on polymerization-induced phase separation. The overall geometries reflected typical LC characteristics such as schlieren and focal-conic fan textures. It was found that the hydrogen bond between benzoic acid groups in the monomer was rigid enough to fix the anisotropic phase-separated structure forming during the early stage of phase separation; however, it could not permanently maintain the fibre structure due to dissociation at elevated temperature. X-ray measurements revealed that a well developed layer structure of the hydrogen-bonded mesogen existed in the polymer obtained from the smectic phase of 11OCB, whereas a polymer layer structure could develop only partially from the nematic phase of 6OCB.     

Growth of large La2−xSrxCuO4 single crystals using tilting-mirror-type infrared heating image furnace

Large single crystals of La_2−xSr_xCuO₄ (LSCO) high-T_c superconductors were grown by the infrared heating floating zone (IR-FZ) method using a tilting-mirror-type image furnace. The maximum diameter of the LSCO crystals increased to 10 mm in the tilting-mirror-type image furnace from 6 mm in the conventional image furnace. CuO rich feeds were required for the crystal growth using the tilting-mirror-type image furnace to compensate for the lack of CuO caused by the significant evaporation of CuO during the growth. The evaporation of CuO was affected by the tilting angle of the mirrors of the image furnace and by feed diameter. The optimized growth conditions were as follows: mirror tilting angle, 20°; feed diameter, 10 mm∅; and feed composition 50.7 mol% CuO.     

Numerical study of QCD phase diagram at high temperature and density by a histogram method

We study the QCD phase structure at high temperature and density adopting a histogram method. Because the quark determinant is complex at finite density, the Monte-Carlo method cannot be applied directly. We use a reweighting method and try to solve the problems which arise in the reweighting method, i.e. the sign problem and the overlap problem. We discuss the chemical potential dependence of the probability distribution function in the heavy quark mass region and examine the applicability of the approach in the light quark region.