Identification of rat urinary glycoproteome captured by three lectins using gel and LC-based proteomics

Many different types of urine proteome studies have been done, but urine glycoprotein studies are insufficient. Therefore, we studied the glycoproteins from rat urine, which could be used to identify biomarkers in an animal model. First, urinary proteins were prepared by using the dialysis and lyophilizing methods from rat urine. Glycoproteins enriched with lectin affinity purification, concanavalin A, jacalin and wheat germ agglutinin from the urinary proteins were separated by means of reverse-phase fast protein LC (FPLC) or 1-D PAGE. Each FPLC fraction and 1-D PAGE gel band were trypsin-digested and analyzed by means of nanoLC-MS/MS. LC-MS/MS analyses were carried out by using linear ion trap MS. A total of 318 rat urinary glycoproteins were identified from the FPLC fractions and gel bands; approximately 90% of identified proteins were confirmed as glycoproteins in Swiss-Prot. Many glycoproteins, known as biomarkers, including C-reactive protein, uromodulin, amyloid beta A4 protein, alpha-1-inhibitor 3, vitamin D-binding protein, kallikrein 3 and fetuin-A were identified in this study. By studying urinary glycoproteins collected from rat, these results may help to assist in identifying urinary biomarkers regarding various types of disease models.     

Dendritic macromolecules for organic light-emitting diodes

The general concepts, design criteria, and physical parameters, such as component placement and electroluminescence, that relate to the construction of OLED devices are described, followed by a discussion of the current literature detailing the use of branched and dendritic materials as the key electroluminescent elements of single- and multi-layered fabricated devices. Their configurations, efficiencies, emission intensities, and molecular structural implications are also delineated and discussed. This critical review should appeal to researchers in the synthetic, material, and physical sciences (122 references).     

Expression of hepatitis C virus nonstructural 4B in transgenic mice

Hepatitis C virus (HCV) is a pathogen that is of great medical significance in chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma worldwide. Although the HCV proteins have been intensively investigated over the past decade, the biochemical functions of the NS4B protein are still largely unknown. To investigate NS4B as a potential causative agent of liver disease, transgenic mice expressing the NS4B protein in liver tissue were produced. The transgenic animals were phenotypically similar to their normal littermates for up to 18 months of age. Our results suggest that the HCV NS4B protein is not directly cytopathic or oncogenic in our transgenic mice model.     

Comparative study of pesticide multi-residue extraction in tobacco for gas chromatography-triple quadrupole mass spectrometry

Coacervates made of surfactant aggregates, namely aqueous and reverse micelles and vesicles, were firstly used as solvents in single-drop microextraction (SDME) and proposed for the extraction and concentration of chlorophenols prior to liquid chromatography. The formation of coacervate drops in the needle tip of conventional microsyringes depended on the type of intermolecular forces established between the surfactant headgroups making up the supramolecular aggregates; hydrogen bond interactions were strong enough to permit the formation of spherical drops. Stability of 1-50 microL coacervate drops was achieved by introducing the microsyringe needle tip in a PTFE rod, the end of which had been machined out with a heated flanging-tool to get circular flanges (diameters in the range 3.5-6 mm). The parameters affecting the efficiency of single-drop coacervative microextraction (SDCME) were investigated using vesicular coacervates as a solvent and 2-chlorophenol (CP), 2,4-dichlorophenol (DCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP) as model analytes. Coacervative microextraction dynamics fit to the general rate equation of liquid-liquid extraction. The effect of variables such as extraction time, drop volume, stirring rate, pH and temperature, on the extraction of chlorophenols was similar to that described for organic solvent drops. Electrolyte concentrations above 0.1 M caused drop instability. Under the optimum conditions, detection limits were in the range 0.1-0.3 microg L(-1). The relative standard deviation was between 4.3 and 5.6 at 20 microg L(-1) spiked level. The method was applied to the determination of the four chlorophenols in wastewater, superficial water from a reservoir and groundwater and the recoveries were in the range 79 and 106% at 5-20 microg L(-1) spiked level.     

Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport.     

Oxygen excess nonstoichiometry and thermodynamic quantities of La2NiO4?+?δ

The oxygen excess nonstoichiometry of La₂NiO_4 + δ is measured as a function of temperature and oxygen partial pressure (pO₂) by coulometric titration method. A positive deviation from the ideal dilution solution behavior is exhibited, and the partial molar thermodynamic quantities of La₂NiO_4 + δ are calculated from the Gibbs–Helmholtz equation for regular solution by introducing the activity coefficient of the charge carriers. The activity coefficient of holes is successfully calculated by using the Joyce–Dixon approximation of the Fermi–Dirac integral. The effective mass of holes ( m_\texth^* m_{\text{h}}^{{*}} ) is 1.27–1.29 times the rest mass (m _h), which indicate the action of band-like conduction and allow the effect of the small degree of polaron hopping to be ignored. The activity coefficient of holes calculated against the oxygen nonstoichiometry clearly illustrates the early positive deviation of the activity coefficient of holes from unit, leading to g_{\texth ^·} \gamma_{{{\text{h}}^{ \bullet }}}  ≈ 14 at δ ≈ 0.08, which is quite close to the literature value of g_{\texth ^·} \gamma_{{{\text{h}}^{ \bullet }}}  ≈ 10 at δ ≈ 0.08. All the evaluated thermodynamic quantities are in good agreement with the experimental literature values.     

Nucleation and growth mechanism of Pd/Pt bimetallic clusters in sodium bis(2-ethylhexyl)sulfosuccinate (AOT) reverse micelles as studied by in situ X-ray absorption spectroscopy

We report in situ X-ray absorption spectroscopy (XAS) investigations on the formation of palladium-platinum (Pd/Pt) bimetallic clusters at the early stage within the water-in-oil microemulsion system of water/AOT/n-heptane. The reduction of palladium and platinum ions and the formation of corresponding clusters are monitored as a function of dosage of reducing agent, hydrazine (N(2)H(5)OH). Upon successive addition of the reducing agent, hydrazine (N(2)H(5)OH), five distinguishable steps are observed in the formation process of Pd/Pt clusters at the early stage. Both in situ X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analysis for both the Pd K-edge and Pt L(III)-edge revealed the formation of Pd/Pt bimetallic clusters. A corresponding structural model is proposed for each step to provide a detailed insight into the nucleation and growth mechanism of Pd/Pt bimetallic clusters. We also discussed the atomic distribution of Pd and Pt atoms in Pd/Pt bimetallic clusters based on the calculated XAS structural parameters.     

Construction of triangular metallomacrocycles: [M3(1,2-bis(2,2':6',2''-terpyridin-4-yl-ethynyl)benzene)3][M = Ru(II), Fe(II), 2Ru(II)Fe(II)

Complexation of a predesigned (1,2-bis(2,2':6',2'-terpyridin-4-yl-ethynyl)benzene) ligand possessing a 60 degrees angle between two terpyridines with transition metals [Fe(II) and Ru(II)] afforded the self-assembled, triangular metallomacrocycles.     

Measuring Submicron-Sized Fractionated Particulate Matter on Aluminum Impactor Disks

Sub-micron sized airborne particulate matter (PM) is not collected well on regular quartz or glass fiber filter papers. We used a micro-orifice uniform deposit impactor (MOUDI) to fractionate PM into six size fractions and deposit it on specially designed high purity thin aluminum disks. The MOUDI separated PM into fractions 56-100 nm, 100-180 nm, 180-320 nm, 320-560 nm, 560-1000 nm, and 1000-1800 nm. Since the MOUDI has a low flow rate (30 L/min), it takes several days to collect sufficient carbon on 47 mm foil disks. The small carbon mass (20-200 microgram C) and large aluminum substrate (~25 mg Al) present several challenges to production of graphite targets for accelerator mass spectrometry (AMS) analysis. The Al foil consumes large amounts of oxygen as it is heated and tends to melt into quartz combustion tubes, causing gas leaks. We describe sample processing techniques to reliably produce graphitic targets for (14)C-AMS analysis of PM deposited on Al impact foils.     

Inhibition of phospholipase D2 induces autophagy in colorectal cancer cells

Autophagy is a conserved lysosomal self-digestion process used for the breakdown of long-lived proteins and damaged organelles, and it is associated with a number of pathological processes, including cancer. Phospholipase D (PLD) isozymes are dysregulated in various cancers. Recently, we reported that PLD1 is a new regulator of autophagy and is a potential target for cancer therapy. Here, we investigated whether PLD2 is involved in the regulation of autophagy. A PLD2-specific inhibitor and siRNA directed against PLD2 were used to treat HT29 and HCT116 colorectal cancer cells, and both inhibition and genetic knockdown of PLD2 in these cells significantly induced autophagy, as demonstrated by the visualization of light chain 3 (LC3) puncta and autophagic vacuoles as well as by determining the LC3-II protein level. Furthermore, PLD2 inhibition promoted autophagic flux via the canonical Atg5-, Atg7- and AMPK-Ulk1-mediated pathways. Taken together, these results suggest that PLD2 might have a role in autophagy and that its inhibition might provide a new therapeutic basis for targeting autophagy.