Serum proteomics of hepatitis C virus infection reveals retinol-binding protein 4 as a novel regulator

Persistent infection of hepatitis C virus (HCV) can lead to liver cirrhosis and hepatocellular carcinoma, which are currently diagnosed by invasive liver biopsy. Approximately 15-20% of cases of chronic liver diseases in India are caused by HCV infection. In North India, genotype 3 is predominant, whereas genotype 1 is predominant in southern parts of India. The aim of this study was to identify differentially regulated serum proteins in HCV-infected Indian patients (genotypes 1 and 3) using a two-dimensional electrophoresis approach. We identified eight differentially expressed proteins by MS. Expression levels of one of the highly upregulated proteins, retinol-binding protein 4 (RBP4), was validated by ELISA and Western blotting in two independent cohorts. We also confirmed our observation in the JFH1 infectious cell culture system. Interestingly, the HCV core protein enhanced RBP4 levels and partial knockdown of RBP4 had a positive impact on HCV replication, suggesting a possible role for this cellular protein in regulating HCV infection. Analysis of RBP4-interacting partners using a bioinformatic approach revealed novel insights into the possible involvement of RBP4 in HCV-induced pathogenesis. Taken together, this study provided information on the proteome profile of the HCV-infected Indian population, and revealed a link between HCV infection, RBP4 and insulin resistance.

Spectral intensity distribution of trapped

To calculate static response properties of a many-body system, local density approximation (LDA) can be safely applied. But, to obtain dynamical response functions, the applicability of LDA is limited bacause dynamics of the system needs to be considered as well. To examine this in the context of cold atoms, we consider a system of non-interacting spin4 fermions confined by a harmonic trapping potential. We have calculated a very important response function, the spectral intensity distribution function (SIDF), both exactly and using LDA at zero temperature and compared with each other for different dimensions, trap frequencies and momenta. The behaviour of the SIDF at a particular momentum can be explained by noting the behaviour of the density of states (DoS) of the free system (without trap) in that particular dimension. The agreement between exact and LDA SIDFs becomes better with increase in dimensions and number of particles.

Ischaemic concentrations of lactate increase TREK1 channel activity by interacting with a single histidine residue in the carboxy terminal domain

Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change. AbstractA rise in lactate concentration and the leak potassium channel TREK1 have been independently associated with cerebral ischaemia. Recent literature suggests lactate to be neuroprotective and TREK1 knockout mice show an increased sensitivity to brain and spinal cord ischaemia; however, the connecting link between the two is missing. Therefore we hypothesized that lactate might interact with TREK1 channels. In the present study, we show that lactate at ischaemic concentrations (15-30mm) at pH7.4 increases TREK1 current in CA1 stratum radiatum astrocytes and causes membrane hyperpolarization. We confirm the intracellular action of lactate on TREK1 in hippocampal slices using monocarboxylate transporter blockers and at single channel level in cell-free inside-out membrane patches. The intracellular effect of lactate on TREK1 is specific since other monocarboxylates such as pyruvate and acetate at pH7.4 failed to increase TREK1 current. Deletion and point mutation experiments suggest that lactate decreases the longer close dwell time incrementally with increase in lactate concentration by interacting with the histidine residue at position 328 (H328) in the carboxy terminal domain of the TREK1 channel. The interaction of lactate with H328 is dependent on the charge on the histidine residue since isosteric mutation of H328 to glutamine did not show an increase in TREK1 channel activity with lactate. This is the first demonstration of a direct effect of lactate on ion channel activity. The action of lactate on the TREK1 channel signifies a separate neuroprotective mechanism in ischaemia since it was found to be independent of the effect of acidic pH on channel activity. Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change.

Coded Illumination for Motion-blur Free Imaging of Cells on Cell-phone Based Imaging Flow Cytometer

Cell-phone based imaging flow cytometry can be realized by flowing cells through the microfluidic devices, and capturing their images with an optically enhanced camera of the cell-phone. Throughput in flow cytometers is usually enhanced by increasing the flow rate of cells. However, maximum frame rate of camera system limits the achievable flow rate. Beyond this, the images become highly blurred due to motion-smear. We propose to address this issue with coded illumination, which enables recovery of high-fidelity images of cells far beyond their motion-blur limit. This paper presents simulation results of deblurring the synthetically generated cell/bead images under such coded illumination.

Free energy landscape of a dense hard-sphere system

The topography of the free energy landscape in phase space of a dense hard-sphere system characterized by a discretized free energy functional of the Ramakishnan-Yussouff form is investigated numerically using a specially devised Monte Carlo procedure. We locate a considerable number of glassy local minima of the free energy and analyze the distributions of the free energy at a minimum and an appropriately defined phase-space "distance" between different minima. We find evidence for the existence of pairs of closely related glassy minima("two-level systems"). We also investigate the way the system makes transitions as it moves from the basin of attraction of a minimum to that of another one after a start under nonequilibrium conditions. This allows us to determine the effective height of free energy barriers that separate a glassy minimum from the others. The dependence of the height of free energy barriers on the density is investigated in detail. The general appearance of the free energy landscape resembles that of a putting green: relatively deep minima separated by a fairly flat structure. We discuss the connection of our results with the Vogel-Fulcher law and relate our observations to other work on the glass transition.

Free vibrations of a reservoir-foundation system

The natural frequencies of a reservoir-foundation system are calculated by treating the foundation as a system of linear springs with inertia. The reservoir is treated as consisting of compressible liquid, and the influence of waves at the free surface is included. It is shown that the natural frequencies decrease monotonically as the depth of foundation participating in the motion increases. The influence of waves at the reservoir surface is negligible for the cases normally occurring in practice. It is also shown that the wavelength of motion along the reservoir has no influence on the frequencies when the foundation depth is large compared to the reservoir depth.

System integration design in MEMS - A case study of micromachined load cell

One of the critical issues in large scale commercial exploitation of MEMS technology is its system integration. In MEMS, a system design approach requires integration of varied and disparate subsystems with one of a kind interface. The physical scales as well as the magnitude of signals of various subsystems vary widely. Known and proven integration techniques often lead to considerable loss in advantages the tiny MEMS sensors have to offer. Therefore, it becomes imperative to think of the entire system at the outset, at least in terms of the concept design. Such design entails various aspects of the system ranging from selection of material, transduction mechanism, structural configuration, interface electronics, and packaging. One way of handling this problem is the system-in-package approach that uses optimized technology for each function using the concurrent hybrid engineering approach. The main strength of this design approach is the fast time to prototype development. In the present work, we pursue this approach for a MEMS load cell to complete the process of system integration for high capacity load sensing. The system includes; a micromachined sensing gauge, interface electronics and a packaging module representing a system-in-package ready for end characterization. The various subsystems are presented in a modular stacked form using hybrid technologies. The micromachined sensing subsystem works on principles of piezo-resistive sensing and is fabricated using CMOS compatible processes. The structural configuration of the sensing layer is designed to reduce the offset, temperature drift, and residual stress effects of the piezo-resistive sensor. ANSYS simulations are carried out to study the effect of substrate coupling on sensor structure and its sensitivity. The load cell system has built-in electronics for signal conditioning, processing, and communication, taking into consideration the issues associated with resolution of minimum detectable signal. The packaged system represents a compact and low cost solution for high capacity load sensing in the category of compressive type load sensor.

Free-to-bound and bound exciton transitions at isoelectronic impurities: GaP(Zn,O)

We show, for sufficiently high temperatures and sufficiently weak majority-carrier binding energies, that the dominant radiative transition at an isoelectronic acceptor (donor) in p-type (n-type) material consists of the recombination of singly trapped minority carriers (bound by central-cell forces) with free majority carriers attracted by a Coulomb interaction. There are two reasons why the radiative recombination rate of the free-to-bound process is greater than the bound exciton process, which dominates at lower temperatures: (i) The population of free majority-carrier states greatly exceeds that of exciton states at higher temperatures, and (ii) the oscillator strength of the free-to-bound transition is greatly enhanced by the Coulomb attraction between the free carrier and the charged isoelectronic impurity. This enhancement is important for isoelectronic centers and is easily calculable from existing exciton models. We show that the free carrier attracted by a Coulomb interaction can be viewed as a continuum excited state of the bound exciton. When we apply the results of our calculations to the GaP(Zn, O) system, we find that the major part of the room-temperature luminescence from nearest-neighbor isoelectronic Zn-O complexes results from free-to-bound recombination and not exciton recombination as has been thought previously. Recent experiments on impulse excitation of luminescence in GaP(Zn, O) are reevaluated in the light of our calculations and are shown to be consistent with a strong free-to-bound transition. For deep isoelectronic centers with weakly bound majority carriers, we predict an overwhelming dominance of the free-to-bound process at 300°K.

Grid interfacing of a photovoltaic system using a chain cell converter

With the rapid development of photovoltaic system installations and increased number of grid connected power systems, it has become imperative to develop an efficient grid interfacing instrumentation suitable for photovoltaic systems ensuring maximum power transfer. The losses in the power converter play an important role in the overall efficiency of a PV system. Chain cell converter is considered to be efficient as compared to PWM converters due to lower switching losses, modularized circuit layout, reduced voltage rating of the converter switches, reduced EMI. The structure of separate dc sources in chain cell converter is well suited for photovoltaic systems as there will b several separate PV modules in the PV array which can act as an individual dc source. In this work, a single phase multilevel chain cell converter is used to interface the photovoltaic array to a single phase grid at a frequency of 50Hz. Control algorithms are developed for efficient interfacing of the PV system with grid and isolating the PV system from grid under faulty conditions. Digital signal processor TMS320F 2812 is used to implement the control algorithms developed and for the generation of other control signals.

Characterization of Alloy-Spinel-Corundum Equilibrium in the System Fe-Ni-Al-O

The three phase equilibrium between alloy, spinel solid solution and α-alumina in the Fe-Ni-Al-O system has been fully characterized at 1823K as a function of alloy composition using both experimental and computational methods. The oxygen potential was measured using a solid state cell incorporating yttria-doped thoria as the electrolyte and Cr+ Cr2O3 as the reference electrode. Oxygen concentration of the alloy was determined by an inert gas fusion technique. The composition of the spinel solid solution, formed at the interface between the alloy and an alumina crucible, was determined by EPMA. The variation of the oxygen concentration and potential and composition of the spinel solid solution with mole fraction of nickel in the alloy have been computed using activities in binary Fe-Ni system, free energies of formation of end member spinels FeO•(1+x)Al2O3 and NiO•(1+x)Al2O3 and free energies of solution of oxygen in liquid iron and nickel, available in the literature. Activities in the spinel solid solution were computed using a cation distribution model. The variation of the activity coefficient of oxygen with alloy composition in Fe-Ni-O system was calculated using both the quasichemical model of Jacob and Alcock and the Wagner's model, with the correlation of Chiang and Chang. The computed results for the oxygen potential and the composition of the spinel solid solution are in good agreement with the measurements. The measured oxygen concentration lies between the values computed using models of Wagner and Jacob and Alcock. The results of the study indicate that the deoxidation hyper-surface in multicomponent systems can be computed with useful accuracy using data for end member systems and thermodynamic models.

Glioblastoma-Specific Protein Interaction Network Identifies PP1A and CSK21 as Connecting Molecules between Cell Cycle-Associated Genes

Glioblastoma (GBM; grade IV astrocytoma) is a very aggressive form of brain cancer with a poor survival and few qualified predictive markers. This study integrates experimentally validated genes that showed specific upregulation in GBM along with their protein-protein interaction information. A system level analysis was used to construct GBM-specific network. Computation of topological parameters of networks showed scale-free pattern and hierarchical organization. From the large network involving 1,447 proteins, we synthesized subnetworks and annotated them with highly enriched biological processes. A careful dissection of the functional modules, important nodes, and their connections identified two novel intermediary molecules CSK21 and protein phosphatase 1 alpha (PP1A) connecting the two subnetworks CDC2-PTEN-TOP2A-CAV1-P53 and CDC2-CAV1-RB-P53-PTEN, respectively. Real-time quantitative reverse transcription-PCR analysis revealed CSK21 to be moderately upregulated and PP1A to be overexpressed by 20-fold in GBM tumor samples. Immunohistochemical staining revealed nuclear expression of PP1A only in GBM samples. Thus, CSK21 and PP1A, whose functions are intimately associated with cell cycle regulation, might play key role in gliomagenesis. Cancer Res; 70(16); 6437-47. (C)2010 AACR.

Activity–Composition Relations in the Nickel Oxide–Magnesium Oxide System at 1300 K by the Solid-State Galvanic Cell Technique

The activity of NiO in NiO-MgO rock salt solid solution has been measured at 1300 K by employing a solid-state galvanic cell: Pt,Ni+ NiO||(CaO)ZrO2||Ni + (Nix,Mgl-x)O, Pt. A high-density tube of Zr02-15 mol% CaO has been used as the solid electrolyte for the emf measurements. The activities of the component oxides in the rock salt solid solution exhibit negative deviation from ideality at the temperature of investigation. The solid solution obeys regular solution behavior at 1300 K. The value of the regular solution parameter is found to be -12000 ((l000) J mol-1. The composition dependence of ΔGEx obtained in this study agrees reasonably well with the calorimetric data reported in the literature for NiO-MgO solid solution.

Terminal solid solubilities at 900–1000°C in the magnesium oxide-zinc oxide system measured using a magnesium fluoride solid-electrolyte galvanic cell

The terminal solid solubilities of the periclase (MgO-rich) and zincite (ZnO-rich) solid solutions in the MgO---ZnO system have been determined by measuring the activity of MgO using a solid-state galvanic cell of the type 02(g), Pt/MgO, MgF2//MgF2//{χMgO+(1-χ)ZnO}(s, sln), MgF2/Pt, O2(g) in the temperature range 900–1050°C. The ZnO activity was calculated by graphical Gibbs-Duhem integration. The activity-composition plots of both components exhibit a strong positive deviation from ideality and are characterised by a miscibility gap. The terminal solid solubilities of the periclase and zincite solid solutions obtained from the activity-composition plots are found to be in reasonable agreement with those reported in the literature.

Phase relationships in the system Ni-W-O and thermodynamic properties of NiWO,

The phase diagram of the Ni-W-O system at 1200 K was established by metallographic and X-ray identification of the phases present after equilibration at controlled oxygen potentials. The oxygen partial pressures over the samples were fixed by metered streams of CO+CO2 gas mixtures. There was only one ternary oxide, nickel tungstate (NiWO4), in the Ni-W-O system at a total pressure of 1 atm, and this compound decomposed to a mixture of Ni+WO2.72 on lowering the oxygen potential. The Gibbs' free energy of formation of NiWO4 was determined from the measurement of the e.m.f. of the solid oxide galvanic cell, Pt, Ni+NiWO4+WO2.72/CaO-ZrO2/Ni+NiO, Pt and thermodynamic properties of tungsten and nickel oxides available in the literature. For the reaction, NiO(s)+WO3(s)rarrNiWO4(s) DeltaG°=–10500–0.708 T (±250) cal mol–1.