Generation of a fusion protein containing the two functional coiled-coil domain of t- SNARE, SNAP-23 and a transmembrane domain for mast cell

SNAREs (Soluble N-Ethylmaleimide-Sensitive Fusion Protein Attachment Protein Receptor) are a class of membrane proteins that mediate membrane-membrane fusion in eukaryotic cells. SNAP-23 is a t-SNARE which is a component of cellular machinery is required for membrane fusion. SNAP-23 lacks transmembrane domain. Cysteines in the linker region of SNAP-23 are involved in targeting of SNAP-23 to the membrane. In the present work, a portion of MDR3 gene (MDR3 1-145) and CLP24 (CLP134-195) was subcloned into a plasmid encoding EGFP-SNAP-23 Cys- mutant for the generation of a fusion protein containing the two functional coiled-coil domain of t-SNARE, SNAP 23 and a transmembrane domain of MDR3 gene and CLP24 for mast cell. This fusion protein will be important to study the membrane targeting and raft association of the chimeric SNAP23 protein, which plays an important role in mast cell exocytosis in the mammalian system. A novel bioinformatics approach has been applied to identify the specific transmembrane domain. This novel approach can be used to construct other fusion proteins

OPTIMIZATION TO INCREASE ENERGY EFFICIENCY OF A SIROCCO CENTRIFUGAL FAN USING COMPUTATIONAL FLUID DYNAMICS (CFD)

This paper presents a numerical and experimental study on the aerodynamic performance of Sirocco centrifugal fans seeking an increase in energy efficiency. Numerical simulations are performed by the Finite-Volume Method commercial code ANSYS Fluent. Characteristics such as flow rate at the outlet, consumed power and sound pressure levels emitted by centrifugal fans with the original model of 16 blades and the optimized models of 16 and 14 blades are compared. Numerical calculations are performed by the continuity equation, the Reynolds Averaged Navier- Stokes (RANS) equations and the k-ω SST turbulence model. The quality of the mesh is evaluated for three different mesh densities. Results demonstrate that it was possible to obtain an increase of flow rate up to 22.7%, and reductions in the noise levels without increasing the consumption of the electric motor

Computational protein profile similarity screening for quantitative mass spectrometry experiments

Motivation: The qualitative and quantitative characterization of protein abundance profiles over a series of time points or a set of environmental conditions is becoming increasingly important. Using isobaric mass tagging experiments, mass spectrometry-based quantitative proteomics deliver accurate peptide abundance profiles for relative quantitation. Associated data analysis workflows need to provide tailored statistical treatment that (i) takes the correlation structure of the normalized peptide abundance profiles into account and (ii) allows inference of protein-level similarity. We introduce a suitable distance measure for relative abundance profiles, derive a statistical test for equality and propose a protein-level representation of peptide-level measurements. This yields a workflow that delivers a similarity ranking of protein abundance profiles with respect to a defined reference. All procedures have in common that they operate based on the true correlation structure that underlies the measurements. This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account. Results: We use protein profile similarity screening to identify candidate proteins whose abundances are post-transcriptionally controlled by the Anaphase Promoting Complex/Cyclosome (APC/C), a specific E3 ubiquitin ligase that is a master regulator of the cell cycle. Results are compared with an established protein correlation profiling method. The proposed procedure yields a 50.9-fold enrichment of co-regulated protein candidates and a 2.5-fold improvement over the previous method

Realtime calibration of the A4 electromagnetic lead fluoride calorimeter

Sufficient energy resolution is the key issue for the calorimetry in particle and nuclear physics. The calorimeter of the A4 parity violation experiment at MAMI is a segmented calorimeter where the energy of an event is determined by summing the signals of neighbouring channels. In this case the precise matching of the individual modules is crucial to obtain a good energy resolution. We have developped a calibration procedure for our total absorbing electromagnetic calorimeter which consists of 1022 lead fluoride (PbF_2) crystals. This procedure reconstructs the the single-module contributions to the events by solving a linear system of equations, involving the inversion of a 1022 x 1022-matrix. The system has shown its functionality at beam energies between 300 and 1500 MeV and represents a new and fast method to keep the calorimeter permanently in a well-calibrated state

Differential gene expression and co-regulated expression of genes in leukemia: an in-silico approach to identify potent biomarker

A biomarker can be measured, used to diagnose or classify disease, and measure progress as well as the therapeutic response of the disease. Early diagnosis and selection of appropriate treatment can be critical for the successful treatment of diseases. Identification and characterization of potent diagnostic biomarkers, and therapeutic targets rely heavily on traditional in vitro screens which require extensive resources and time. Integration of in silico screens prior to experimental validation can improve the efficiency and potency of biomarkers as well as reduce the cost and time of biomarker discovery. Considering the need, present work was undertaken to identify biomarkers for different classes of leukemia. Differential Gene Expression (DGE) analysis and co-regulated expression analysis were used for in silico identification and characterise a potent biomarker for leukemia. On the basis of in silico screening, the present study proposed seven protein-coding (CD38, TSC22D3, TNFRSF25, AGL, LARGE1, ARHGAP32, and PARM1) genes for the diagnosis of leukemia. The study also proposed a novel three-step lineage-specific model for the diagnosis of leukemia. In the three-step diagnosis model, the first group of biomarkers with an association of clinical and hematological parameters diagnose leukemia. The second group of biomarkers diagnoses acute and chronic form of leukemia. The third group of biomarkers identifies whether it belongs to myeloid lineage or lymphoid lineage

Evidence for Strange Quark Contributions to the Nucleon's Form Factors at Q2Q^2 = 0.108 (GeV/c)2^2

We report on a measurement of the parity violating asymmetry in the elastic scattering of polarized electrons off unpolarized protons with the A4 apparatus at MAMI in Mainz at a four momentum transfer value of $Q^2$ = \Qsquare (GeV/c)$^2$ and at a forward electron scattering angle of 30$^\circ < \theta_e < 40^\circ$. The measured asymmetry is $A_{LR}(\vec{e}p)$ = (\Aphys $\pm$ \Deltastat$_{stat}$ $\pm$ \Deltasyst$_{syst}$) $\times$ 10$^{-6}$. The expectation from the Standard Model assuming no strangeness contribution to the vector current is A$_0$ = (\Azero $\pm$ \DeltaAzero) $\times$ 10$^{-6}$. We have improved the statistical accuracy by a factor of 3 as compared to our previous measurements at a higher $Q^2$. We have extracted the strangeness contribution to the electromagnetic form factors from our data to be $G_E^s$ + \FakGMs $G_M^s$ = \GEsGMs $\pm$ \DeltaGEsGMs at $Q^2$ = \Qsquare (GeV/c)$^2$. As in our previous measurement at higher momentum transfer for $G_E^s$ + 0.230 $G_M^s$, we again find the value for $G_E^s$ + \FakGMs $G_M^s$ to be positive, this time at an improved significance level of 2 $\sigma$.Comment: 4 pages, 3 figure

Measurement of the Transverse Beam Spin Asymmetry in Elastic Electron Proton Scattering and the Inelastic Contribution to the Imaginary Part of the Two-Photon Exchange Amplitude

We report on a measurement of the asymmetry in the scattering of transversely polarized electrons off unpolarized protons, A$_\perp$, at two Q$^2$ values of \qsquaredaveragedlow (GeV/c)$^2$ and \qsquaredaveragedhighII (GeV/c)$^2$ and a scattering angle of $30^\circ < \theta_e < 40^\circ$. The measured transverse asymmetries are A$_{\perp}$(Q$^2$ = \qsquaredaveragedlow (GeV/c)$^2$) = (\experimentalasymmetry alulowcorr $\pm$ \statisticalerrorlow$_{\rm stat}$ $\pm$ \combinedsyspolerrorlowalucor$_{\rm sys}$) $\times$ 10$^{-6}$ and A$_{\perp}$(Q$^2$ = \qsquaredaveragedhighII (GeV/c)$^2$) = (\experimentalasymme tryaluhighcorr $\pm$ \statisticalerrorhigh$_{\rm stat}$ $\pm$ \combinedsyspolerrorhighalucor$_{\rm sys}$) $\times$ 10$^{-6}$. The first errors denotes the statistical error and the second the systematic uncertainties. A$_\perp$ arises from the imaginary part of the two-photon exchange amplitude and is zero in the one-photon exchange approximation. From comparison with theoretical estimates of A$_\perp$ we conclude that $\pi$N-intermediate states give a substantial contribution to the imaginary part of the two-photon amplitude. The contribution from the ground state proton to the imaginary part of the two-photon exchange can be neglected. There is no obvious reason why this should be different for the real part of the two-photon amplitude, which enters into the radiative corrections for the Rosenbluth separation measurements of the electric form factor of the proton.Comment: 4 figures, submitted to PRL on Oct.

Measurement of Strange Quark Contributions to the Nucleon's Form Factors at Q^2=0.230 (GeV/c)^2

We report on a measurement of the parity-violating asymmetry in the scattering of longitudinally polarized electrons on unpolarized protons at a $Q^2$ of 0.230 (GeV/c)^2 and a scattering angle of \theta_e = 30^o - 40^o. Using a large acceptance fast PbF_2 calorimeter with a solid angle of \Delta\Omega = 0.62 sr the A4 experiment is the first parity violation experiment to count individual scattering events. The measured asymmetry is A_{phys} =(-5.44 +- 0.54_{stat} +- 0.27_{\rm sys}) 10^{-6}. The Standard Model expectation assuming no strangeness contributions to the vector form factors is $A_0=(-6.30 +- 0.43) 10^{-6}$. The difference is a direct measurement of the strangeness contribution to the vector form factors of the proton. The extracted value is G^s_E + 0.225 G^s_M = 0.039 +- 0.034 or F^s_1 + 0.130 F^s_2 = 0.032 +- 0.028.Comment: 5 pages, 3 figures, submitted to Phys. Rev. Letters on Dec 11, 200

Capillary filling with wall corrugations] Capillary filling in microchannels with wall corrugations: A comparative study of the Concus-Finn criterion by continuum, kinetic and atomistic approaches

We study the impact of wall corrugations in microchannels on the process of capillary filling by means of three broadly used methods - Computational Fluid Dynamics (CFD), Lattice-Boltzmann Equations (LBE) and Molecular Dynamics (MD). The numerical results of these approaches are compared and tested against the Concus-Finn (CF) criterion, which predicts pinning of the contact line at rectangular ridges perpendicular to flow for contact angles theta > 45. While for theta = 30, theta = 40 (no flow) and theta = 60 (flow) all methods are found to produce data consistent with the CF criterion, at theta = 50 the numerical experiments provide different results. Whilst pinning of the liquid front is observed both in the LB and CFD simulations, MD simulations show that molecular fluctuations allow front propagation even above the critical value predicted by the deterministic CF criterion, thereby introducing a sensitivity to the obstacle heigth.Comment: 25 pages, 8 figures, Langmuir in pres