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Sample records for accelerating protein gap

  1. Phospholipases as GTPase activity accelerating proteins (GAPs) in plants.

    PubMed

    Pandey, Sona

    2016-05-01

    GTPase activity accelerating proteins (GAPs) are key regulators of the G-protein signaling cycle. By facilitating effective hydrolysis of the GTP bound on Gα proteins, GAPs control the timing and amplitude of the signaling cycle and ascertain the availability of the inactive heterotrimer for the next round of activation. Until very recently, the studies of GAPs in plants were focused exclusively on the regulator of G-protein signaling (RGS) protein. We now show that phospholipase Dα1 (PLDα1) is also a bona fide GAP in plants and together with the RGS protein controls the level of active Gα protein. PMID:27124090

  2. Stacked insulator induction accelerator gaps

    SciTech Connect

    Houck, T.I.; Westenskow, G.A.; Kim, J.S.; Eylon, S.; Henestroza, E.; Yu, S.S.; Vanecek, D.

    1997-05-01

    Stacked insulators, with alternating layers of insulating material and conducting film, have been shown to support high surface electrical field stresses. We have investigated the application of the stacked insulator technology to the design of induction accelerator modules for the Relativistic-Klystron Two-Beam Accelerator program. The rf properties of the accelerating gaps using stacked insulators, particularly the impedance at frequencies above the beam pipe cutoff frequency, are investigated. Low impedance is critical for Relativistic-Klystron Two-Beam Accelerator applications where a high current, bunched beam is trsnsported through many accelerating gaps. An induction accelerator module designs using a stacked insulator is presented.

  3. Virtual gap dielectric wall accelerator

    SciTech Connect

    Caporaso, George James; Chen, Yu-Jiuan; Nelson, Scott; Sullivan, Jim; Hawkins, Steven A

    2013-11-05

    A virtual, moving accelerating gap is formed along an insulating tube in a dielectric wall accelerator (DWA) by locally controlling the conductivity of the tube. Localized voltage concentration is thus achieved by sequential activation of a variable resistive tube or stalk down the axis of an inductive voltage adder, producing a "virtual" traveling wave along the tube. The tube conductivity can be controlled at a desired location, which can be moved at a desired rate, by light illumination, or by photoconductive switches, or by other means. As a result, an impressed voltage along the tube appears predominantly over a local region, the virtual gap. By making the length of the tube large in comparison to the virtual gap length, the effective gain of the accelerator can be made very large.

  4. Particle acceleration in the vacuum gaps in black hole magnetospheres

    NASA Astrophysics Data System (ADS)

    Ptitsyna, K.; Neronov, A.

    2016-08-01

    Aims: We consider particle acceleration in the vacuum gaps in magnetospheres of black holes powered by the Blandford-Znajek mechanism and embedded in the radiatively-inefficient accretion flow (RIAF) environment. In this situation, the gap height is limited by the onset of gamma-gamma pair production on the infrared photons originating in the RIAF. Methods: We numerically calculated the acceleration and propagation of charged particles by taking the detailed structure of the electric and magnetic fields in the gap and in the entire black hole magnetosphere into account, as well as the radiative energy losses and interactions of γ-rays produced by the propagated charged particles with the background radiation field of the RIAF. Results: We show that the presence of the vacuum gap has clear observational signatures. The spectra of emission from gaps embedded in a relatively high-luminosity RIAF are dominated by the inverse Compton emission with a sharp, super-exponential cut-off in the very-high-energy gamma-ray band. The cut-off energy is determined by the properties of the RIAF and is largely independent of the structure of magnetosphere and geometry of the gap. The spectra of the gap residing in low-luminosity RIAFs are dominated by synchrotron or curvature emission with the spectra extending into 1-100 GeV energy range. We also consider the effect of possible acceleration of protons in the gap and find that proton energies could reach the ultra-high-energy cosmic ray (UHECR) range only in extremely low-luminosity RIAFs.

  5. Photonic Band Gap structures: A new approach to accelerator cavities

    SciTech Connect

    Kroll, N. |; Smith, D.R.; Schultz, S.

    1992-12-31

    We introduce a new accelerator cavity design based on Photonic Band Gap (PGB) structures. The PGB cavity consists of a two-dimensional periodic array of high dielectric, low loss cylinders with a single removal defect, bounded on top and bottom by conducting sheets. We present the results of both numerical simulations and experimental measurements on the PGB cavity.

  6. Photonic Band Gap resonators for high energy accelerators

    SciTech Connect

    Schultz, S.; Smith, D.R.; Kroll, N. |

    1993-12-31

    We have proposed that a new type of microwave resonator, based on Photonic Band Gap (PBG) structures, may be particularly useful for high energy accelerators. We provide an explanation of the PBG concept and present data which illustrate some of the special properties associated with such structures. Further evaluation of the utility of PBG resonators requires laboratory testing of model structures at cryogenic temperatures, and at high fields. We provide a brief discussion of our test program, which is currently in progress.

  7. Recent progress on photonic band gap accelerator cavities

    SciTech Connect

    Smith, D.R.; Li, D.; Vier, D.C.

    1997-02-01

    We report on the current status of our program to apply Photonic Band Gap (PBG) concepts to produce novel high-energy, high-intensity accelerator cavities. The PBG design on which we have concentrated our initial efforts consists of a square array of metal cylinders, terminated by conducting or superconducting sheets, and surrounded by microwave absorber on the periphery of the structure. A removed cylinder from the center of the array constitutes a site defect where a localized electromagnetic mode can occur. In previous work, we have proposed that this structure could be utilized as an accelerator cavity, with advantageous properties over conventional cavity designs. In the present work, we present further studies, including MAFIA-based numerical calculations and experimental measurements, demonstrating the feasibility of using the proposed structure in a real accelerator application.

  8. TBC-Domain GAPs for Rab GTPases Accelerate GTP Hydrolysis by a Dual-Finger Mechanism

    SciTech Connect

    Pan,X.; Eathiraj, S.; Lambright, D.

    2006-01-01

    Rab GTPases regulate membrane trafficking by cycling between inactive (GDP-bound) and active (GTP-bound) conformations. The duration of the active state is limited by GTPase-activating proteins (GAPs), which accelerate the slow intrinsic rate of GTP hydrolysis. Proteins containing TBC (Tre-2, Bub2 and Cdc16) domains are broadly conserved in eukaryotic organisms and function as GAPs for Rab GTPases as well as GTPases that control cytokinesis. An exposed arginine residue is a critical determinant of GAP activity in vitro and in vivo. It has been expected that the catalytic mechanism of TBC domains would parallel that of Ras and Rho family GAPs. Here we report crystallographic, mutational and functional analyses of complexes between Rab GTPases and the TBC domain of Gyp1p. In the crystal structure of a TBC-domain-Rab-GTPase-aluminium fluoride complex, which approximates the transition-state intermediate for GTP hydrolysis, the TBC domain supplies two catalytic residues in trans, an arginine finger analogous to Ras/Rho family GAPs and a glutamine finger that substitutes for the glutamine in the DxxGQ motif of the GTPase. The glutamine from the Rab GTPase does not stabilize the transition state as expected but instead interacts with the TBC domain. Strong conservation of both catalytic fingers indicates that most TBC-domain GAPs may accelerate GTP hydrolysis by a similar dual-finger mechanism.

  9. Hollow-Core Photonic Band Gap Fibers for Particle Acceleration

    SciTech Connect

    Noble, Robert J.; Spencer, James E.; Kuhlmey, Boris T.; /Sydney U.

    2011-08-19

    Photonic band gap (PBG) dielectric fibers with hollow cores are being studied both theoretically and experimentally for use as laser driven accelerator structures. The hollow core functions as both a longitudinal waveguide for the transverse-magnetic (TM) accelerating fields and a channel for the charged particles. The dielectric surrounding the core is permeated by a periodic array of smaller holes to confine the mode, forming a photonic crystal fiber in which modes exist in frequency pass-bands, separated by band gaps. The hollow core acts as a defect which breaks the crystal symmetry, and so-called defect, or trapped modes having frequencies in the band gap will only propagate near the defect. We describe the design of 2-D hollow-core PBG fibers to support TM defect modes with high longitudinal fields and high characteristic impedance. Using as-built dimensions of industrially-made fibers, we perform a simulation analysis of the first prototype PBG fibers specifically designed to support speed-of-light TM modes.

  10. Phosphorylation of Serine 402 Regulates RacGAP Protein Activity of FilGAP Protein.

    PubMed

    Morishita, Yuji; Tsutsumi, Koji; Ohta, Yasutaka

    2015-10-23

    FilGAP is a Rho GTPase-activating protein (GAP) that specifically regulates Rac. FilGAP is phosphorylated by ROCK, and this phosphorylation stimulates its RacGAP activity. However, it is unclear how phosphorylation regulates cellular functions and localization of FilGAP. We found that non-phosphorylatable FilGAP (ST/A) mutant is predominantly localized to the cytoskeleton along actin filaments and partially co-localized with vinculin around cell periphery, whereas phosphomimetic FilGAP (ST/D) mutant is diffusely cytoplasmic. Moreover, phosphorylated FilGAP detected by Phos-tag is also mainly localized in the cytoplasm. Of the six potential phosphorylation sites in FilGAP tested, only mutation of serine 402 to alanine (S402A) resulted in decreased cell spreading on fibronectin. FilGAP phosphorylated at Ser-402 is localized to the cytoplasm but not at the cytoskeleton. Although Ser-402 is highly phosphorylated in serum-starved quiescent cells, dephosphorylation of Ser-402 is accompanied with the cell spreading on fibronectin. Treatment of the cells expressing wild-type FilGAP with calyculin A, a Ser/Thr phosphatase inhibitor, suppressed cell spreading on fibronectin, whereas cells transfected with FilGAP S402A mutant were not affected by calyculin A. Expression of constitutively activate Arf6 Q67L mutant stimulated membrane blebbing activity of both non-phosphorylatable (ST/A) and phosphomimetic (ST/D) FilGAP mutants. Conversely, depletion of endogenous Arf6 suppressed membrane blebbing induced by FilGAP (ST/A) and (ST/D) mutants. Our study suggests that Arf6 and phosphorylation of FilGAP may regulate FilGAP, and phosphorylation of Ser-402 may play a role in the regulation of cell spreading on fibronectin. PMID:26359494

  11. Wake-field studies on photonic band gap accelerator cavities

    NASA Astrophysics Data System (ADS)

    Li, Derun; Kroll, N.; Smith, D. R.; Schultz, S.

    1997-03-01

    We have studied the wake-field of several metal Photonic Band Gap (PBG) cavities which consist of either a square or a hexagonal array of metal cylinders, bounded on top and bottom by conducting or superconducting sheets, surrounded by placing microwave absorber at the periphery or by replacing outer rows of metal cylinders with lossy dielectric ones, or by metallic walls. A removed cylinder from the center of the array constitutes a site defect where a localized electromagnetic mode can occur. While both monopole and dipole wake-fields have been studied, we confine our attention here mainly to the dipole case. The dipole wake-field is produced by modes in the propagation bands which tend to fill the entire cavity more or less uniformly and are thus easy to damp selectively. MAFIA time domain simulation of the transverse wake-field has been compared with that of a cylindrical pill-box comparison cavity. Even without damping the wake-field of the metal PBG cavity is substantially smaller than that of the pill-box cavity and may be further reduced by increasing the size of the lattice. By introducing lossy material at the periphery we have been able to produce Q factors for the dipole modes in the 40 to 120 range without significantly degrading the accelerating mode.

  12. Noncanonical Myo9b-RhoGAP Accelerates RhoA GTP Hydrolysis by a Dual-Arginine-Finger Mechanism.

    PubMed

    Yi, Fengshuang; Kong, Ruirui; Ren, Jinqi; Zhu, Li; Lou, Jizhong; Wu, Jane Y; Feng, Wei

    2016-07-31

    The GTP hydrolysis activities of Rho GTPases are stimulated by GTPase-activating proteins (GAPs), which contain a RhoGAP domain equipped with a characteristic arginine finger and an auxiliary asparagine for catalysis. However, the auxiliary asparagine is missing in the RhoGAP domain of Myo9b (Myo9b-RhoGAP), a unique motorized RhoGAP that specifically targets RhoA for controlling cell motility. Here, we determined the structure of Myo9b-RhoGAP in complex with GDP-bound RhoA and magnesium fluoride. Unexpectedly, Myo9b-RhoGAP contains two arginine fingers at its catalytic site. The first arginine finger resembles the one within the canonical RhoGAP domains and inserts into the nucleotide-binding pocket of RhoA, whereas the second arginine finger anchors the Switch I loop of RhoA and interacts with the nucleotide, stabilizing the transition state of GTP hydrolysis and compensating for the lack of the asparagine. Mutating either of the two arginine fingers impaired the catalytic activity of Myo9b-RhoGAP and affected the Myo9b-mediated cell migration. Our data indicate that Myo9b-RhoGAP accelerates RhoA GTP hydrolysis by a previously unknown dual-arginine-finger mechanism, which may be shared by other noncanonical RhoGAP domains lacking the auxiliary asparagine. PMID:27363609

  13. Experimental Work With Photonic Band Gap Fiber: Building A Laser Electron Accelerator

    SciTech Connect

    Lincoln, Melissa; Ischebeck, Rasmus; Nobel, Robert; Siemann, Robert; /SLAC

    2006-09-29

    In the laser acceleration project E-163 at the Stanford Linear Accelerator Center, work is being done toward building a traveling wave accelerator that uses as its accelerating structure a length of photonic band gap fiber. The small scale of the optical fiber allows radiation at optical wavelengths to be used to provide the necessary accelerating energy. Optical wavelength driving energy in a small structure yields higher accelerating fields. The existence of a speed-of-light accelerating mode in a photonic band gap fiber has been calculated previously [1]. This paper presents an overview of several of the experimental challenges posed in the development of the proposed photonic band gap fiber accelerator system.

  14. Longitudinal impedance measurement of an RK-TBA induction accelerating gap

    SciTech Connect

    Eylon, S.; Henestroza, E.; Kim, J.-S.; Houck, T.L.; Westenskow, G.A.; Yu, S.S.

    1997-05-01

    Induction accelerating gap designs are being studied for Relativistic Klystron Two-Beam Accelerator (RK-TBA) applications. The accelerating gap has to satisfy the following major requirements: hold-off of the applied accelerating voltage pulse, low transverse impedance to limit beam breakup, low longitudinal impedance at the beam-modulation frequency to minimize power loss. Various gap geometries, materials and novel insulating techniques were explored to optimize the gap design. We report on the experimental effort to evaluate the rf properties of the accelerating gaps in a simple pillbox cavity structure. The experimental cavity setup was designed using the AMOS, MAFIA and URMEL numerical codes. Longitudinal impedance measurements above beam-tube cut-off frequency using a single-wire measuring system are presented.

  15. Accelerated Plan for Closing the Gaps by 2015

    ERIC Educational Resources Information Center

    Texas Higher Education Coordinating Board, 2010

    2010-01-01

    Texas launched its ambitious strategic plan for higher education, "Closing the Gaps by 2015," in the year 2000 to create a statewide vision for closing the higher education gaps within Texas and between Texas and other leading states. The plan focuses on bringing Texas to national parity in four critical areas of higher education: participation,…

  16. Mercury BLASTP: Accelerating Protein Sequence Alignment.

    PubMed

    Jacob, Arpith; Lancaster, Joseph; Buhler, Jeremy; Harris, Brandon; Chamberlain, Roger D

    2008-06-01

    Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we describe the architecture of the portions of the application that are accelerated in the FPGA, and we also describe the integration of these FPGA-accelerated portions with the existing BLASTP software. We have implemented Mercury BLASTP on a commodity workstation with two Xilinx Virtex-II 6000 FPGAs. We show that the new design runs 11-15 times faster than software BLASTP on a modern CPU while delivering close to 99% identical results. PMID:19492068

  17. Mercury BLASTP: Accelerating Protein Sequence Alignment

    PubMed Central

    Jacob, Arpith; Lancaster, Joseph; Buhler, Jeremy; Harris, Brandon; Chamberlain, Roger D.

    2008-01-01

    Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we describe the architecture of the portions of the application that are accelerated in the FPGA, and we also describe the integration of these FPGA-accelerated portions with the existing BLASTP software. We have implemented Mercury BLASTP on a commodity workstation with two Xilinx Virtex-II 6000 FPGAs. We show that the new design runs 11-15 times faster than software BLASTP on a modern CPU while delivering close to 99% identical results. PMID:19492068

  18. Regulators of G-protein signaling accelerate GPCR signaling kinetics and govern sensitivity solely by accelerating GTPase activity.

    PubMed

    Lambert, Nevin A; Johnston, Christopher A; Cappell, Steven D; Kuravi, Sudhakiranmayi; Kimple, Adam J; Willard, Francis S; Siderovski, David P

    2010-04-13

    G-protein heterotrimers, composed of a guanine nucleotide-binding G alpha subunit and an obligate G betagamma dimer, regulate signal transduction pathways by cycling between GDP- and GTP-bound states. Signal deactivation is achieved by G alpha-mediated GTP hydrolysis (GTPase activity) which is enhanced by the GTPase-accelerating protein (GAP) activity of "regulator of G-protein signaling" (RGS) proteins. In a cellular context, RGS proteins have also been shown to speed up the onset of signaling, and to accelerate deactivation without changing amplitude or sensitivity of the signal. This latter paradoxical activity has been variably attributed to GAP/enzymatic or non-GAP/scaffolding functions of these proteins. Here, we validated and exploited a G alpha switch-region point mutation, known to engender increased GTPase activity, to mimic in cis the GAP function of RGS proteins. While the transition-state, GDP x AlF(4)(-)-bound conformation of the G202A mutant was found to be nearly identical to wild-type, G alpha(i1)(G202A) x GDP assumed a divergent conformation more closely resembling the GDP x AlF(4)(-)-bound state. When placed within Saccharomyces cerevisiae G alpha subunit Gpa1, the fast-hydrolysis mutation restored appropriate dose-response behaviors to pheromone signaling in the absence of RGS-mediated GAP activity. A bioluminescence resonance energy transfer (BRET) readout of heterotrimer activation with high temporal resolution revealed that fast intrinsic GTPase activity could recapitulate in cis the kinetic sharpening (increased onset and deactivation rates) and blunting of sensitivity also engendered by RGS protein action in trans. Thus G alpha-directed GAP activity, the first biochemical function ascribed to RGS proteins, is sufficient to explain the activation kinetics and agonist sensitivity observed from G-protein-coupled receptor (GPCR) signaling in a cellular context. PMID:20351284

  19. Observation of Wakefield Suppression in a Photonic-Band-Gap Accelerator Structure

    DOE PAGESBeta

    Simakov, Evgenya I.; Arsenyev, Sergey A.; Buechler, Cynthia E.; Edwards, Randall L.; Romero, William P.; Conde, Manoel; Ha, Gwanghui; Power, John G.; Wisniewski, Eric E.; Jing, Chunguang

    2016-02-10

    We report experimental observation of higher order mode (HOM) wakefield suppression in a room-temperature traveling-wave photonic band gap (PBG) accelerating structure at 11.700 GHz. It has been long recognized that PBG structures have potential for reducing long-range wakefields in accelerators. The first ever demonstration of acceleration in a room-temperature PBG structure was conducted in 2005. Since then, the importance of PBG accelerator research has been recognized by many institutions. However, the full experimental characterization of the wakefield spectrum and demonstration of wakefield suppression when the accelerating structure is excited by an electron beam has not been performed to date. Wemore » conducted an experiment at the Argonne Wakefield Accelerator (AWA) test facility and observed wakefields excited by a single high charge electron bunch when it passes through a PBG accelerator structure. Lastly, excellent HOM suppression properties of the PBG accelerator were demonstrated in the beam test.« less

  20. Observation of Wakefield Suppression in a Photonic-Band-Gap Accelerator Structure.

    PubMed

    Simakov, Evgenya I; Arsenyev, Sergey A; Buechler, Cynthia E; Edwards, Randall L; Romero, William P; Conde, Manoel; Ha, Gwanghui; Power, John G; Wisniewski, Eric E; Jing, Chunguang

    2016-02-12

    We report experimental observation of higher order mode (HOM) wakefield suppression in a room-temperature traveling-wave photonic-band-gap (PBG) accelerating structure at 11.700 GHz. It has been long recognized that PBG structures have the potential for reducing long-range wakefields in accelerators. The first ever demonstration of acceleration in a room-temperature PBG structure was conducted in 2005. Since then, the importance of PBG accelerator research has been recognized by many institutions. However, the full experimental characterization of the wakefield spectrum and demonstration of wakefield suppression when the accelerating structure is excited by an electron beam has not been performed to date. We conducted an experiment at the Argonne Wakefield Accelerator test facility and observed wakefields excited by a single high charge electron bunch when it passes through a PBG accelerator structure. Excellent HOM suppression properties of the PBG accelerator were demonstrated in the beam test. PMID:26918995

  1. Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover

    PubMed Central

    Farkas, Zoltán; Horvath, Peter; Bódi, Zoltán; Daraba, Andreea; Szamecz, Béla; Gut, Ivo; Bayes, Mónica; Santos, Manuel A. S.; Pál, Csaba

    2015-01-01

    Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome–mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that

  2. Extended Acceleration in Slot Gaps and Pulsar High-Energy Emission

    NASA Technical Reports Server (NTRS)

    White, Nicholas E. (Technical Monitor); Muslimov, Alex G.; Harding, Alice K.

    2003-01-01

    We revise the physics of primary electron acceleration in the "slot gap" (SG) above the pulsar polar caps (PCs), a regime originally proposed by Arons and Scharlemann (1979) in their electrodynamic model of pulsar PCs. We employ the standard definition of the SG as a pair-free space between the last open field lines and the boundary of the pair plasma column which is expected to develop above the bulk of the PC. The rationale for our revision is that the proper treatment of primary acceleration within the pulsar SGs should take into account the effect of the narrow geometry of the gap on the electrodynamics within the gap and also to include the effect of inertial frame dragging on the particle acceleration. We show that the accelerating electric field within the gap, being significantly boosted by the effect of frame dragging, becomes reduced because of the gap geometry by a factor proportional to the square of the SG width. The combination of the effects of frame dragging and geometrical screening in the gap region naturally gives rise to a regime of extended acceleration, that is not limited to favorably curved field lines as in earlier models, and the possibility of multiple-pair production by curvature photons at very high altitudes, up to several stellar radii. We present our estimates of the characteristic SG thickness across the PC, energetics of primaries accelerated within the gap, high-energy bolometric luminosities emitted from the high altitudes in the gaps, and maximum heating luminosities produced by positrons returning from the elevated pair fronts. The estimated theoretical high-energy luminosities are in good agreement with the corresponding empirical relationships for gamma-ray pulsars. We illustrate the results of our modeling of the pair cascades and gamma-ray emission from the high altitudes in the SG for the Crab pulsar. The combination of the frame-dragging field and high-altitude SG emission enables both acceleration at the smaller

  3. Correlation of pulsar radio emission spectrum with peculiarities of particle acceleration in a polar gap

    SciTech Connect

    Kontorovich, V. M. Flanchik, A. B.

    2013-01-15

    The analytical expression for the frequency of radio emission intensity maximum in pulsars with free electron emission from the stellar surface has been found. Peculiarities of the electron acceleration in a polar gap are considered. The correlation between the high-frequency cutoff and low-frequency turnover in the radio emission spectrum of pulsars known from observations has been explained.

  4. Observation of wakefields in a beam-driven photonic band gap accelerating structure.

    SciTech Connect

    Conde, M.; Yusof, Z.; Power, J. G.; Jing, C.; Gao, F.; Antipov, S.; Xu, P.; Zheng, S.; Chen, H.; Tang, C.; Gai, W.; High Energy Physics; Euclid Techlabs LLC; Tsinghua Univ.

    2009-12-01

    Wakefield excitation has been experimentally studied in a three-cell X-band standing wave photonic band gap (PBG) accelerating structure. Major monopole (TM{sub 01}- and TM{sub 02}-like) and dipole (TM{sub 11}- and TM{sub 12}-like) modes were identified and characterized by precisely controlling the position of beam injection. The quality factor Q of the dipole modes was measured to be {approx}10 times smaller than that of the accelerating mode. A charge sweep, up to 80 nC, has been performed, equivalent to {approx} 30 MV/m accelerating field on axis. A variable delay low charge witness bunch following a high charge drive bunch was used to calibrate the gradient in the PBG structure by measuring its maximum energy gain and loss. Experimental results agree well with numerical simulations.

  5. Differences between liver gap junction protein and lens MIP 26 from rat: implications for tissue specificity of gap junctions.

    PubMed

    Nicholson, B J; Takemoto, L J; Hunkapiller, M W; Hood, L E; Revel, J P

    1983-03-01

    Liver gap junctions and gap-junction-like structures from eye lenses are each comprised of a single major protein (Mr 28,000 and 26,000, respectively). These proteins display different two-dimensional peptide fingerprints, distinct amino acid compositions, nonhomologous N-terminal amino acid sequences and different sensitivities to proteases when part of the intact junction. However, the junctional protein of each tissue is well conserved between species, as demonstrated previously for lens and now for liver in several mammalian species. The possiblity of tissue-specific gap junction proteins is discussed in the light of data suggesting that rat heart gap junctions are comprised of yet a third protein. PMID:6299583

  6. Human Articular Chondrocytes Express Multiple Gap Junction Proteins

    PubMed Central

    Mayan, Maria D.; Carpintero-Fernandez, Paula; Gago-Fuentes, Raquel; Martinez-de-Ilarduya, Oskar; Wang, Hong-Zhang; Valiunas, Virginijus; Brink, Peter; Blanco, Francisco J.

    2014-01-01

    Osteoarthritis (OA) is the most common joint disease and involves progressive degeneration of articular cartilage. The aim of this study was to investigate if chondrocytes from human articular cartilage express gap junction proteins called connexins (Cxs). We show that human chondrocytes in tissue express Cx43, Cx45, Cx32, and Cx46. We also find that primary chondrocytes from adults retain the capacity to form functional voltage-dependent gap junctions. Immunohistochemistry experiments in cartilage from OA patients revealed significantly elevated levels of Cx43 and Cx45 in the superficial zone and down through the next approximately 1000 μm of tissue. These zones corresponded with regions damaged in OA that also had high levels of proliferative cell nuclear antigen. An increased number of Cxs may help explain the increased proliferation of cells in clusters that finally lead to tissue homeostasis loss. Conversely, high levels of Cxs in OA cartilage reflect the increased number of adjacent cells in clusters that are able to interact directly by gap junctions as compared with hemichannels on single cells in normal cartilage. Our data provide strong evidence that OA patients have a loss of the usual ordered distribution of Cxs in the damaged zones and that the reductions in Cx43 levels are accompanied by the loss of correct Cx localization in the nondamaged areas. PMID:23416160

  7. Nerve ending "signal" proteins GAP-43, MARCKS, and BASP1.

    PubMed

    Mosevitsky, Mark I

    2005-01-01

    Mechanisms of growth cone pathfinding in the course of neuronal net formation as well as mechanisms of learning and memory have been under intense investigation for the past 20 years, but many aspects of these phenomena remain unresolved and even mysterious. "Signal" proteins accumulated mainly in the axon endings (growth cones and the presynaptic area of synapses) participate in the main brain processes. These proteins are similar in several essential structural and functional properties. The most prominent similarities are N-terminal fatty acylation and the presence of an "effector domain" (ED) that dynamically binds to the plasma membrane, to calmodulin, and to actin fibrils. Reversible phosphorylation of ED by protein kinase C modulates these interactions. However, together with similarities, there are significant differences among the proteins, such as different conditions (Ca2+ contents) for calmodulin binding and different modes of interaction with the actin cytoskeleton. In light of these facts, we consider GAP-43, MARCKS, and BASP1 both separately and in conjunction. Special attention is devoted to a discussion of apparent inconsistencies in results and opinions of different authors concerning specific questions about the structure of proteins and their interactions. PMID:16125549

  8. Gap junction proteins and their role in spinal cord injury

    PubMed Central

    Tonkin, Ryan S.; Mao, Yilin; O’Carroll, Simon J.; Nicholson, Louise F. B.; Green, Colin R.; Gorrie, Catherine A.; Moalem-Taylor, Gila

    2015-01-01

    Gap junctions are specialized intercellular communication channels that are formed by two hexameric connexin hemichannels, one provided by each of the two adjacent cells. Gap junctions and hemichannels play an important role in regulating cellular metabolism, signaling, and functions in both normal and pathological conditions. Following spinal cord injury (SCI), there is damage and disturbance to the neuronal elements of the spinal cord including severing of axon tracts and rapid cell death. The initial mechanical disruption is followed by multiple secondary cascades that cause further tissue loss and dysfunction. Recent studies have implicated connexin proteins as playing a critical role in the secondary phase of SCI by propagating death signals through extensive glial networks. In this review, we bring together past and current studies to outline the distribution, changes and roles of various connexins found in neurons and glial cells, before and in response to SCI. We discuss the contribution of pathologically activated connexin proteins, in particular connexin 43, to functional recovery and neuropathic pain, as well as providing an update on potential connexin specific pharmacological agents to treat SCI. PMID:25610368

  9. High-Altitude Particle Acceleration and Radiation in Pulsar Slot Gaps

    NASA Technical Reports Server (NTRS)

    Muslimov, Alex G.; Harding, Alice K.

    2004-01-01

    We explore the pulsar slot gap (SG) electrodynamics up to very high altitudes, where for most relatively rapidly rotating pulsars both the standard small-angle approximation and the assumption that the magnetic field lines are ideal stream lines break down. We address the importance of the electrodynamic conditions at the SG boundaries and the occurrence of a steady-state drift of charged particles across the SG field lines at very high altitudes. These boundary conditions and the cross-field particle motion determine the asymptotic behavior of the scalar potential at all radii from the polar cap (PC) to near the light cylinder. As a result, we demonstrate that the steady-state accelerating electric field, E(sub ll), must approach a small and constant value at high altitude above the PC. This E(sub ll) is capable of maintaining electrons moving with high Lorentz factors (approx. a few x 10(exp 7)) and emitting curvature gamma-ray photons up to nearly the light cylinder. By numerical simulations, we show that primary electrons accelerating from the PC surface to high altitude in the SG along the outer edge of the open field region will form caustic emission patterns on the trailing dipole field lines. Acceleration and emission in such an extended SG may form the physical basis of a model that can successfully reproduce some pulsar high-energy light curves.

  10. Electrical stimulation accelerates axonal and functional peripheral nerve regeneration across long gaps.

    PubMed

    Haastert-Talini, Kirsten; Schmitte, Ruth; Korte, Nele; Klode, Dorothee; Ratzka, Andreas; Grothe, Claudia

    2011-04-01

    Short-term low-frequency electrical stimulation (ESTIM) of proximal peripheral nerve stumps prior to end-to-end coaptation or tubular bridging of small distances has been reported to increase preferential motor reinnervation and functional motor recovery in animal models and human patients undergoing carpal tunnel release surgery. We investigated the effects of ESTIM on regeneration across rat sciatic nerve gaps, which exceed distances that allow spontaneous regeneration. Three different reconstruction approaches were combined with ESTIM in the experimental groups. Nerve gaps (13 mm) were bridged using (I) nerve autotransplantation, (II) transplantation of differentially filled silicone tubes, or (III) transplantation of tubular grafts containing fibroblast growth factor-2 overexpressing Schwann cells (SCs) for gene therapy. The regeneration outcome was followed for up to 8 weeks, and functionally as well as histomorphometrically analyzed in comparison to non-stimulated control groups. Combining ESTIM with nerve autotransplantation significantly increased the nerve fiber density in the regenerated nerve, and the grade of functional recovery as detected by electrodiagnostic recordings from the gastrocnemius muscle. The combination of ESTIM with transplantation of naïve SCs increased the regeneration of gap-bridging nerve tissue. Although macroscopic tissue regeneration was not further improved after combining ESTIM with FGF-2(21/23-kD) gene therapy, the latter resulted in a high rate of regenerated nerves that functionally reconnected to the target muscle. Based on our results, brief ESTIM shows high potential to accelerate axonal as well as functional (motor and sensory) outcomes in the clinical setting of peripheral nerve gap reconstruction in human patients. PMID:21265597

  11. X-Band Photonic Band-Gap Accelerator Structure Breakdown Experiment

    SciTech Connect

    Marsh, Roark A.; Shapiro, Michael A.; Temkin, Richard J.; Dolgashev, Valery A.; Laurent, Lisa L.; Lewandowski, James R.; Yeremian, A.Dian; Tantawi, Sami G.; /SLAC

    2012-06-11

    In order to understand the performance of photonic band-gap (PBG) structures under realistic high gradient, high power, high repetition rate operation, a PBG accelerator structure was designed and tested at X band (11.424 GHz). The structure consisted of a single test cell with matching cells before and after the structure. The design followed principles previously established in testing a series of conventional pillbox structures. The PBG structure was tested at an accelerating gradient of 65 MV/m yielding a breakdown rate of two breakdowns per hour at 60 Hz. An accelerating gradient above 110 MV/m was demonstrated at a higher breakdown rate. Significant pulsed heating occurred on the surface of the inner rods of the PBG structure, with a temperature rise of 85 K estimated when operating in 100 ns pulses at a gradient of 100 MV/m and a surface magnetic field of 890 kA/m. A temperature rise of up to 250 K was estimated for some shots. The iris surfaces, the location of peak electric field, surprisingly had no damage, but the inner rods, the location of the peak magnetic fields and a large temperature rise, had significant damage. Breakdown in accelerator structures is generally understood in terms of electric field effects. These PBG structure results highlight the unexpected role of magnetic fields in breakdown. The hypothesis is presented that the moderate level electric field on the inner rods, about 14 MV/m, is enhanced at small tips and projections caused by pulsed heating, leading to breakdown. Future PBG structures should be built to minimize pulsed surface heating and temperature rise.

  12. The 7-gap-resonator-accelerator for the REX-ISOLDE-experiment at CERN

    NASA Astrophysics Data System (ADS)

    Podlech, H.; Grieser, M.; von Hahn, R.; Papureanu, S.; Repnow, R.; Schwalm, D.

    1998-04-01

    The Radioactive Beam Experiment at ISOLDE (REX-ISOLDE-Experiment) which presently is being developed and under construction at CERN serves to investigate exotic, very neutron rich, radioactive nuclei [1](Radioactive beam EXperiment at ISOLDE: Coloumb Excitation and Neutron Transfer Reactions of Exotic Nuclei, Proposal to the ISOLDE commitee, CERNSIC94-25). A linear accelerator delivers radioactive ions which are produced by the isotope separator ISOLDE with energies between 0.85 and 2.2 MeV/u. The Linac will consist of a RFQ-accelerator, an interdigital H-Structure (IH) and three 7-gap-resonators with variable energy. While the LMU Munich is responsible for the frontpart of the accelerator, the backpart is being built by the MPI [2](H. Podlech, Master Thesis, MPI-H-V21-1997, Heidelburg, 1997). After estimation of the voltage of one resonator to 1.75 MV at 90 kW, the design velocities were fixed to 5.4%, 6.0% and 6.6% of the velocity of light. Three downscaled models (1:2.5) were built in order to optimize the shuntimpedance and the field-distribution at the operation frequency of the amplifiers of 101.28 MHz. The optimization of all low power resonators is now successfully finished. Extensive beam dynamic calculations were made in order to optimize the transmission of the beam up to the target. It turned out that final energies between 0.85 and 2.2 MeV/u with nearly 100% transmission can be achieved. The acceptance in the x-plane is 1.2π mm mrad (norm.) and in the y-plane 3.0π mm mrad (norm.). The bunchlength of the fully accelerated beam (2.2 MeV/u) is 2.4 ns at the target. The development of the resonators was accompanied by extensive MAFIA calculations. It could be demonstrated that spiral-resonators like 7-gap-resonators can be calculated with MAFIA with an accuracy of 1% in comparison with experimental results. Presently, the tanks and the half shells of the power type resonators are manufactured in the workshops of the MPI.

  13. Experimental high gradient testing of a 17.1 GHz photonic band-gap accelerator structure

    NASA Astrophysics Data System (ADS)

    Munroe, Brian J.; Zhang, JieXi; Xu, Haoran; Shapiro, Michael A.; Temkin, Richard J.

    2016-03-01

    We report the design, fabrication, and high gradient testing of a 17.1 GHz photonic band-gap (PBG) accelerator structure. Photonic band-gap (PBG) structures are promising candidates for electron accelerators capable of high-gradient operation because they have the inherent damping of high order modes required to avoid beam breakup instabilities. The 17.1 GHz PBG structure tested was a single cell structure composed of a triangular array of round copper rods of radius 1.45 mm spaced by 8.05 mm. The test assembly consisted of the test PBG cell located between conventional (pillbox) input and output cells, with input power of up to 4 MW from a klystron supplied via a TM01 mode launcher. Breakdown at high gradient was observed by diagnostics including reflected power, downstream and upstream current monitors and visible light emission. The testing procedure was first benchmarked with a conventional disc-loaded waveguide structure, which reached a gradient of 87 MV /m at a breakdown probability of 1.19 ×10-1 per pulse per meter. The PBG structure was tested with 100 ns pulses at gradient levels of less than 90 MV /m in order to limit the surface temperature rise to 120 K. The PBG structure reached up to 89 MV /m at a breakdown probability of 1.09 ×10-1 per pulse per meter. These test results show that a PBG structure can simultaneously operate at high gradients and low breakdown probability, while also providing wakefield damping.

  14. GapIII, a new brain-enriched member of the GTPase-activating protein family.

    PubMed

    Baba, H; Fuss, B; Urano, J; Poullet, P; Watson, J B; Tamanoi, F; Macklin, W B

    1995-08-15

    Ras GTPase-activating proteins (GAPs) are negative regulators of ras, which controls proliferation and differentiation in many cells. Ras GAPs have been found in a variety of species from yeast to mammals. We describe here a newly identified mammalian GAP, GapIII, which was obtained by differential screening of a rat oligodendrocyte cDNA library. GapIII putatively encodes a 834 amino acid protein with a predicted molecular weight of 96 kDa, which contains a consensus GAP-related domain (GRD). The protein encoded by this cDNA has high homology with Gap1m, which was recently identified as a putative mammalian homolog of Drosophila Gap1. These proteins contain three structural domains, an N-terminal calcium-dependent phospholipid binding domain, GRD, and a C-terminal PH/Btk domain. Because of the sequence homology and the structural similarities of this protein with Gap1m, we hypothesize that GapIII and Gap1m may be members of a mammalian GAP gene family, separate from p120GAP, neurofibromin (NF1), and IQGAP. To confirm the GapIII protein activity, constructs containing different GapIII-GRD domains were transformed into iral mutant yeast to determine their relative ability to replace IRA1 functionally. Constructs that contained essentially the full-length protein (all three domains), the GRD alone, or the GRD plus PH/Btk domain suppressed heat shock sensitivity of ira1, whereas constructs that contained the GRD with part of the PH/Btk domain had only a weak ability to suppress heat shock sensitivity. These results suggest that the GapIII GRD itself is sufficient to down-regulate ras proteins in yeast. Expression of GapIII mRNA (4.2 kb) was examined by Northern analysis and in situ hybridization. This mRNA was expressed at highest levels in the brain, where its expression increased with development. Lower levels of the mRNA were expressed in the spleen and lung. Among neural cells, GapIII mRNA was expressed in neurons and oligodendrocytes, but not in astrocytes

  15. Attomole quantitation of protein separations with accelerator mass spectrometry

    SciTech Connect

    Vogel, J S; Grant, P G; Buccholz, B A; Dingley, K; Turteltaub, K W

    2000-12-15

    Quantification of specific proteins depends on separation by chromatography or electrophoresis followed by chemical detection schemes such as staining and fluorophore adhesion. Chemical exchange of short-lived isotopes, particularly sulfur, is also prevalent despite the inconveniences of counting radioactivity. Physical methods based on isotopic and elemental analyses offer highly sensitive protein quantitation that has linear response over wide dynamic ranges and is independent of protein conformation. Accelerator mass spectrometry quantifies long-lived isotopes such as 14C to sub-attomole sensitivity. We quantified protein interactions with small molecules such as toxins, vitamins, and natural biochemicals at precisions of 1-5% . Micro-proton-induced-xray-emission quantifies elemental abundances in separated metalloprotein samples to nanogram amounts and is capable of quantifying phosphorylated loci in gels. Accelerator-based quantitation is a possible tool for quantifying the genome translation into proteome.

  16. Closing the gap: accelerating the translational process in nanomedicine by proposing standardized characterization techniques

    PubMed Central

    Khorasani, Ali A; Weaver, James L; Salvador-Morales, Carolina

    2014-01-01

    On the cusp of widespread permeation of nanomedicine, academia, industry, and government have invested substantial financial resources in developing new ways to better treat diseases. Materials have unique physical and chemical properties at the nanoscale compared with their bulk or small-molecule analogs. These unique properties have been greatly advantageous in providing innovative solutions for medical treatments at the bench level. However, nanomedicine research has not yet fully permeated the clinical setting because of several limitations. Among these limitations are the lack of universal standards for characterizing nanomaterials and the limited knowledge that we possess regarding the interactions between nanomaterials and biological entities such as proteins. In this review, we report on recent developments in the characterization of nanomaterials as well as the newest information about the interactions between nanomaterials and proteins in the human body. We propose a standard set of techniques for universal characterization of nanomaterials. We also address relevant regulatory issues involved in the translational process for the development of drug molecules and drug delivery systems. Adherence and refinement of a universal standard in nanomaterial characterization as well as the acquisition of a deeper understanding of nanomaterials and proteins will likely accelerate the use of nanomedicine in common practice to a great extent. PMID:25525356

  17. Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

    NASA Astrophysics Data System (ADS)

    Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

    2014-03-01

    A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.

  18. Distinct roles of the RasGAP family proteins in C. elegans associative learning and memory

    PubMed Central

    Gyurkó, M. Dávid; Csermely, Péter; Sőti, Csaba; Steták, Attila

    2015-01-01

    The Ras GTPase activating proteins (RasGAPs) are regulators of the conserved Ras/MAPK pathway. Various roles of some of the RasGAPs in learning and memory have been reported in different model systems, yet, there is no comprehensive study to characterize all gap genes in any organism. Here, using reverse genetics and neurobehavioural tests, we studied the role of all known genes of the rasgap family in C. elegans in associative learning and memory. We demonstrated that their proteins are implicated in different parts of the learning and memory processes. We show that gap-1 contribute redundantly with gap-3 to the chemosensation of volatile compounds, gap-1 plays a major role in associative learning, while gap-2 and gap-3 are predominantly required for short- and long-term associative memory. Our results also suggest that the C. elegans Ras orthologue let-60 is involved in multiple processes during learning and memory. Thus, we show that the different classes of RasGAP proteins are all involved in cognitive function and their complex interplay ensures the proper formation and storage of novel information in C. elegans. PMID:26469632

  19. Quality Protein Maize for Africa: Closing the Protein Inadequacy Gap in Vulnerable Populations12

    PubMed Central

    Nuss, Emily T.; Tanumihardjo, Sherry A.

    2011-01-01

    Africa shares a unique relationship with maize (Zea mays). After its introduction from New World explorers, maize was quickly adopted as the cornerstone of local cuisine, especially in sub-Saharan countries. Although maize provides macro- and micronutrients required for humans, it lacks adequate amounts of the essential amino acids lysine and tryptophan. For those consuming >50% of their daily energy from maize, pandemic protein malnutrition may exist. Severe protein and energy malnutrition increases susceptibility to life-threatening diseases such as tuberculosis and gastroenteritis. A nutritionally superior maize cultivar named quality protein maize (QPM) represents nearly one-half century of research dedicated to malnutrition eradication. Compared with traditional maize types, QPM has twice the amount of lysine and tryptophan, as well as protein bioavailability that rivals milk casein. Animal and human studies suggest that substituting QPM for common maize results in improved health. However, QPM’s practical contribution to maize-subsisting populations remains unresolved. Herein, total protein and essential amino acid requirements recommended by the WHO and the Institute of Medicine were applied to estimate QPM target intake levels for young children and adults, and these were compared with mean daily maize intakes by African country. The comparisons revealed that ∼100 g QPM is required for children to maintain adequacy of lysine, the most limiting amino acid, and nearly 500 g is required for adults. This represents a 40% reduction in maize intake relative to common maize to meet protein requirements. The importance of maize in Africa underlines the potential for QPM to assist in closing the protein inadequacy gap. PMID:22332054

  20. Large full band gaps for photonic crystals in two dimensions computed by an inverse method with multigrid acceleration

    NASA Astrophysics Data System (ADS)

    Chern, R. L.; Chang, C. Chung; Chang, Chien C.; Hwang, R. R.

    2003-08-01

    In this study, two fast and accurate methods of inverse iteration with multigrid acceleration are developed to compute band structures of photonic crystals of general shape. In particular, we report two-dimensional photonic crystals of silicon air with an optimal full band gap of gap-midgap ratio Δω/ωmid=0.2421, which is 30% larger than ever reported in the literature. The crystals consist of a hexagonal array of circular columns, each connected to its nearest neighbors by slender rectangular rods. A systematic study with respect to the geometric parameters of the photonic crystals was made possible with the present method in drawing a three-dimensional band-gap diagram with reasonable computing time.

  1. Large full band gaps for photonic crystals in two dimensions computed by an inverse method with multigrid acceleration.

    PubMed

    Chern, R L; Chang, C Chung; Chang, Chien C; Hwang, R R

    2003-08-01

    In this study, two fast and accurate methods of inverse iteration with multigrid acceleration are developed to compute band structures of photonic crystals of general shape. In particular, we report two-dimensional photonic crystals of silicon air with an optimal full band gap of gap-midgap ratio Deltaomega/omega(mid)=0.2421, which is 30% larger than ever reported in the literature. The crystals consist of a hexagonal array of circular columns, each connected to its nearest neighbors by slender rectangular rods. A systematic study with respect to the geometric parameters of the photonic crystals was made possible with the present method in drawing a three-dimensional band-gap diagram with reasonable computing time. PMID:14525145

  2. Accelerated chemical synthesis of peptides and small proteins

    PubMed Central

    Miranda, Les P.; Alewood, Paul F.

    1999-01-01

    The chemical synthesis of peptides and small proteins is a powerful complementary strategy to recombinant protein overexpression and is widely used in structural biology, immunology, protein engineering, and biomedical research. Despite considerable improvements in the fidelity of peptide chain assembly, side-chain protection, and postsynthesis analysis, a limiting factor in accessing polypeptides containing greater than 50 residues remains the time taken for chain assembly. The ultimate goal of this work is to establish highly efficient chemical procedures that achieve chain-assembly rates of approximately 10–15 residues per hour, thus underpinning the rapid chemical synthesis of long polypeptides and proteins, including cytokines, growth factors, protein domains, and small enzymes. Here we report Boc chemistry that employs O-(7-azabenzotriazol-1-yl)-N,N,N′,N′-tetramethyluronium hexafluorophosphate (HATU)/dimethyl sulfoxide in situ neutralization as the coupling agent and incorporates a protected amino acid residue every 5 min to produce peptides of good quality. This rapid coupling chemistry was successfully demonstrated by synthesizing several small to medium peptides, including the “difficult” C-terminal sequence of HIV-1 proteinase (residues 81–99); fragment 65–74 of the acyl carrier protein; conotoxin PnIA(A10L), a potent neuronal nicotinic receptor antagonist; and the pro-inflammatory chemotactic protein CP10, an 88-residue protein, by means of native chemical ligation. The benefits of this approach include enhanced ability to identify and characterize “difficult couplings,” rapid access to peptides for biological and structure–activity studies, and accelerated synthesis of tailored large peptide segments (<50 residues) for use in chemoselective ligation methods. PMID:9989998

  3. LRP6 acts as a scaffold protein in cardiac gap junction assembly.

    PubMed

    Li, Jun; Li, Changming; Liang, Dandan; Lv, Fei; Yuan, Tianyou; The, Erlinda; Ma, Xiue; Wu, Yahan; Zhen, Lixiao; Xie, Duanyang; Wang, Shiyi; Liu, Yuan; Huang, Jian; Shi, Jingyi; Liu, Yi; Shi, Dan; Xu, Liang; Lin, Li; Peng, Luying; Cui, Jianmin; Zhu, Weidong; Chen, Yi-Han

    2016-01-01

    Low-density lipoprotein receptor-related protein 6 (LRP6) is a Wnt co-receptor in the canonical Wnt/β-catenin signalling. Here, we report the scaffold function of LRP6 in gap junction formation of cardiomyocytes. Cardiac LRP6 is spatially restricted to intercalated discs and binds to gap junction protein connexin 43 (Cx43). A deficiency in LRP6 disrupts Cx43 gap junction formation and thereby impairs the cell-to-cell coupling, which is independent of Wnt/β-catenin signalling. The defect in Cx43 gap junction resulting from LRP6 reduction is attributable to the defective traffic of de novo Cx43 proteins from the endoplasmic reticulum to the Golgi apparatus, leading to the lysosomal degradation of Cx43 proteins. Accordingly, the hearts of conditional cardiac-specific Lrp6-knockout mice consistently exhibit overt reduction of Cx43 gap junction plaques without any abnormality in Wnt signalling and are predisposed to lethal arrhythmias. These findings uncover a distinct role of LRP6 as a platform for intracellular protein trafficking. PMID:27250245

  4. LRP6 acts as a scaffold protein in cardiac gap junction assembly

    PubMed Central

    Li, Jun; Li, Changming; Liang, Dandan; Lv, Fei; Yuan, Tianyou; The, Erlinda; Ma, Xiue; Wu, Yahan; Zhen, Lixiao; Xie, Duanyang; Wang, Shiyi; Liu, Yuan; Huang, Jian; Shi, Jingyi; Liu, Yi; Shi, Dan; Xu, Liang; Lin, Li; Peng, Luying; Cui, Jianmin; Zhu, Weidong; Chen, Yi-Han

    2016-01-01

    Low-density lipoprotein receptor-related protein 6 (LRP6) is a Wnt co-receptor in the canonical Wnt/β-catenin signalling. Here, we report the scaffold function of LRP6 in gap junction formation of cardiomyocytes. Cardiac LRP6 is spatially restricted to intercalated discs and binds to gap junction protein connexin 43 (Cx43). A deficiency in LRP6 disrupts Cx43 gap junction formation and thereby impairs the cell-to-cell coupling, which is independent of Wnt/β-catenin signalling. The defect in Cx43 gap junction resulting from LRP6 reduction is attributable to the defective traffic of de novo Cx43 proteins from the endoplasmic reticulum to the Golgi apparatus, leading to the lysosomal degradation of Cx43 proteins. Accordingly, the hearts of conditional cardiac-specific Lrp6-knockout mice consistently exhibit overt reduction of Cx43 gap junction plaques without any abnormality in Wnt signalling and are predisposed to lethal arrhythmias. These findings uncover a distinct role of LRP6 as a platform for intracellular protein trafficking. PMID:27250245

  5. Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules.

    PubMed

    Lever, Greg; Cole, Daniel J; Hine, Nicholas D M; Haynes, Peter D; Payne, Mike C

    2013-04-17

    A detailed study of energy differences between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO gaps) in protein systems and water clusters is presented. Recent work questioning the applicability of Kohn-Sham density-functional theory to proteins and large water clusters (Rudberg 2012 J. Phys.: Condens. Matter 24 072202) has demonstrated vanishing HOMO-LUMO gaps for these systems, which is generally attributed to the treatment of exchange in the functional used. The present work shows that the vanishing gap is, in fact, an electrostatic artefact of the method used to prepare the system. Practical solutions for ensuring the gap is maintained when the system size is increased are demonstrated. This work has important implications for the use of large-scale density-functional theory in biomolecular systems, particularly in the simulation of photoemission, optical absorption and electronic transport, all of which depend critically on differences between energies of molecular orbitals. PMID:23470878

  6. An Update on the DOE Early Career Project on Photonic Band Gap Accelerator Structures

    SciTech Connect

    Simakov, Evgenya I.; Edwards, Randall L.; Haynes, William B.; Madrid, Michael A.; Romero, Frank P.; Tajima, Tsuyoshi; Tuzel, Walter M.; Boulware , Chase H.; Grimm, Terry

    2012-06-07

    We performed fabrication of two SRF PBG resonators at 2.1 GHz and demonstrated their proof-of-principle operation at high gradients. Measured characteristics of the resonators were in good agreement with theoretical predictions. We demonstrated that SRF PBG cavities can be operated at 15 MV/m accelerating gradients. We completed the design and started fabrication of the 16-cell PBG accelerating structure at 11.7 GHz for wakefield testing at AWA.

  7. Acceleration of calcite kinetics by abalone nacre proteins

    SciTech Connect

    Fu, G; Qiu, S R; Orme, C A; Morse, D E; De Yoreo, J J

    2005-06-09

    The fascinating shapes and hierarchical designs of biomineralized structures have long been an inspiration to materials scientists because of the potential they suggest for biomolecular control over synthesis of crystalline materials. One prevailing view is that mineral-associated macromolecules are responsible for initiating and stabilizing non-equilibrium crystal polymorphs and morphologies through interactions between anionic moieties and cations in solution or at mineral surfaces. Indeed, numerous studies have demonstrated that bio-organic additives can dramatically alter crystal shapes and growth-rates in vitro. However, previous molecular-scale studies revealing mechanisms of growth modification focused on small molecules such as amino acids or peptides and always observed growth inhibition. In contrast, studies using full proteins were non-quantitative and underlying sources of growth modification were ill-defined. Here we investigate interactions between proteins isolated from abalone shell nacre and growing surfaces of calcite. We find that these proteins significantly accelerate the molecular-scale kinetics and, though much larger than atomic steps, alter growth morphology through step-specific interactions that lower their free energies. We propose that these proteins act as surfactants to promote ion attachment at calcite surfaces.

  8. Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling.

    PubMed

    De Los Rios, Paolo; Ben-Zvi, Anat; Slutsky, Olga; Azem, Abdussalam; Goloubinoff, Pierre

    2006-04-18

    Hsp70s are highly conserved ATPase molecular chaperones mediating the correct folding of de novo synthesized proteins, the translocation of proteins across membranes, the disassembly of some native protein oligomers, and the active unfolding and disassembly of stress-induced protein aggregates. Here, we bring thermodynamic arguments and biochemical evidences for a unifying mechanism named entropic pulling, based on entropy loss due to excluded-volume effects, by which Hsp70 molecules can convert the energy of ATP hydrolysis into a force capable of accelerating the local unfolding of various protein substrates and, thus, perform disparate cellular functions. By means of entropic pulling, individual Hsp70 molecules can accelerate unfolding and pulling of translocating polypeptides into mitochondria in the absence of a molecular fulcrum, thus settling former contradictions between the power-stroke and the Brownian ratchet models for Hsp70-mediated protein translocation across membranes. Moreover, in a very different context devoid of membrane and components of the import pore, the same physical principles apply to the forceful unfolding, solubilization, and assisted native refolding of stable protein aggregates by individual Hsp70 molecules, thus providing a mechanism for Hsp70-mediated protein disaggregation. PMID:16606842

  9. Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling

    PubMed Central

    De Los Rios, Paolo; Ben-Zvi, Anat; Slutsky, Olga; Azem, Abdussalam; Goloubinoff, Pierre

    2006-01-01

    Hsp70s are highly conserved ATPase molecular chaperones mediating the correct folding of de novo synthesized proteins, the translocation of proteins across membranes, the disassembly of some native protein oligomers, and the active unfolding and disassembly of stress-induced protein aggregates. Here, we bring thermodynamic arguments and biochemical evidences for a unifying mechanism named entropic pulling, based on entropy loss due to excluded-volume effects, by which Hsp70 molecules can convert the energy of ATP hydrolysis into a force capable of accelerating the local unfolding of various protein substrates and, thus, perform disparate cellular functions. By means of entropic pulling, individual Hsp70 molecules can accelerate unfolding and pulling of translocating polypeptides into mitochondria in the absence of a molecular fulcrum, thus settling former contradictions between the power-stroke and the Brownian ratchet models for Hsp70-mediated protein translocation across membranes. Moreover, in a very different context devoid of membrane and components of the import pore, the same physical principles apply to the forceful unfolding, solubilization, and assisted native refolding of stable protein aggregates by individual Hsp70 molecules, thus providing a mechanism for Hsp70-mediated protein disaggregation. PMID:16606842

  10. HIV-1 proteins accelerate HPA axis habituation in female rats.

    PubMed

    Panagiotakopoulos, Leonidas; Kelly, Sean; Neigh, Gretchen N

    2015-10-15

    Congenital infection by the Human Immunodeficiency Virus (HIV) has been shown to lead to multiple co-morbidities, and people living with HIV have a higher incidence of affective and anxiety disorders. A marked increase in mood disorders is evident during the sensitive phase of adolescence and this is further pronounced in females. Depression has been linked to dysfunction of the intracellular response system to corticosteroids at the level of the hippocampus (HC) and prefrontal cortex (PFC) with a notable role of the glucocorticoid receptor (GR) and its co-chaperones (FKBP5 and FKBP4). The current study examined the extent to which HIV protein expression in adolescent female rats altered the stress response at both the level of corticosterone output and molecular regulation of the glucocorticoid receptor in the brain. WT and HIV-1 genotype female rats were randomly allocated in control, acute stress and repeat stress groups. Corticosterone plasma levels and expression of GR, FKBP4, and FKBP5 in the HC and PFC were measured. The presence of HIV-1 proteins facilitates habituation of the corticosterone response to repeated stressors, such that HIV-1 TG rats habituated to repeated restraint and WT rats did not. This was reflected by interactions between stress exposure and HIV-1 protein expression at the level of GR co-chaperones. Although expression of the GR was similarly reduced after acute and repeat stress in both genotypes, expression of FKBP5 and FKBP4 was altered in a brain-region specific manner depending on the duration of the stress exposure and the presence or absence of HIV-1 proteins. Collectively, the data presented demonstrate that HIV-1 proteins accelerate habituation to repeated stressors and modify the influence of acute and repeat stressors on GR co-chaperones in a brain region-specific manner. PMID:25666308

  11. ArfGAP1 interacts with coat proteins through tryptophan-based motifs

    SciTech Connect

    Rawet, Moran; Levi-Tal, Sharon; Szafer-Glusman, Edith; Parnis, Anna; Cassel, Dan

    2010-04-09

    The Arf1 GTPase-activating protein ArfGAP1 regulates vesicular traffic through the COPI system. This protein consists of N-terminal catalytic domain, lipid packing sensors (the ALPS motifs) in the central region, and a carboxy part of unknown function. The carboxy part contains several diaromatic sequences that are reminiscent of motifs known to interact with clathrin adaptors. In pull-down experiments using GST-fused peptides from rat ArfGAP1, a peptide containing a {sup 329}WETF sequence interacted strongly with clathrin adaptors AP1 and AP2, whereas a major coatomer-binding determinant was identified within the extreme carboxy terminal peptide ({sup 405}AADEGWDNQNW). Mutagenesis and peptide competition experiments revealed that this determinant is required for coatomer binding to full-length ArfGAP1, and that interaction is mediated through the {delta}-subunit of the coatomer adaptor-like subcomplex. Evidence for a role of the carboxy motif in ArfGAP1-coatomer interaction in vivo is provided by means of a reporter fusion assay. Our findings point to mechanistic differences between ArfGAP1 and the other ArfGAPs known to function in the COPI system.

  12. cDNA cloning and chromosomal mapping of a novel human GAP (GAP1M), GTPase-activating protein of Ras

    SciTech Connect

    Li, Shaowei; Nakamura, Shun; Hattori, Seisuke

    1996-08-01

    We have previously isolated a novel Ras GTPase-activating protein (Ras GAP), Gapl{sup m}, from rat brain. Gap1{sup m} is considered to be a negative regulator of the Ras signaling pathways, like other Ras GAPs, neurofibromin, which is a gene product of the neurofibromatosis type I gene, and p120GAP. In this study we have isolated a human cDNA of this Gap and mapped the gene. The gene encodes a protein of 853 amino acids that shows 89% sequence identity to rat Gapl{sup m}. The human gene was mapped to chromosome 3 by PCR analysis on a panel of human-mouse hybrid cells. FISH analysis refined the location of the gene further to 3q22-q23. 11 refs., 2 figs.

  13. The Mr 28,000 gap junction proteins from rat heart and liver are different but related.

    PubMed

    Nicholson, B J; Gros, D B; Kent, S B; Hood, L E; Revel, J P

    1985-06-10

    The sequence of the amino-terminal 32 residues of the rat heart Mr 28,000 gap junction protein presented here allows, for the first time, a sequence comparison of gap junctional proteins from different tissues (heart and liver). Comparison of the rat heart gap junction protein sequence and that available from rat liver reveals 43% sequence identity and conservative changes at an additional 25% of the positions. Both proteins exhibit a hydrophobic domain which could represent a transmembrane span of the junction. This result unequivocally demonstrates the existence of at least two forms of the gap junction protein. As yet, no homology is evident between the gap junctional proteins of either heart or liver and main intrinsic protein from rat eye lens. PMID:2987225

  14. Bone morphogenetic protein-7 accelerates fracture healing in osteoporotic rats

    PubMed Central

    Diwan, Ashish D; Leong, Anthony; Appleyard, Richard; Bhargav, Divya; Fang, Zhi Ming; Wei, Aiqun

    2013-01-01

    Background: Osteoporosis is characterized by low bone mass, bone fragility and increased susceptibility to fracture. Fracture healing in osteoporosis is delayed and rates of implant failure are high with few biological treatment options available. This study aimed to determine whether a single dose of bone morphogenetic protein-7 (BMP-7) in a collagen/carboxy-methyl cellulose (CMC) composite enhanced fracture healing in an osteoporotic rat model. Materials and Methods: An open femoral midshaft osteotomy was performed in female rats 3 months post-ovarectomy. Rats were randomized to receive either BMP-7 composite (n = 30) or composite alone (n = 30) at the fracture site during surgery. Thereafter calluses were collected on days 12, 20 and 31. Callus cross-sectional area, bone mineral density, biomechanical stiffness and maximum torque, radiographic bony union and histological callus maturity were evaluated at each time point. Results: There were statistically significant increases in bone mineral density and callus cross-section area at all time points in the BMP-7 group as compared to controls and biomechanical readings showed stronger bones at day 31 in the BMP-7 group. Histological and radiographic evaluation indicated significant acceleration of bony union in the BMP-7 group as compared to controls. Conclusion: This study demonstrated that BMP-7 accelerates fracture healing in an oestrogen-deficient environment in a rat femoral fracture healing model to scientific relevance level I. The use of BMP-7 composite could offer orthopedic surgeons an advantage over oestrogen therapy, enhancing osteoporotic fracture healing with a single, locally applied dose at the time of surgery, potentially overcoming delays in healing caused by the osteoporotic state. PMID:24379457

  15. Protein Kinase Cδ-mediated Phosphorylation of Connexin43 Gap Junction Channels Causes Movement within Gap Junctions followed by Vesicle Internalization and Protein Degradation*

    PubMed Central

    Cone, Angela C.; Cavin, Gabriel; Ambrosi, Cinzia; Hakozaki, Hiroyuki; Wu-Zhang, Alyssa X.; Kunkel, Maya T.; Newton, Alexandra C.; Sosinsky, Gina E.

    2014-01-01

    Phosphorylation of gap junction proteins, connexins, plays a role in global signaling events involving kinases. Connexin43 (Cx43), a ubiquitous and important connexin, has several phosphorylation sites for specific kinases. We appended an imaging reporter tag for the activity of the δ isoform of protein kinase C (PKCδ) to the carboxyl terminus of Cx43. The FRET signal of this reporter is inversely related to the phosphorylation of serine 368 of Cx43. By activating PKC with the phorbol ester phorbol 12,13-dibutyrate (PDBu) or a natural stimulant, UTP, time lapse live cell imaging movies indicated phosphorylated Ser-368 Cx43 separated into discrete domains within gap junctions and was internalized in small vesicles, after which it was degraded by lysosomes and proteasomes. Mutation of Ser-368 to an Ala eliminated the response to PDBu and changes in phosphorylation of the reporter. A phosphatase inhibitor, calyculin A, does not change this pattern, indicating PKC phosphorylation causes degradation of Cx43 without dephosphorylation, which is in accordance with current hypotheses that cells control their intercellular communication by a fast and constant turnover of connexins, using phosphorylation as part of this mechanism. PMID:24500718

  16. Protein-Protein Interaction Inhibition (2P2I)-Oriented Chemical Library Accelerates Hit Discovery.

    PubMed

    Milhas, Sabine; Raux, Brigitt; Betzi, Stéphane; Derviaux, Carine; Roche, Philippe; Restouin, Audrey; Basse, Marie-Jeanne; Rebuffet, Etienne; Lugari, Adrien; Badol, Marion; Kashyap, Rudra; Lissitzky, Jean-Claude; Eydoux, Cécilia; Hamon, Véronique; Gourdel, Marie-Edith; Combes, Sébastien; Zimmermann, Pascale; Aurrand-Lions, Michel; Roux, Thomas; Rogers, Catherine; Müller, Susanne; Knapp, Stefan; Trinquet, Eric; Collette, Yves; Guillemot, Jean-Claude; Morelli, Xavier

    2016-08-19

    Protein-protein interactions (PPIs) represent an enormous source of opportunity for therapeutic intervention. We and others have recently pinpointed key rules that will help in identifying the next generation of innovative drugs to tackle this challenging class of targets within the next decade. We used these rules to design an oriented chemical library corresponding to a set of diverse "PPI-like" modulators with cores identified as privileged structures in therapeutics. In this work, we purchased the resulting 1664 structurally diverse compounds and evaluated them on a series of representative protein-protein interfaces with distinct "druggability" potential using homogeneous time-resolved fluorescence (HTRF) technology. For certain PPI classes, analysis of the hit rates revealed up to 100 enrichment factors compared with nonoriented chemical libraries. This observation correlates with the predicted "druggability" of the targets. A specific focus on selectivity profiles, the three-dimensional (3D) molecular modes of action resolved by X-ray crystallography, and the biological activities of identified hits targeting the well-defined "druggable" bromodomains of the bromo and extraterminal (BET) family are presented as a proof-of-concept. Overall, our present study illustrates the potency of machine learning-based oriented chemical libraries to accelerate the identification of hits targeting PPIs. A generalization of this method to a larger set of compounds will accelerate the discovery of original and potent probes for this challenging class of targets. PMID:27219844

  17. Application of Gap-Constraints Given Sequential Frequent Pattern Mining for Protein Function Prediction

    PubMed Central

    Park, Hyeon Ah; Kim, Taewook; Li, Meijing; Shon, Ho Sun; Park, Jeong Seok; Ryu, Keun Ho

    2015-01-01

    Objectives Predicting protein function from the protein–protein interaction network is challenging due to its complexity and huge scale of protein interaction process along with inconsistent pattern. Previously proposed methods such as neighbor counting, network analysis, and graph pattern mining has predicted functions by calculating the rules and probability of patterns inside network. Although these methods have shown good prediction, difficulty still exists in searching several functions that are exceptional from simple rules and patterns as a result of not considering the inconsistent aspect of the interaction network. Methods In this article, we propose a novel approach using the sequential pattern mining method with gap-constraints. To overcome the inconsistency problem, we suggest frequent functional patterns to include every possible functional sequence—including patterns for which search is limited by the structure of connection or level of neighborhood layer. We also constructed a tree-graph with the most crucial interaction information of the target protein, and generated candidate sets to assign by sequential pattern mining allowing gaps. Results The parameters of pattern length, maximum gaps, and minimum support were given to find the best setting for the most accurate prediction. The highest accuracy rate was 0.972, which showed better results than the simple neighbor counting approach and link-based approach. Conclusion The results comparison with other approaches has confirmed that the proposed approach could reach more function candidates that previous methods could not obtain. PMID:25938021

  18. Phylogenetic and bioinformatic analysis of gap junction-related proteins, innexins, pannexins and connexins.

    PubMed

    Fushiki, Daisuke; Hamada, Yasuo; Yoshimura, Ryoichi; Endo, Yasuhisa

    2010-04-01

    All multi-cellular animals, including hydra, insects and vertebrates, develop gap junctions, which communicate directly with neighboring cells. Gap junctions consist of protein families called connexins in vertebrates and innexins in invertebrates. Connexins and innexins have no homology in their amino acid sequence, but both are thought to have some similar characteristics, such as a tetra-membrane-spanning structure, formation of a channel by hexamer, and transmission of small molecules (e.g. ions) to neighboring cells. Pannexins were recently identified as a homolog of innexins in vertebrate genomes. Although pannexins are thought to share the function of intercellular communication with connexins and innexins, there is little information about the relationship among these three protein families of gap junctions. We phylgenetically and bioinformatically examined these protein families and other tetra-membrane-spanning proteins using a database and three analytical softwares. The clades formed by pannexin families do not belong to the species classification but do to paralogs of each member of pannexins. Amino acid sequences of pannexins are closely related to those of innexins but less to those of connexins. These data suggest that innexins and pannexins have a common origin, but the relationship between innexins/pannexins and connexins is as slight as that of other tetra-membrane-spanning members. PMID:20460741

  19. ELMO Domains, Evolutionary and Functional Characterization of a Novel GTPase-activating Protein (GAP) Domain for Arf Protein Family GTPases*

    PubMed Central

    East, Michael P.; Bowzard, J. Bradford; Dacks, Joel B.; Kahn, Richard A.

    2012-01-01

    The human family of ELMO domain-containing proteins (ELMODs) consists of six members and is defined by the presence of the ELMO domain. Within this family are two subclassifications of proteins, based on primary sequence conservation, protein size, and domain architecture, deemed ELMOD and ELMO. In this study, we used homology searching and phylogenetics to identify ELMOD family homologs in genomes from across eukaryotic diversity. This demonstrated not only that the protein family is ancient but also that ELMOs are potentially restricted to the supergroup Opisthokonta (Metazoa and Fungi), whereas proteins with the ELMOD organization are found in diverse eukaryotes and thus were likely the form present in the last eukaryotic common ancestor. The segregation of the ELMO clade from the larger ELMOD group is consistent with their contrasting functions as unconventional Rac1 guanine nucleotide exchange factors and the Arf family GTPase-activating proteins, respectively. We used unbiased, phylogenetic sorting and sequence alignments to identify the most highly conserved residues within the ELMO domain to identify a putative GAP domain within the ELMODs. Three independent but complementary assays were used to provide an initial characterization of this domain. We identified a highly conserved arginine residue critical for both the biochemical and cellular GAP activity of ELMODs. We also provide initial evidence of the function of human ELMOD1 as an Arf family GAP at the Golgi. These findings provide the basis for the future study of the ELMOD family of proteins and a new avenue for the study of Arf family GTPases. PMID:23014990

  20. Targeted protein-omic methods are bridging the gap between proteomic and hypothesis-driven protein analysis approaches

    PubMed Central

    Hause, Ronald J.; Kim, Hyung-Do; Leung, Kin; Jones, Richard Baker

    2011-01-01

    While proteomic methods have illuminated many areas of biological protein space, many fundamental questions remain with regard to systems-level relationships between mRNAs, proteins, and cell behaviors. While mass spectrometric methods offer a panoramic picture of the relative expression and modification of large numbers of proteins, they are neither optimal for the analysis of pre-defined targets across large numbers of samples nor for assessing differences in proteins between individual cells or cell compartments. Conversely, traditional antibody-based methods are effective at sensitively analyzing small numbers of proteins across small numbers of conditions, and can be used to analyze relative differences in protein abundance and modification between cells and cell compartments. However, traditional antibody-based approaches are not optimal for analyzing large numbers of protein abundances and modifications across many samples. In this perspective article, we will review recent advances in methodologies and philosophies behind several microarray-based, intermediate-level, “protein-omic” methods including a focus on reverse phase lysate arrays and micro-western arrays that have been helpful for bridging gaps between large- and small-scale protein analysis approaches and have provided insight into the roles that protein systems play in several biological processes. PMID:21999828

  1. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

    PubMed

    Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P; Kasif, Simon; Roberts, Richard J; Steffen, Martin

    2016-01-01

    The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue. PMID:26635392

  2. Antofine-induced connexin43 gap junction disassembly in rat astrocytes involves protein kinase Cβ.

    PubMed

    Huang, Yu-Fang; Liao, Chih-Kai; Lin, Jau-Chen; Jow, Guey-Mei; Wang, Hwai-Shi; Wu, Jiahn-Chun

    2013-03-01

    Antofine, a phenanthroindolizidine alkaloid derived from Cryptocaryachinensis and Ficusseptica in the Asclepiadaceae milkweed family, is cytotoxic for various cancer cell lines. In this study, we demonstrated that treatment of rat primary astrocytes with antofine induced dose-dependent inhibition of gap junction intercellular communication (GJIC), as assessed by scrape-loading 6-carboxyfluorescein dye transfer. Levels of Cx43 protein were also decreased in a dose- and time-dependent manner following antofine treatment. Double-labeling immunofluorescence microscopy showed that antofine (10ng/ml) induced endocytosis of surface gap junctions into the cytoplasm, where Cx43 was co-localized with the early endosome marker EEA1. Inhibition of lysosomes or proteasomes by co-treatment with antofine and their respective specific inhibitors, NH4Cl or MG132, partially inhibited the antofine-induced decrease in Cx43 protein levels, but did not inhibit the antofine-induced inhibition of GJIC. After 30min of treatment, antofine induced a rapid increase in the intracellular Ca(2+) concentration and activation of protein kinase C (PKC)α/βII, which was maintained for at least 6h. Co-treatment of astrocytes with antofine and the intracellular Ca(2+) chelator BAPTA-AM prevented downregulation of Cx43 and inhibition of GJIC. Moreover, co-treatment with antofine and a specific PKCβ inhibitor prevented endocytosis of gap junctions, downregulation of Cx43, and inhibition of GJIC. Taken together, these findings indicate that antofine induces Cx43 gap junction disassembly by the PKCβ signaling pathway. Inhibition of GJIC by antofine may undermine the neuroprotective effect of astrocytes in CNS. PMID:23403203

  3. Fast gap-free enumeration of conformations and sequences for protein design.

    PubMed

    Roberts, Kyle E; Gainza, Pablo; Hallen, Mark A; Donald, Bruce R

    2015-10-01

    Despite significant successes in structure-based computational protein design in recent years, protein design algorithms must be improved to increase the biological accuracy of new designs. Protein design algorithms search through an exponential number of protein conformations, protein ensembles, and amino acid sequences in an attempt to find globally optimal structures with a desired biological function. To improve the biological accuracy of protein designs, it is necessary to increase both the amount of protein flexibility allowed during the search and the overall size of the design, while guaranteeing that the lowest-energy structures and sequences are found. DEE/A*-based algorithms are the most prevalent provable algorithms in the field of protein design and can provably enumerate a gap-free list of low-energy protein conformations, which is necessary for ensemble-based algorithms that predict protein binding. We present two classes of algorithmic improvements to the A* algorithm that greatly increase the efficiency of A*. First, we analyze the effect of ordering the expansion of mutable residue positions within the A* tree and present a dynamic residue ordering that reduces the number of A* nodes that must be visited during the search. Second, we propose new methods to improve the conformational bounds used to estimate the energies of partial conformations during the A* search. The residue ordering techniques and improved bounds can be combined for additional increases in A* efficiency. Our enhancements enable all A*-based methods to more fully search protein conformation space, which will ultimately improve the accuracy of complex biomedically relevant designs. PMID:26235965

  4. Fast Gap-Free Enumeration of Conformations and Sequences for Protein Design

    PubMed Central

    Hallen, Mark A.; Donald, Bruce R.

    2016-01-01

    Despite significant successes in structure-based computational protein design in recent years, protein design algorithms must be improved to increase the biological accuracy of new designs. Protein design algorithms search through an exponential number of protein conformations, protein ensembles, and amino acid sequences in an attempt to find globally optimal structures with a desired biological function. To improve the biological accuracy of protein designs, it is necessary to increase both the amount of protein flexibility allowed during the search and the overall size of the design, while guaranteeing that the lowest-energy structures and sequences are found. DEE/A*-based algorithms are the most prevalent provable algorithms in the field of protein design and can provably enumerate a gap-free list of low-energy protein conformations, which is necessary for ensemble-based algorithms that predict protein binding. We present two classes of algorithmic improvements to the A* algorithm that greatly increase the efficiency of A*. First, we analyze the effect of ordering the expansion of mutable residue positions within the A* tree and present a dynamic residue ordering that reduces the number of A* nodes that must be visited during the search. Second, we propose new methods to improve the conformational bounds used to estimate the energies of partial conformations during the A* search. The residue ordering techniques and improved bounds can be combined for additional increases in A* efficiency. Our enhancements enable all A*-based methods to more fully search protein conformation space, which will ultimately improve the accuracy of complex biomedically-relevant designs. PMID:26235965

  5. Lateral interactions among membrane proteins. Implications for the organization of gap junctions.

    PubMed Central

    Abney, J R; Braun, J; Owicki, J C

    1987-01-01

    We have studied the relationship between interprotein forces and the lateral distribution of proteins in disordered mouse liver gap junctions. Data on protein positions are obtained from freeze-fracture electron micrographs. Short-ranged correlations in observed positions are characteristic of interacting particles in a fluid state. An analysis derived from statistical mechanics allows the determination of the magnitude and functional form of interprotein forces. We find that jap junction proteins are mutually repulsive, in a manner consistent with electrostatics and excluded volume. This dictates that long-ranged protein aggregation into jap junction plaques cannot arise solely from interparticle interactions. An alternative is the balance of lateral pressures between the junction and the surrounding glycocalyx. This idea is quantified into a model. Junctional pressure arises from protein-protein interactions and is computed from a pressure equation based on the force and a radial distribution function describing order. The pressure from the glycocalyx is assumed to arise from mixing, electrostatic, and elastic interactions of sugar residues, and is described with terms from Flory-Krigbaum and McMillan-Mayer theories. The results of this modeling are in reasonable agreement with available experimental data. Images FIGURE 1 PMID:3651562

  6. Connexin 33: a rodent-specific member of the gap junction protein family?

    PubMed

    Fischer, Petra; Brehm, Ralph; Konrad, Lutz; Hartmann, Sonja; Kliesch, Sabine; Bohle, Rainer M; Bergmann, Martin

    2005-01-01

    Gap junctional intercellular communication between Sertoli cells and between Sertoli cells and spermatogonia is considered to play a key role in the regulation of both proliferation and differentiation of germ cells. A member of the gap junction protein family, Connexin 33 (cx33), probably has an inhibitory effect on the formation of gap junctions and so far it is the only cx that has been exclusively found in rat and mouse testes. Thus, this connexin seems to be a special member of the cx family. Using immunohistochemistry, Western blot analysis, polymerase chain reaction, and reverse transcription (RT)-PCR (tissue homogenate and microdissected cells), we studied the possible occurrence of cx33 at the protein, the DNA, and the RNA level in human testis. Whereas immunohistochemistry using the only commercially available anti-cx33 antibody showed similar labeling to the rat within the seminiferous epithelium, we could not find any further evidence for the existence of cx33 using Western blot analysis, PCR, and RT-PCR in human testis. Based on the demonstration of the staining pattern of mitochondria in human germ cells and on preabsorption studies, we could demonstrate anti-cx33 antibody cross-reacting with mitochondrial ferritin, a protein localized in the mitochondria of human testicular spermatids. Therefore, we were not able to abide by the suspicion that cx33 is present in human testis. Additionally, it was not possible to demonstrate cx33 via PCR and immunohistochemistry in the testis of different mammals (dog, cattle, pig, horse, and marmoset monkey) with normal spermatogenesis. These data indicate that cx33 seems to be the first rodent-specific testicular cx. PMID:15611570

  7. Switch in Gap Junction Protein Expression is Associated with Selective Changes in Junctional Permeability During Keratinocyte Differentiation

    NASA Astrophysics Data System (ADS)

    Brissette, Janice L.; Kumar, Nalin M.; Gilula, Norton B.; Hall, James E.; Dotto, G. Paolo

    1994-07-01

    Gap junctional communication provides a mechanism for regulating multicellular activities by allowing the exchange of small diffusible molecules between neighboring cells. The diversity of gap junction proteins may exist to form channels that have different permeability properties. We report here that induction of terminal differentiation in mouse primary keratinocytes by calcium results in a specific switch in gap junction protein expression. Expression of α_1 (connexin 43) and β_2 (connexin 26) gap junction proteins is down-modulated, whereas that of β_3 (connexin 31) and β_4 (connexin 31.1) proteins is induced. Although both proliferating and differentiating keratinocytes are electrically coupled, there are significant changes in the permeability properties of the junctions to small molecules. In parallel with the changes in gap junction protein expression during differentiation, the intercellular transfer of the small dyes neurobiotin, carboxyfluorescein, and Lucifer yellow is significantly reduced, whereas that of small metabolites, such as nucleotides and amino acids, proceeds unimpeded. Thus, a switch in gap junction protein expression in differentiating keratinocytes is accompanied by selective changes in junctional permeability that may play an important role in the coordinate control of the differentiation process.

  8. Tumor cell migration and invasion are enhanced by depletion of Rap1 GTPase-activating protein (Rap1GAP).

    PubMed

    Tsygankova, Oxana M; Wang, Hongbin; Meinkoth, Judy L

    2013-08-23

    The functional significance of the widespread down-regulation of Rap1 GTPase-activating protein (Rap1GAP), a negative regulator of Rap activity, in human tumors is unknown. Here we show that human colon cancer cells depleted of Rap1GAP are endowed with more aggressive migratory and invasive properties. Silencing Rap1GAP enhanced the migration of confluent and single cells. In the latter, migration distance, velocity, and directionality were increased. Enhanced migration was a consequence of increased endogenous Rap activity as silencing Rap expression selectively abolished the migration of Rap1GAP-depleted cells. ROCK-mediated cell contractility was suppressed in Rap1GAP-depleted cells, which exhibited a spindle-shaped morphology and abundant membrane protrusions. Tumor cells can switch between Rho/ROCK-mediated contractility-based migration and Rac1-mediated mesenchymal motility. Strikingly, the migration of Rap1GAP-depleted, but not control cells required Rac1 activity, suggesting that loss of Rap1GAP alters migratory mechanisms. Inhibition of Rac1 activity restored membrane blebbing and increased ROCK activity in Rap1GAP-depleted cells, suggesting that Rac1 contributes to the suppression of contractility. Collectively, these findings identify Rap1GAP as a critical regulator of aggressive tumor cell behavior and suggest that the level of Rap1GAP expression influences the migratory mechanisms that are operative in tumor cells. PMID:23864657

  9. Simvastatin Sodium Salt and Fluvastatin Interact with Human Gap Junction Gamma-3 Protein.

    PubMed

    Marsh, Andrew; Casey-Green, Katherine; Probert, Fay; Withall, David; Mitchell, Daniel A; Dilly, Suzanne J; James, Sean; Dimitri, Wade; Ladwa, Sweta R; Taylor, Paul C; Singer, Donald R J

    2016-01-01

    Finding pleiomorphic targets for drugs allows new indications or warnings for treatment to be identified. As test of concept, we applied a new chemical genomics approach to uncover additional targets for the widely prescribed lipid-lowering pro-drug simvastatin. We used mRNA extracted from internal mammary artery from patients undergoing coronary artery surgery to prepare a viral cardiovascular protein library, using T7 bacteriophage. We then studied interactions of clones of the bacteriophage, each expressing a different cardiovascular polypeptide, with surface-bound simvastatin in 96-well plates. To maximise likelihood of identifying meaningful interactions between simvastatin and vascular peptides, we used a validated photo-immobilisation method to apply a series of different chemical linkers to bind simvastatin so as to present multiple orientations of its constituent components to potential targets. Three rounds of biopanning identified consistent interaction with the clone expressing part of the gene GJC3, which maps to Homo sapiens chromosome 7, and codes for gap junction gamma-3 protein, also known as connexin 30.2/31.3 (mouse connexin Cx29). Further analysis indicated the binding site to be for the N-terminal domain putatively 'regulating' connexin hemichannel and gap junction pores. Using immunohistochemistry we found connexin 30.2/31.3 to be present in samples of artery similar to those used to prepare the bacteriophage library. Surface plasmon resonance revealed that a 25 amino acid synthetic peptide representing the discovered N-terminus did not interact with simvastatin lactone, but did bind to the hydrolysed HMG CoA inhibitor, simvastatin acid. This interaction was also seen for fluvastatin. The gap junction blockers carbenoxolone and flufenamic acid also interacted with the same peptide providing insight into potential site of binding. These findings raise key questions about the functional significance of GJC3 transcripts in the vasculature and

  10. Transportation of high-current ion and electron beams in the accelerator drift gap in the presence of an additional electron background

    NASA Astrophysics Data System (ADS)

    Karas', V. I.; Kornilov, E. A.; Manuilenko, O. V.; Tarakanov, V. P.; Fedorovskaya, O. V.

    2015-12-01

    The dynamics of a high-current ion beam propagating in the drift gap of a linear induction accelerator with collective focusing is studied using 3D numerical simulations in the framework of the full system of the Vlasov-Maxwell equations (code KARAT). The ion beam is neutralized by a comoving electron beam in the current density and, partially, in space charge, since the velocities of electrons and ions differ substantially. The dynamics of the high-current ion beam is investigated for different versions of additional neutralization of its space charge. It is established that, for a given configuration of the magnetic field and in the presence of a specially programmed injection of additional electrons from the boundary opposite to the ion injection boundary, the angular divergence of the ion beam almost vanishes, whereas the current of the ion beam at the exit from the accelerator drift gap changes insignificantly and the beam remains almost monoenergetic.

  11. Transportation of high-current ion and electron beams in the accelerator drift gap in the presence of an additional electron background

    SciTech Connect

    Karas’, V. I. Kornilov, E. A.; Manuilenko, O. V.; Tarakanov, V. P.; Fedorovskaya, O. V.

    2015-12-15

    The dynamics of a high-current ion beam propagating in the drift gap of a linear induction accelerator with collective focusing is studied using 3D numerical simulations in the framework of the full system of the Vlasov–Maxwell equations (code KARAT). The ion beam is neutralized by a comoving electron beam in the current density and, partially, in space charge, since the velocities of electrons and ions differ substantially. The dynamics of the high-current ion beam is investigated for different versions of additional neutralization of its space charge. It is established that, for a given configuration of the magnetic field and in the presence of a specially programmed injection of additional electrons from the boundary opposite to the ion injection boundary, the angular divergence of the ion beam almost vanishes, whereas the current of the ion beam at the exit from the accelerator drift gap changes insignificantly and the beam remains almost monoenergetic.

  12. Accelerated protein engineering for chemical biotechnology via homologous recombination.

    PubMed

    Nordwald, Erik M; Garst, Andrew; Gill, Ryan T; Kaar, Joel L

    2013-12-01

    Protein engineering has traditionally relied on random mutagenesis strategies to generate diverse libraries, which require high-throughput screening or selection methods to identify rare variants. Alternatively, approaches to semi-rational library construction can be used to minimize the screening load and enhance the efficiency by which improved mutants may be identified. Such methods are typically limited to characterization of relatively few variants due to the difficulties in generating large rational libraries. New tools from synthetic biology, namely multiplexed DNA synthesis and homologous recombination, provide a promising avenue to rapidly construct large, rational libraries. These technologies also enable incorporation of synthetically encoded features that permit efficient characterization of the fitness of each mutant. Extension of these tools to protein library design could complement rational protein design cycles in an effort to more systematically search complex fitness landscapes. The highly parallelized nature with which such libraries can be generated also has the potential to expand directed protein evolution from single protein targets to protein networks whose concerted activities are required for the biological function of interest. PMID:23540421

  13. Accelerated Nucleation of Hydroxyapatite Using an Engineered Hydrophobin Fusion Protein.

    PubMed

    Melcher, Melanie; Facey, Sandra J; Henkes, Thorsten M; Subkowski, Thomas; Hauer, Bernhard

    2016-05-01

    Calcium phosphate mineralization is of particular interest in dental repair. A biomimetic approach using proteins or peptides is a highly promising way to reconstruct eroded teeth. In this study, the screening of several proteins is described for their binding and nucleating activities toward hydroxyapatite. Out of 27 tested candidates, only two hydrophobin fusion proteins showed binding abilities to hydroxyapatite in a mouthwash formulation and an increased nucleation in artificial saliva. Using a semirational approach, one of the two candidates (DEWA_5), a fusion protein consisting of a truncated section of the Bacillus subtilis synthase YaaD, the Aspergillus nidulans hydrophobin DEWA, and the rationally designed peptide P11-4 described in the literature, could be further engineered toward a faster mineral formation. The variants DEWA_5a (40aaYaaD-SDSDSD-DEWA) and DEWA_5b (40aaYaaD-RDRDRD-DEWA) were able to enhance the nucleation activity without losing the ability to form hydroxyapatite. In the case of variant DEWA_5b, an additional increase in the binding toward hydroxyapatite could be achieved. Especially with the variant DEWA_5a, the protein engineering of the rationally designed peptide sequence resulted in a resemblance of an amino acid motif that is found in nature. The engineered peptide resembles the amino acid motif in dentin phosphoprotein, one of the major proteins involved in dentinogenesis. PMID:27010648

  14. GPU-accelerated visualization of protein dynamics in ribbon mode

    NASA Astrophysics Data System (ADS)

    Wahle, Manuel; Birmanns, Stefan

    2011-01-01

    Proteins are biomolecules present in living organisms and essential for carrying out vital functions. Inherent to their functioning is folding into different spatial conformations, and to understand these processes, it is crucial to visually explore the structural changes. In recent years, significant advancements in experimental techniques and novel algorithms for post-processing of protein data have routinely revealed static and dynamic structures of increasing sizes. In turn, interactive visualization of the systems and their transitions became more challenging. Therefore, much research for the efficient display of protein dynamics has been done, with the focus being space filling models, but for the important class of abstract ribbon or cartoon representations, there exist only few methods for an efficient rendering. Yet, these models are of high interest to scientists, as they provide a compact and concise description of the structure elements along the protein main chain. In this work, a method was developed to speed up ribbon and cartoon visualizations. Separating two phases in the calculation of geometry allows to offload computational work from the CPU to the GPU. The first phase consists of computing a smooth curve along the protein's main chain on the CPU. In the second phase, conducted independently by the GPU, vertices along that curve are moved to set up the final geometrical representation of the molecule.

  15. Sequence heterogeneity accelerates protein search for targets on DNA

    NASA Astrophysics Data System (ADS)

    Shvets, Alexey A.; Kolomeisky, Anatoly B.

    2015-12-01

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

  16. Sequence heterogeneity accelerates protein search for targets on DNA

    SciTech Connect

    Shvets, Alexey A.; Kolomeisky, Anatoly B.

    2015-12-28

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

  17. Maternal treatment with glucocorticoids modulates gap junction protein expression in the ovine fetal brain.

    PubMed

    Sadowska, G B; Stonestreet, B S

    2014-09-01

    Gap junctions facilitate intercellular communication and are important in brain development. Connexins (Cx) comprise a transmembrane protein family that forms gap junctions. Cx-32 is expressed in oligodendrocytes and neurons, Cx-36 in neurons, and Cx-43 in astrocytes. Although single antenatal steroid courses are recommended for fetal lung maturation, multiple courses can be given to women at recurrent risk for premature delivery. We examined the effects of single and multiple glucocorticoid courses on Cx-32, Cx-36, and Cx-43 protein expressions in the fetal cerebral cortex, cerebellum, and spinal cord, and differences in Cx expression among brain regions under basal conditions. In the single-course groups, the ewes received dexamethasone (6 mg) or placebo as four intramuscular injections every 12h over 48 h. In the multiple-course groups, the ewes received the same treatment, once a week for 5 weeks starting at 76-78 days of gestation. Cx were measured by Western immunoblot on brain samples from 105 to 108-day gestation fetuses. A single dexamethasone course was associated with increases (P<0.05) in cerebral cortical and spinal cord Cx-36 and Cx-43 and multiple courses with increases in cerebellar and spinal cord Cx-36, and cerebral cortical and cerebellar Cx-43. Cx-32 did not change. Cx-32 was higher in the cerebellum than cerebral cortex and spinal cord, Cx-36 higher in the spinal cord than cerebellum, and Cx-43 higher in the cerebellum and spinal cord than cerebral cortex during basal conditions. In conclusion, maternal glucocorticoid therapy increases specific Cx, responses to different maternal courses vary among Cx and brain regions, and Cx expression differs among brain regions under basal conditions. Maternal treatment with glucocorticoids differentially modulates Cx in the fetal brain. PMID:24929069

  18. An efficient parallel algorithm for accelerating computational protein design

    PubMed Central

    Zhou, Yichao; Xu, Wei; Donald, Bruce R.; Zeng, Jianyang

    2014-01-01

    Motivation: Structure-based computational protein design (SCPR) is an important topic in protein engineering. Under the assumption of a rigid backbone and a finite set of discrete conformations of side-chains, various methods have been proposed to address this problem. A popular method is to combine the dead-end elimination (DEE) and A* tree search algorithms, which provably finds the global minimum energy conformation (GMEC) solution. Results: In this article, we improve the efficiency of computing A* heuristic functions for protein design and propose a variant of A* algorithm in which the search process can be performed on a single GPU in a massively parallel fashion. In addition, we make some efforts to address the memory exceeding problem in A* search. As a result, our enhancements can achieve a significant speedup of the A*-based protein design algorithm by four orders of magnitude on large-scale test data through pre-computation and parallelization, while still maintaining an acceptable memory overhead. We also show that our parallel A* search algorithm could be successfully combined with iMinDEE, a state-of-the-art DEE criterion, for rotamer pruning to further improve SCPR with the consideration of continuous side-chain flexibility. Availability: Our software is available and distributed open-source under the GNU Lesser General License Version 2.1 (GNU, February 1999). The source code can be downloaded from http://www.cs.duke.edu/donaldlab/osprey.php or http://iiis.tsinghua.edu.cn/∼compbio/software.html. Contact: zengjy321@tsinghua.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24931991

  19. Sequence Heterogeneity Accelerates Protein Search for Targets on DNA

    NASA Astrophysics Data System (ADS)

    Shvets, Alexey; Kolomeisky, Anatoly

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry and heterogeneity of a genome. The work was supported by the Welch Foundation (Grant C-1559), by the NSF (Grant CHE-1360979), and by the Center for Theoretical Biological Physics sponsored by the NSF (Grant PHY-1427654).

  20. Simvastatin Sodium Salt and Fluvastatin Interact with Human Gap Junction Gamma-3 Protein

    PubMed Central

    Marsh, Andrew; Casey-Green, Katherine; Probert, Fay; Withall, David; Mitchell, Daniel A.; Dilly, Suzanne J.; James, Sean; Dimitri, Wade; Ladwa, Sweta R.; Taylor, Paul C.; Singer, Donald R. J.

    2016-01-01

    Finding pleiomorphic targets for drugs allows new indications or warnings for treatment to be identified. As test of concept, we applied a new chemical genomics approach to uncover additional targets for the widely prescribed lipid-lowering pro-drug simvastatin. We used mRNA extracted from internal mammary artery from patients undergoing coronary artery surgery to prepare a viral cardiovascular protein library, using T7 bacteriophage. We then studied interactions of clones of the bacteriophage, each expressing a different cardiovascular polypeptide, with surface-bound simvastatin in 96-well plates. To maximise likelihood of identifying meaningful interactions between simvastatin and vascular peptides, we used a validated photo-immobilisation method to apply a series of different chemical linkers to bind simvastatin so as to present multiple orientations of its constituent components to potential targets. Three rounds of biopanning identified consistent interaction with the clone expressing part of the gene GJC3, which maps to Homo sapiens chromosome 7, and codes for gap junction gamma-3 protein, also known as connexin 30.2/31.3 (mouse connexin Cx29). Further analysis indicated the binding site to be for the N-terminal domain putatively ‘regulating’ connexin hemichannel and gap junction pores. Using immunohistochemistry we found connexin 30.2/31.3 to be present in samples of artery similar to those used to prepare the bacteriophage library. Surface plasmon resonance revealed that a 25 amino acid synthetic peptide representing the discovered N-terminus did not interact with simvastatin lactone, but did bind to the hydrolysed HMG CoA inhibitor, simvastatin acid. This interaction was also seen for fluvastatin. The gap junction blockers carbenoxolone and flufenamic acid also interacted with the same peptide providing insight into potential site of binding. These findings raise key questions about the functional significance of GJC3 transcripts in the vasculature and

  1. A Rab-GAP TBC Domain Protein Binds Hepatitis C Virus NS5A and Mediates Viral Replication▿

    PubMed Central

    Sklan, Ella H.; Staschke, Kirk; Oakes, Tina M.; Elazar, Menashe; Winters, Mark; Aroeti, Benjamin; Danieli, Tsafi; Glenn, Jeffrey S.

    2007-01-01

    Hepatitis C virus (HCV) is an important cause of liver disease worldwide. Current therapies are inadequate for most patients. Using a two-hybrid screen, we isolated a novel cellular binding partner interacting with the N terminus of HCV nonstructural protein NS5A. This partner contains a TBC Rab-GAP (GTPase-activating protein) homology domain found in all known Rab-activating proteins. As the first described interaction between such a Rab-GAP and a viral protein, this finding suggests a new mechanism whereby viruses may subvert host cell machinery for mediating the endocytosis, trafficking, and sorting of their own proteins. Moreover, depleting the expression of this partner severely impairs HCV RNA replication with no obvious effect on cell viability. These results suggest that pharmacologic disruption of this NS5A-interacting partner can be contemplated as a potential new antiviral strategy against a pathogen affecting nearly 3% of the world's population. PMID:17686842

  2. Isotope Coded Labeling for Accelerated Protein Interaction Profiling using MS

    PubMed Central

    Venable, John D.; Steckler, Caitlin; Ou, Weijia; Grünewald, Jan; Agarwalla, Sanjay; Brock, Ansgar

    2015-01-01

    Protein interaction surface mapping using MS is widely applied but comparatively resource intensive. Here a workflow adaptation for use of isotope coded tandem mass tags for the purpose is reported. The key benefit of improved throughput derived from sample acquisition multiplexing and automated analysis is shown to be maintained in the new application. Mapping of the epitopes of two monoclonal antibodies on their respective targets serves to illustrate the novel approach. We conclude that the approach enables mapping of interactions by MS at significantly larger scales than hereto possible. PMID:26151661

  3. The cyst nematode SPRYSEC protein RBP-1 elicits Gpa2- and RanGAP2-dependent plant cell death.

    PubMed

    Sacco, Melanie Ann; Koropacka, Kamila; Grenier, Eric; Jaubert, Marianne J; Blanchard, Alexandra; Goverse, Aska; Smant, Geert; Moffett, Peter

    2009-08-01

    Plant NB-LRR proteins confer robust protection against microbes and metazoan parasites by recognizing pathogen-derived avirulence (Avr) proteins that are delivered to the host cytoplasm. Microbial Avr proteins usually function as virulence factors in compatible interactions; however, little is known about the types of metazoan proteins recognized by NB-LRR proteins and their relationship with virulence. In this report, we demonstrate that the secreted protein RBP-1 from the potato cyst nematode Globodera pallida elicits defense responses, including cell death typical of a hypersensitive response (HR), through the NB-LRR protein Gpa2. Gp-Rbp-1 variants from G. pallida populations both virulent and avirulent to Gpa2 demonstrated a high degree of polymorphism, with positive selection detected at numerous sites. All Gp-RBP-1 protein variants from an avirulent population were recognized by Gpa2, whereas virulent populations possessed Gp-RBP-1 protein variants both recognized and non-recognized by Gpa2. Recognition of Gp-RBP-1 by Gpa2 correlated to a single amino acid polymorphism at position 187 in the Gp-RBP-1 SPRY domain. Gp-RBP-1 expressed from Potato virus X elicited Gpa2-mediated defenses that required Ran GTPase-activating protein 2 (RanGAP2), a protein known to interact with the Gpa2 N terminus. Tethering RanGAP2 and Gp-RBP-1 variants via fusion proteins resulted in an enhancement of Gpa2-mediated responses. However, activation of Gpa2 was still dependent on the recognition specificity conferred by amino acid 187 and the Gpa2 LRR domain. These results suggest a two-tiered process wherein RanGAP2 mediates an initial interaction with pathogen-delivered Gp-RBP-1 proteins but where the Gpa2 LRR determines which of these interactions will be productive. PMID:19714238

  4. The Cyst Nematode SPRYSEC Protein RBP-1 Elicits Gpa2- and RanGAP2-Dependent Plant Cell Death

    PubMed Central

    Sacco, Melanie Ann; Blanchard, Alexandra; Goverse, Aska; Smant, Geert; Moffett, Peter

    2009-01-01

    Plant NB-LRR proteins confer robust protection against microbes and metazoan parasites by recognizing pathogen-derived avirulence (Avr) proteins that are delivered to the host cytoplasm. Microbial Avr proteins usually function as virulence factors in compatible interactions; however, little is known about the types of metazoan proteins recognized by NB-LRR proteins and their relationship with virulence. In this report, we demonstrate that the secreted protein RBP-1 from the potato cyst nematode Globodera pallida elicits defense responses, including cell death typical of a hypersensitive response (HR), through the NB-LRR protein Gpa2. Gp-Rbp-1 variants from G. pallida populations both virulent and avirulent to Gpa2 demonstrated a high degree of polymorphism, with positive selection detected at numerous sites. All Gp-RBP-1 protein variants from an avirulent population were recognized by Gpa2, whereas virulent populations possessed Gp-RBP-1 protein variants both recognized and non-recognized by Gpa2. Recognition of Gp-RBP-1 by Gpa2 correlated to a single amino acid polymorphism at position 187 in the Gp-RBP-1 SPRY domain. Gp-RBP-1 expressed from Potato virus X elicited Gpa2-mediated defenses that required Ran GTPase-activating protein 2 (RanGAP2), a protein known to interact with the Gpa2 N terminus. Tethering RanGAP2 and Gp-RBP-1 variants via fusion proteins resulted in an enhancement of Gpa2-mediated responses. However, activation of Gpa2 was still dependent on the recognition specificity conferred by amino acid 187 and the Gpa2 LRR domain. These results suggest a two-tiered process wherein RanGAP2 mediates an initial interaction with pathogen-delivered Gp-RBP-1 proteins but where the Gpa2 LRR determines which of these interactions will be productive. PMID:19714238

  5. Bisphenol A accelerates capacitation-associated protein tyrosine phosphorylation of rat sperm by activating protein kinase A.

    PubMed

    Wan, Xiaofeng; Ru, Yanfei; Chu, Chen; Ni, Zimei; Zhou, Yuchuan; Wang, Shoulin; Zhou, Zuomin; Zhang, Yonglian

    2016-06-01

    Bisphenol A (BPA) is a synthetic estrogen-mimic chemical. It has been shown to affect many reproductive endpoints. However, the effect of BPA on the mature sperm and the mechanism of its action are not clear yet. Here, our in vitro studies indicated that BPA could accelerate sperm capacitation-associated protein tyrosine phosphorylation in time- and dose-dependent manners. In vivo, the adult male rats exposed to a high dose of BPA could result in a significant increase in sperm activity. Further investigation demonstrated that BPA could accelerate capacitation-associated protein tyrosine phosphorylation even if sperm were incubated in medium devoid of BSA, HCO3 (-), and Ca(2+) However, this action of BPA stimulation could be blocked by H89, a highly selective blocker of protein kinase A (PKA), but not by KH7, a specific inhibitor of adenylyl cyclase. These data suggest that BPA may activate PKA to affect sperm functions and male fertility. PMID:27174873

  6. Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model

    PubMed Central

    Neuwald, Andrew F; Liu, Jun S

    2004-01-01

    Background Certain protein families are highly conserved across distantly related organisms and belong to large and functionally diverse superfamilies. The patterns of conservation present in these protein sequences presumably are due to selective constraints maintaining important but unknown structural mechanisms with some constraints specific to each family and others shared by a larger subset or by the entire superfamily. To exploit these patterns as a source of functional information, we recently devised a statistically based approach called contrast hierarchical alignment and interaction network (CHAIN) analysis, which infers the strengths of various categories of selective constraints from co-conserved patterns in a multiple alignment. The power of this approach strongly depends on the quality of the multiple alignments, which thus motivated development of theoretical concepts and strategies to improve alignment of conserved motifs within large sets of distantly related sequences. Results Here we describe a hidden Markov model (HMM), an algebraic system, and Markov chain Monte Carlo (MCMC) sampling strategies for alignment of multiple sequence motifs. The MCMC sampling strategies are useful both for alignment optimization and for adjusting position specific background amino acid frequencies for alignment uncertainties. Associated statistical formulations provide an objective measure of alignment quality as well as automatic gap penalty optimization. Improved alignments obtained in this way are compared with PSI-BLAST based alignments within the context of CHAIN analysis of three protein families: Giα subunits, prolyl oligopeptidases, and transitional endoplasmic reticulum (p97) AAA+ ATPases. Conclusion While not entirely replacing PSI-BLAST based alignments, which likewise may be optimized for CHAIN analysis using this approach, these motif-based methods often more accurately align very distantly related sequences and thus can provide a better measure of

  7. Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.

    PubMed

    Neuwald, Andrew F; Altschul, Stephen F

    2016-05-01

    We describe a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA) that, as implemented in the program GISMO and applied to large numbers of diverse sequences, is more accurate than the popular MSA programs MUSCLE, MAFFT, Clustal-Ω and Kalign. Features of GISMO central to its performance are: (i) It employs a "top-down" strategy with a favorable asymptotic time complexity that first identifies regions generally shared by all the input sequences, and then realigns closely related subgroups in tandem. (ii) It infers position-specific gap penalties that favor insertions or deletions (indels) within each sequence at alignment positions in which indels are invoked in other sequences. This favors the placement of insertions between conserved blocks, which can be understood as making up the proteins' structural core. (iii) It uses a Bayesian statistical measure of alignment quality based on the minimum description length principle and on Dirichlet mixture priors. Consequently, GISMO aligns sequence regions only when statistically justified. This is unlike methods based on the ad hoc, but widely used, sum-of-the-pairs scoring system, which will align random sequences. (iv) It defines a system for exploring alignment space that provides natural avenues for further experimentation through the development of new sampling strategies for more efficiently escaping from suboptimal traps. GISMO's superior performance is illustrated using 408 protein sets containing, on average, 235 sequences. These sets correspond to NCBI Conserved Domain Database alignments, which have been manually curated in the light of available crystal structures, and thus provide a means to assess alignment accuracy. GISMO fills a different niche than other MSA programs, namely identifying and aligning a conserved domain present within a large, diverse set of full length sequences. The GISMO program is available at http://gismo.igs.umaryland.edu/. PMID:27192614

  8. Extracellular Superoxide Dismutase Regulates the Expression of Small GTPase Regulatory Proteins GEFs, GAPs, and GDI

    PubMed Central

    Laukkanen, Mikko O.; Cammarota, Francesca; Esposito, Tiziana; Salvatore, Marco; Castellone, Maria D.

    2015-01-01

    Extracellular superoxide dismutase (SOD3), which catalyzes the dismutation of superoxide anions to hydrogen peroxide at the cell membranes, regulates the cellular growth in a dose-dependent manner. This enzyme induces primary cell proliferation and immortalization at low expression levels whereas it activates cancer barrier signaling through the p53-p21 pathway at high expression levels, causing growth arrest, senescence, and apoptosis. Because previous reports suggested that the SOD3–induced reduction in the rates of cellular growth and migration also occurred in the absence of functional p53 signaling, in the current study we investigated the SOD3-induced growth-suppressive mechanisms in anaplastic thyroid cancer cells. Based on our data, the robust over-expression of SOD3 increased the level of phosphorylation of the EGFR, ERBB2, RYK, ALK, FLT3, and EPHA10 receptor tyrosine kinases with the consequent downstream activation of the SRC, FYN, YES, HCK, and LYN kinases. However, pull-down experiments focusing on the small GTPase RAS, RAC, CDC42, and RHO revealed a reduced level of growth and migration signal transduction, such as the lack of stimulation of the mitogen pathway, in the SOD3 over-expressing cells, which was confirmed by MEK1/2 and ERK1/2 Western blotting analysis. Interestingly, the mRNA expression analyses indicated that SOD3 regulated the expression of guanine nucleotide-exchange factors (RHO GEF16, RAL GEF RGL1), GTPase-activating proteins (ARFGAP ADAP2, RAS GAP RASAL1, RGS4), and a Rho guanine nucleotide-disassociation inhibitor (RHO GDI 2) in a dose dependent manner, thus controlling signaling through the small G protein GTPases. Therefore, our current data may suggest the occurrence of dose-dependent SOD3–driven control of the GTP loading of small G proteins indicating a novel growth regulatory mechanism of this enzyme. PMID:25751262

  9. Extracellular superoxide dismutase regulates the expression of small gtpase regulatory proteins GEFs, GAPs, and GDI.

    PubMed

    Laukkanen, Mikko O; Cammarota, Francesca; Esposito, Tiziana; Salvatore, Marco; Castellone, Maria D

    2015-01-01

    Extracellular superoxide dismutase (SOD3), which catalyzes the dismutation of superoxide anions to hydrogen peroxide at the cell membranes, regulates the cellular growth in a dose-dependent manner. This enzyme induces primary cell proliferation and immortalization at low expression levels whereas it activates cancer barrier signaling through the p53-p21 pathway at high expression levels, causing growth arrest, senescence, and apoptosis. Because previous reports suggested that the SOD3-induced reduction in the rates of cellular growth and migration also occurred in the absence of functional p53 signaling, in the current study we investigated the SOD3-induced growth-suppressive mechanisms in anaplastic thyroid cancer cells. Based on our data, the robust over-expression of SOD3 increased the level of phosphorylation of the EGFR, ERBB2, RYK, ALK, FLT3, and EPHA10 receptor tyrosine kinases with the consequent downstream activation of the SRC, FYN, YES, HCK, and LYN kinases. However, pull-down experiments focusing on the small GTPase RAS, RAC, CDC42, and RHO revealed a reduced level of growth and migration signal transduction, such as the lack of stimulation of the mitogen pathway, in the SOD3 over-expressing cells, which was confirmed by MEK1/2 and ERK1/2 Western blotting analysis. Interestingly, the mRNA expression analyses indicated that SOD3 regulated the expression of guanine nucleotide-exchange factors (RHO GEF16, RAL GEF RGL1), GTPase-activating proteins (ARFGAP ADAP2, RAS GAP RASAL1, RGS4), and a Rho guanine nucleotide-disassociation inhibitor (RHO GDI 2) in a dose dependent manner, thus controlling signaling through the small G protein GTPases. Therefore, our current data may suggest the occurrence of dose-dependent SOD3-driven control of the GTP loading of small G proteins indicating a novel growth regulatory mechanism of this enzyme. PMID:25751262

  10. Expression of gap junctional connexin proteins in ovine fetal ovaries: Effects of maternal diet

    PubMed Central

    Grazul-Bilska, A.T.; Vonnahme, K.A.; Bilski, J.J.; Borowczyk, E.; Soni, D.; Mikkelson, B.; Johnson, M.L.; Reynolds, L.P.; Redmer, D.A.; Caton, J.S.

    2011-01-01

    Gap junctions have been implicated in the regulation of cellular metabolism and the coordination of cellular functions during growth and differentiation of organs and tissues, and gap junctions play a major role in direct cell-cell communication. Gap junctional channels and connexin (Cx) proteins have been detected in adult ovaries in several species. Furthermore, it has been demonstrated that several environmental factors including maternal diet may affect fetal organ growth and function. To determine if maternal diet impacts expression of connexin (Cx) 26, 32, 37 and 43 in fetal ovaries, sheep were fed a maintenance (M) diet with adequate (A) selenium (Se) or high (H) Se levels from 21 days before breeding to day 132 of pregnancy. From day 50 to 132 of pregnancy (tissue collection day), a portion of the ewes from ASe and HSe groups was fed restricted (R; 60% of M) diet. Sections of fetal ovaries were immunostained for the presence of connexins followed by image analysis. All four connexins were detected, but the distribution pattern differed. Cx26 was immunolocalized in the oocytes from primordial, primary, secondary and antral follicles, in granulosa and theca layers of secondary and antral follicles, stroma and blood vessels; Cx32 was in oocytes, granulosa and theca cells in a portion of antral follicles; Cx37 was on the borders between oocyte and granulosa/cumulus cells of primordial to antral follicles, and in endothelium; and Cx43 was on cellular borders in granulosa and theca layers, and between oocyte and granulosa/cumulus cells of primordial to antral follicles. Maternal diet affected Cx26 and Cx43 expression; Cx26 in granulosa layer of antral follicles was decreased (P<0.01) by HSe in M and R diets, and Cx43 in granulosa layer of primary and granulosa and theca of antral follicles was increased (P<0.05) by M diet with HSe. Thus, connexins may be differentially involved in regulation of fetal ovarian function in sheep. These data emphasize the importance

  11. Three-dimensional Non-vacuum Pulsar Outer-gap Model: Localized Acceleration Electric Field in the Higher Altitudes

    NASA Astrophysics Data System (ADS)

    Hirotani, Kouichi

    2015-01-01

    We investigate the particle accelerator that arises in a rotating neutron-star magnetosphere. Simultaneously solving the Poisson equation for the electro-static potential, the Boltzmann equations for relativistic electrons and positrons, and the radiative transfer equation, we demonstrate that the electric field is substantially screened along the magnetic field lines by pairs that are created and separated within the accelerator. As a result, the magnetic-field-aligned electric field is localized in higher altitudes near the light cylinder and efficiently accelerates the positrons created in the lower altitudes outward but does not accelerate the electrons inward. The resulting photon flux becomes predominantly outward, leading to typical double-peak light curves, which are commonly observed from many high-energy pulsars.

  12. THREE-DIMENSIONAL NON-VACUUM PULSAR OUTER-GAP MODEL: LOCALIZED ACCELERATION ELECTRIC FIELD IN THE HIGHER ALTITUDES

    SciTech Connect

    Hirotani, Kouichi

    2015-01-10

    We investigate the particle accelerator that arises in a rotating neutron-star magnetosphere. Simultaneously solving the Poisson equation for the electro-static potential, the Boltzmann equations for relativistic electrons and positrons, and the radiative transfer equation, we demonstrate that the electric field is substantially screened along the magnetic field lines by pairs that are created and separated within the accelerator. As a result, the magnetic-field-aligned electric field is localized in higher altitudes near the light cylinder and efficiently accelerates the positrons created in the lower altitudes outward but does not accelerate the electrons inward. The resulting photon flux becomes predominantly outward, leading to typical double-peak light curves, which are commonly observed from many high-energy pulsars.

  13. Revisiting G3BP1 as a RasGAP Binding Protein: Sensitization of Tumor Cells to Chemotherapy by the RasGAP 317–326 Sequence Does Not Involve G3BP1

    PubMed Central

    Annibaldi, Alessandro; Dousse, Aline; Martin, Sophie; Tazi, Jamal; Widmann, Christian

    2011-01-01

    RasGAP is a multifunctional protein that controls Ras activity and that is found in chromosomal passenger complexes. It also negatively or positively regulates apoptosis depending on the extent of its cleavage by caspase-3. RasGAP has been reported to bind to G3BP1 (RasGAP SH3-domain-binding protein 1), a protein regulating mRNA stability and stress granule formation. The region of RasGAP (amino acids 317–326) thought to bind to G3BP1 corresponds exactly to the sequence within fragment N2, a caspase-3-generated fragment of RasGAP, that mediates sensitization of tumor cells to genotoxins. While assessing the contribution of G3BP1 in the anti-cancer function of a cell-permeable peptide containing the 317–326 sequence of RasGAP (TAT-RasGAP317–326), we found that, in conditions where G3BP1 and RasGAP bind to known partners, no interaction between G3BP1 and RasGAP could be detected. TAT-RasGAP317–326 did not modulate binding of G3BP1 to USP10, stress granule formation or c-myc mRNA levels. Finally, TAT-RasGAP317–326 was able to sensitize G3BP1 knock-out cells to cisplatin-induced apoptosis. Collectively these results indicate that G3BP1 and its putative RasGAP binding region have no functional influence on each other. Importantly, our data provide arguments against G3BP1 being a genuine RasGAP-binding partner. Hence, G3BP1-mediated signaling may not involve RasGAP. PMID:22205990

  14. Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties

    PubMed Central

    Neuwald, Andrew F.; Altschul, Stephen F.

    2016-01-01

    We describe a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA) that, as implemented in the program GISMO and applied to large numbers of diverse sequences, is more accurate than the popular MSA programs MUSCLE, MAFFT, Clustal-Ω and Kalign. Features of GISMO central to its performance are: (i) It employs a “top-down” strategy with a favorable asymptotic time complexity that first identifies regions generally shared by all the input sequences, and then realigns closely related subgroups in tandem. (ii) It infers position-specific gap penalties that favor insertions or deletions (indels) within each sequence at alignment positions in which indels are invoked in other sequences. This favors the placement of insertions between conserved blocks, which can be understood as making up the proteins’ structural core. (iii) It uses a Bayesian statistical measure of alignment quality based on the minimum description length principle and on Dirichlet mixture priors. Consequently, GISMO aligns sequence regions only when statistically justified. This is unlike methods based on the ad hoc, but widely used, sum-of-the-pairs scoring system, which will align random sequences. (iv) It defines a system for exploring alignment space that provides natural avenues for further experimentation through the development of new sampling strategies for more efficiently escaping from suboptimal traps. GISMO’s superior performance is illustrated using 408 protein sets containing, on average, 235 sequences. These sets correspond to NCBI Conserved Domain Database alignments, which have been manually curated in the light of available crystal structures, and thus provide a means to assess alignment accuracy. GISMO fills a different niche than other MSA programs, namely identifying and aligning a conserved domain present within a large, diverse set of full length sequences. The GISMO program is available at http://gismo.igs.umaryland.edu/. PMID

  15. Closing the Achievement Gap: A Summer School Program to Accelerate the Academic Performance of Economically Disadvantaged Students

    ERIC Educational Resources Information Center

    Gonzalez, Ramon Michael

    2013-01-01

    With the increasing disparity in educational outcomes among economically and racially different groups of students, summer school has received attention from school reformers as a means to close the achievement gap. Given the interest in this topic by educators, researchers, and policymakers, there is little research on the impact of summer school…

  16. Displacement of plasma protein and conduction velocity in rats under action of acceleration forces and hypokinesia

    NASA Technical Reports Server (NTRS)

    Baranski, S.; Edelwejn, Z.; Wojtkowiak, M.

    1980-01-01

    The permeability of capillary vessels was investigated in order to determine if acceleration alone or following prolonged hypokinesia would induce changes in the vascular wall leading to the penetration by l-albumins and/or proteins with larger molecules. In rats undergoing action of +5 Gz accelerations, no increase in vascular permeability, as tested with the use of (Cr-5k)-globulin, was demostrated. In rats immobilized for 4 weeks before centrifugation, rather weak migration of (Cr-51)-globulin from the vessels was observed. Immobilization resulted also in lowering of conduction velocity in the sciatic nerve.

  17. Identification of a novel zinc finger protein gene (ZNF298) in the GAP2 of human chromosome 21q

    SciTech Connect

    Shibuya, Kazunori; Kudoh, Jun; Okui, Michiyo; Shimizu, Nobuyoshi . E-mail: shimizu@dmb.med.keio.ac.jp

    2005-07-01

    We have isolated a novel zinc finger protein gene, designated ZNF298, as a candidate gene for a particular phenotype of Down syndrome or bipolar affective disorder (BPAD) which maps to human chromosome 21q22.3. ZNF298 gene consists of 25 exons spanning approximately 80 kb in a direction from the telomere to centromere. There are four kinds of transcripts that harbor three types of 3' UTR. These four transcripts (ZNF298a, ZNF298b, ZNF298c, and ZNF298d) contain putative open reading frames encoding 1178, 1198, 555, and 515 amino acids, respectively. ZNF298 gene was ubiquitously expressed in various tissues at very low level. The protein motif analysis revealed that ZNF298 proteins contain a SET [Su(var)3-9, Enhancer-of-zeste, Trithorax] domain, multiple C2H2-type zinc finger (ZnF{sub C}2H2) domains, several nuclear localization signals (NLSs), and PEST sequences. Nuclear localization of ZNF298 protein was confirmed by transfection of expression vector of GFP-tagged protein into two human cell lines. Interestingly, this gene crosses over a clone gap (GAP2) remaining in the band 21q22.3. We obtained the DNA fragments corresponding to GAP2 using ZNF298 cDNA sequence as anchor primers for PCR and determined its genomic DNA sequence.

  18. Non-catalytic roles for TET1 protein negatively regulating neuronal differentiation through srGAP3 in neuroblastoma cells.

    PubMed

    Gao, Jie; Ma, Yue; Fu, Hua-Lin; Luo, Qian; Wang, Zhen; Xiao, Yu-Huan; Yang, Hao; Cui, Da-Xiang; Jin, Wei-Lin

    2016-05-01

    The methylcytosine dioxygenases TET proteins (TET1, TET2, and TET3) play important regulatory roles in neural function. In this study, we investigated the role of TET proteins in neuronal differentiation using Neuro2a cells as a model. We observed that knockdown of TET1, TET2 or TET3 promoted neuronal differentiation of Neuro2a cells, and their overexpression inhibited VPA (valproic acid)-induced neuronal differentiation, suggesting all three TET proteins negatively regulate neuronal differentiation of Neuro2a cells. Interestingly, the inducing activity of TET protein is independent of its enzymatic activity. Our previous studies have demonstrated that srGAP3 can negatively regulate neuronal differentiation of Neuro2a cells. Furthermore, we revealed that TET1 could positively regulate srGAP3 expression independent of its catalytic activity, and srGAP3 is required for TET-mediated neuronal differentiation of Neuro2a cells. The results presented here may facilitate better understanding of the role of TET proteins in neuronal differentiation, and provide a possible therapy target for neuroblastoma. PMID:27113584

  19. FPGA accelerator for protein secondary structure prediction based on the GOR algorithm

    PubMed Central

    2011-01-01

    Background Protein is an important molecule that performs a wide range of functions in biological systems. Recently, the protein folding attracts much more attention since the function of protein can be generally derived from its molecular structure. The GOR algorithm is one of the most successful computational methods and has been widely used as an efficient analysis tool to predict secondary structure from protein sequence. However, the execution time is still intolerable with the steep growth in protein database. Recently, FPGA chips have emerged as one promising application accelerator to accelerate bioinformatics algorithms by exploiting fine-grained custom design. Results In this paper, we propose a complete fine-grained parallel hardware implementation on FPGA to accelerate the GOR-IV package for 2D protein structure prediction. To improve computing efficiency, we partition the parameter table into small segments and access them in parallel. We aggressively exploit data reuse schemes to minimize the need for loading data from external memory. The whole computation structure is carefully pipelined to overlap the sequence loading, computing and back-writing operations as much as possible. We implemented a complete GOR desktop system based on an FPGA chip XC5VLX330. Conclusions The experimental results show a speedup factor of more than 430x over the original GOR-IV version and 110x speedup over the optimized version with multi-thread SIMD implementation running on a PC platform with AMD Phenom 9650 Quad CPU for 2D protein structure prediction. However, the power consumption is only about 30% of that of current general-propose CPUs. PMID:21342582

  20. Acceleration through passive destabilization: protein folding in a weak hydrophobic environment

    NASA Astrophysics Data System (ADS)

    Jewett, Andrew; Baumketner, Andrij; Shea, Joan-Emma

    2004-03-01

    The GroEL chaperonin is a biomolecule which assists the folding of an extremely diverse range of proteins in Eubacteria. Some proteins undergo many rounds of ATP-regulated binding and dissociation from GroEL/ES before folding. It has been proposed that transient stress from ATP-regulated binding and release from GroEL/ES frees frustrated proteins from misfolded conformations. However recent evidence suggests that chaperonin-accelerated protein folding can take place entirely within a mutated GroEL+ES cavity that is unable to open and release the protein. Using molecular dynamics, we demonstrate that static confinement within a weakly hydrophobic (attractive) cavity (similar to the interior of the cavity formed by the GroEL+ES complex) is sufficient to significantly accelerate the folding of a highly frustrated protein-like heteropolymer. Our frustrated molecule benifits kinetically from a static hydrophobic environment that destabilizes misfolded conformations. This may shed light on the mechanisms used by other chaperones which do not depend on ATP.

  1. Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamics

    PubMed Central

    Mohammad Hosseini Naveh, Zeynab; Malliavin, Therese E.; Maragliano, Luca; Cottone, Grazia; Ciccotti, Giovanni

    2014-01-01

    Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit. PMID:24551117

  2. Nitrogen catabolite repressible GAP1 promoter, a new tool for efficient recombinant protein production in S. cerevisiae

    PubMed Central

    2013-01-01

    Background Decades of work requiring heterologous expression of eukaryotic proteins have shown that no expression system can be considered as the panacea and the appropriate expression strategy is often protein-dependent. In a large number of cases, yeasts have proven to be reliable organisms for heterologous protein expression by combining eukaryotic cellular organization with the ease of use of simpler microorganisms. Results During this work, a novel promoter system based on the nitrogen catabolite regulation has been developed to produce the general amino acid permease (Gap1) in its natural host, the yeast Saccharomyces cerevisiae. A simple purification protocol was also established that allows to purify milligrams of Gap1 from cells cultivated in a five liters bio-reactor. In order to test the ability of the system to be used for expression of other proteins, the yeast specific transporter of γ-aminobutyric acid (Uga4), a human vesicular transporter of glutamate (Vglut1) and a small secreted glycoprotein (MD-2) were also expressed using the nitrogen catabolite regulation. All proteins were fused to GFP and their presence and localization were confirmed by western blot analysis and fluorescence microscopy. Conclusions Our work shows that the nitrogen catabolite repressible GAP1 promoter can be used to obtain high levels of recombinant protein while allowing for large biomass production in S. cerevisiae. This approach can be used to express membrane and soluble proteins from higher eukaryotes (from yeast to human). Therefore, this system stands as a promising alternative to commonly used expression procedure in yeasts. PMID:24369062

  3. GTPase acceleration as the rate-limiting step in Arabidopsis G protein-coupled sugar signaling.

    PubMed

    Johnston, Christopher A; Taylor, J Philip; Gao, Yajun; Kimple, Adam J; Grigston, Jeffrey C; Chen, Jin-Gui; Siderovski, David P; Jones, Alan M; Willard, Francis S

    2007-10-30

    Heterotrimeric G protein signaling is important for cell-proliferative and glucose-sensing signal transduction pathways in the model plant organism Arabidopsis thaliana. AtRGS1 is a seven-transmembrane, RGS domain-containing protein that is a putative membrane receptor for d-glucose. Here we show, by using FRET, that d-glucose alters the interaction between the AtGPA1 and AtRGS1 in vivo. AtGPA1 is a unique heterotrimeric G protein alpha subunit that is constitutively GTP-bound given its high spontaneous nucleotide exchange coupled with slow GTP hydrolysis. Analysis of a point mutation in AtRGS1 that abrogates GTPase-accelerating activity demonstrates that the regulation of AtGPA1 GTP hydrolysis mediates sugar signal transduction during Arabidopsis development, in contrast to animals where nucleotide exchange is the limiting step in the heterotrimeric G protein nucleotide cycle. PMID:17951432

  4. Photoperiod-Dependent Effects of 4-tert-Octylphenol on Adherens and Gap Junction Proteins in Bank Vole Seminiferous Tubules

    PubMed Central

    Kuras, Paulina; Lydka-Zarzycka, Marta; Bilinska, Barbara

    2013-01-01

    In the present study we evaluated in vivo and in vitro effects of 4-tert-octylphenol (OP) on the expression and distribution of adherens and gap junction proteins, N-cadherin, β-catenin, and connexin 43 (Cx43), in testes of seasonally breeding rodents, bank voles. We found that in bank vole testes expression and distribution of N-cadherin, β-catenin, and Cx43 were photoperiod dependent. Long-term treatment with OP (200 mg/kg b.w.) resulted in the reduction of junction proteins expressions (P < 0.05, P < 0.01) and their delocalization in the testes of males kept in long photoperiod, whereas in short-day animals slight increase of Cx43 (P < 0.05), N-cadherin, and β-catenin (statistically nonsignificant) levels was observed. Effects of OP appeared to be independent of FSH and were maintained during in vitro organ culture, indicating that OP acts directly on adherens and gap junction proteins in the testes. An experiment performed using an antiestrogen ICI 182,780 demonstrated that the biological effects of OP on β-catenin and Cx43 involve an estrogen receptor-mediated response. Taken together, in bank vole organization of adherens and gap junctions and their susceptibility to OP are related to the length of photoperiod. Alterations in cadherin/catenin and Cx43-based junction may partially result from activation of estrogen receptor α and/or β signaling pathway. PMID:23737770

  5. Tyrosine-rich acidic matrix protein (TRAMP) accelerates collagen fibril formation in vitro.

    PubMed

    MacBeath, J R; Shackleton, D R; Hulmes, D J

    1993-09-15

    Tyrosine-rich acidic matrix protein (TRAMP) is a recently discovered protein that co-purifies with porcine skin lysyl oxidase and is equivalent to the M(r) 22,000 extracellular matrix protein from bovine skin that co-purifies with dermatan sulfate proteoglycans (Cronshaw, A. D., MacBeath, J. R. E., Shackleton, D. R., Collins, J. F., Fothergill-Gilmore, L. A., and Hulmes, D. J. S. (1993) Matrix 13, 255-266; Neame, P. J., Choi, H. U., and Rosenberg, L. C. (1989) J. Biol. Chem. 264, 5474-5479). The effect of TRAMP on collagen fibril formation was studied in vitro by reconstitution of fibrils from lathyritic rat skin collagen I. Fibril formation was initiated by the warm start procedure, in which acidic collagen solutions and double strength neutral buffer, both preincubated separately at 34 degrees C, were mixed. When monitored by turbidimetry, TRAMP was found to accelerate collagen fibril formation. Acceleration occurred at sub-stoichiometric molar ratios of TRAMP collagen, and the presence of TRAMP stabilized the fibrils against low temperature dissociation. It was confirmed by centrifugation that the amount of fibrillar collagen formed in the presence of TRAMP was greater than in its absence. By SDS-polyacrylamide gel electrophoresis and scanning densitometry, binding of TRAMP to collagen was detected that approached saturation with a molar ratio of TRAMP to collagen of approximately 1:2. Fibrils formed in the presence of TRAMP were normal when observed by electron microscopy, although fibril diameters were smaller than the controls. TRAMP was found to partially reverse the inhibitory effects of urea and increased ionic strength on the kinetics of fibril formation, although inhibition by glucose was unaffected. TRAMP also accelerated the assembly of pepsin-treated collagen, where the non-helical, telopeptide regions were partially removed. Acceleration of collagen fibril formation by TRAMP is discussed in the light of the known effects of other extracellular matrix

  6. Retention of chimeric Tat2-Gap1 permease in the endoplasmic reticulum induces unfolded protein response in Saccharomyces cerevisiae.

    PubMed

    Mochizuki, Takahiro; Kimata, Yukio; Uemura, Satoshi; Abe, Fumiyoshi

    2015-08-01

    In Saccharomyces cerevisiae, high-affinity tryptophan import is performed by subtle mechanisms involving tryptophan permease Tat2. We have shown that Tat2 requires 15 amino acid residues in the transmembrane domains (TMDs) for its import activity, whereas leucine permease Bap2 requires only seven corresponding residues for its leucine import. For this reason, the structure of Tat2 is elaborately designed to transport the hydrophobic and bulky tryptophan. Newly synthesized cell surface proteins first undergo endoplasmic reticulum (ER)-associated quality check before entering the secretory pathway. In this study, we used domain replacement with general amino acid permease Gap1 to show that Tat2 chimeric proteins were dysfunctional when TMD10 or TMD11 was replaced. These chimeras formed large 270-800-kDa protein complexes and were stably retained in the ER membrane without efficient degradation. In contrast, Tat2 chimeras of TMD9 or TMD12 retained some of their tryptophan import activity and underwent vacuolar degradation as observed with wild-type Tat2. Thus, ours results suggest that TMD10 and TMD11 are essential for the correct folding of Tat2, probably because of their interdomain interactions. Notably, overexpression of Tat2-Gap1 chimera of TMD10 activated the unfolded protein response (UPR) element-lacZ reporter, suggesting that ER retention of the protein aggregates induces the UPR. PMID:26071436

  7. Automated Technologies and Novel Techniques to Accelerate Protein Crystallography for Structrual Genomics

    SciTech Connect

    Manjasetty,B.; Turnbull, A.; Panjikar, S.; Bussow, K.; Chance, M.

    2008-01-01

    The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis.

  8. Distribution of the gap junction protein connexin 35 in the central nervous system of developing zebrafish larvae

    PubMed Central

    Jabeen, Shaista; Thirumalai, Vatsala

    2013-01-01

    Gap junctions are membrane specializations that allow the passage of ions and small molecules from one cell to another. In vertebrates, connexins are the protein subunits that assemble to form gap junctional plaques. Connexin-35 (Cx35) is the fish ortholog of mammalian Cx36, which is enriched in the retina and the brain and has been shown to form neuronal gap junctions. As a first step toward understanding the role of neuronal gap junctions in central nervous system (CNS) development, we describe here the distribution of Cx35 in the CNS during zebrafish development. Cx35 expression is first seen at 1 day post fertilization (dpf) along cell boundaries throughout the nervous system. At 2 dpf, Cx35 immunoreactivity appears in commissures and fiber tracts throughout the CNS and along the edges of the tectal neuropil. In the rhombencephalon, the Mauthner neurons and fiber tracts show strong Cx35 immunoreactivity. As the larva develops, the commissures and fiber tracts continue to be immunoreactive for Cx35. In addition, the area of the tectal neuropil stained increases vastly and tectal commissures are visible. Furthermore, at 4–5 dpf, Cx35 is seen in the habenulae, cerebellum and in radial glia lining the rhombencephalic ventricle. This pattern of Cx35 immunoreactivity is stable at least until 15 dpf. To test whether the Cx35 immunoreactivity seen corresponds to functional gap junctional coupling, we documented the number of dye-coupled neurons in the hindbrain. We found several dye-coupled neurons within the reticulospinal network indicating functional gap junctional connectivity in the developing zebrafish brain. PMID:23717264

  9. A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation.

    PubMed

    Patel, Avinash; Lee, Hyun O; Jawerth, Louise; Maharana, Shovamayee; Jahnel, Marcus; Hein, Marco Y; Stoynov, Stoyno; Mahamid, Julia; Saha, Shambaditya; Franzmann, Titus M; Pozniakovski, Andrej; Poser, Ina; Maghelli, Nicola; Royer, Loic A; Weigert, Martin; Myers, Eugene W; Grill, Stephan; Drechsel, David; Hyman, Anthony A; Alberti, Simon

    2015-08-27

    Many proteins contain disordered regions of low-sequence complexity, which cause aging-associated diseases because they are prone to aggregate. Here, we study FUS, a prion-like protein containing intrinsically disordered domains associated with the neurodegenerative disease ALS. We show that, in cells, FUS forms liquid compartments at sites of DNA damage and in the cytoplasm upon stress. We confirm this by reconstituting liquid FUS compartments in vitro. Using an in vitro "aging" experiment, we demonstrate that liquid droplets of FUS protein convert with time from a liquid to an aggregated state, and this conversion is accelerated by patient-derived mutations. We conclude that the physiological role of FUS requires forming dynamic liquid-like compartments. We propose that liquid-like compartments carry the trade-off between functionality and risk of aggregation and that aberrant phase transitions within liquid-like compartments lie at the heart of ALS and, presumably, other age-related diseases. PMID:26317470

  10. Impact of obesity on 7,12-dimethylbenz[a]anthracene-induced altered ovarian connexin gap junction proteins in female mice

    SciTech Connect

    Ganesan, Shanthi Nteeba, Jackson Keating, Aileen F.

    2015-01-01

    The ovarian gap junction proteins alpha 4 (GJA4 or connexin 37; CX37), alpha 1 (GJA1 or connexin 43; CX43) and gamma 1 (GJC1 or connexin 45; CX45) are involved in cell communication and folliculogenesis. 7,12-dimethylbenz[a]anthracene (DMBA) alters Cx37 and Cx43 expression in cultured neonatal rat ovaries. Additionally, obesity has an additive effect on DMBA-induced ovarian cell death and follicle depletion, thus, we investigated in vivo impacts of obesity and DMBA on CX protein levels. Ovaries were collected from lean and obese mice aged 6, 12, 18, or 24 wks. A subset of 18 wk old mice (lean and obese) were dosed with sesame oil or DMBA (1 mg/kg; ip) for 14 days and ovaries collected 3 days thereafter. Cx43 and Cx45 mRNA and protein levels decreased (P < 0.05) after 18 wks while Cx37 mRNA and protein levels decreased (P < 0.05) after 24 wks in obese ovaries. Cx37 mRNA and antral follicle protein staining intensity were reduced (P < 0.05) by obesity while total CX37 protein was reduced (P < 0.05) in DMBA exposed obese ovaries. Cx43 mRNA and total protein levels were decreased (P < 0.05) by DMBA in both lean and obese ovaries while basal protein staining intensity was reduced (P < 0.05) in obese controls. Cx45 mRNA, total protein and protein staining intensity level were decreased (P < 0.05) by obesity. These data support that obesity temporally alters gap junction protein expression and that DMBA-induced ovotoxicity may involve reduced gap junction protein function. - Highlights: • Ovarian gap junction proteins are affected by ovarian aging and obesity. • DMBA exposure negatively impacts gap junction proteins. • Altered gap junction proteins may contribute to infertility.

  11. Anabolic therapy with growth hormone accelerates protein gain in surgical patients requiring nutritional rehabilitation.

    PubMed Central

    Byrne, T A; Morrissey, T B; Gatzen, C; Benfell, K; Nattakom, T V; Scheltinga, M R; LeBoff, M S; Ziegler, T R; Wilmore, D W

    1993-01-01

    .05). GH administration altered substrate oxidation (respiratory quotient = 0.94 +/- 0.02 GH vs. 1.17 +/- 0.05 STD, p < or = 0.0002) and the use of available energy, resulting in a 66% increase in the efficiency of protein deposition (13.37 +/- 0.8 g/1000 kcal vs. 8.04 g +/- 3.06 g/1000 kcal, p < or = 0.04). CONCLUSIONS: GH administration accelerated protein gain in stable adult patients receiving aggressive nutritional therapy without a significant increase in body fat or a disproportionate expansion of ECW. GH therapy accelerated nutritional repletion and, therefore, may shorten the convalescence of the malnourished patient requiring a major surgical procedure. PMID:8215633

  12. Conditioning nerve crush accelerates cytoskeletal protein transport in sprouts that form after a subsequent crush

    SciTech Connect

    McQuarrie, I.G.; Jacob, J.M. )

    1991-03-01

    To examine the relationship between axonal outgrowth and the delivery of cytoskeletal proteins to the growing axon tip, outgrowth was accelerated by using a conditioning nerve crush. Because slow component b (SCb) of axonal transport is the most rapid vehicle for carrying cytoskeletal proteins to the axon tip, the rate of SCb was measured in conditioned vs. sham-conditioned sprouts. In young Sprague-Dawley rats, the conditioning crush was made to sciatic nerve branches at the knee; 14 days later, the test crush was made where the L4 and L5 spinal nerves join to form the sciatic nerve in the flank. Newly synthesized proteins were labeled in motor neurons by injecting {sup 35}S-methionine into the lumbar spinal cord 7 days before the test crush. The wave of pulse-labeled SCb proteins reached the crush by the time it was made and subsequently entered sprouts. The nerve was removed and sectioned for SDS-PAGE and fluorography 4-12 days after the crush. Tubulins, neurofilament proteins, and representative 'cytomatrix' proteins (actin, calmodulin, and putative microtubule-associated proteins) were removed from gels for liquid scintillation counting. Labeled SCb proteins entered sprouts without first accumulating in parent axon stumps, presumably because sprouts begin to grow within hours after axotomy. The peak of SCb moved 11% faster in conditioned than in sham-conditioned sprouts: 3.0 vs. 2.7 mm/d (p less than 0.05). To confirm that sprouts elongate more rapidly when a test crush is preceded by a conditioning crush, outgrowth distances were measured in a separate group of rats by labeling fast axonal transport with {sup 3}H-proline 24 hours before nerve retrieval.

  13. Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics

    NASA Astrophysics Data System (ADS)

    Chen, Chun-Long; Qi, Jiahui; Tao, Jinhui; Zuckermann, Ronald N.; Deyoreo, James J.

    2014-09-01

    In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic and hydrophobic interactions, with hydrophobic interactions playing the dominant role. While either strong electrostatic or hydrophobic interactions inhibit growth and reduces expression of the {104} faces, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate electrostatic interactions allow peptoids to weakly adsorb while moderate hydrophobic interactions cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of the {104} faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications.

  14. Tuning calcite morphology and growth acceleration by a rational design of highly stable protein-mimetics

    SciTech Connect

    Chen, Chunlong; Qi, Jiahui; Tao, Jinhui; Zuckermann, Ronald; De Yoreo, James J.

    2014-09-05

    In nature, proteins play a significant role in biomineral formation. One of the ultimate goals of bioinspired materials science is to develop highly stable synthetic molecules that mimic the function of these natural proteins by controlling crystal formation. Here, we demonstrate that both the morphology and the degree of acceleration or inhibition observed during growth of calcite in the presence of peptoids can be rationally tuned by balancing the electrostatic interactions (EI) and hydrophobic interactions (HI), with HI playing the dominant role. While either strong EI or HI inhibit growth and suppress (104) face expression, correlations between peptoid-crystal binding energies and observed changes in calcite growth indicate moderate EI allow peptoids to weakly adsorb while moderate HI cause disruption of surface-adsorbed water layers, leading to growth acceleration with retained expression of (104) faces. This study provides fundamental principles for designing peptoids as crystallization promoters, and offers a straightforward screening method based on macroscopic crystal morphology. Because peptoids are sequence-specific, highly stable, and easily synthesized, peptoid-enhanced crystallization offers a broad range of potential applications.

  15. Decreased Gap Width in a Cylindrical High-Field Asymmetric Waveform Ion Mobility Spectrometry Device Improves Protein Discovery.

    PubMed

    Swearingen, Kristian E; Winget, Jason M; Hoopmann, Michael R; Kusebauch, Ulrike; Moritz, Robert L

    2015-12-15

    High-field asymmetric waveform ion mobility spectrometry (FAIMS) is an atmospheric pressure ion mobility technique that separates gas phase ions according to their characteristic dependence of ion mobility on electric field strength. FAIMS can be implemented as a means of automated gas-phase fractionation in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments. We modified a commercially available cylindrical FAIMS device by enlarging the inner electrode, thereby narrowing the gap and increasing the effective field strength. This modification provided a nearly 4-fold increase in FAIMS peak capacity over the optimally configured unmodified device. We employed the modified FAIMS device for on-line fractionation in a proteomic analysis of a complex sample and observed major increases in protein discovery. NanoLC-FAIMS-MS/MS of an unfractionated yeast tryptic digest using the modified FAIMS device identified 53% more proteins than were identified using an unmodified FAIMS device and 98% more proteins than were identified with unaided nanoLC-MS/MS. We describe here the development of a nanoLC-FAIMS-MS/MS protocol that provides automated gas-phase fractionation for proteomic analysis of complex protein digests. We compare this protocol against prefractionation of peptides with isoelectric focusing and demonstrate that FAIMS fractionation yields comparable protein recovery while significantly reducing the amount of sample required and eliminating the need for additional sample handling. PMID:26560994

  16. RhoGAP68F controls transport of adhesion proteins in Rab4 endosomes to modulate epithelial morphogenesis of Drosophila leg discs

    PubMed Central

    de Madrid, Beatriz Hernandez; Greenberg, Lina; Hatini, Victor

    2015-01-01

    SUMMARY Elongation and invagination of epithelial tissues are fundamental developmental processes that contribute to the morphogenesis of embryonic and adult structures and are dependent on coordinated remodeling of cell-cell contacts. The morphogenesis of Drosophila leg imaginal discs depends on extensive remodeling of cell contacts and thus provides a useful system with which to investigate the underlying mechanisms. The small Rho GTPase regulator RhoGAP68F has been previously implicated in leg morphogenesis. It consists of an N-terminal Sec14 domain and a C-terminal GAP domain. Here we examined the molecular function and role of RhoGAP68F in epithelial remodeling. We find that depletion of RhoGAP68F impairs epithelial remodeling from a pseudostratified to simple, while overexpression of RhoGAP68F causes tears of lateral cell-cell contacts and thus impairs epithelial integrity. We show that the RhoGAP68F protein localizes to Rab4 recycling endosomes and forms a complex with the Rab4 protein. The Sec14 domain is sufficient for localizing to Rab4 endosomes, while the activity of the GAP domain is dispensable. RhoGAP68F, in turn, inhibits the scission and movement of Rab4 endosomes involved in transport the adhesion proteins Fasciclin3 and E-cadherin back to cell-cell contacts. Expression of RhoGAP68F is upregulated during prepupal development suggesting that RhoGAP68F decreases the transport of key adhesion proteins to the cell surface during this developmental stage to decrease the strength of adhesive cell-cell contacts and thereby facilitate epithelial remodeling and leg morphogenesis. PMID:25617722

  17. Acceleration of crossbridge kinetics by protein kinase A phosphorylation of cardiac myosin binding protein C modulates cardiac function.

    PubMed

    Tong, Carl W; Stelzer, Julian E; Greaser, Marion L; Powers, Patricia A; Moss, Richard L

    2008-10-24

    Normal cardiac function requires dynamic modulation of contraction. beta1-adrenergic-induced protein kinase (PK)A phosphorylation of cardiac myosin binding protein (cMyBP)-C may regulate crossbridge kinetics to modulate contraction. We tested this idea with mechanical measurements and echocardiography in a mouse model lacking 3 PKA sites on cMyBP-C, ie, cMyBP-C(t3SA). We developed the model by transgenic expression of mutant cMyBP-C with Ser-to-Ala mutations on the cMyBP-C knockout background. Western blots, immunofluorescence, and in vitro phosphorylation combined to show that non-PKA-phosphorylatable cMyBP-C expressed at 74% compared to normal wild-type (WT) and was correctly positioned in the sarcomeres. Similar expression of WT cMyBP-C at 72% served as control, ie, cMyBP-C(tWT). Skinned myocardium responded to stretch with an immediate increase in force, followed by a transient relaxation of force and finally a delayed development of force, ie, stretch activation. The rate constants of relaxation, k(rel) (s-1), and delayed force development, k(df) (s-1), in the stretch activation response are indicators of crossbridge cycling kinetics. cMyBP-C(t3SA) myocardium had baseline k(rel) and k(df) similar to WT myocardium, but, unlike WT, k(rel) and k(df) were not accelerated by PKA treatment. Reduced dobutamine augmentation of systolic function in cMyBP-C(t3SA) hearts during echocardiography corroborated the stretch activation findings. Furthermore, cMyBP-C(t3SA) hearts exhibited basal echocardiographic findings of systolic dysfunction, diastolic dysfunction, and hypertrophy. Conversely, cMyBP-C(tWT) hearts performed similar to WT. Thus, PKA phosphorylation of cMyBP-C accelerates crossbridge kinetics and loss of this regulation leads to cardiac dysfunction. PMID:18802026

  18. Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding

    PubMed Central

    Basu, Sankar; Bhattacharyya, Dhananjay; Banerjee, Rahul

    2012-01-01

    Complementarity, in terms of both shape and electrostatic potential, has been quantitatively estimated at protein-protein interfaces and used extensively to predict the specific geometry of association between interacting proteins. In this work, we attempted to place both binding and folding on a common conceptual platform based on complementarity. To that end, we estimated (for the first time to our knowledge) electrostatic complementarity (Em) for residues buried within proteins. Em measures the correlation of surface electrostatic potential at protein interiors. The results show fairly uniform and significant values for all amino acids. Interestingly, hydrophobic side chains also attain appreciable complementarity primarily due to the trajectory of the main chain. Previous work from our laboratory characterized the surface (or shape) complementarity (Sm) of interior residues, and both of these measures have now been combined to derive two scoring functions to identify the native fold amid a set of decoys. These scoring functions are somewhat similar to functions that discriminate among multiple solutions in a protein-protein docking exercise. The performances of both of these functions on state-of-the-art databases were comparable if not better than most currently available scoring functions. Thus, analogously to interfacial residues of protein chains associated (docked) with specific geometry, amino acids found in the native interior have to satisfy fairly stringent constraints in terms of both Sm and Em. The functions were also found to be useful for correctly identifying the same fold for two sequences with low sequence identity. Finally, inspired by the Ramachandran plot, we developed a plot of Sm versus Em (referred to as the complementarity plot) that identifies residues with suboptimal packing and electrostatics which appear to be correlated to coordinate errors. PMID:22713576

  19. The gap junctional protein INX-14 functions in oocyte precursors to promote C. elegans sperm guidance

    PubMed Central

    Edmonds, Johnathan W.; McKinney, Shauna L.; Prasain, Jeevan K.; Miller, Michael A.

    2011-01-01

    Innexins are the subunits of invertebrate gap junctions. Here we show that the innexin INX-14 promotes sperm guidance to the fertilization site in the C. elegans hermaphrodite reproductive tract. inx-14 loss causes cell nonautonomous defects in sperm migration velocity and directional velocity. Results from genetic and immunocytochemical analyses provide strong evidence that INX-14 acts in transcriptionally active oocyte precursors in the distal gonad, not in transcriptionally inactive oocytes that synthesize prostaglandin sperm-attracting cues. Somatic gonadal sheath cell interaction is necessary for INX-14 function, likely via INX-8 and INX-9 expressed in sheath cells. However, electron microscopy has not identified gap junctions in oocyte precursors, suggesting that INX-14 acts in a channel-independent manner or INX-14 channels are difficult to document. INX-14 promotes prostaglandin signaling to sperm at a step after F-series prostaglandin synthesis in oocytes. Taken together, our results support the model that INX-14 functions in a somatic gonad/germ cell signaling mechanism essential for sperm function. We propose that this mechanism regulates the transcription of a factor(s) that modulates prostaglandin metabolism, transport, or activity in the reproductive tract. PMID:21889935

  20. Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution

    PubMed Central

    Barrozo, Alexandre; Borstnar, Rok; Marloie, Gaël; Kamerlin, Shina Caroline Lynn

    2012-01-01

    Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies. PMID:23202907

  1. Toxicity of TDCPP and TCEP on PC12 cell: changes in CAMKII, GAP43, tubulin and NF-H gene and protein levels.

    PubMed

    Ta, Na; Li, Chaonan; Fang, Yanjun; Liu, Huanliang; Lin, Bencheng; Jin, Hong; Tian, Lei; Zhang, Huashan; Zhang, Wei; Xi, Zhuge

    2014-06-16

    TDCPP and TCEP are two major types of organophosphorus flame retardants (OPFRs) that are bioaccumulative and persistent in the environment. The toxicity effects of TDCPP and TCEP on PC12 cell are not well understood. In the present study, we investigated morphology, viability and apoptosis in cultured PC12 cells in response to TDCPP and TCEP. The mRNA and protein expression levels of CAMKII, GAP43, tubulin and NF-H were quantified in PC12 cells treated with varying concentrations of the two agents. Results indicate that, upon treatment with the two OPFRs, cell growth decreased, apoptosis increased, morphology was altered and significant changes were found in the gene and protein levels. Treatment with TDCPP caused a reduction in the levels of each of the six proteins studied and in the gene levels of GAP43, NF-H and the two tubulins, but it resulted in an increase in CAMKII gene levels. Treatment with TCEP resulted in similar changes in gene levels to TDCPP and led to decreases in the protein levels of GAP43 and the tubulins while increasing the CAMKII and NF-H protein levels. These results suggest that changes in the gene and protein levels of the regulatory proteins (CAMKII, GAP43) and the structural proteins (tubulin, NF-H) are due to different mechanisms of the toxins, and these proteins may be useful biomarkers for the cytotoxicity and neurotoxicity. PMID:24717766

  2. Characterization of the Rac-GAP (Rac-GTPase-activating protein) activity of beta2-chimaerin, a 'non-protein kinase C' phorbol ester receptor.

    PubMed Central

    Caloca, Maria Jose; Wang, HongBin; Kazanietz, Marcelo G

    2003-01-01

    The regulation and function of beta2-chimaerin, a novel receptor for the phorbol ester tumour promoters and the second messenger DAG (diacylglycerol), is largely unknown. As with PKC (protein kinase C) isoenzymes, phorbol esters bind to beta2-chimaerin with high affinity and promote its subcellular distribution. beta2-Chimaerin has GAP (GTPase-activating protein) activity for the small GTP-binding protein Rac1, but for not Cdc42 or RhoA. We show that acidic phospholipids enhanced its catalytic activity markedly in vitro, but the phorbol ester PMA had no effect. beta2-Chimaerin and other chimaerin isoforms decreased cellular levels of Rac-GTP markedly in COS-1 cells and impaired GTP loading on to Rac upon EGF (epidermal growth factor) receptor stimulation. Deletional and mutagenesis analysis determined that the beta2-chimaerin GAP domain is essential for this effect. Interestingly, PMA has a dual effect on Rac-GTP levels in COS-1 cells. PMA increased Rac-GTP levels in the absence of a PKC inhibitor, whereas under conditions in which PKC activity is inhibited, PMA markedly decreased Rac-GTP levels and potentiated the effect of beta2-chimaerin. Chimaerin isoforms co-localize at the plasma membrane with active Rac, and these results were substantiated by co-immunoprecipitation assays. In summary, the novel phorbol ester receptor beta2-chimaerin regulates the activity of the Rac GTPase through its GAP domain, leading to Rac inactivation. These results strongly emphasize the high complexity of DAG signalling due to the activation of PKC-independent pathways, and cast doubts regarding the selectivity of phorbol esters and DAG analogues as selective PKC activators. PMID:12877655

  3. Meeting report on protein particles and immunogenicity of therapeutic proteins: filling in the gaps in risk evaluation and mitigation.

    PubMed

    Carpenter, John; Cherney, Barry; Lubinecki, Anthony; Ma, Stacey; Marszal, Ewa; Mire-Sluis, Anthony; Nikolai, Thomas; Novak, Jeanne; Ragheb, Jack; Simak, Jan

    2010-09-01

    This meeting was successful in achieving its main goals: (1) summarize currently available information on the origin, detection, quantification and characterization of sub-visible particulates in protein products, available information on their clinical importance, and potential strategies for evaluating and mitigating risk to product quality, and (2) foster communication among academic, industry, and regulatory scientists to define the capabilities of current analytical methods, to promote the development of improved methods, and to stimulate investigations into the impact of large protein aggregates on immunogenicity. There was a general consensus that a considerable amount of interesting scientific information was presented and many stimulating conversations were begun. It is clear that this aspect of protein characterization is in its initial stages. As the development of these new methods progress, it is hoped that they will shed light on the role of protein particulates on product quality, safety, and efficacy. A topic which seemed appropriate for short term follow up was to hold further discussions concerning the development and preparation of one or more standard preparations of protein particulates. This would be generally useful to facilitate comparison of results among different studies, methods, and laboratories, and to foster further development of a common understanding among laboratories and health authorities which is essential to making further progress in this emerging field. PMID:20702108

  4. Chondroitin Sulfate Accelerates Trans-Golgi-to-Surface Transport of Proteoglycan Amyloid Precursor Protein.

    PubMed

    Mihov, Deyan; Raja, Eva; Spiess, Martin

    2015-08-01

    The amyloid precursor protein (APP) is a membrane protein implicated in the pathogenesis of Alzheimer's disease. APP is a part-time proteoglycan, as splice variants lacking exon 15 are modified by a chondroitin sulfate glycosaminoglycan (GAG) chain. Investigating the effect of the GAG chain on the trafficking of APP in non-polarized cells, we found it to increase the steady-state surface-to-intracellular distribution, to reduce the rate of endocytosis and to accelerate transport kinetics from the trans-Golgi network (TGN) to the plasma membrane. Deletion of the cytosolic domain resulted in delayed surface arrival of GAG-free APP, but did not affect the rapid export kinetics of the proteoglycan form. Protein-free GAG chains showed the same TGN-to-cell surface transport kinetics as proteoglycan APP. Endosome ablation experiments were performed to distinguish between indirect endosomal and direct pathways to the cell surface. Surprisingly, TGN-to-cell surface transport of both GAG-free and proteoglycan APP was found to be indirect via transferrin-positive endosomes. Our results show that GAGs act as alternative sorting determinants in cellular APP transport that are dominant over cytoplasmic signals and involve distinct sorting mechanisms. PMID:25951880

  5. Mitochondrial Complex I Deficiency Increases Protein Acetylation and Accelerates Heart Failure

    PubMed Central

    Karamanlidis, Georgios; Lee, Chi Fung; Garcia-Menendez, Lorena; Kolwicz, Stephen C.; Suthammarak, Wichit; Gong, Guohua; Sedensky, Margaret M.; Morgan, Philip G.; Wang, Wang; Tian, Rong

    2013-01-01

    Summary Mitochondrial respiratory dysfunction is linked to the pathogenesis of multiple diseases including heart failure but the specific mechanisms for this link remain largely elusive. We modeled the impairment of mitochondrial respiration by inactivation of the Ndufs4 gene, a protein critical for Complex I (C-I) assembly, in the mouse heart (cKO). While C-I supported respiration decreased by >40%, the cKO mice maintained normal cardiac function in vivo and high-energy phosphate content in isolated perfused hearts. However, the cKO mice developed accelerated heart failure after pressure overload or repeated pregnancy. Decreased NAD+/NADH ratio by C-I deficiency inhibited Sirt3 activity, leading to increase in protein acetylation, and sensitization of the permeability transition in mitochondria (mPTP). NAD+ precursor supplementation to cKO mice partially normalized the NAD+/NADH ratio, protein acetylation and mPTP sensitivity. These findings describe a mechanism connecting mitochondrial dysfunction to the susceptibility to diseases and propose a potential therapeutic target. PMID:23931755

  6. Lymphocytes accelerate epithelial tight junction assembly: role of AMP-activated protein kinase (AMPK).

    PubMed

    Tang, Xiao Xiao; Chen, Hao; Yu, Sidney; Zhang, Li; Caplan, Michael J; Chan, Hsiao Chang

    2010-01-01

    The tight junctions (TJs), characteristically located at the apicolateral borders of adjacent epithelial cells, are required for the proper formation of epithelial cell polarity as well as for sustaining the mucosal barrier to the external environment. The observation that lymphocytes are recruited by epithelial cells to the sites of infection [1] suggests that they may play a role in the modulation of epithelial barrier function and thus contribute to host defense. To test the ability of lymphocytes to modulate tight junction assembly in epithelial cells, we set up a lymphocyte-epithelial cell co-culture system, in which Madin-Darby canine kidney (MDCK) cells, a well-established model cell line for studying epithelial TJ assembly [2], were co-cultured with mouse lymphocytes to mimic an infection state. In a typical calcium switch experiment, the TJ assembly in co-culture was found to be accelerated compared to that in MDCK cells alone. This accelaration was found to be mediated by AMP-activated protein kinase (AMPK). AMPK activation was independent of changes in cellular ATP levels but it was found to be activated by the pro-inflammatory cytokine TNF-alpha. Forced suppression of AMPK, either with a chemical inhibitor or by knockdown, abrogated the accelerating effect of lymphocytes on TJ formation. Similar results were also observed in a co-culture with lymphocytes and Calu-3 human airway epithelial cells, suggesting that the activation of AMPK may be a general mechanism underlying lymphocyte-accelerated TJ assembly in different epithelia. These results suggest that signals from lymphocytes, such as cytokines, facilitate TJ assembly in epithelial cells via the activation of AMPK. PMID:20808811

  7. Expression and modulation of connexin 30.2, a novel gap junction protein in the mouse retina.

    PubMed

    Müller, Luis Pérez de Sevilla; Dedek, Karin; Janssen-Bienhold, Ulrike; Meyer, Arndt; Kreuzberg, Maria M; Lorenz, Susanne; Willecke, Klaus; Weiler, Reto

    2010-07-01

    Mammalian retinae express multiple connexins that mediate the metabolic and electrical coupling of various cell types. In retinal neurons, only connexin 36, connexin 45, connexin 50, and connexin 57 have been described so far. Here, we present an analysis of a novel retinal connexin, connexin 30.2 (Cx30.2), and its regulation in the mouse retina. To analyze the expression of Cx30.2, we used a transgenic mouse line in which the coding region of Cx30.2 was replaced by lacZ reporter DNA. We detected the lacZ signal in the nuclei of neurons located in the inner nuclear layer and the ganglion cell layer (GCL). In this study, we focused on the GCL and characterized the morphology of the Cx30.2-expressing cells. Using immunocytochemistry and intracellular dye injections, we found six different types of Cx30.2-expressing ganglion cells: one type of ON-OFF, three types of OFF, and two types of ON ganglion cells; among the latter was the RG A1 type. We show that RG A1 cells were heterologously coupled to numerous displaced amacrine cells. Our results suggest that these gap junction channels may be heterotypic, involving Cx30.2 and a connexin yet unidentified in the mouse retina. Gap junction coupling can be modulated by protein kinases, a process that plays a major role in retinal adaptation. Therefore, we studied the protein kinase-induced modulation of coupling between RG A1 and displaced amacrine cells. Our data provide evidence that coupling of RG A1 cells to displaced amacrine cells is mediated by Cx30.2 and that the extent of this coupling is modulated by protein kinase C. PMID:20537217

  8. Metal-assisted and microwave accelerated-evaporative crystallization: Application to lysozyme protein

    NASA Astrophysics Data System (ADS)

    Mauge-Lewis, Kevin

    In response to the growing need for new crystallization techniques that afford for rapid processing times along with control over crystal size and distribution, the Aslan Research Group has recently demonstrated the use of Metal-Assisted and Microwave-Accelerated Evaporative Crystallization MA-MAEC technique in conjunction with metal nanoparticles and nanostructures for the crystallization of amino acids and organic small molecules. In this study, we have employed the newly developed MA-MAEC technique to the accelerated crystallization of chicken egg-white lysozyme on circular crystallization platforms in order to demonstrate the proof-of-principle application of the method for protein crystallization. The circular crystallization platforms are constructed in-house from poly (methyl methacrylate) (PMMA) and silver nanoparticle films (SNFs), indium tin oxide (ITO) and iron nano-columns. In this study, we prove the MA-MAEC method to be a more effective technique in the rapid crystallization of macromolecules in comparison to other conventional methods. Furthermore, we demonstrate the use of the novel iCrystal system, which incorporates the use of continuous, low wattage heating to facilitate the rapid crystallization of the lysozyme while still retaining excellent crystal quality. With the incorporation of the iCrystal system, we observe crystallization times that are even shorter than those produced by the MA-MAEC technique using a conventional microwave oven in addition to significantly improved crystal quality.

  9. Replacing a single atom accelerates the folding of a protein and increases its thermostability.

    PubMed

    Arnold, Ulrich; Raines, Ronald T

    2016-07-12

    The conformational attributes of proline can have a substantial effect on the folding of polypeptide chains into a native structure and on the stability of that structure. Replacing the 4S hydrogen of a proline residue with fluorine is known to elicit stereoelectronic effects that favor a cis peptide bond. Here, semisynthesis is used to replace a cis-proline residue in ribonuclease A with (2S,4S)-4-fluoroproline. This subtle substitution accelerates the folding of the polypeptide chain into its three-dimensional structure and increases the thermostability of that structure without compromising its catalytic activity. Thus, an appropriately situated fluorine can serve as a prosthetic atom in the context of a protein. PMID:27336677

  10. Acceleration of protein folding by four orders of magnitude through a single amino acid substitution

    PubMed Central

    Roderer, Daniel J. A.; Schärer, Martin A.; Rubini, Marina; Glockshuber, Rudi

    2015-01-01

    Cis prolyl peptide bonds are conserved structural elements in numerous protein families, although their formation is energetically unfavorable, intrinsically slow and often rate-limiting for folding. Here we investigate the reasons underlying the conservation of the cis proline that is diagnostic for the fold of thioredoxin-like thiol-disulfide oxidoreductases. We show that replacement of the conserved cis proline in thioredoxin by alanine can accelerate spontaneous folding to the native, thermodynamically most stable state by more than four orders of magnitude. However, the resulting trans alanine bond leads to small structural rearrangements around the active site that impair the function of thioredoxin as catalyst of electron transfer reactions by more than 100-fold. Our data provide evidence for the absence of a strong evolutionary pressure to achieve intrinsically fast folding rates, which is most likely a consequence of proline isomerases and molecular chaperones that guarantee high in vivo folding rates and yields. PMID:26121966

  11. Acceleration of protein folding by four orders of magnitude through a single amino acid substitution.

    PubMed

    Roderer, Daniel J A; Schärer, Martin A; Rubini, Marina; Glockshuber, Rudi

    2015-01-01

    Cis prolyl peptide bonds are conserved structural elements in numerous protein families, although their formation is energetically unfavorable, intrinsically slow and often rate-limiting for folding. Here we investigate the reasons underlying the conservation of the cis proline that is diagnostic for the fold of thioredoxin-like thiol-disulfide oxidoreductases. We show that replacement of the conserved cis proline in thioredoxin by alanine can accelerate spontaneous folding to the native, thermodynamically most stable state by more than four orders of magnitude. However, the resulting trans alanine bond leads to small structural rearrangements around the active site that impair the function of thioredoxin as catalyst of electron transfer reactions by more than 100-fold. Our data provide evidence for the absence of a strong evolutionary pressure to achieve intrinsically fast folding rates, which is most likely a consequence of proline isomerases and molecular chaperones that guarantee high in vivo folding rates and yields. PMID:26121966

  12. Rescue of perfluorooctanesulfonate (PFOS)-mediated Sertoli cell injury by overexpression of gap junction protein connexin 43

    PubMed Central

    Li, Nan; Mruk, Dolores D.; Chen, Haiqi; Wong, Chris K. C.; Lee, Will M.; Cheng, C. Yan

    2016-01-01

    Perfluorooctanesulfonate (PFOS) is an environmental toxicant used in developing countries, including China, as a stain repellent for clothing, carpets and draperies, but it has been banned in the U.S. and Canada since the late 2000s. PFOS perturbed the Sertoli cell tight junction (TJ)-permeability barrier, causing disruption of actin microfilaments in cell cytosol, perturbing the localization of cell junction proteins (e.g., occluden-ZO-1, N-cadherin-ß-catenin). These changes destabilized Sertoli cell blood-testis barrier (BTB) integrity. These findings suggest that human exposure to PFOS might induce BTB dysfunction and infertility. Interestingly, PFOS-induced Sertoli cell injury associated with a down-regulation of the gap junction (GJ) protein connexin43 (Cx43). We next investigated if overexpression of Cx43 in Sertoli cells could rescue the PFOS-induced cell injury. Indeed, overexpression of Cx43 in Sertoli cells with an established TJ-barrier blocked the disruption in PFOS-induced GJ-intercellular communication, resulting in the re-organization of actin microfilaments, which rendered them similar to those in control cells. Furthermore, cell adhesion proteins that utilized F-actin for attachment became properly distributed at the cell-cell interface, resealing the disrupted TJ-barrier. In summary, Cx43 is a good target that might be used to manage PFOS-induced reproductive dysfunction. PMID:27436542

  13. Rescue of perfluorooctanesulfonate (PFOS)-mediated Sertoli cell injury by overexpression of gap junction protein connexin 43.

    PubMed

    Li, Nan; Mruk, Dolores D; Chen, Haiqi; Wong, Chris K C; Lee, Will M; Cheng, C Yan

    2016-01-01

    Perfluorooctanesulfonate (PFOS) is an environmental toxicant used in developing countries, including China, as a stain repellent for clothing, carpets and draperies, but it has been banned in the U.S. and Canada since the late 2000s. PFOS perturbed the Sertoli cell tight junction (TJ)-permeability barrier, causing disruption of actin microfilaments in cell cytosol, perturbing the localization of cell junction proteins (e.g., occluden-ZO-1, N-cadherin-ß-catenin). These changes destabilized Sertoli cell blood-testis barrier (BTB) integrity. These findings suggest that human exposure to PFOS might induce BTB dysfunction and infertility. Interestingly, PFOS-induced Sertoli cell injury associated with a down-regulation of the gap junction (GJ) protein connexin43 (Cx43). We next investigated if overexpression of Cx43 in Sertoli cells could rescue the PFOS-induced cell injury. Indeed, overexpression of Cx43 in Sertoli cells with an established TJ-barrier blocked the disruption in PFOS-induced GJ-intercellular communication, resulting in the re-organization of actin microfilaments, which rendered them similar to those in control cells. Furthermore, cell adhesion proteins that utilized F-actin for attachment became properly distributed at the cell-cell interface, resealing the disrupted TJ-barrier. In summary, Cx43 is a good target that might be used to manage PFOS-induced reproductive dysfunction. PMID:27436542

  14. Rescue of perfluorooctanesulfonate (PFOS)-mediated Sertoli cell injury by overexpression of gap junction protein connexin 43

    NASA Astrophysics Data System (ADS)

    Li, Nan; Mruk, Dolores D.; Chen, Haiqi; Wong, Chris K. C.; Lee, Will M.; Cheng, C. Yan

    2016-07-01

    Perfluorooctanesulfonate (PFOS) is an environmental toxicant used in developing countries, including China, as a stain repellent for clothing, carpets and draperies, but it has been banned in the U.S. and Canada since the late 2000s. PFOS perturbed the Sertoli cell tight junction (TJ)-permeability barrier, causing disruption of actin microfilaments in cell cytosol, perturbing the localization of cell junction proteins (e.g., occluden-ZO-1, N-cadherin-ß-catenin). These changes destabilized Sertoli cell blood-testis barrier (BTB) integrity. These findings suggest that human exposure to PFOS might induce BTB dysfunction and infertility. Interestingly, PFOS-induced Sertoli cell injury associated with a down-regulation of the gap junction (GJ) protein connexin43 (Cx43). We next investigated if overexpression of Cx43 in Sertoli cells could rescue the PFOS-induced cell injury. Indeed, overexpression of Cx43 in Sertoli cells with an established TJ-barrier blocked the disruption in PFOS-induced GJ-intercellular communication, resulting in the re-organization of actin microfilaments, which rendered them similar to those in control cells. Furthermore, cell adhesion proteins that utilized F-actin for attachment became properly distributed at the cell-cell interface, resealing the disrupted TJ-barrier. In summary, Cx43 is a good target that might be used to manage PFOS-induced reproductive dysfunction.

  15. A split-ubiquitin two-hybrid screen for proteins physically interacting with the yeast amino acid transceptor Gap1 and ammonium transceptor Mep2.

    PubMed

    Van Zeebroeck, Griet; Kimpe, Marlies; Vandormael, Patrick; Thevelein, Johan M

    2011-01-01

    Several nutrient permeases have been identified in yeast, which combine a transport and receptor function, and are called transceptors. The Gap1 general amino acid permease and the Mep2 ammonium permease mediate rapid activation by amino acids and by ammonium, respectively, of the protein kinase A (PKA) pathway in nitrogen-starved cells. Their mode of action is not well understood. Both proteins are subject to complex controls governing their intracellular trafficking. Using a split-ubiquitin yeast two-hybrid screen with Gap1 or Mep2 as bait, we identified proteins putatively interacting with Gap1 and/or Mep2. They are involved in glycosylation, the secretory pathway, sphingolipid biosynthesis, cell wall biosynthesis and other processes. For several candidate interactors, determination of transport and signaling capacity, as well as localization of Gap1 or Mep2 in the corresponding deletion strains, confirmed a functional interaction with Gap1 and/or Mep2. Also common interacting proteins were identified. Transport and signaling were differentially affected in specific deletion strains, clearly separating the two functions of the transceptors and confirming that signaling does not require transport. We identified two new proteins, Bsc6 and Yir014w, that affect trafficking or downregulation of Gap1. Deletion of EGD2, YNL024c or SPC2 inactivates Gap1 transport and signaling, while its plasma membrane level appears normal.. Vma4 is required for Mep2 expression, while Gup1 appears to be required for proper distribution of Mep2 over the plasma membrane. Some of the interactions were confirmed by GST pull-down assay, using the C-terminal tail of Gap1 or Mep2 expressed in E.coli. Our results reveal the effectiveness of split-ubiquitin two-hybrid screening for identification of proteins functionally interacting with membrane proteins. They provide several candidate proteins involved in the transport and signaling function or in the complex trafficking control of the Gap1

  16. Identification of two proteins that bind to a pyrimidine-rich sequence in the 3'-untranslated region of GAP-43 mRNA.

    PubMed Central

    Irwin, N; Baekelandt, V; Goritchenko, L; Benowitz, L I

    1997-01-01

    GAP-43 is a membrane phosphoprotein that is important for the development and plasticity of neural connections. In undifferentiated PC12 pheochromocytoma cells, GAP-43 mRNA degrades rapidly ( t = 5 h), but becomes stable when cells are treated with nerve growth factor. To identify trans- acting factors that may influence mRNA stability, we combined column chromatography and gel mobility shift assays to isolate GAP-43 mRNA binding proteins from neonatal bovine brain tissue. This resulted in the isolation of two proteins that bind specifically and competitively to a pyrimidine-rich sequence in the 3'-untranslated region of GAP-43 mRNA. Partial amino acid sequencing revealed that one of the RNA binding proteins coincides with FBP (far upstream element binding protein), previously characterized as a protein that resembles hnRNP K and which binds to a single-stranded, pyrimidine-rich DNA sequence upstream of the c -myc gene to activate its expression. The other binding protein shares sequence homology with PTB, a polypyrimidine tract binding protein implicated in RNA splicing and regulation of translation initiation. The two proteins bind to a 26 nt pyrimidine-rich sequence lying 300 nt downstream of the end of the coding region, in an area shown by others to confer instability on a reporter mRNA in transient transfection assays. We therefore propose that FBP and the PTB-like protein may compete for binding at the same site to influence the stability of GAP-43 mRNA. PMID:9092640

  17. UV Irradiation Accelerates Amyloid Precursor Protein (APP) Processing and Disrupts APP Axonal Transport

    PubMed Central

    Almenar-Queralt, Angels; Falzone, Tomas L.; Shen, Zhouxin; Lillo, Concepcion; Killian, Rhiannon L.; Arreola, Angela S.; Niederst, Emily D.; Ng, Kheng S.; Kim, Sonia N.; Briggs, Steven P.; Williams, David S.

    2014-01-01

    Overexpression and/or abnormal cleavage of amyloid precursor protein (APP) are linked to Alzheimer's disease (AD) development and progression. However, the molecular mechanisms regulating cellular levels of APP or its processing, and the physiological and pathological consequences of altered processing are not well understood. Here, using mouse and human cells, we found that neuronal damage induced by UV irradiation leads to specific APP, APLP1, and APLP2 decline by accelerating their secretase-dependent processing. Pharmacological inhibition of endosomal/lysosomal activity partially protects UV-induced APP processing implying contribution of the endosomal and/or lysosomal compartments in this process. We found that a biological consequence of UV-induced γ-secretase processing of APP is impairment of APP axonal transport. To probe the functional consequences of impaired APP axonal transport, we isolated and analyzed presumptive APP-containing axonal transport vesicles from mouse cortical synaptosomes using electron microscopy, biochemical, and mass spectrometry analyses. We identified a population of morphologically heterogeneous organelles that contains APP, the secretase machinery, molecular motors, and previously proposed and new residents of APP vesicles. These possible cargoes are enriched in proteins whose dysfunction could contribute to neuronal malfunction and diseases of the nervous system including AD. Together, these results suggest that damage-induced APP processing might impair APP axonal transport, which could result in failure of synaptic maintenance and neuronal dysfunction. PMID:24573290

  18. A RabGAP Regulates Life-Cycle Duration via Trimeric G-protein Cascades in Dictyostelium discoideum

    PubMed Central

    Kuwayama, Hidekazu; Miyanaga, Yukihiro; Urushihara, Hideko; Ueda, Masahiro

    2013-01-01

    Background The life-cycle of cellular slime molds comprises chronobiologically regulated processes. During the growth phase, the amoeboid cells proliferate at a definite rate. Upon starvation, they synthesize cAMP as both first and second messengers in signalling pathways and form aggregates, migrating slugs, and fruiting bodies, consisting of spores and stalk cells, within 24 h. In Dictyostelium discoideum, because most growth-specific events cease during development, proliferative and heterochronic mutations are not considered to be interrelated and no genetic factor governing the entire life-cycle duration has ever been identified. Methodology/Principal Findings Using yeast 2-hybrid library screening, we isolated a Dictyostelium discoideum RabGAP, Dd Rbg-3, as a candidate molecule by which the Dictyostelium Gα2 subunit directs its effects. Rab GTPase-activating protein, RabGAP, acts as a negative regulator of Rab small GTPases, which orchestrate the intracellular membrane trafficking involved in cell proliferation. Deletion mutants of Dd rbg-3 exhibited an increased growth rate and a shortened developmental period, while an overexpression mutant demonstrated the opposite effects. We also show that Dd Rbg-3 interacts with 2 Gα subunits in an activity-dependent manner in vitro. Furthermore, both human and Caenorhabditis elegans rbg-3 homologs complemented the Dd rbg-3–deletion phenotype in D. discoideum, indicating that similar pathways may be generally conserved in multicellular organisms. Conclusions/Significance Our findings suggest that Dd Rbg-3 acts as a key element regulating the duration of D. discoideum life-span potentially via trimeric G-protein cascades. PMID:24349132

  19. The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation.

    PubMed

    Weidmann, Chase A; Raynard, Nathan A; Blewett, Nathan H; Van Etten, Jamie; Goldstrohm, Aaron C

    2014-08-01

    PUF proteins are potent repressors that serve important roles in stem cell maintenance, neurological processes, and embryonic development. These functions are driven by PUF protein recognition of specific binding sites within the 3' untranslated regions of target mRNAs. In this study, we investigated mechanisms of repression by the founding PUF, Drosophila Pumilio, and its human orthologs. Here, we evaluated a previously proposed model wherein the Pumilio RNA binding domain (RBD) binds Argonaute, which in turn blocks the translational activity of the eukaryotic elongation factor 1A. Surprisingly, we found that Argonautes are not necessary for repression elicited by Drosophila and human PUFs in vivo. A second model proposed that the RBD of Pumilio represses by recruiting deadenylases to shorten the mRNA's polyadenosine tail. Indeed, the RBD binds to the Pop2 deadenylase and accelerates deadenylation; however, this activity is not crucial for regulation. Rather, we determined that the poly(A) is necessary for repression by the RBD. Our results reveal that poly(A)-dependent repression by the RBD requires the poly(A) binding protein, pAbp. Furthermore, we show that repression by the human PUM2 RBD requires the pAbp ortholog, PABPC1. Pumilio associates with pAbp but does not disrupt binding of pAbp to the mRNA. Taken together, our data support a model wherein the Pumilio RBD antagonizes the ability of pAbp to promote translation. Thus, the conserved function of the PUF RBD is to bind specific mRNAs, antagonize pAbp function, and promote deadenylation. PMID:24942623

  20. Narrowing the gap in understanding protein structure and function through computer simulations

    NASA Astrophysics Data System (ADS)

    Guo, Hong

    2012-06-01

    Quantum mechanical/molecular mechanical (QM/MM) free energy simulations are applied for understanding mechanisms of different enzyme-catalyzed reactions and for determining some of the key factors in transition state (TS) stabilization and substrate specificity, two of the most important properties of enzymes. It is demonstrated here based on the results of computer simulations on kumamolisin-As, a member of sedolisin family, and DIM-5 and SET7/9, two of protein lysine methyltransferases, that transition state stabilization may be achieved in part through the general acid/base mechanism or the binding of the substrate in the TS-like configuration. Moreover, it is shown that dynamic substrate assisted catalysis may play an important role in the substrate specificity of enzymes.

  1. Co-ordination between membrane phospholipid synthesis and accelerated biosynthesis of cytoplasmic ribonucleic acid and protein

    PubMed Central

    Tata, J. R.

    1970-01-01

    1. The rate of synthesis of membrane phospholipid was studied in rat liver and seminal vesicles by following the incorporation of [32P]orthophosphate, [14C]choline and [14C]glycerol. Particular emphasis was laid on the endoplasmic reticulum, which was fractionated into smooth microsomal membranes, heavy rough membranes, light rough membranes and free polyribosomes. 2. Phospholipid labelling patterns suggested a heterogeneity in the synthesis and turnover of the different lipid moieties of smooth and rough endoplasmic membranes. The major phospholipids, phosphatidylcholine and phosphatidylethanolamine, were labelled relatively rapidly with 32P over a short period of time whereas incorporation of radioisotope into the minor phospholipids, sphingomyelin, lysolecithin and phosphatidylinositol proceeded slowly but over a longer period of time. 3. The incorporation of orotic acid into RNA and labelled amino acids into protein of the four submicrosomal fractions was also studied. 4. Rapid growth of the liver was induced by the administration of growth hormone and tri-iodothyronine to hypophysectomized and thyroidectomized rats and by partial hepatectomy. Growth of seminal vesicles of castrated rats was stimulated with testosterone propionate. 5. The rate of labelling of membrane phospholipids was enhanced in all major subcellular particulate fractions (nuclear, mitochondrial and microsomal) during induced growth. However, it was in the rough endoplasmic reticulum that the accumulation of phospholipids, RNA and protein was most marked. The effect of hormone administration was also to accelerate preferentially the labelling with 32P of sphingomyelin relative to that of phosphatidylcholine or phosphatidylethanolamine. 6. Time-course analyses showed that, in all four growth systems studied, the enhancement of the rate of membrane phospholipid synthesis coincided with the rather abrupt increase in the synthesis of RNA and protein of the rough endoplasmic reticulum. Growth

  2. Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter

    PubMed Central

    Gedeon, Patrick C.; Thomas, James R.; Madura, Jeffry D.

    2015-01-01

    Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis. PMID:25330967

  3. Impact of obesity on 7,12-dimethylbenz[a]anthracene-induced altered ovarian connexin gap junction proteins in female mice

    PubMed Central

    Ganesan, Shanthi; Nteeba, Jackson; Keating, Aileen F.

    2014-01-01

    The ovarian gap junction proteins alpha 4 (GJA4 or connexin 37; CX37), alpha 1 (GJA1 or connexin 43; CX43) and gamma 1 (GJC1 or connexin 45; CX45) are involved in cell communication and folliculogenesis. 7,12-dimethylbenz[a]anthracene (DMBA) alters Cx37 and Cx43 expression in cultured neonatal rat ovaries. Additionally, obesity has an additive effect on DMBA-induced ovarian cell death and follicle depletion, thus, we investigated in vivo impacts of obesity and DMBA on CX protein levels. Ovaries were collected from lean and obese mice aged 6, 12, 18, or 24 wks. A subset of 18 wk old mice (lean and obese) were dosed with sesame oil or DMBA (1mg/kg; ip) for 14 days and ovaries collected 3 days thereafter. Cx43 and Cx45 mRNA and protein levels decreased (P < 0.05) after 18 wks while Cx37 mRNA and protein levels decreased (P < 0.05) after 24 wks in obese ovaries. Cx37 mRNA and antral follicle protein staining intensity were reduced (P < 0.05) by obesity while total CX37 protein was reduced (P < 0.05) in DMBA exposed obese ovaries. Cx43 mRNA and total protein levels were decreased (P < 0.05) by DMBA in both lean and obese ovaries while basal protein staining intensity was reduced (P < 0.05) in obese controls. Cx45 mRNA, total protein and protein staining intensity level were decreased (P < 0.05) by obesity. These data support that obesity temporally alters gap junction protein expression and that DMBA-induced ovotoxicity may involve reduced gap junction protein function. PMID:25447408

  4. Identification of a Conserved Linear B-Cell Epitope of Streptococcus dysgalactiae GapC Protein by Screening Phage-Displayed Random Peptide Library

    PubMed Central

    Fan, Ziyao; Zhou, Xue; Yu, Liquan; Sun, Hunan; Wu, Zhijun; Yu, Yongzhong; Song, Baifen; Ma, Jinzhu; Tong, Chunyu; Wang, Xintong; Zhu, Zhanbo; Cui, Yudong

    2015-01-01

    The GapC of Streptococcus dysgalactiae (S. dysgalactiae) is a highly conserved surface protein that can induce protective humoral immune response in animals. However, B-cell epitopes on the S. dysgalactiae GapC have not been well identified. In this study, a monoclonal antibody (mAb5B7) against the GapC1-150 protein was prepared. After passive transfer, mAb5B7 could partially protect mice against S. dysgalactiae infection. Eleven positive phage clones recognized by mAb5B7 were identified by screening phage-displayed random 12-peptide library, most of which matched the consensus motif DTTQGRFD. The motif sequence exactly matches amino acids 48-55 of the S. dysgalactiae GapC protein. In addition, the motif 48DTTQGRFD55 shows high homology among various streptococcus species. Site-directed mutagenic analysis further confirmed that residues D48, T50, Q51, G52 and F54 formed the core motif of 48DTTQGRFD55. This motif was the minimal determinant of the B-cell epitope recognized by the mAb5B7. As expected, epitope-peptide evoked protective immune response against S. dysgalactiae infection in immunized mice. Taken together, this identified conserved B-cell epitope within S. dysgalactiae GapC could provide very valuable insights for vaccine design against S. dysgalactiae infection. PMID:26121648

  5. Overexpression of protein O-fucosyltransferase 1 accelerates hepatocellular carcinoma progression via the Notch signaling pathway.

    PubMed

    Ma, Lijie; Dong, Pingping; Liu, Longzi; Gao, Qiang; Duan, Meng; Zhang, Si; Chen, She; Xue, Ruyi; Wang, Xiaoying

    2016-04-29

    Aberrant activation of Notch signaling frequently occurs in liver cancer, and is associated with liver malignancies. However, the mechanisms regulating pathologic Notch activation in hepatocellular carcinoma (HCC) remain unclear. Protein O-fucosyltransferase 1 (Pofut1) catalyzes the addition of O-linked fucose to the epidermal growth factor-like repeats of Notch. In the present study, we detected the expression of Pofut1 in 8 HCC cell lines and 253 human HCC tissues. We reported that Pofut1 was overexpressed in HCC cell lines and clinical HCC tissues, and Pofut1 overexpression clinically correlated with the unfavorable survival and high disease recurrence in HCC. The in vitro assay demonstrated that Pofut1 overexpression accelerated the cell proliferation and migration in HCC cells. Furthermore, Pofut1 overexpression promoted the binding of Notch ligand Dll1 to Notch receptor, and hence activated Notch signaling pathway in HCC cells, indicating that Pofut1 overexpression could be a reason for the aberrant activation of Notch signaling in HCC. Taken together, our findings indicated that an aberrant activated Pofut1-Notch pathway was involved in HCC progression, and blockage of this pathway could be a promising strategy for the therapy of HCC. PMID:27003260

  6. LINEAR ACCELERATOR

    DOEpatents

    Christofilos, N.C.; Polk, I.J.

    1959-02-17

    Improvements in linear particle accelerators are described. A drift tube system for a linear ion accelerator reduces gap capacity between adjacent drift tube ends. This is accomplished by reducing the ratio of the diameter of the drift tube to the diameter of the resonant cavity. Concentration of magnetic field intensity at the longitudinal midpoint of the external sunface of each drift tube is reduced by increasing the external drift tube diameter at the longitudinal center region.

  7. Accelerated degradation of caspase-8 protein correlates with TRAIL resistance in a DLD1 human colon cancer cell line.

    PubMed

    Zhang, Lidong; Zhu, Hongbo; Teraishi, Fuminori; Davis, John J; Guo, Wei; Fan, Zhen; Fang, Bingliang

    2005-06-01

    The tumor-selective cytotoxic effect of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) makes TRAIL an attractive candidate as an anticancer agent. However, resistance to TRAIL poses a challenge in anticancer therapy with TRAIL. Therefore, characterizing the mechanisms of resistance and developing strategies to overcome the resistance are important steps toward successful TRAIL-mediated cancer therapy. In this study, we investigated mechanisms of acquired TRAIL resistance in a colon cancer DLD1 cell line. Compared with the TRAIL-susceptible DLD1 cell line, TRAIL-resistant DLD1/TRAIL-R cells have a low level of caspase-8 protein, but not its mRNA. Suppression of caspase-8 expression by siRNA in parental DLD1 cells led to TRAIL resistance. Restoration of caspase-8 protein expression by stable transfection rendered the DLD1/TRAIL-R cell line fully sensitive to TRAIL protein, suggesting that the low level of caspase-8 protein expression might be the culprit in TRAIL resistance in DLD1/TRAIL-R cells. Sequencing analysis of the caspase-8 coding region revealed a missense mutation that is present in both TRAIL-sensitive and TRAIL-resistant DLD1 cells. Subsequent study showed that the degradation of caspase-8 protein was accelerated in DLD1/TRAIL-R cells compared to parental DLD1 cells. Thus, accelerated degradation of caspase-8 protein is one of the mechanisms that lead to TRAIL resistance. PMID:16036110

  8. Hydrolysis of Guanosine Triphosphate (GTP) by the Ras·GAP Protein Complex: Reaction Mechanism and Kinetic Scheme.

    PubMed

    Khrenova, Maria G; Grigorenko, Bella L; Kolomeisky, Anatoly B; Nemukhin, Alexander V

    2015-10-01

    Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by the Ras·GAP protein complex are fully investigated by using modern modeling tools. The previously hypothesized stages of the cleavage of the phosphorus-oxygen bond in GTP and the formation of the imide form of catalytic Gln61 from Ras upon creation of Pi are confirmed by using the higher-level quantum-based calculations. The steps of the enzyme regeneration are modeled for the first time, providing a comprehensive description of the catalytic cycle. It is found that for the reaction Ras·GAP·GTP·H2O → Ras·GAP·GDP·Pi, the highest barriers correspond to the process of regeneration of the active site but not to the process of substrate cleavage. The specific shape of the energy profile is responsible for an interesting kinetic mechanism of the GTP hydrolysis. The analysis of the process using the first-passage approach and consideration of kinetic equations suggest that the overall reaction rate is a result of the balance between relatively fast transitions and low probability of states from which these transitions are taking place. Our theoretical predictions are in excellent agreement with available experimental observations on GTP hydrolysis rates. PMID:26374425

  9. Combination of adrenomedullin with its binding protein accelerates cutaneous wound healing.

    PubMed

    Idrovo, Juan-Pablo; Yang, Weng-Lang; Jacob, Asha; Ajakaiye, Michael A; Cheyuo, Cletus; Wang, Zhimin; Prince, Jose M; Nicastro, Jeffrey; Coppa, Gene F; Wang, Ping

    2015-01-01

    Cutaneous wound continues to cause significant morbidity and mortality in the setting of diseases such as diabetes and cardiovascular diseases. Despite advances in wound care management, there is still an unmet medical need exists for efficient therapy for cutaneous wound. Combined treatment of adrenomedullin (AM) and its binding protein-1 (AMBP-1) is protective in various disease conditions. To examine the effect of the combination treatment of AM and AMBP-1 on cutaneous wound healing, full-thickness 2.0-cm diameter circular excision wounds were surgically created on the dorsum of rats, saline (vehicle) or AM/AMBP-1 (96/320 μg kg BW) was topically applied to the wound daily and wound size measured. At days 3, 7, and 14, skin samples were collected from the wound sites. AM/AMBP-1 treated group had significantly smaller wound surface area than the vehicle group over the 14-day time course. At day 3, AM/AMBP-1 promoted neutrophil infiltration (MPO), increased cytokine levels (IL-6 and TNF-α), angiogenesis (CD31, VEGF and TGFβ-1) and cell proliferation (Ki67). By day 7 and 14, AM/AMBP-1 treatment decreased MPO, followed by a rapid resolution of inflammation characterized by a decrease in cytokines. At the matured stage, AM/AMBP-1 treatment increased the alpha smooth muscle actin expression (mature blood vessels) and Masson-Trichrome staining (collagen deposition) along the granulation area, and increased MMP-9 and decreased MMP-2 mRNA expressions. TGFβ-1 mRNA levels in AM/AMBP-1 group were 5.3 times lower than those in the vehicle group. AM/AMBP-1 accelerated wound healing by promoting angiogenesis, collagen deposition and remodeling. Treatment also shortened the days to reach plateau for wound closure. Thus, AM/AMBP-1 may be further developed as a therapeutic for cutaneous wound healing. PMID:25781901

  10. Temporal dissociation of frequency-dependent acceleration of relaxation and protein phosphorylation by CaMKII.

    PubMed

    Huke, Sabine; Bers, Donald M

    2007-03-01

    Frequency-dependent acceleration of relaxation (FDAR) is an important intrinsic mechanism that allows for diastolic filling of the ventricle at higher heart rates, yet its molecular mechanism is still not understood. Previous studies showed that FDAR is dependent on functional sarcoplasmic reticulum (SR) and can be abolished by phosphatase or by Ca/CaM kinase (CaMKII) inhibition. Additionally, CaMKII activity/autophosphorylation has been shown to be frequency-dependent. Thus, we tested the hypothesis that CaMKII phosphorylation of SR Ca(2+)-handling proteins (Phospholamban (PLB), Ca(2+) release channel (RyR)) mediates FDAR. Here we show that FDAR occurs abruptly in fluo-4 loaded isolated rat ventricular myocytes when frequency is raised from 0.1 to 2 Hz. The effect is essentially complete within four beats (2 s) with the tau of [Ca(2+)](i) decline decreasing by 42+/-3%. While there is a detectable increase in PLB Thr-17 and RyR Ser-2814 phosphorylation, the increase is quantitatively small (PLB<5%, RyR approximately 8%) and the time-course is clearly delayed with regard to FDAR. The low substrate phosphorylation indicates that pacing of myocytes only mildly activates CaMKII and consistent with this CaMKIIdelta autophosphorylation did not increase with pacing alone. However, in the presence of phosphatase 1 inhibition pacing triggered a net-increase in autophosphorylated CaMKII and also greatly enhanced PLB and RyR phosphorylation. We conclude that FDAR does not rely on phosphorylation of PLB or RyR. Even though CaMKII does become activated when myocytes are paced, phosphatases immediately antagonize CaMKII action, limit substrate phosphorylation and also prevent sustained CaMKII autophosphorylation (thereby suppressing global CaMKII effects). PMID:17239900

  11. [Therapeutical effect of growth-associated protein 43 (GAP43) gene-modified bone marrow mesenchymal stem cell transplantation on rat retinal degenerative diseases].

    PubMed

    Yang, Juan; Xie, Maosong; Zheng, Weidong; Hu, Jianzhang; Qu, Qiang

    2016-08-01

    Objective To investigate the potential of the treatment of growth-associated protein 43 (GAP43) gene-modified bone marrow-derived mesenchymal stem cells (BMSCs) for retinitis pigmentosa (RP). Methods BMSCs were isolated and cultured by adherence method. By transfecting GAP43 gene into BMSCs via a lentivirus vector, we got GAP43 gene-modified BMSCs. Sixty-three Royal College of Surgeons (RCS) rats were randomly divided into three groups: experimental group, negative control group and blank control group. The experimental rats received subretinal injection of GAP43 gene-modified BMSCs. The negative control rats received subretinal injection of BMSCs. The control rats received subretinal injection of PBS. Thirty days after transplanting, the retinal thickness was detected by optical coherence tomography (OCT), and the expression of rhodopsin in RCS rat retinas was examined by Western blotting. Results Compared with the blank control group and the negative control group, 30 days after GAP43 gene-modified BMSC transplantation, the retinal thickness of the experimental group remarkably increased and the expression of rhodopsin significantly rose. Conclusion GAP43 gene-modified BMSC transplantation can increase survival photoreceptor cells and delay retinal degeneration. PMID:27412933

  12. A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase - Structural and modeling insight into its functions

    SciTech Connect

    Li, Hui-Guang; Huang, Philip L.; Zhang, Dawei; Sun, Yongtao; Chen, Hao-Chia; Zhang, John; Huang, Paul L.; Kong, Xiang-Peng; Lee-Huang, Sylvia

    2010-01-01

    We report here the high-resolution atomic structures of GAP31 crystallized in the presence of HIV-LTR DNA oligonucleotides systematically designed to examine the adenosine glycosidase activity of this anti-HIV and anti-tumor plant protein. Structural analysis and molecular modeling lead to several novel findings. First, adenine is bound at the active site in the crystal structures of GAP31 to HIV-LTR duplex DNA with 5' overhanging adenosine ends, such as the 3'-processed HIV-LTR DNA but not to DNA duplex with blunt ends. Second, the active site pocket of GAP31 is ideally suited to accommodate the 5' overhanging adenosine of the 3'-processed HIV-LTR DNA and the active site residues are positioned to perform the adenosine glycosidase activity. Third, GAP31 also removes the 5'-end adenine from single-stranded HIV-LTR DNA oligonucleotide as well as any exposed adenosine, including that of single nucleotide dAMP but not from AMP. Fourth, GAP31 does not de-purinate guanosine from di-nucleotide GT. These results suggest that GAP31 has DNA adenosine glycosidase activity against accessible adenosine. This activity is distinct from the generally known RNA N-glycosidase activity toward the 28S rRNA. It may be an alternative function that contributes to the antiviral and anti-tumor activities of GAP31. These results provide molecular insights consistent with the anti-HIV mechanisms of GAP31 in its inhibition on the integration of viral DNA into the host genome by HIV-integrase as well as irreversible topological relaxation of the supercoiled viral DNA.

  13. A New Activity of Anti-HIV and Anti-tumor Protein GAP31: DNA Adenosine Glycosidase – Structural and Modeling Insight into its Functions

    SciTech Connect

    Li, H.; Huang, P; Zhang, D; Sun, Y; Chen, H; Zhang, J; Huang, P; Kong, X; Lee-Huang, S

    2010-01-01

    We report here the high-resolution atomic structures of GAP31 crystallized in the presence of HIV-LTR DNA oligonucleotides systematically designed to examine the adenosine glycosidase activity of this anti-HIV and anti-tumor plant protein. Structural analysis and molecular modeling lead to several novel findings. First, adenine is bound at the active site in the crystal structures of GAP31 to HIV-LTR duplex DNA with 5' overhanging adenosine ends, such as the 3'-processed HIV-LTR DNA but not to DNA duplex with blunt ends. Second, the active site pocket of GAP31 is ideally suited to accommodate the 5' overhanging adenosine of the 3'-processed HIV-LTR DNA and the active site residues are positioned to perform the adenosine glycosidase activity. Third, GAP31 also removes the 5'-end adenine from single-stranded HIV-LTR DNA oligonucleotide as well as any exposed adenosine, including that of single nucleotide dAMP but not from AMP. Fourth, GAP31 does not de-purinate guanosine from di-nucleotide GT. These results suggest that GAP31 has DNA adenosine glycosidase activity against accessible adenosine. This activity is distinct from the generally known RNA N-glycosidase activity toward the 28S rRNA. It may be an alternative function that contributes to the antiviral and anti-tumor activities of GAP31. These results provide molecular insights consistent with the anti-HIV mechanisms of GAP31 in its inhibition on the integration of viral DNA into the host genome by HIV-integrase as well as irreversible topological relaxation of the supercoiled viral DNA.

  14. Role of gap junctions and protein kinase A during the development of oocyte maturational competence in Ayu (Plecoglossus altivelis)

    USGS Publications Warehouse

    Yamamoto, Y.; Yoshizaki, G.; Takeuchi, T.; Soyano, K.; Patino, R.

    2008-01-01

    Meiotic resumption in teleost oocytes is induced by a maturation-inducing hormone (MIH). The sensitivity of oocytes to MIH, also known as oocyte maturational competence (OMC), is induced by LH via mechanisms that are not fully understood. A previous study of Ayu (Plecoglossus altivelis) showed the presence of functional heterologous gap junctions (GJs) between oocytes and their surrounding granulosa cells. The objectives of this study were to determine the role of ovarian GJs and of protein kinase A (PKA) during the acquisition of OMC. We examined the effects of the specific GJ inhibitor carbenoxolone (CBX) and 18??-glycyrrhetinic acid (??-GA) on the LH-(hCG)-dependent acquisition of OMC and on MIH-(17,20??-dihydroxy-4-pregnen-3-one)-dependent meiotic resumption; measured the cAMP content of ovarian follicles during the hCG-dependent acquisition of OMC; and determined the effects of PK activators and inhibitors on hCG-dependent OMC. Production of follicular cAMP increased during the hCG-dependent acquisition of OMC. Both GJ inhibitors and the PKA inhibitor H8-dihydrochloride, but not the PKC inhibitor GF109203X, suppressed the hCG-dependent acquisition of OMC in a dose-dependent manner. The PKA activator forskolin induced OMC with a similar potency to hCG. Unlike previous observations with teleosts where disruption of heterologous GJ either blocks or stimulates meiotic resumption, treatment with GJ inhibitors did not affect MIH-dependent meiotic resumption in maturationally competent follicles of Ayu. These observations suggest that ovarian GJs are essential for LH-dependent acquisition of OMC but not for MIH-dependent meiotic resumption, and that the stimulation of OMC by LH is mediated by cAMP-dependent PKA. They are also consistent with the view that a precise balance between GJ-mediated signals (positive or negative) and oocyte maturational readiness is required for hormonally regulated meiotic resumption. ?? 2007 Elsevier Inc. All rights reserved.

  15. A cell-free approach to accelerate the study of protein–protein interactions in vitro

    PubMed Central

    Sierecki, E.; Giles, N.; Polinkovsky, M.; Moustaqil, M.; Alexandrov, K.; Gambin, Y.

    2013-01-01

    Protein–protein interactions are highly desirable targets in drug discovery, yet only a fraction of drugs act as binding inhibitors. Here, we review the different technologies used to find and validate protein–protein interactions. We then discuss how the novel combination of cell-free protein expression, AlphaScreen and single-molecule fluorescence spectroscopy can be used to rapidly map protein interaction networks, determine the architecture of protein complexes, and find new targets for drug discovery. PMID:24511386

  16. Sphingosine 1-Phosphate Induces Myoblast Differentiation through Cx43 Protein Expression: A Role for a Gap Junction-dependent and -independent Function

    PubMed Central

    Squecco, R.; Sassoli, C.; Nuti, F.; Martinesi, M.; Chellini, F.; Nosi, D.; Zecchi-Orlandini, S.; Francini, F.; Formigli, L.

    2006-01-01

    Although sphingosine 1-phosphate (S1P) has been considered a potent regulator of skeletal muscle biology, acting as a physiological anti-mitogenic and prodifferentiating agent, its downstream effectors are poorly known. In the present study, we provide experimental evidence for a novel mechanism by which S1P regulates skeletal muscle differentiation through the regulation of gap junctional protein connexin (Cx) 43. Indeed, the treatment with S1P greatly enhanced Cx43 expression and gap junctional intercellular communication during the early phases of myoblast differentiation, whereas the down-regulation of Cx43 by transfection with short interfering RNA blocked myogenesis elicited by S1P. Moreover, calcium and p38 MAPK-dependent pathways were required for S1P-induced increase in Cx43 expression. Interestingly, enforced expression of mutated Cx43Δ130–136 reduced gap junction communication and totally inhibited S1P-induced expression of the myogenic markers, myogenin, myosin heavy chain, caveolin-3, and myotube formation. Notably, in S1P-stimulated myoblasts, endogenous or wild-type Cx43 protein, but not the mutated form, coimmunoprecipitated and colocalized with F-actin and cortactin in a p38 MAPK-dependent manner. These data, together with the known role of actin remodeling in cell differentiation, strongly support the important contribution of gap junctional communication, Cx43 expression and Cx43/cytoskeleton interaction in skeletal myogenesis elicited by S1P. PMID:16957055

  17. Dynamic recruitment of the curvature-sensitive protein ArhGAP44 to nanoscale membrane deformations limits exploratory filopodia initiation in neurons

    PubMed Central

    Galic, Milos; Tsai, Feng-Chiao; Collins, Sean R; Matis, Maja; Bandara, Samuel; Meyer, Tobias

    2014-01-01

    In the vertebrate central nervous system, exploratory filopodia transiently form on dendritic branches to sample the neuronal environment and initiate new trans-neuronal contacts. While much is known about the molecules that control filopodia extension and subsequent maturation into functional synapses, the mechanisms that regulate initiation of these dynamic, actin-rich structures have remained elusive. Here, we find that filopodia initiation is suppressed by recruitment of ArhGAP44 to actin-patches that seed filopodia. Recruitment is mediated by binding of a membrane curvature-sensing ArhGAP44 N-BAR domain to plasma membrane sections that were deformed inward by acto-myosin mediated contractile forces. A GAP domain in ArhGAP44 triggers local Rac-GTP hydrolysis, thus reducing actin polymerization required for filopodia formation. Additionally, ArhGAP44 expression increases during neuronal development, concurrent with a decrease in the rate of filopodia formation. Together, our data reveals a local auto-regulatory mechanism that limits initiation of filopodia via protein recruitment to nanoscale membrane deformations. DOI: http://dx.doi.org/10.7554/eLife.03116.001 PMID:25498153

  18. Insulin accelerates global and mitochondrial protein synthesis rates in neonatal muscle during sepsis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In neonatal pigs, sepsis decreases protein synthesis in skeletal muscle by decreasing translation initiation. However, insulin stimulates muscle protein synthesis despite persistent repression of translation initiation signaling. To determine whether the insulin-induced increase in global rates of m...

  19. MIIP accelerates epidermal growth factor receptor protein turnover and attenuates proliferation in non-small cell lung cancer

    PubMed Central

    Wen, Jing; Fu, Jianhua; Ling, Yihong; Zhang, Wei

    2016-01-01

    The migration and invasion inhibitory protein (MIIP) has been discovered recently to have inhibitory functions in cell proliferation and migration. Overexpression of MIIP reduced the intracellular steady-state level of epidermal growth factor receptor (EGFR) protein in lung cancer cells with no effect on EGFR mRNA expression compared to that in the control cells. This MIIP-promoted EGFR protein degradation was reversed by proteasome and lysosome inhibitors, suggesting the involvement of both proteasomal and lysosomal pathways in this degradation. This finding was further validated by pulse-chase experiments using 35S-methionine metabolic labeling. We found that MIIP accelerates EGFR protein turnover via proteasomal degradation in the endoplasmic reticulum and then via the lysosomal pathway after its entry into endocytic trafficking. MIIP-stimulated downregulation of EGFR inhibits downstream activation of Ras and blocks the MEK signal transduction pathway, resulting in inhibition of cell proliferation. The negative correlation between MIIP and EGFR protein expression was validated in lung adenocarcinoma samples. Furthermore, the higher MIIP protein expression predicts a better overall survival of Stage IA-IIIA lung adenocarcinoma patients who underwent radical surgery. These findings reveal a new mechanism by which MIIP inhibits cell proliferation. PMID:26824318

  20. Atomic-level description of protein-lipid interactions using an accelerated membrane model.

    PubMed

    Baylon, Javier L; Vermaas, Josh V; Muller, Melanie P; Arcario, Mark J; Pogorelov, Taras V; Tajkhorshid, Emad

    2016-07-01

    Peripheral membrane proteins are structurally diverse proteins that are involved in fundamental cellular processes. Their activity of these proteins is frequently modulated through their interaction with cellular membranes, and as a result techniques to study the interfacial interaction between peripheral proteins and the membrane are in high demand. Due to the fluid nature of the membrane and the reversibility of protein-membrane interactions, the experimental study of these systems remains a challenging task. Molecular dynamics simulations offer a suitable approach to study protein-lipid interactions; however, the slow dynamics of the lipids often prevents sufficient sampling of specific membrane-protein interactions in atomistic simulations. To increase lipid dynamics while preserving the atomistic detail of protein-lipid interactions, in the highly mobile membrane-mimetic (HMMM) model the membrane core is replaced by an organic solvent, while short-tailed lipids provide a nearly complete representation of natural lipids at the organic solvent/water interface. Here, we present a brief introduction and a summary of recent applications of the HMMM to study different membrane proteins, complementing the experimental characterization of the presented systems, and we offer a perspective of future applications of the HMMM to study other classes of membrane proteins. This article is part of a Special Issue entitled: Membrane proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26940626

  1. Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages

    NASA Astrophysics Data System (ADS)

    Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine

    2008-12-01

    This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave-accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MALDI-TOF and LC-ESI-MS to identify the peptide products. RNase A and B each contains four disulfide bonds, and the addition of a reducing reagent, such as dithiothreitol, was found to be required to achieve efficient acidic proteolysis. The linkage of the glycosidic group to the asparagine side chain in ribonuclease B was found not to be cleaved by brief microwave treatment in 12.5% acetic acid. The distribution of the heterogeneous carbohydrate side chain in the glycopeptide products of acid cleavage was compared to that of the glycopeptide products of tryptic digestion. Hydrolysis within the carbohydrate chain itself is minimal under the conditions used. The O-linked side chain on alpha crystalline A was found to be cleaved during acid cleavage of the protein.

  2. Methoprene and protein supplements accelerate reproductive development and improve mating success of male tephritid flies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have been studying the physiological mechanisms responsible for coordination of reproductive maturity and sex pheromone communication in males of tephritid flies in order to develop methods for acceleration of reproductive maturity among sterilized males. Our studies revealed that the juvenile ho...

  3. Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.

    PubMed

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Shaw, David E

    2016-01-01

    Molecular dynamics (MD) simulation is a well-established tool for the computational study of protein structure and dynamics, but its application to the important problem of protein structure prediction remains challenging, in part because extremely long timescales can be required to reach the native structure. Here, we examine the extent to which the use of low-resolution information in the form of residue-residue contacts, which can often be inferred from bioinformatics or experimental studies, can accelerate the determination of protein structure in simulation. We incorporated sets of 62, 31, or 15 contact-based restraints in MD simulations of ubiquitin, a benchmark system known to fold to the native state on the millisecond timescale in unrestrained simulations. One-third of the restrained simulations folded to the native state within a few tens of microseconds-a speedup of over an order of magnitude compared with unrestrained simulations and a demonstration of the potential for limited amounts of structural information to accelerate structure determination. Almost all of the remaining ubiquitin simulations reached near-native conformations within a few tens of microseconds, but remained trapped there, apparently due to the restraints. We discuss potential methodological improvements that would facilitate escape from these near-native traps and allow more simulations to quickly reach the native state. Finally, using a target from the Critical Assessment of protein Structure Prediction (CASP) experiment, we show that distance restraints can improve simulation accuracy: In our simulations, restraints stabilized the native state of the protein, enabling a reasonable structural model to be inferred. PMID:26266489

  4. Accelerated simulation of unfolding and refolding of a large single chain globular protein

    PubMed Central

    Seddon, Gavin M.; Bywater, Robert P.

    2012-01-01

    We have developed novel strategies for contracting simulation times in protein dynamics that enable us to study a complex protein with molecular weight in excess of 34 kDa. Starting from a crystal structure, we produce unfolded and then refolded states for the protein. We then compare these quantitatively using both established and new metrics for protein structure and quality checking. These include use of the programs Concoord and Darvols. Simulation of protein-folded structure well beyond the molten globule state and then recovery back to the folded state is itself new, and our results throw new light on the protein-folding process. We accomplish this using a novel cooling protocol developed for this work. PMID:22870389

  5. Accelerated simulation of unfolding and refolding of a large single chain globular protein.

    PubMed

    Seddon, Gavin M; Bywater, Robert P

    2012-07-01

    We have developed novel strategies for contracting simulation times in protein dynamics that enable us to study a complex protein with molecular weight in excess of 34 kDa. Starting from a crystal structure, we produce unfolded and then refolded states for the protein. We then compare these quantitatively using both established and new metrics for protein structure and quality checking. These include use of the programs Concoord and Darvols. Simulation of protein-folded structure well beyond the molten globule state and then recovery back to the folded state is itself new, and our results throw new light on the protein-folding process. We accomplish this using a novel cooling protocol developed for this work. PMID:22870389

  6. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

    PubMed

    Cetinbaş, Murat; Shakhnovich, Eugene I

    2013-01-01

    Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI) network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics. PMID:24244114

  7. Investigation of carbohydrate and protein metabolism in the digestive organs of the rabbit under the combined influence of vibration, acceleration and irradiation

    NASA Technical Reports Server (NTRS)

    Yuy, R. I.

    1975-01-01

    During spaceflight, the organism is subjected to the influence of various extremal factors such as acceleration, vibration, irradiation, etc. The study of the influence of these factors on metabolism, especially carbohydrate and protein metabolism, in young rabbits is of great significance in simulation experiments. Dynamic factors and irradiation, depending on dose and duration, lead to reduced RNA and protein metabolism.

  8. Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP

    NASA Astrophysics Data System (ADS)

    Khrenova, Maria G.; Grigorenko, Bella L.; Nemukhin, Alexander V.

    2016-09-01

    The structures and vibrational spectra of the reacting species upon guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate and inorganic phosphate (Pi) trapped inside the protein complex Ras-GAP were analyzed following the results of QM/MM simulations. The frequencies of the phosphate vibrations referring to the reactants and to Pi were compared to those observed in the experimental FTIR studies. A good correlation between the theoretical and experimental vibrational data provides a strong support to the reaction mechanism of GTP hydrolysis by the Ras-GAP enzyme system revealed by the recent QM/MM modeling. Evolution of the vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted.

  9. Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP.

    PubMed

    Khrenova, Maria G; Grigorenko, Bella L; Nemukhin, Alexander V

    2016-09-01

    The structures and vibrational spectra of the reacting species upon guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate and inorganic phosphate (Pi) trapped inside the protein complex Ras-GAP were analyzed following the results of QM/MM simulations. The frequencies of the phosphate vibrations referring to the reactants and to Pi were compared to those observed in the experimental FTIR studies. A good correlation between the theoretical and experimental vibrational data provides a strong support to the reaction mechanism of GTP hydrolysis by the Ras-GAP enzyme system revealed by the recent QM/MM modeling. Evolution of the vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted. PMID:27214270

  10. Proteomic identification of less oxidized brain proteins in aged senescence-accelerated mice following administration of antisense oligonucleotide directed at the Abeta region of amyloid precursor protein.

    PubMed

    Poon, H Fai; Farr, Susan A; Banks, William A; Pierce, William M; Klein, Jon B; Morley, John E; Butterfield, D Allan

    2005-07-29

    Amyloid beta-peptide (Abeta) is the major constituent of senile plaques, a pathological hallmark of Alzheimer's disease (AD) brain. It is generally accepted that Abeta plays a central role in the pathophysiology of AD. Abeta is released from cells under entirely normal cellular conditions during the internalization and endosomal processing of amyloid precursor protein (APP). However, accumulation of Abeta can induce neurotoxicity. Our previous reports showed that decreasing the production of Abeta by giving an intracerebroventricular injection of a 42-mer phosphorothiolated antisense oligonucleotide (AO) directed at the Abeta region of the APP gene reduces lipid peroxidation and protein oxidation and improves cognitive deficits in aged senescence-accelerated mice prone 8 (SAMP8) mice. In order to investigate how Abeta level reduction improves learning and memory performance of SAMP8 mice through reduction of oxidative stress in brains, we used proteomics to identify the proteins that are less oxidized in 12-month-old SAMP8 mice brains treated with AO against the Abeta region of APP (12 mA) compared to that of the age-control SAMP8 mice. We found that the specific protein carbonyl levels of aldoase 3 (Aldo3), coronin 1a (Coro1a) and peroxiredoxin 2 (Prdx2) are significantly decreased in the brains of 12 mA SAMP8 mice compared to the age-controlled SAMP8 treated with random AO (12 mR). We also found that the expression level of alpha-ATP synthase (Atp5a1) was significantly decreased, whereas the expression of profilin 2 (Pro-2) was significantly increased in brains from 12 mA SAMP8 mice. Our results suggest that decreasing Abeta levels in aged brain in aged accelerated mice may contribute to the mechanism of restoring the learning and memory improvement in aged SAMP8 mice and may provide insight into the role of Abeta in the memory and cognitive deficits in AD. PMID:15932783

  11. The E6 Oncoproteins of High-Risk Papillomaviruses Bind to a Novel Putative GAP Protein, E6TP1, and Target It for Degradation

    PubMed Central

    Gao, Qingshen; Srinivasan, Seetha; Boyer, Sarah N.; Wazer, David E.; Band, Vimla

    1999-01-01

    The high-risk human papillomaviruses (HPVs) are associated with carcinomas of the cervix and other genital tumors. Previous studies have identified two viral oncoproteins, E6 and E7, which are expressed in the majority of HPV-associated carcinomas. The ability of high-risk HPV E6 protein to immortalize human mammary epithelial cells (MECs) has provided a single-gene model to study the mechanisms of E6-induced oncogenic transformation. In this system, the E6 protein targets the p53 tumor suppressor protein for degradation, and mutational analyses have shown that E6-induced degradation of p53 protein is required for MEC immortalization. However, the inability of most dominant-negative p53 mutants to induce efficient immortalization of MECs suggests the existence of additional targets of the HPV E6 oncoprotein. Using the yeast two-hybrid system, we have isolated a novel E6-binding protein. This polypeptide, designated E6TP1 (E6-targeted protein 1), exhibits high homology to GTPase-activating proteins for Rap, including SPA-1, tuberin, and Rap1GAP. The mRNA for E6TP1 is widely expressed in tissues and in vitro-cultured cell lines. The gene for E6TP1 localizes to chromosome 14q23.2-14q24.3 within a locus that has been shown to undergo loss of heterozygosity in malignant meningiomas. Importantly, E6TP1 is targeted for degradation by the high-risk but not the low-risk HPV E6 proteins both in vitro and in vivo. Furthermore, the immortalization-competent but not the immortalization-incompetent HPV16 E6 mutants target the E6TP1 protein for degradation. Our results identify a novel target for the E6 oncoprotein and provide a potential link between HPV E6 oncogenesis and alteration of a small G protein signaling pathway. PMID:9858596

  12. Mevastatin accelerates loss of synaptic proteins and neurite degeneration in aging cortical neurons in a heme-independent manner.

    PubMed

    Kannan, Madhuvanthi; Steinert, Joern R; Forsythe, Ian D; Smith, Andrew G; Chernova, Tatyana

    2010-09-01

    The therapeutic use of statins in reducing cholesterol requires careful assessment of potential neuroprotective and/or neurotoxic mechanisms. Chronic treatment with mevastatin (MV) exerts effects on cortical neuron morphology, protein expression and synaptic function in primary culture. MV impaired expression of synaptic proteins, reduced N-methyl-d-aspartate receptor (NMDAR) currents and accelerated neurodegeneration associated with aging. The down-regulating effect of MV on neuronal protein expression was additive with aging-associated decline in culture. Induction of Heme oxygenase-1 (HMOX1) by MV was superimposed on age-related up-regulation. Comparison of MV-treated and heme-deficient neurons showed that inhibition of heme synthesis (by succinyl acetone) had similar damaging effect on neurite integrity and MNDAR expression and function but not on expression of the receptor for neuropeptide Y1 (NPY1R). Replacement of heme in heme-deficient cultures restored protein expression but had no effect in those cultures co-treated with MV. Despite the dramatic induction of HMOX1, intracellular heme remained sufficient in MV-treated cultures, consistent with a heme-independent mechanism of MV-induced neurotoxicity and this was confirmed by analysing neurons with lentiviral over-expression of HMOX1. We conclude that MV exerts a neurotoxic effect in cultured neurons in a heme-independent manner. PMID:18951667

  13. Low-Level Laser-Accelerated Peripheral Nerve Regeneration within a Reinforced Nerve Conduit across a Large Gap of the Transected Sciatic Nerve in Rats

    PubMed Central

    Shen, Chiung-Chyi; Yang, Yi-Chin; Huang, Tsung-Bin; Chan, Shiuh-Chuan; Liu, Bai-Shuan

    2013-01-01

    This study proposed a novel combination of neural regeneration techniques for the repair of damaged peripheral nerves. A biodegradable nerve conduit containing genipin-cross-linked gelatin was annexed using beta-tricalcium phosphate (TCP) ceramic particles (genipin-gelatin-TCP, GGT) to bridge the transection of a 15 mm sciatic nerve in rats. Two trigger points were irradiated transcutaneously using 660 nm of gallium-aluminum arsenide phosphide (GaAlAsP) via laser diodes for 2 min daily over 10 consecutive days. Walking track analysis showed a significant improvement in sciatic functional index (SFI) (P < 0.01) and pronounced improvement in the toe spreading ability of rats undergoing laser stimulation. Electrophysiological measurements (peak amplitude and area) illustrated by compound muscle action potential (CMAP) curves demonstrated that laser stimulation significantly improved nerve function and reduced muscular atrophy. Histomorphometric assessments revealed that laser stimulation accelerated nerve regeneration over a larger area of neural tissue, resulting in axons of greater diameter and myelin sheaths of greater thickness than that observed in rats treated with nerve conduits alone. Motor function, electrophysiological reactions, muscular reinnervation, and histomorphometric assessments all demonstrate that the proposed therapy accelerated the repair of transected peripheral nerves bridged using a GGT nerve conduit. PMID:23737818

  14. ACCELERATION INTEGRATOR

    DOEpatents

    Pope, K.E.

    1958-01-01

    This patent relates to an improved acceleration integrator and more particularly to apparatus of this nature which is gyrostabilized. The device may be used to sense the attainment by an airborne vehicle of a predetermined velocitv or distance along a given vector path. In its broad aspects, the acceleration integrator utilizes a magnetized element rotatable driven by a synchronous motor and having a cylin drical flux gap and a restrained eddy- current drag cap deposed to move into the gap. The angular velocity imparted to the rotatable cap shaft is transmitted in a positive manner to the magnetized element through a servo feedback loop. The resultant angular velocity of tae cap is proportional to the acceleration of the housing in this manner and means may be used to measure the velocity and operate switches at a pre-set magnitude. To make the above-described dcvice sensitive to acceleration in only one direction the magnetized element forms the spinning inertia element of a free gyroscope, and the outer housing functions as a gimbal of a gyroscope.

  15. Accelerated Evolution of Schistosome Genes Coding for Proteins Located at the Host–Parasite Interface

    PubMed Central

    Philippsen, Gisele S.; Wilson, R. Alan; DeMarco, Ricardo

    2015-01-01

    Study of proteins located at the host–parasite interface in schistosomes might provide clues about the mechanisms utilized by the parasite to escape the host immune system attack. Micro-exon gene (MEG) protein products and venom allergen-like (VAL) proteins have been shown to be present in schistosome secretions or associated with glands, which led to the hypothesis that they are important components in the molecular interaction of the parasite with the host. Phylogenetic and structural analysis of genes and their transcripts in these two classes shows that recent species-specific expansion of gene number for these families occurred separately in three different species of schistosomes. Enrichment of transposable elements in MEG and VAL genes in Schistosoma mansoni provides a credible mechanism for preferential expansion of gene numbers for these families. Analysis of the ratio between synonymous and nonsynonymous substitution rates (dN/dS) in the comparison between schistosome orthologs for the two classes of genes reveals significantly higher values when compared with a set of a control genes coding for secreted proteins, and for proteins previously localized in the tegument. Additional analyses of paralog genes indicate that exposure of the protein to the definitive host immune system is a determining factor leading to the higher than usual dN/dS values in those genes. The observation that two genes encoding S. mansoni vaccine candidate proteins, known to be exposed at the parasite surface, also display similar evolutionary dynamics suggests a broad response of the parasite to evolutionary pressure imposed by the definitive host immune system. PMID:25567667

  16. Gap Junction Proteins in the Blood-Brain Barrier Control Nutrient-Dependent Reactivation of Drosophila Neural Stem Cells

    PubMed Central

    Spéder, Pauline; Brand, Andrea H.

    2014-01-01

    Summary Neural stem cells in the adult brain exist primarily in a quiescent state but are reactivated in response to changing physiological conditions. How do stem cells sense and respond to metabolic changes? In the Drosophila CNS, quiescent neural stem cells are reactivated synchronously in response to a nutritional stimulus. Feeding triggers insulin production by blood-brain barrier glial cells, activating the insulin/insulin-like growth factor pathway in underlying neural stem cells and stimulating their growth and proliferation. Here we show that gap junctions in the blood-brain barrier glia mediate the influence of metabolic changes on stem cell behavior, enabling glia to respond to nutritional signals and reactivate quiescent stem cells. We propose that gap junctions in the blood-brain barrier are required to translate metabolic signals into synchronized calcium pulses and insulin secretion. PMID:25065772

  17. Accelerating molecular simulations of proteins using Bayesian inference on weak information.

    PubMed

    Perez, Alberto; MacCallum, Justin L; Dill, Ken A

    2015-09-22

    Atomistic molecular dynamics (MD) simulations of protein molecules are too computationally expensive to predict most native structures from amino acid sequences. Here, we integrate "weak" external knowledge into folding simulations to predict protein structures, given their sequence. For example, we instruct the computer "to form a hydrophobic core," "to form good secondary structures," or "to seek a compact state." This kind of information has been too combinatoric, nonspecific, and vague to help guide MD simulations before. Within atomistic replica-exchange molecular dynamics (REMD), we develop a statistical mechanical framework, modeling using limited data with coarse physical insight(s) (MELD + CPI), for harnessing weak information. As a test, we apply MELD + CPI to predict the native structures of 20 small proteins. MELD + CPI samples to within less than 3.2 Å from native for all 20 and correctly chooses the native structures (<4 Å) for 15 of them, including ubiquitin, a millisecond folder. MELD + CPI is up to five orders of magnitude faster than brute-force MD, satisfies detailed balance, and should scale well to larger proteins. MELD + CPI may be useful where physics-based simulations are needed to study protein mechanisms and populations and where we have some heuristic or coarse physical knowledge about states of interest. PMID:26351667

  18. Accelerating molecular simulations of proteins using Bayesian inference on weak information

    PubMed Central

    Perez, Alberto; MacCallum, Justin L.; Dill, Ken A.

    2015-01-01

    Atomistic molecular dynamics (MD) simulations of protein molecules are too computationally expensive to predict most native structures from amino acid sequences. Here, we integrate “weak” external knowledge into folding simulations to predict protein structures, given their sequence. For example, we instruct the computer “to form a hydrophobic core,” “to form good secondary structures,” or “to seek a compact state.” This kind of information has been too combinatoric, nonspecific, and vague to help guide MD simulations before. Within atomistic replica-exchange molecular dynamics (REMD), we develop a statistical mechanical framework, modeling using limited data with coarse physical insight(s) (MELD + CPI), for harnessing weak information. As a test, we apply MELD + CPI to predict the native structures of 20 small proteins. MELD + CPI samples to within less than 3.2 Å from native for all 20 and correctly chooses the native structures (<4 Å) for 15 of them, including ubiquitin, a millisecond folder. MELD + CPI is up to five orders of magnitude faster than brute-force MD, satisfies detailed balance, and should scale well to larger proteins. MELD + CPI may be useful where physics-based simulations are needed to study protein mechanisms and populations and where we have some heuristic or coarse physical knowledge about states of interest. PMID:26351667

  19. Interaction of HTLV-1 Tax with minichromosome maintenance proteins accelerates the replication timing program.

    PubMed

    Boxus, Mathieu; Twizere, Jean-Claude; Legros, Sébastien; Kettmann, Richard; Willems, Luc

    2012-01-01

    The Tax oncoprotein encoded by the human T-cell leukemia virus type 1 plays a pivotal role in viral persistence and pathogenesis. Human T-cell leukemia virus type 1-infected cells proliferate faster than normal lymphocytes, expand through mitotic division, and accumulate genomic lesions. Here, we show that Tax associates with the minichromosome maintenance MCM2-7 helicase complex and localizes to origins of replication. Tax modulates the spatiotemporal program of origin activation and fires supplementary origins at the onset of S phase. Thereby, Tax increases the DNA replication rate, accelerates S phase progression, but also generates a replicative stress characterized by the presence of genomic lesions. Mechanistically, Tax favors p300 recruitment and histone hyperacetylation at late replication domains, advancing their replication timing in early S phase. PMID:22058115

  20. Role of Polymer Architecture on the Activity of Polymer-Protein Conjugates for the Treatment of Accelerated Bone Loss Disorders.

    PubMed

    Tucker, Bryan S; Stewart, Jon D; Aguirre, J Ignacio; Holliday, L Shannon; Figg, C Adrian; Messer, Jonathan G; Sumerlin, Brent S

    2015-08-10

    Polymers of similar molecular weights and chemical constitution but varying in their macromolecular architectures were conjugated to osteoprotegerin (OPG) to determine the effect of polymer topology on protein activity in vitro and in vivo. OPG is a protein that inhibits bone resorption by preventing the formation of mature osteoclasts from the osteoclast precursor cell. Accelerated bone loss disorders, such as osteoporosis, rheumatoid arthritis, and metastatic bone disease, occur as a result of increased osteoclastogenesis, leading to the severe weakening of the bone. OPG has shown promise as a treatment in bone disorders; however, it is rapidly cleared from circulation through rapid liver uptake, and frequent, high doses of the protein are necessary to achieve a therapeutic benefit. We aimed to improve the effectiveness of OPG by creating OPG-polymer bioconjugates, employing reversible addition-fragmentation chain transfer polymerization to create well-defined polymers with branching densities varying from linear, loosely branched to densely branched. Polymers with each of these architectures were conjugated to OPG using a "grafting-to" approach, and the bioconjugates were characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The OPG-polymer bioconjugates showed retention of activity in vitro against osteoclasts, and each bioconjugate was shown to be nontoxic. Preliminary in vivo studies further supported the nontoxic characteristics of the bioconjugates, and measurement of the bone mineral density in rats 7 days post-treatment via peripheral quantitative computed tomography suggested a slight increase in bone mineral density after administration of the loosely branched OPG-polymer bioconjugate. PMID:26151628

  1. [Gap junction and diabetic foot].

    PubMed

    Zou, Xiao-rong; Tao, Jian; Wang, Yun-kai

    2015-11-01

    Gap junctions play a critical role in electrical synchronization and exchange of small molecules between neighboring cells; connexins are a family of structurally related transmembrane proteins that assemble to form vertebrate gap junctions. Hyperglycemia changes the structure gap junction proteins and their expression, resulting in obstruction of neural regeneration, vascular function and wound healing, and also promoting vascular atherosclerosis. These pathogenic factors would cause diabetic foot ulcers. This article reviews the involvement of connexins in pathogenesis of diabetic foot. PMID:26822053

  2. Accelerated Profile HMM Searches

    PubMed Central

    Eddy, Sean R.

    2011-01-01

    Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call “sparse rescaling”. These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. PMID:22039361

  3. The chloroplast protein LTO1/AtVKOR is involved in the xanthophyll cycle and the acceleration of D1 protein degradation.

    PubMed

    Yu, Zhi-Bo; Lu, Ying; Du, Jia-Jia; Peng, Jun-Jie; Wang, Xiao-Yun

    2014-01-01

    The thylakoid protein LTO1/AtVKOR-DsbA is recently found to be an oxidoreductase involved in disulfide bond formation and the assembly of photosystem II (PSII) in Arabidopsis thaliana. In this study, experimental evidence showed that LTO1 deficiency caused severe photoinhibition which was related to the xanthophyll cycle and D1 protein degradation. The lto1-2 mutant was more sensitive to intense irradiance than wild type. When treated with different concentrations of dithiothreitol (DTT), an inhibitor of violaxanthin de-epoxidase (VDE) in the xanthophyll cycle, there was a larger reduction in NPQ in the wild type than in the lto1-2 mutant under high irradiance, indicating that lto1-2 had a lower sensitivity to DTT gradients than did the wild type. Zeaxanthin in the xanthophyll cycle, which participates in the thermal dissipation of excess absorbed light energy, was much less active in lto1-2 than in the wild type under intense light levels, and the de-epoxidation state of the xanthophyll cycle was consistent with the susceptibility of NPQ. Together these observations indicated that aggravated photoinhibition in lto1-2 was related to a reduction in xanthophyll cycle-associated energy dissipation. When D1 protein synthesis was suppressed by an inhibitor of chloroplast protein synthesis (streptomycin sulfate), the levels of D1 protein decreased more in the lto1-2 mutant than in the wild type when exposed to intense light levels, implying that a deficiency in LTO1 accelerated the degradation of D1 and thus affected D1 turnover. Transgenic complementation of plants with lto1-2 ultimately allowed for the recovery of the photoinhibition properties of leaves. PMID:24300993

  4. The GroEL protein of Porphyromonas gingivalis accelerates tumor growth by enhancing endothelial progenitor cell function and neovascularization.

    PubMed

    Lin, F-Y; Huang, C-Y; Lu, H-Y; Shih, C-M; Tsao, N-W; Shyue, S-K; Lin, C-Y; Chang, Y-J; Tsai, C-S; Lin, Y-W; Lin, S-J

    2015-06-01

    Porphyromonas gingivalis is a bacterial species that causes destruction of periodontal tissues. Additionally, previous evidence indicates that GroEL from P. gingivalis may possess biological activities involved in systemic inflammation, especially inflammation involved in the progression of periodontal diseases. The literature has established a relationship between periodontal disease and cancer. However, it is unclear whether P. gingivalis GroEL enhances tumor growth. Here, we investigated the effects of P. gingivalis GroEL on neovasculogenesis in C26 carcinoma cell-carrying BALB/c mice and chick eggs in vivo as well as its effect on human endothelial progenitor cells (EPC) in vitro. We found that GroEL treatment accelerated tumor growth (tumor volume and weight) and increased the mortality rate in C26 cell-carrying BALB/c mice. GroEL promoted neovasculogenesis in chicken embryonic allantois and increased the circulating EPC level in BALB/c mice. Furthermore, GroEL effectively stimulated EPC migration and tube formation and increased E-selectin expression, which is mediated by eNOS production and p38 mitogen-activated protein kinase activation. Additionally, GroEL may enhance resistance against paclitaxel-induced cell cytotoxicity and senescence in EPC. In conclusion, P. gingivalis GroEL may act as a potent virulence factor, contributing to the neovasculogenesis of tumor cells and resulting in accelerated tumor growth. PMID:25220060

  5. Invited review: Small GTPases and their GAPs.

    PubMed

    Mishra, Ashwini K; Lambright, David G

    2016-08-01

    Widespread utilization of small GTPases as major regulatory hubs in many different biological systems derives from a conserved conformational switch mechanism that facilitates cycling between GTP-bound active and GDP-bound inactive states under control of guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), which accelerate slow intrinsic rates of activation by nucleotide exchange and deactivation by GTP hydrolysis, respectively. Here we review developments leading to current understanding of intrinsic and GAP catalyzed GTP hydrolytic reactions in small GTPases from structural, molecular and chemical mechanistic perspectives. Despite the apparent simplicity of the GTPase cycle, the structural bases underlying the hallmark hydrolytic reaction and catalytic acceleration by GAPs are considerably more diverse than originally anticipated. Even the most fundamental aspects of the reaction mechanism have been challenging to decipher. Through a combination of experimental and in silico approaches, the outlines of a consensus view have begun to emerge for the best studied paradigms. Nevertheless, recent observations indicate that there is still much to be learned. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 431-448, 2016. PMID:26972107

  6. Comparative changes in plasma protein concentration, hematocrit and plasma volume during exercise, bedrest and + Gz acceleration.

    NASA Technical Reports Server (NTRS)

    Van Beaumont, W.; Greenleaf, J. E.

    1972-01-01

    Discussion of experiments which indicate that under conditions of a constant red cell volume the proportional changes in hematocrit and plasma volume during exercise are never equal. On the basis of direct measurements and calculated changes of plasma volume it is concluded that during maximal exercise there is a small loss of protein from the plasma. It is clear that changes in content of blood constituents can only be evaluated correctly after determination of changes in plasma volume.

  7. Target disruption of ribosomal protein pNO40 accelerates aging and impairs osteogenic differentiation of mesenchymal stem cells.

    PubMed

    Lin, Yen-Ming; Wu, Chih-Ching; Chang, Yu-Chen; Wu, Chu-Han; Ho, Hsien Li; Hu, Ji Wei; Chang, Ren-Chi; Wang, Chung-Ta; Ouyang, Pin

    2016-01-22

    pNO40/PS1D, a novel nucleolar protein, has been characterized as a core protein of eukaryotic 60S ribosome and at least two splicing forms of pNO40 mRNAs with alternative starting sites have been identified. Through production of knockout (ko) mice with either exon 2 (△E2), exon 4 (△E4) or △E2+E4 targeted disruption we identified a cryptic splicing product occurring in the ko tissues examined which in general cannot be observed in regular RT-PCR detection of wild-type (wt) animals. Among ko animals, △E4 null embryos exhibited prominent senescence-associated β-galactosidase (SA-β-gal) staining, a marker for senescent cells, in notochord, forelimbs and heart while bone marrow-derived mesenchymal stem cells (MSCs) from △E4 null mice developed accelerated aging and osteogenic differentiation defects compared to those from wt and other isoform mutant mice. Examination of the causal relationship between pNO40 deficiency and MSC-accelerated aging revealed △E4 null disruption in MSCs elicits high levels of ROS and elevated expression levels of p16 and Rb but not p53. Further analysis with iTraq identified CYP1B1, a component of the cytochrome p450 system, as a potential molecule mediating ROS generation in pNO40 deficient MSCs. We herein established a mouse model of MSC aging through pNO40-targeted depletion and demonstrated the effects of loss of pNO40 on bone homeostasis. PMID:26721440

  8. Regulator of G protein signaling 2 (RGS2) deficiency accelerates the progression of kidney fibrosis.

    PubMed

    Jang, Hee-Seong; Kim, Jee In; Noh, Mira; Rhee, Man Hee; Park, Kwon Moo

    2014-09-01

    The regulator of G protein signaling 2 (RGS2) is a potent negative regulator of Gq protein signals including the angiotensin II (AngII)/AngII receptor signal, which plays a critical role in the progression of fibrosis. However, the role of RGS2 on the progression of kidney fibrosis has not been assessed. Here, we investigated the role of RGS2 in kidney fibrosis induced by unilateral ureteral obstruction (UUO) in mice. UUO resulted in increased expression of RGS2 mRNA and protein in the kidney along with increases of AngII and its type 1 receptor (AT1R) signaling and fibrosis. Furthermore, UUO increased the levels of F4/80, Ly6G, myeloperoxidase, and CXCR4 in the kidneys. RGS2 deficiency significantly enhanced these changes in the kidney. RGS2 deletion in the bone marrow-derived cells by transplanting the bone marrow of RGS2 knock-out mice into wild type mice enhanced UUO-induced kidney fibrosis. Overexpression of RGS2 in HEK293 cells, a human embryonic kidney cell line, and RAW264.7 cells, a monocyte/macrophage line, inhibited the AngII-induced activation of ERK and increase of CXCR4 expression. These findings provide the first evidence that RGS2 negatively regulates the progression of kidney fibrosis following UUO, likely by suppressing fibrogenic and inflammatory responses through the inhibition of AngII/AT1R signaling. PMID:24973550

  9. Functional expression of Ca²⁺ dependent mammalian transmembrane gap junction protein Cx43 in slime mold Dictyostelium discoideum.

    PubMed

    Kaufmann, Stefan; Weiss, Ingrid M; Eckstein, Volker; Tanaka, Motomu

    2012-03-01

    In this paper, we expressed murine gap junction protein Cx43 in Dictyostelium discoideum by introducing the specific vector pDXA. In the first step, the successful expression of Cx43 and Cx43-eGFP was verified by (a) Western blot (anti-Cx43, anti-GFP), (b) fluorescence microscopy (eGFP-Cx43 co-expression, Cx43 immunostaining), and (c) flow cytometry analysis (eGFP-Cx43 co-expression). Although the fluorescence signals from cells expressing Cx43-eGFP detected by fluorescence microscopy seem relatively low, analysis by flow cytometry demonstrated that more than 60% of cells expressed Cx43-eGFP. In order to evaluate the function of expressed Cx43 in D. discoideum, we examined the hemi-channel function of Cx43. In this series of experiments, the passive uptake of carboxyfluorescein was monitored using flow cytometric analysis. A significant number of the transfected cells showed a prominent dye uptake in the absence of Ca(2+). The dye uptake by transfected cells in the presence of Ca(2+) was even lower than the non-specific dye uptake by non-transformed Ax3 orf+ cells, confirming that Cx43 expressed in D. discoideum retains its Ca(2+)-dependent, specific gating function. The expression of gap junction proteins expressed in slime molds opens a possibility to the biological significance of intercellular communications in development and maintenance of multicellular organisms. PMID:22330805

  10. Targeted disruption of fibrinogen like protein-1 accelerates hepatocellular carcinoma development

    SciTech Connect

    Nayeb-Hashemi, Hamed; Desai, Anal; Demchev, Valeriy; Bronson, Roderick T.; Hornick, Jason L.; Cohen, David E.; Ukomadu, Chinweike

    2015-09-18

    Fibrinogen like protein-1 (Fgl1) is a predominantly liver expressed protein that has been implicated as both a hepatoprotectant and a hepatocyte mitogen. Fgl1 expression is decreased in hepatocellular carcinoma (HCC) and its loss correlates with a poorly differentiated phenotype. To better elucidate the role of Fgl1 in hepatocarcinogenesis, we treated mice wild type or null for Fgl1 with diethyl nitrosamine and monitored for incidence of hepatocellular cancer. We find that mice lacking Fgl1 develop HCC at more than twice the rate of wild type mice. We show that hepatocellular cancers from Fgl1 null mice are molecularly distinct from those of the wild type mice. In tumors from Fgl1 null mice there is enhanced activation of Akt and downstream targets of the mammalian target of rapamycin (mTOR). In addition, there is paradoxical up regulation of putative hepatocellular cancer tumor suppressors; tripartite motif-containing protein 35 (Trim35) and tumor necrosis factor super family 10b (Tnfrsf10b). Taken together, these findings suggest that Fgl1 acts as a tumor suppressor in hepatocellular cancer through an Akt dependent mechanism and supports its role as a potential therapeutic target in HCC. - Highlights: • Fgl1 knockout mice (Fgl1KO) are more prone to carcinogen-induced liver cancer compared to wild type (WT) mates. • Tumors from the Fgl1KO are molecularly distinct with enhanced Akt and mTOR activity in comparison with Fgl1WT tumors. • Tumors from the Fgl1KO have enhanced expression of Trim35 and Tnfrsf10b, putative HCC tumor suppressors.

  11. Human carcinomas variably express the complement inhibitory proteins CD46 (membrane cofactor protein), CD55 (decay-accelerating factor), and CD59 (protectin).

    PubMed Central

    Niehans, G. A.; Cherwitz, D. L.; Staley, N. A.; Knapp, D. J.; Dalmasso, A. P.

    1996-01-01

    Normal human tissues express membrane-associated complement inhibitory proteins that protect these tissues from damage by autologous complement. To determine whether neoplasms also express these proteins, we examined the distribution of the complement inhibitors decay-accelerating factor (DAF), CD59 (protectin), and membrane cofactor protein in frozen samples of human breast, colon, kidney, and lung carcinomas and in adjacent non-neoplastic tissues, using immunohistochemistry. All samples were also studied for deposition of C3 fragments and activated C5b-9. Differences between normal tissues and the corresponding neoplasms were often observed, with loss or gain of expression of one or more inhibitors. Ductal carcinomas of the breast showed the most variation in phenotype; some tumors expressed only one inhibitor while others expressed different combinations of two or three inhibitors. Colon carcinomas, by contrast, stained intensely for all inhibitors. Renal cell carcinomas had weak to moderate expression of one to three inhibitors, generally DAF and CD59, whereas non-small cell carcinomas of the lung usually expressed CD59 and membrane cofactor protein with variable DAF immunoreactivity. The two small cell carcinomas of the lung showed little or no staining for any inhibitor. Activated C5b-9 deposition was seen adjacent to tumor nests in a minority of carcinomas and showed no correlation with complement inhibitor expression. C3 fragment deposition was minimal. Our results demonstrate that most carcinomas, with the exception of small cell carcinomas of the lung, do express one or more complement inhibitors at a level likely to inhibit complement-mediated cellular damage. Unexpectedly, large quantities of DAF and CD59 were often observed in tumor stroma, with only limited deposition in normal connective tissue. This suggests that carcinomas may supplement the activity of membrane-associated complement inhibitors by release of soluble forms of DAF and CD59 into the

  12. Impact of 7,12-dimethylbenz[a]anthracene exposure on connexin gap junction proteins in cultured rat ovaries

    PubMed Central

    Ganesan, Shanthi; Keating, Aileen F.

    2014-01-01

    7,12-dimethylbenz[a]anthracene (DMBA) destroys ovarian follicles in a concentration-dependent manner. The impact of DMBA on connexin (CX) proteins that mediate communication between follicular cell types along with pro-apoptotic factors p53 and Bax were investigated. Postnatal day (PND) 4 Fisher 344 rat ovaries were cultured for 4 days in vehicle medium (1% DMSO) followed by a single exposure to vehicle control (1% DMSO) or DMBA (12.5 nM or 75 nM) and cultured for 4 or 8 days. RT-PCR was performed to quantify Cx37, Cx43, p53 and Bax mRNA level. Western blotting and immunofluorescence staining were performed to determine CX37 or CX43 level and/or localization. Cx37 mRNA and protein increased (P < 0.05) at 4 days of 12.5 nM DMBA exposure. Relative to vehicle control-treated ovaries, mRNA encoding Cx43 decreased (P < 0.05) but CX43 protein increased (P < 0.05) at 4 days by both DMBA exposures. mRNA expression of pro-apoptotic p53 was decreased (P < 0.05) but no changes in Bax expression were observed after 4 days of DMBA exposures. In contrast, after 8 days, DMBA decreased Cx37 and Cx43 mRNA and protein but increased both p53 and Bax mRNA levels. CX43 protein was located between granulosa cells, while CX37 was located at the oocyte cell surface of all follicle stages. These findings support that DMBA exposure impacts ovarian Cx37 and Cx43 mRNA and protein prior to both observed changes in pro-apoptotic p53 and Bax and follicle loss. It is possible that such interference in follicular cell communication is detrimental to follicle viability, and may play a role in DMBA-induced follicular atresia. PMID:24269759

  13. Gap Junctions

    PubMed Central

    Nielsen, Morten Schak; Axelsen, Lene Nygaard; Sorgen, Paul L.; Verma, Vandana; Delmar, Mario; Holstein-Rathlou, Niels-Henrik

    2013-01-01

    Gap junctions are essential to the function of multicellular animals, which require a high degree of coordination between cells. In vertebrates, gap junctions comprise connexins and currently 21 connexins are known in humans. The functions of gap junctions are highly diverse and include exchange of metabolites and electrical signals between cells, as well as functions, which are apparently unrelated to intercellular communication. Given the diversity of gap junction physiology, regulation of gap junction activity is complex. The structure of the various connexins is known to some extent; and structural rearrangements and intramolecular interactions are important for regulation of channel function. Intercellular coupling is further regulated by the number and activity of channels present in gap junctional plaques. The number of connexins in cell-cell channels is regulated by controlling transcription, translation, trafficking, and degradation; and all of these processes are under strict control. Once in the membrane, channel activity is determined by the conductive properties of the connexin involved, which can be regulated by voltage and chemical gating, as well as a large number of posttranslational modifications. The aim of the present article is to review our current knowledge on the structure, regulation, function, and pharmacology of gap junctions. This will be supported by examples of how different connexins and their regulation act in concert to achieve appropriate physiological control, and how disturbances of connexin function can lead to disease. © 2012 American Physiological Society. Compr Physiol 2:1981-2035, 2012. PMID:23723031

  14. Impact of 7,12-dimethylbenz[a]anthracene exposure on connexin gap junction proteins in cultured rat ovaries

    SciTech Connect

    Ganesan, Shanthi Keating, Aileen F.

    2014-01-15

    7,12-Dimethylbenz[a]anthracene (DMBA) destroys ovarian follicles in a concentration-dependent manner. The impact of DMBA on connexin (CX) proteins that mediate communication between follicular cell types along with pro-apoptotic factors p53 and Bax were investigated. Postnatal day (PND) 4 Fisher 344 rat ovaries were cultured for 4 days in vehicle medium (1% DMSO) followed by a single exposure to vehicle control (1% DMSO) or DMBA (12.5 nM or 75 nM) and cultured for 4 or 8 days. RT-PCR was performed to quantify Cx37, Cx43, p53 and Bax mRNA level. Western blotting and immunofluorescence staining were performed to determine CX37 or CX43 level and/or localization. Cx37 mRNA and protein increased (P < 0.05) at 4 days of 12.5 nM DMBA exposure. Relative to vehicle control-treated ovaries, mRNA encoding Cx43 decreased (P < 0.05) but CX43 protein increased (P < 0.05) at 4 days by both DMBA exposures. mRNA expression of pro-apoptotic p53 was decreased (P < 0.05) but no changes in Bax expression were observed after 4 days of DMBA exposures. In contrast, after 8 days, DMBA decreased Cx37 and Cx43 mRNA and protein but increased both p53 and Bax mRNA levels. CX43 protein was located between granulosa cells, while CX37 was located at the oocyte cell surface of all follicle stages. These findings support that DMBA exposure impacts ovarian Cx37 and Cx43 mRNA and protein prior to both observed changes in pro-apoptotic p53 and Bax and follicle loss. It is possible that such interference in follicular cell communication is detrimental to follicle viability, and may play a role in DMBA-induced follicular atresia. - Highlights: • DMBA increases Cx37 and Cx43 expression prior to follicle loss. • During follicle loss both Cx37 and Cx43 expressions are reduced. • CX43 protein is absent in follicle remnants lacking an oocyte.

  15. Fibroblast Activation Protein (FAP) Accelerates Collagen Degradation and Clearance from Lungs in Mice.

    PubMed

    Fan, Ming-Hui; Zhu, Qiang; Li, Hui-Hua; Ra, Hyun-Jeong; Majumdar, Sonali; Gulick, Dexter L; Jerome, Jacob A; Madsen, Daniel H; Christofidou-Solomidou, Melpo; Speicher, David W; Bachovchin, William W; Feghali-Bostwick, Carol; Puré, Ellen

    2016-04-01

    Idiopathic pulmonary fibrosis is a disease characterized by progressive, unrelenting lung scarring, with death from respiratory failure within 2-4 years unless lung transplantation is performed. New effective therapies are clearly needed. Fibroblast activation protein (FAP) is a cell surface-associated serine protease up-regulated in the lungs of patients with idiopathic pulmonary fibrosis as well as in wound healing and cancer. We postulate that FAP is not only a marker of disease but influences the development of pulmonary fibrosis after lung injury. In two different models of pulmonary fibrosis, intratracheal bleomycin instillation and thoracic irradiation, we find increased mortality and increased lung fibrosis in FAP-deficient mice compared with wild-type mice. Lung extracellular matrix analysis reveals accumulation of intermediate-sized collagen fragments in FAP-deficient mouse lungs, consistent within vitrostudies showing that FAP mediates ordered proteolytic processing of matrix metalloproteinase (MMP)-derived collagen cleavage products. FAP-mediated collagen processing leads to increased collagen internalization without altering expression of the endocytic collagen receptor, Endo180. Pharmacologic FAP inhibition decreases collagen internalization as expected. Conversely, restoration of FAP expression in the lungs of FAP-deficient mice decreases lung hydroxyproline content after intratracheal bleomycin to levels comparable with that of wild-type controls. Our findings indicate that FAP participates directly, in concert with MMPs, in collagen catabolism and clearance and is an important factor in resolving scar after injury and restoring lung homeostasis. Our study identifies FAP as a novel endogenous regulator of fibrosis and is the first to show FAP's protective effects in the lung. PMID:26663085

  16. Loss of Gi G-Protein-Coupled Receptor Signaling in Osteoblasts Accelerates Bone Fracture Healing.

    PubMed

    Wang, Liping; Hsiao, Edward C; Lieu, Shirley; Scott, Mark; O'Carroll, Dylan; Urrutia, Ashley; Conklin, Bruce R; Colnot, Celine; Nissenson, Robert A

    2015-10-01

    G-protein-coupled receptors (GPCRs) are key regulators of skeletal homeostasis and are likely important in fracture healing. Because GPCRs can activate multiple signaling pathways simultaneously, we used targeted disruption of G(i) -GPCR or activation of G(s) -GPCR pathways to test how each pathway functions in the skeleton. We previously demonstrated that blockade of G(i) signaling by pertussis toxin (PTX) transgene expression in maturing osteoblastic cells enhanced cortical and trabecular bone formation and prevented age-related bone loss in female mice. In addition, activation of G(s) signaling by expressing the G(s) -coupled engineered receptor Rs1 in maturing osteoblastic cells induced massive trabecular bone formation but cortical bone loss. Here, we test our hypothesis that the G(i) and G(s) pathways also have distinct functions in fracture repair. We applied closed, nonstabilized tibial fractures to mice in which endogenous G(i) signaling was inhibited by PTX, or to mice with activated G(s) signaling mediated by Rs1. Blockade of endogenous G(i) resulted in a smaller callus but increased bone formation in both young and old mice. PTX treatment decreased expression of Dkk1 and increased Lef1 mRNAs during fracture healing, suggesting a role for endogenous G(i) signaling in maintaining Dkk1 expression and suppressing Wnt signaling. In contrast, adult mice with activated Gs signaling showed a slight increase in the initial callus size with increased callus bone formation. These results show that G(i) blockade and G(s) activation of the same osteoblastic lineage cell can induce different biological responses during fracture healing. Our findings also show that manipulating the GPCR/cAMP signaling pathway by selective timing of G(s) and G(i) -GPCR activation may be important for optimizing fracture repair. PMID:25917236

  17. A deficiency in cold-inducible RNA-binding protein accelerates the inflammation phase and improves wound healing.

    PubMed

    Idrovo, Juan Pablo; Jacob, Asha; Yang, Weng Lang; Wang, Zhimin; Yen, Hao Ting; Nicastro, Jeffrey; Coppa, Gene F; Wang, Ping

    2016-02-01

    Chronic or non-healing wounds are a major concern in clinical practice and these wounds are mostly associated with diabetes, and venous and pressure ulcers. Wound healing is a complex process involving overlapping phases and the primary phase in this complex cascade is the inflammatory state. While inflammation is necessary for wound healing, a prolonged inflammatory phase leads to impaired healing. Cold-inducible RNA-binding protein (CIRP) belongs to a family of cold-shock proteins that are expressed in high levels under stress conditions. Recently, we demonstrated that a deficiency in CIRP led to decreased inflammation and mortality in an experimental model of hemorrhagic shock. Thus, we hypothesized that a deficiency in CIRP would accelerate the inflammatory phase and lead to an improvement in cutaneous wound healing. In this study, to examine this hypothesis, a full-thickness wound was created on the dorsum of wild-type (WT) and CIRP-/- mice. The wound size was measured every other day for 14 days. The wound area was significantly decreased in the CIRP-/- mice by day 9 and continued to decrease until day 14 compared to the WT mice. In a separate cohort, mice were sacrificed on days 3 and 7 after wounding and the skin tissues were harvested for histological analysis and RNA measurements. On day 3, the mRNA expression of tumor necrossis factor (TNF)-α in the skin tissues was increased by 16-fold in the WT mice, whereas these levels were increased by 65-fold in the CIRP-/- mice. Of note on day 7, while the levels of TNF-α remained high in the WT mice, these levels were significantly decreased in the CIRP-/- mice. The histological analysis of the wounded skin tissue indicated an improvement as early as day 3 in the CIRP-/- mice, whereas in the WT mice, infiltrated immune cells were still present on day 7. On day 7 in the CIRP-/- mice, Gr-1 expression was low and CD31 expression was high, whereas in the WT mice, Gr-1 expression was high and CD31 expression was low

  18. Functional Requirement for a Highly Conserved Charged Residue at Position 75 in the Gap Junction Protein Connexin 32*

    PubMed Central

    Abrams, Charles K.; Islam, Mahee; Mahmoud, Rola; Kwon, Taekyung; Bargiello, Thaddeus A.; Freidin, Mona M.

    2013-01-01

    Charcot Marie Tooth disease (CMT) is a group of inherited disorders characterized clinically by exclusively or predominantly peripheral nerve dysfunction. CMT1X, the most common form of X-linked CMT is caused by mutations in connexin 32 (Cx32). In this work, we used dual whole cell patch clamp recording to examine the functional effects of mutations at the Arg75 position. This residue is highly conserved among members of the connexin family, and disease-causing mutations have been identified at this (or the corresponding) position in Cx26, Cx43, and Cx46. Thus, a better understanding of the effects of mutations of this position in Cx32 may have relevance to pathogenesis of a number of different human diseases. All three mutants associated with CMT1X (R75P, R75Q, and R75W) showed very low levels of coupling similar to those of the cells transfected with vector alone. Heterotypic pairing with Cx32 WT showed that the absence of coupling for these mutants in the homotypic configuration could be explained by shifts in their hemichannel Gj-Vj relations. Examination of the expression levels and gating characteristics of seven additional mutants (R75A, R75D, R75E, R75H, R75K, R75L, and R75V) at this position suggest that the positive charge at position 75 in Cx32 is required for normal channel function but not for gap junction assembly. Our studies also suggest that disease treatment strategies for CMT1X, which correct trafficking abnormalities in Cx32, may be ineffective for the group of mutations also conferring changes in gating properties of Cx32 channels. PMID:23209285

  19. Identification of Atg2 and ArfGAP1 as Candidate Genetic Modifiers of the Eye Pigmentation Phenotype of Adaptor Protein-3 (AP-3) Mutants in Drosophila melanogaster

    PubMed Central

    Rodriguez-Fernandez, Imilce A.; Dell’Angelica, Esteban C.

    2015-01-01

    The Adaptor Protein (AP)-3 complex is an evolutionary conserved, molecular sorting device that mediates the intracellular trafficking of proteins to lysosomes and related organelles. Genetic defects in AP-3 subunits lead to impaired biogenesis of lysosome-related organelles (LROs) such as mammalian melanosomes and insect eye pigment granules. In this work, we have performed a forward screening for genetic modifiers of AP-3 function in the fruit fly, Drosophila melanogaster. Specifically, we have tested collections of large multi-gene deletions–which together covered most of the autosomal chromosomes–to identify chromosomal regions that, when deleted in single copy, enhanced or ameliorated the eye pigmentation phenotype of two independent AP-3 subunit mutants. Fine-mapping led us to define two non-overlapping, relatively small critical regions within fly chromosome 3. The first critical region included the Atg2 gene, which encodes a conserved protein involved in autophagy. Loss of one functional copy of Atg2 ameliorated the pigmentation defects of mutants in AP-3 subunits as well as in two other genes previously implicated in LRO biogenesis, namely Blos1 and lightoid, and even increased the eye pigment content of wild-type flies. The second critical region included the ArfGAP1 gene, which encodes a conserved GTPase-activating protein with specificity towards GTPases of the Arf family. Loss of a single functional copy of the ArfGAP1 gene ameliorated the pigmentation phenotype of AP-3 mutants but did not to modify the eye pigmentation of wild-type flies or mutants in Blos1 or lightoid. Strikingly, loss of the second functional copy of the gene did not modify the phenotype of AP-3 mutants any further but elicited early lethality in males and abnormal eye morphology when combined with mutations in Blos1 and lightoid, respectively. These results provide genetic evidence for new functional links connecting the machinery for biogenesis of LROs with molecules implicated

  20. Curcuma purpurascens BI. rhizome accelerates rat excisional wound healing: involvement of Hsp70/Bax proteins, antioxidant defense, and angiogenesis activity

    PubMed Central

    Rouhollahi, Elham; Moghadamtousi, Soheil Zorofchian; Hajiaghaalipour, Fatemeh; Zahedifard, Maryam; Tayeby, Faezeh; Awang, Khalijah; Abdulla, Mahmood Ameen; Mohamed, Zahurin

    2015-01-01

    Purpose Curcuma purpurascens BI. is a member of Zingiberaceae family. The purpose of this study is to investigate the wound healing properties of hexane extract of C. purpurascens rhizome (HECP) against excisional wound healing in rats. Materials and methods Twenty four rats were randomly divided into 4 groups: A) negative control (blank placebo, acacia gum), B) low dose of HECP, C) high dose of HECP, and D) positive control, with 6 rats in each group. Full-thickness incisions (approximately 2.00 cm) were made on the neck area of each rat. Groups 1–4 were treated two-times a day for 20 days with blank placebo, HECP (100 mg/kg), HECP (200 mg/kg), and intrasite gel as a positive control, respectively. After 20 days, hematoxylin and eosin and Masson’s trichrome stainings were employed to investigate the histopathological alterations. Protein expressions of Bax and Hsp70 were examined in the wound tissues using immunohistochemistry analysis. In addition, levels of enzymatic antioxidants and malondialdehyde representing lipid peroxidation were measured in wound tissue homogenates. Results Macroscopic evaluation of wounds showed conspicuous elevation in wound contraction after topical administration of HECP at both doses. Moreover, histopathological analysis revealed noteworthy reduction in the scar width correlated with the enhanced collagen content and fibroblast cells, accompanied by a reduction of inflammatory cells in the granulation tissues. At the molecular level, HECP facilitates wound-healing process by downregulating Bax and upregulating Hsp70 protein at the wound site. The formation of new blood vessel was observed in Masson’s trichrome staining of wounds treated with HECP (100 and 200 mg/kg). In addition, HECP administration caused a significant surge in enzymatic antioxidant activities and a decline in lipid peroxidation. Conclusion These findings suggested that HECP accelerated wound-healing process in rats via antioxidant activity, angiogenesis

  1. Gap Resolution

    SciTech Connect

    2009-06-16

    With the continued improvements of next generation DNA sequencing technologies and their advantages over traditional Sanger sequencing, the Joint Genome Institute (JGI) has modified its sequencing pipeline to take advantage of the benefits of such technologies. Currently, standard 454 Titanium, paired end 454 Titanium, and Illumina GAll data are generated for all microbial projects and then assembled using draft assemblies at a much greater throughput than before. However, it also presents us with new challenges. In addition to the increased throughput, we also have to deal with a larger number of gaps in the Newbler genome assemblies. Gaps in these assemblies are usually caused by repeats (Newbler collapses repeat copies into individual contigs, thus creating gaps), strong secondary structures, and artifacts of the PCR process (specific to 454 paired end libraries). Some gaps in draft assemblies can be resolved merely by adding back the collapsed data from repeats. To expedite gap closure and assembly improvement on large numbers of these assemblies, we developed software to address this issue.

  2. Gap Resolution

    2009-06-16

    With the continued improvements of next generation DNA sequencing technologies and their advantages over traditional Sanger sequencing, the Joint Genome Institute (JGI) has modified its sequencing pipeline to take advantage of the benefits of such technologies. Currently, standard 454 Titanium, paired end 454 Titanium, and Illumina GAll data are generated for all microbial projects and then assembled using draft assemblies at a much greater throughput than before. However, it also presents us with new challenges.more » In addition to the increased throughput, we also have to deal with a larger number of gaps in the Newbler genome assemblies. Gaps in these assemblies are usually caused by repeats (Newbler collapses repeat copies into individual contigs, thus creating gaps), strong secondary structures, and artifacts of the PCR process (specific to 454 paired end libraries). Some gaps in draft assemblies can be resolved merely by adding back the collapsed data from repeats. To expedite gap closure and assembly improvement on large numbers of these assemblies, we developed software to address this issue.« less

  3. Atherosclerosis in ancient humans, accelerated aging syndromes and normal aging: is lamin a protein a common link?

    PubMed

    Miyamoto, Michael I; Djabali, Karima; Gordon, Leslie B

    2014-06-01

    Imaging studies of ancient human mummies have demonstrated the presence of vascular calcification that is consistent with the presence of atherosclerosis. These findings have stimulated interest in the underlying biological processes that might impart to humans an inherent predisposition to the development of atherosclerosis. Clues to these processes may possibly be found in accelerated aging syndromes, such as Hutchinson-Gilford progeria syndrome (HGPS), an ultra-rare disorder characterized by premature aging phenotypes, including very aggressive forms of atherosclerosis, occurring in childhood. The genetic defect in HGPS eventuates in the production of a mutant form of the nuclear structural protein lamin A, called progerin, which is thought to interfere with normal nuclear functioning. Progerin appears to be expressed in vascular cells, resulting in vessel wall cell loss and replacement by fibrous tissue, reducing vessel compliance and promoting calcification, leading to the vascular dysfunction and atherosclerosis seen in HGPS. Interestingly, vascular progerin is detectable in lower levels, in an age-related manner, in the general population, providing the basis for further study of the potential role of abnormal forms of lamin A in the atherosclerotic process of normal aging. PMID:25667091

  4. The Huntington disease protein accelerates breast tumour development and metastasis through ErbB2/HER2 signalling

    PubMed Central

    Moreira Sousa, Cristovão; McGuire, John Russel; Thion, Morgane Sonia; Gentien, David; de la Grange, Pierre; Tezenas du Montcel, Sophie; Vincent-Salomon, Anne; Durr, Alexandra; Humbert, Sandrine

    2013-01-01

    In Huntington disease (HD), polyglutamine expansion in the huntingtin protein causes specific neuronal death. The consequences of the presence of mutant huntingtin in other tissues are less well understood. Here we propose that mutant huntingtin influences breast cancer progression. Indeed, we show that mammary tumours appear earlier in mouse breast cancer models expressing mutant huntingtin as compared to control mice expressing wild-type huntingtin. Tumours bearing mutant huntingtin have a modified gene expression pattern that reflects enhanced aggressiveness with the overexpression of genes favouring invasion and metastasis. In agreement, mutant huntingtin accelerates epithelial to mesenchymal transition and enhances cell motility and invasion. Also, lung metastasis is higher in HD conditions than in control mice. Finally, we report that in HD, the dynamin dependent endocytosis of the ErbB2/HER2 receptor tyrosine kinase is reduced. This leads to its accumulation and to subsequent increases in cell motility and proliferation. Our study may thus have important implications for both cancer and HD. PMID:23300147

  5. Salicylic acid signaling controls the maturation and localization of the arabidopsis defense protein ACCELERATED CELL DEATH6.

    PubMed

    Zhang, Zhongqin; Shrestha, Jay; Tateda, Chika; Greenberg, Jean T

    2014-08-01

    ACCELERATED CELL DEATH6 (ACD6) is a multipass membrane protein with an ankyrin domain that acts in a positive feedback loop with the defense signal salicylic acid (SA). This study implemented biochemical approaches to infer changes in ACD6 complexes and localization. In addition to forming endoplasmic reticulum (ER)- and plasma membrane (PM)-localized complexes, ACD6 forms soluble complexes, where it is bound to cytosolic HSP70, ubiquitinated, and degraded via the proteasome. Thus, ACD6 constitutively undergoes ER-associated degradation. During SA signaling, the soluble ACD6 pool decreases, whereas the PM pool increases. Similarly, ACD6-1, an activated version of ACD6 that induces SA, is present at low levels in the soluble fraction and high levels in the PM. However, ACD6 variants with amino acid substitutions in the ankyrin domain form aberrant, inactive complexes, are induced by a SA agonist, but show no PM localization. SA signaling also increases the PM pools of FLAGELLIN SENSING2 (FLS2) and BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1). FLS2 forms complexes ACD6; both FLS2 and BAK1 require ACD6 for maximal accumulation at the PM in response to SA signaling. A plausible scenario is that SA increases the efficiency of productive folding and/or complex formation in the ER, such that ACD6, together with FLS2 and BAK1, reaches the cell surface to more effectively promote immune responses. PMID:24923602

  6. Accelerating the Association of the Most Stable Protein-Ligand Complex by More than Two Orders of Magnitude.

    PubMed

    Giese, Christoph; Eras, Jonathan; Kern, Anne; Schärer, Martin A; Capitani, Guido; Glockshuber, Rudi

    2016-08-01

    The complex between the bacterial type 1 pilus subunit FimG and the peptide corresponding to the N-terminal extension (termed donor strand, Ds) of the partner subunit FimF (DsF) shows the strongest reported noncovalent molecular interaction, with a dissociation constant (KD ) of 1.5×10(-20)  m. However, the complex only exhibits a slow association rate of 330 m(-1)  s(-1) that limits technical applications, such as its use in affinity purification. Herein, a structure-based approach was used to design pairs of FimGt (a FimG variant lacking its own N-terminal extension) and DsF variants with enhanced electrostatic surface complementarity. Association of the best mutant FimGt/DsF pairs was accelerated by more than two orders of magnitude, while the dissociation rates and 3D structures of the improved complexes remained essentially unperturbed. A KD  value of 8.8×10(-22)  m was obtained for the best mutant complex, which is the lowest value reported to date for a protein/ligand complex. PMID:27351462

  7. Multiplexed Electrochemical Immunoassay of Phosphorylated Proteins Based on Enzyme-Functionalized Gold Nanorod Labels and Electric Field-Driven Acceleration

    SciTech Connect

    Du, Dan; Wang, Jun; Lu, Donglai; Dohnalkova, Alice; Lin, Yuehe

    2011-09-09

    A multiplexed electrochemical immunoassay integrating enzyme amplification and electric field-driven strategy was developed for fast and sensitive quantification of phosphorylated p53 at Ser392 (phospho-p53 392), Ser15 (phospho-p53 15), Ser46 (phospho-p53 46) and total p53 simultaneously. The disposable sensor array has four spatially separated working electrodes and each of them is modified with different capture antibody, which enables simultaneous immunoassay to be conducted without cross-talk between adjacent electrodes. The enhanced sensitivity was achieved by multi-enzymes amplification strategy using gold nanorods (AuNRs) as nanocarrier for co-immobilization of horseradish peroxidase (HRP) and detection antibody (Ab2) at high ratio of HRP/Ab2, which produced an amplified electrocatalytic response by the reduction of HRP oxidized thionine in the presence of hydrogen peroxide. The immunoreaction processes were accelerated by applying +0.4 V for 3 min and then -0.2 V for 1.5 min, thus the whole sandwich immunoreactions could be completed in less than 5 min. The disposable immunosensor array shows excellent promise for clinical screening of phosphorylated proteins and convenient point-of-care diagnostics.

  8. Fiber Accelerating Structures

    SciTech Connect

    Hammond, Andrew P.; /Reed Coll. /SLAC

    2010-08-25

    One of the options for future particle accelerators are photonic band gap (PBG) fiber accelerators. PBG fibers are specially designed optical fibers that use lasers to excite an electric field that is used to accelerate electrons. To improve PBG accelerators, the basic parameters of the fiber were tested to maximize defect size and acceleration. Using the program CUDOS, several accelerating modes were found that maximized these parameters for several wavelengths. The design of multiple defects, similar to having closely bound fibers, was studied to find possible coupling or the change of modes. The amount of coupling was found to be dependent on distance separated. For certain distances accelerating coupled modes were found and examined. In addition, several non-periodic fiber structures were examined using CUDOS. The non-periodic fibers produced several interesting results and promised more modes given time to study them in more detail.

  9. Flooding Vocabulary Gaps to Accelerate Word Learning

    ERIC Educational Resources Information Center

    Brabham, Edna; Buskist, Connie; Henderson, Shannon Coman; Paleologos, Timon; Baugh, Nikki

    2012-01-01

    Students entering school with limited vocabularies are at a disadvantage compared to classmates with robust knowledge of words and meanings. Teaching a few unrelated words at a time is insufficient for catching these students up with peers and preparing them to comprehend texts they will encounter across the grades. This article presents…

  10. Mutation Analysis of Gap Junction Protein Beta 1 and Genotype–Phenotype Correlation in X-linked Charcot–Marie–Tooth Disease in Chinese Patients

    PubMed Central

    Sun, Bo; Chen, Zhao-Hui; Ling, Li; Li, Yi-Fan; Liu, Li-Zhi; Yang, Fei; Huang, Xu-Sheng

    2016-01-01

    Background: Among patients with Charcot–Marie–Tooth disease (CMT), the X-linked variant (CMTX) caused by gap junction protein beta 1 (GJB1) gene mutation is the second most frequent type, accounting for approximately 90% of all CMTX. More than 400 mutations have been identified in the GJB1 gene that encodes connexin 32 (CX32). CX32 is thought to form gap junctions that promote the diffusion pathway between cells. GJB1 mutations interfere with the formation of the functional channel and impair the maintenance of peripheral myelin, and novel mutations are continually discovered. Methods: We included 79 unrelated patients clinically diagnosed with CMT at the Department of Neurology of the Chinese People's Liberation Army General Hospital from December 20, 2012, to December 31, 2015. Clinical examination, nerve conduction studies, and molecular and bioinformatics analyses were performed to identify patients with CMTX1. Results: Nine GJB1 mutations (c.283G>A, c.77C>T, c.643C>T, c.515C>T, c.191G>A, c.610C>T, c.490C>T, c.491G>A, and c.44G>A) were discovered in nine patients. Median motor nerve conduction velocities of all nine patients were < 38 m/s, resembling CMT Type 1. Three novel mutations, c.643C>T, c.191G>A, and c.610C>T, were revealed and bioinformatics analyses indicated high pathogenicity. Conclusions: The three novel missense mutations within the GJB1 gene broaden the mutational diversity of CMT1X. Molecular analysis of family members and bioinformatics analyses of the afflicted patients confirmed the pathogenicity of these mutations. PMID:27098783

  11. ArfGAP3 regulates the Transport of Cation-Independent Mannose 6-phosphate Receptor in the post-Golgi compartment

    PubMed Central

    Shiba, Yoko; Kametaka, Satoshi; Waguri, Satoshi; Presley, John F.; Randazzo, Paul Agostino

    2013-01-01

    Summary ArfGAPs are known to be involved in cargo sorting in COPI transport. However, the role of ArfGAPs in post-Golgi membrane traffic has not been defined. To determine the function of ArfGAPs in post-Golgi traffic, we used siRNA to examine each of 25 ArfGAPs for effects on cation-independent mannose 6-phosphate receptor (CIMPR) localization. We found that down-regulation of ArfGAP3 resulted in the peripheral localization of CIMPR. The effect was specific for ArfGAP3 and dependent on its GAP activity, because the phenotype was rescued by ArfGAP3 but not by ArfGAP1, ArfGAP2 or the GAP domain mutants of ArfGAP3. ArfGAP3 localized to the trans-Golgi network and early endosomes. In cells with reduced expression of ArfGAP3, Cathepsin D maturation was slowed and its secretion was accelerated. Also retrograde transport from the endosomes to the trans-Golgi network of endogenous CIMPR, but not truncated CIMPR lacking the luminal domain, was perturbed in cells with reduced expression of ArfGAP3. Furthermore the exit of epidermal growth factor receptor (EGFR) from the early endosomes and degradation of EGFR after EGF stimulation was slowed in cells with reduced expression of ArfGAP3. ArfGAP3 associates with Golgi-localized, γ-ear-containing, ADP-ribosylation factor binding proteins (GGAs), and ArfGAP3 knockdown reduces membrane association of GGAs. A possible mechanism explaining our results is that ArfGAP3 regulates transport from early endosomes to late endosomes. We suggest a model in which ArfGAP3 regulates Golgi association of GGA clathrin adaptors. PMID:24076238

  12. The Nucleoid Occlusion SlmA Protein Accelerates the Disassembly of the FtsZ Protein Polymers without Affecting Their GTPase Activity

    PubMed Central

    Cabré, Elisa J.; Monterroso, Begoña; Alfonso, Carlos; Sánchez-Gorostiaga, Alicia; Reija, Belén; Jiménez, Mercedes

    2015-01-01

    Division site selection is achieved in bacteria by different mechanisms, one of them being nucleoid occlusion, which prevents Z-ring assembly nearby the chromosome. Nucleoid occlusion in E. coli is mediated by SlmA, a sequence specific DNA binding protein that antagonizes FtsZ assembly. Here we show that, when bound to its specific target DNA sequences (SBS), SlmA reduces the lifetime of the FtsZ protofilaments in solution and of the FtsZ bundles when located inside permeable giant vesicles. This effect appears to be essentially uncoupled from the GTPase activity of the FtsZ protofilaments, which is insensitive to the presence of SlmA·SBS. The interaction of SlmA·SBS with either FtsZ protofilaments containing GTP or FtsZ oligomers containing GDP results in the disassembly of FtsZ polymers. We propose that SlmA·SBS complexes control the polymerization state of FtsZ by accelerating the disassembly of the FtsZ polymers leading to their fragmentation into shorter species that are still able to hydrolyze GTP at the same rate. SlmA defines therefore a new class of inhibitors of the FtsZ ring different from the SOS response regulator SulA and from the moonlighting enzyme OpgH, inhibitors of the GTPase activity. SlmA also shows differences compared with MinC, the inhibitor of the division site selection Min system, which shortens FtsZ protofilaments by interacting with the GDP form of FtsZ. PMID:25950808

  13. Evolution and variability of Solanum RanGAP2, a cofactor in the incompatible interaction between the resistance protein GPA2 and the Globodera pallida effector Gp-RBP-1

    PubMed Central

    2013-01-01

    Background The Ran GTPase Activating Protein 2 (RanGAP2) was first described as a regulator of mitosis and nucleocytoplasmic trafficking. It was then found to interact with the Coiled-Coil domain of the Rx and GPA2 resistance proteins, which confer resistance to Potato Virus X (PVX) and potato cyst nematode Globodera pallida, respectively. RanGAP2 is thought to mediate recognition of the avirulence protein GP-RBP-1 by GPA2. However, the Gpa2-induced hypersensitive response appears to be relatively weak and Gpa2 is limited in terms of spectrum of efficiency as it is effective against only two nematode populations. While functional and evolutionary analyses of Gp-Rbp-1 and Gpa2 identified key residues in both the resistance and avirulence proteins that are involved in recognition determination, whether variation in RanGAP2 also plays a role in pathogen recognition has not been investigated. Results We amplified a total of 147 RanGAP2 sequences from 55 accessions belonging to 18 different di-and tetraploid Solanum species from the section Petota. Among the newly identified sequences, 133 haplotypes were obtained and 19.1% of the nucleotide sites were found to be polymorphic. The observed intra-specific nucleotide diversity ranges from 0.1 to 1.3%. Analysis of the selection pressures acting on RanGAP2 suggests that this gene evolved mainly under purifying selection. Nonetheless, we identified polymorphic positions in the protein sequence at the intra-specific level, which could modulate the activity of RanGAP2. Two polymorphic sites and a three amino-acid deletion in RanGAP2 were found to affect the timing and intensity of the Gpa2-induced hypersensitive response to avirulent GP-RBP-1 variants even though they did not confer any gain of recognition of virulent GP-RBP-1 variants. Conclusions Our results highlight how a resistance gene co-factor can manage in terms of evolution both an established role as a cell housekeeping gene and an implication in plant parasite

  14. Differential expression of complement proteins and regulatory decay accelerating factor in relation to differentiation of cultured human colon adenocarcinoma cell lines.

    PubMed Central

    Bernet-Camard, M F; Coconnier, M H; Hudault, S; Servin, A L

    1996-01-01

    Self protection of host cells against inadvertent injury resulting from attack by autologous complement proteins is well reported for vascular epithelium. In intestinal epithelium, the expression of C complement proteins and regulatory proteins remains currently poorly reported. This study looked at the distribution of C complement proteins and regulatory decay accelerating factor (DAF) in four cultured human intestinal cell lines of embryogenic or colon cancer origins. C3 and C4 proteins and DAF were widely present in human colon adenocarcinoma T84, HT-29 glc-/+ cells compared with human embryonic INT407 cells. In contrast, no expression of C5, C5b-9, and CR1 was seen for any of the cell lines. Taking advantage of the Caco-2 cells, which spontaneously differentiate in culture, it was seen that the C3, C4, and DAF were present in undifferentiated cells and that their expression increased as a function of the cell differentiation. These results, taken together with other reports on the presence of C complement proteins and DAF in the intestinal cells infer that the expression of regulatory C complement proteins develops in parallel with the expression of C proteins to protect these cells against the potential injury resulting from the activation of these local C proteins. Moreover, the finding that the pathogenic C1845 Escherichia coli binds to the membrane bound DAF in the cultured human intestinal cells synthetising locally C proteins and regulatory C proteins supports the hypothesis that E coli could promote inflammatory disorders by blocking local regulatory protein function. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:8801206

  15. Amphiregulin co-operates with bone morphogenetic protein 15 to increase bovine oocyte developmental competence: effects on gap junction-mediated metabolite supply.

    PubMed

    Sugimura, Satoshi; Ritter, Lesley J; Sutton-McDowall, Melanie L; Mottershead, David G; Thompson, Jeremy G; Gilchrist, Robert B

    2014-06-01

    This study assessed the participation of amphiregulin (AREG) and bone morphogenetic protein 15 (BMP15) during maturation of bovine cumulus-oocyte complexes (COCs) on cumulus cell function and their impact on subsequent embryo development. AREG treatment of COCs enhanced blastocyst formation and quality only when in the presence of BMP15. Expression of hyaluronan synthase 2 was enhanced by follicle-stimulating hormone (FSH) but not by AREG, which was reflected in the level of cumulus expansion. Although both FSH and AREG stimulated glycolysis, AREG-treated COCs had higher glucose consumption, lactate production and ratio of lactate production to glucose uptake. Autofluorescence levels in oocytes, indicative of NAD(P)H and FAD(++), were increased with combined AREG and BMP15 treatment of COCs. In contrast, these treatments did not alter autofluorescence levels when cumulus cells were removed from oocytes, even in the presence of other COCs, suggesting that oocyte-cumulus gap-junctional communication (GJC) is required. FSH contributed to maintaining GJC for an extended period of time. Remarkably, BMP15 was equally effective at maintaining GJC even in the presence of AREG. Hence, AREG stimulation of COC glycolysis and BMP15 preservation of GJC may facilitate efficient transfer of metabolites from cumulus cells to the oocyte thereby enhancing oocyte developmental competence. These results have implications for improving in vitro oocyte maturation systems. PMID:24557840

  16. MicroRNA-19b Downregulates Gap Junction Protein Alpha1 and Synergizes with MicroRNA-1 in Viral Myocarditis

    PubMed Central

    Lin, Junyi; Xue, Aimin; Li, Liliang; Li, Beixu; Li, Yuhua; Shen, Yiwen; Sun, Ning; Chen, Ruizhen; Xu, Hongfei; Zhao, Ziqin

    2016-01-01

    Viral myocarditis (VMC) is a life-threatening disease that leads to heart failure or cardiac arrhythmia. A large number of researches have revealed that mircroRNAs (miRNAs) participate in the pathological processes of VMC. We previously reported that miR-1 repressed the expression of gap junction protein α1 (GJA1) in VMC. In this study, miR-19b was found to be significantly upregulated using the microarray analysis in a mouse model of VMC, and overexpression of miR-19b led to irregular beating pattern in human cardiomyocytes derived from the induced pluripotent stem cells (hiPSCs-CMs). The upregulation of miR-19b was associated with decreased GJA1 in vivo. Furthermore, a miR-19b inhibitor increased, while its mimics suppressed the expression of GJA1 in HL-1 cells. When GJA1 was overexpressed, the miR-19b mimics-mediated irregular beating was reversed in hiPSCs-CMs. In addition, the effect of miR-19b on GJA1 was enhanced by miR-1 in a dose-dependent manner. These data suggest miR-19b contributes to irregular beating through regulation of GJA1 by cooperating with miR-1. Based on the present and our previous studies, it could be indicated that miR-19b and miR-1 might be critically involved in cardiac arrhythmia associated with VMC. PMID:27213338

  17. MicroRNA-19b Downregulates Gap Junction Protein Alpha1 and Synergizes with MicroRNA-1 in Viral Myocarditis.

    PubMed

    Lin, Junyi; Xue, Aimin; Li, Liliang; Li, Beixu; Li, Yuhua; Shen, Yiwen; Sun, Ning; Chen, Ruizhen; Xu, Hongfei; Zhao, Ziqin

    2016-01-01

    Viral myocarditis (VMC) is a life-threatening disease that leads to heart failure or cardiac arrhythmia. A large number of researches have revealed that mircroRNAs (miRNAs) participate in the pathological processes of VMC. We previously reported that miR-1 repressed the expression of gap junction protein α1 (GJA1) in VMC. In this study, miR-19b was found to be significantly upregulated using the microarray analysis in a mouse model of VMC, and overexpression of miR-19b led to irregular beating pattern in human cardiomyocytes derived from the induced pluripotent stem cells (hiPSCs-CMs). The upregulation of miR-19b was associated with decreased GJA1 in vivo. Furthermore, a miR-19b inhibitor increased, while its mimics suppressed the expression of GJA1 in HL-1 cells. When GJA1 was overexpressed, the miR-19b mimics-mediated irregular beating was reversed in hiPSCs-CMs. In addition, the effect of miR-19b on GJA1 was enhanced by miR-1 in a dose-dependent manner. These data suggest miR-19b contributes to irregular beating through regulation of GJA1 by cooperating with miR-1. Based on the present and our previous studies, it could be indicated that miR-19b and miR-1 might be critically involved in cardiac arrhythmia associated with VMC. PMID:27213338

  18. A GTPase-activating protein for the G protein Galphaz. Identification, purification, and mechanism of action.

    PubMed

    Wang, J; Tu, Y; Woodson, J; Song, X; Ross, E M

    1997-02-28

    A GTPase-activating protein (GAP) specific for Galphaz was identified in brain, spleen, retina, platelet, C6 glioma cells, and several other tissues and cells. Gz GAP from bovine brain is a membrane protein that is refractory to solubilization with most detergents but was solubilized with warm Triton X-100 and purified up to 50,000-fold. Activity is associated with at least two separate proteins of Mr approximately 22,000 and 28,000, both of which have similar specific activities. In an assay that measures the rate of hydrolysis of GTP pre-bound to detergent-soluble Galphaz, the GAP accelerates hydrolysis over 200-fold, from 0.014 to 3 min -1 at 15 degrees C, or to >/=20 min-1 at 30 degrees C. It does not alter rates of nucleotide association or dissociation. When co-reconstituted into phospholipid vesicles with trimeric Gz and m2 muscarinic receptor, Gz GAP accelerates agonist-stimulated steady-state GTP hydrolysis as predicted by its effect on the hydrolytic reaction. In the single turnover assay, the Km of the GAP for Galphaz-GTP is 2 nM. Its activity is inhibited by Galphaz-guanosine 5'-O-thiotriphosphate (Galphaz-GTPgammaS) or by Galphaz-GDP/AlF4 with Ki approximately 1.5 nM for both species; Galphaz-GDP does not inhibit. G protein betagamma subunits inhibit Gz GAP activity, apparently by forming a GTP-Galphazbetagamma complex that is a poor GAP substrate. Gz GAP displays little GAP activity toward Galphai1 or Galphao, but its activity with Galphaz is competitively inhibited by both Galphai1 and Galphao at nanomolar concentrations when they are bound to GTPgammaS but not to GDP. Neither phospholipase C-beta1 (a Gq GAP) nor several adenylyl cyclase isoforms display Gz GAP activity. PMID:9038185

  19. Expression and role of gap junction protein connexin43 in immune challenge-induced extracellular ATP release in Japanese flounder (Paralichthys olivaceus).

    PubMed

    Li, Shuo; Peng, Weijiao; Chen, Xiaoli; Geng, Xuyun; Zhan, Wenbin; Sun, Jinsheng

    2016-08-01

    Connexin43 (Cx43) is the best characterized gap junction protein that allows the direct exchange of signaling molecules during cell-to-cell communications. The immunological functions and ATP permeable properties of Cx43 have been insensitively examined in mammals. The similar biological significance of Cx43 in lower vertebrates, however, is not yet understood. In the present study we identified and characterized a Cx43 ortholog (termed PoCx43) from Japanese flounder (Paralichthys olivaceus) and investigated its role in immune challenge-induced extracellular ATP release. PoCx43 mRNA transcripts are widely distributed in all tested normal tissues and cells with predominant expression in the brain, and are significantly up-regulated by LPS, poly(I:C) and zymosan challenges and Edwardsiella tarda infections as well, suggesting that PoCx43 expression was modulated by the inflammatory stresses. In addition, cyclic AMP (cAMP), an essential second messenger, also plays an important role in regulating PoCx43 gene expression, by which the PoCx43-mediated gap junctional communication may be regulated. Furthermore, overexpression of PoCx43 in Japanese flounder FG-9307 cells significantly potentiates the LPS- and poly(I:C)-induced extracellular ATP release and this enhanced ATP release was attenuated by pre-incubation with Cx43 inhibitor carbenoxolone. In a complementary experiment, down-regulation of PoCx43 endogenous expression in FG-9307 cells with small interfering RNA also significantly reduced the PAMP-induced extracellular ATP release, suggesting that PoCx43 is an important ATP release conduit under the immune challenge conditions. Finally, we showed that extracellular ATP stimulation led to an increased PoCx43 expression which probably provides a feedback mechanism in regulating PoCx43 expression at the transcriptional level. These findings suggest that PoCx43 is an inducible immune response gene and an important conduit for immune challenge-induced extracellular ATP

  20. Linear Accelerators

    NASA Astrophysics Data System (ADS)

    Sidorin, Anatoly

    2010-01-01

    In linear accelerators the particles are accelerated by either electrostatic fields or oscillating Radio Frequency (RF) fields. Accordingly the linear accelerators are divided in three large groups: electrostatic, induction and RF accelerators. Overview of the different types of accelerators is given. Stability of longitudinal and transverse motion in the RF linear accelerators is briefly discussed. The methods of beam focusing in linacs are described.

  1. Linear Accelerators

    SciTech Connect

    Sidorin, Anatoly

    2010-01-05

    In linear accelerators the particles are accelerated by either electrostatic fields or oscillating Radio Frequency (RF) fields. Accordingly the linear accelerators are divided in three large groups: electrostatic, induction and RF accelerators. Overview of the different types of accelerators is given. Stability of longitudinal and transverse motion in the RF linear accelerators is briefly discussed. The methods of beam focusing in linacs are described.

  2. Confronting Twin Paradox Acceleration

    NASA Astrophysics Data System (ADS)

    Murphy, Thomas W.

    2016-05-01

    The resolution to the classic twin paradox in special relativity rests on the asymmetry of acceleration. Yet most students are not exposed to a satisfactory analysis of what exactly happens during the acceleration phase that results in the nonaccelerated observer's more rapid aging. The simple treatment presented here offers both graphical and quantitative solutions to the problem, leading to the correct result that the acceleration-induced age gap is 2Lβ years when the one-way distance L is expressed in light-years and velocity β ≡v/c .

  3. Ion Engine Grid Gap Measurements

    NASA Technical Reports Server (NTRS)

    Soulas, Gerge C.; Frandina, Michael M.

    2004-01-01

    A simple technique for measuring the grid gap of an ion engine s ion optics during startup and steady-state operation was demonstrated with beam extraction. The grid gap at the center of the ion optics assembly was measured with a long distance microscope that was focused onto an alumina pin that protruded through the center accelerator grid aperture and was mechanically attached to the screen grid. This measurement technique was successfully applied to a 30 cm titanium ion optics assembly mounted onto an NSTAR engineering model ion engine. The grid gap and each grid s movement during startup from room temperature to both full and low power were measured. The grid gaps with and without beam extraction were found to be significantly different. The grid gaps at the ion optics center were both significantly smaller than the cold grid gap and different at the two power levels examined. To avoid issues associated with a small grid gap during thruster startup with titanium ion optics, a simple method was to operate the thruster initially without beam extraction to heat the ion optics. Another possible method is to apply high voltage to the grids prior to igniting the discharge because power deposition to the grids from the plasma is lower with beam extraction than without. Further testing would be required to confirm this approach.

  4. Low Level Pro-inflammatory Cytokines Decrease Connexin36 Gap Junction Coupling in Mouse and Human Islets through Nitric Oxide-mediated Protein Kinase Cδ.

    PubMed

    Farnsworth, Nikki L; Walter, Rachelle L; Hemmati, Alireza; Westacott, Matthew J; Benninger, Richard K P

    2016-02-12

    Pro-inflammatory cytokines contribute to the decline in islet function during the development of diabetes. Cytokines can disrupt insulin secretion and calcium dynamics; however, the mechanisms underlying this are poorly understood. Connexin36 gap junctions coordinate glucose-induced calcium oscillations and pulsatile insulin secretion across the islet. Loss of gap junction coupling disrupts these dynamics, similar to that observed during the development of diabetes. This study investigates the mechanisms by which pro-inflammatory cytokines mediate gap junction coupling. Specifically, as cytokine-induced NO can activate PKCδ, we aimed to understand the role of PKCδ in modulating cytokine-induced changes in gap junction coupling. Isolated mouse and human islets were treated with varying levels of a cytokine mixture containing TNF-α, IL-1β, and IFN-γ. Islet dysfunction was measured by insulin secretion, calcium dynamics, and gap junction coupling. Modulators of PKCδ and NO were applied to determine their respective roles in modulating gap junction coupling. High levels of cytokines caused cell death and decreased insulin secretion. Low levels of cytokine treatment disrupted calcium dynamics and decreased gap junction coupling, in the absence of disruptions to insulin secretion. Decreases in gap junction coupling were dependent on NO-regulated PKCδ, and altered membrane organization of connexin36. This study defines several mechanisms underlying the disruption to gap junction coupling under conditions associated with the development of diabetes. These mechanisms will allow for greater understanding of islet dysfunction and suggest ways to ameliorate this dysfunction during the development of diabetes. PMID:26668311

  5. The Structure of the RLIP76 RhoGAP-Ral Binding Domain Dyad: Fixed Position of the Domains Leads to Dual Engagement of Small G Proteins at the Membrane

    PubMed Central

    Rajasekar, Karthik V.; Campbell, Louise J.; Nietlispach, Daniel; Owen, Darerca; Mott, Helen R.

    2013-01-01

    Summary RLIP76 is an effector for Ral small GTPases, which in turn lie downstream of the master regulator Ras. Evidence is growing that Ral and RLIP76 play a role in tumorigenesis, invasion, and metastasis. RLIP76 contains both a RhoGAP domain and a Ral binding domain (GBD) and is, therefore, a node between Ras and Rho family signaling. The structure of the RhoGAP-GBD dyad reveals that the RLIP76 RhoGAP domain adopts a canonical RhoGAP domain structure and that the linker between the two RLIP76 domains is structured, fixing the orientation of the two domains and allowing RLIP76 to interact with Rho-family GTPases and Ral simultaneously. However, the juxtaposed domains do not influence each other functionally, suggesting that the RLIP76-Ral interaction controls cellular localization and that the fixed orientation of the two domains orientates the RhoGAP domain with respect to the membrane, allowing it to be perfectly poised to engage its target G proteins. PMID:24207123

  6. GAP-43 Gene Expression Regulates Information Storage

    ERIC Educational Resources Information Center

    Holahan, Matthew R.; Honegger, Kyle S.; Tabatadze, Nino; Routtenberg, Aryeh

    2007-01-01

    Previous reports have shown that overexpression of the growth- and plasticity-associated protein GAP-43 improves memory. However, the relation between the levels of this protein to memory enhancement remains unknown. Here, we studied this issue in transgenic mice (G-Phos) overexpressing native, chick GAP-43. These G-Phos mice could be divided at…

  7. A decay-accelerating factor-binding strain of coxsackievirus B3 requires the coxsackievirus-adenovirus receptor protein to mediate lytic infection of rhabdomyosarcoma cells.

    PubMed Central

    Shafren, D R; Williams, D T; Barry, R D

    1997-01-01

    The composition of the cellular receptor complex for coxsackievirus B3 (CVB3) has been an area of much contention for the last 30 years. Recently, two individual components of a putative CVB3 cellular receptor complex have been identified as (i) decay-accelerating factor (DAF) and (ii) the coxsackievirus-adenovirus receptor protein (CAR). The present study elucidates the individual roles of DAF and CAR in cell entry of CVB3 Nancy. First, we confirm that the DAF-binding phenotype of CVB3 correlates to the presence of key amino acids located in the viral capsid protein, VP2. Second, using antibody blockade, we show that complete protection of permissive cells from infection by high input multiplicities of CVB3 requires a combination of both anti-DAF and anti-CAR antibodies. Finally, it is shown that expression of the CAR protein on the surface of nonpermissive DAF-expressing RD cells renders them highly susceptible to CVB3-mediated lytic infection. Therefore, although the majority of CVB3 Nancy attaches to the cell via DAF, only virus directly interacting with the CAR protein mediates lytic infection. The role of DAF in CVB3 cell infection may be analogous to that recently described for coxsackievirus A21 (D. R. Shafren, D. J. Dorahy, R. A. Ingham, G. F. Burns, and R. D. Barry, J. Virol. 71:4736-4743, 1997), in that DAF may act as a CVB3 sequestration site, enhancing viral presentation to the functional CAR protein. PMID:9371658

  8. Can Accelerators Accelerate Learning?

    NASA Astrophysics Data System (ADS)

    Santos, A. C. F.; Fonseca, P.; Coelho, L. F. S.

    2009-03-01

    The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ) [1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.

  9. PARTICLE ACCELERATOR

    DOEpatents

    Teng, L.C.

    1960-01-19

    ABS>A combination of two accelerators, a cyclotron and a ring-shaped accelerator which has a portion disposed tangentially to the cyclotron, is described. Means are provided to transfer particles from the cyclotron to the ring accelerator including a magnetic deflector within the cyclotron, a magnetic shield between the ring accelerator and the cyclotron, and a magnetic inflector within the ring accelerator.

  10. Bacoside-A, an anti-amyloid natural substance, inhibits membrane disruption by the amyloidogenic determinant of prion protein through accelerating fibril formation.

    PubMed

    Malishev, Ravit; Nandi, Sukhendu; Kolusheva, Sofiya; Shaham-Niv, Shira; Gazit, Ehud; Jelinek, Raz

    2016-09-01

    Bacosides, class of compounds extracted from the Bacopa monniera plant, exhibit interesting therapeutic properties, particularly enhancing cognitive functions and putative anti-amyloid activity. We show that bacoside-A exerted significant effects upon fibrillation and membrane interactions of the amyloidogenic fragment of the prion protein [PrP(106-126)]. Specifically, when co-incubated with PrP(106-126), bacoside-A accelerated fibril formation in the presence of lipid bilayers and in parallel inhibited bilayer interactions of the peptide aggregates formed in solution. These interesting phenomena were studied by spectroscopic and microscopic techniques, which suggest that bacoside A-promoted fibrillation reduced the concentration of membrane-active pre-fibrillar species of the prion fragment. This study suggests that induction of fibril formation and corresponding inhibition of membrane interactions are likely the underlying factors for ameliorating amyloid protein toxicity by bacoside-A. PMID:27365272

  11. The inhibitory effects of boldine, glaucine, and probucol on TPA-induced down regulation of gap junction function. Relationships to intracellular peroxides, protein kinase C translocation, and connexin 43 phosphorylation.

    PubMed

    Hu, J; Speisky, H; Cotgreave, I A

    1995-11-01

    The naturally occurring antioxidant boldine and its di-methoxy analogue glucine, as well as the drug antioxidant probucol, all inhibit TPA-induced downregulation of gap junctional intercellular communication in WB-F344 rat liver epithelial cells in dose-dependent manners. The compounds were essentially 100% inhibitory to the effect of TPA (10 nM) at 50 microM each. Analysis of the mechanism of the antitumor promotive action of these agents in vitro revealed that boldine and probucol (both at 10 microM) totally inhibited the TPA-induced accumulation of intracellular oxidants. Additionally, boldine, glaucine, and probucol, each at 50 microM, inhibited TPA-induced translocation of protein kinase C (PKC) to the particulate fraction of the cells, with concomitant inhibition of TPA-induced hyperphosphorylation of gap junctional connexin 43 (cx43) and TPA-induced internalisation of cx43 protein from the plasma membrane of the cells. None of the compounds inhibited the binding of (3H)-PDBu to TPA-specific binding sites in the cells. The results indicate that antioxidant molecules, irrespective of structure, possess common antitumor promotive potential in this model of gap junctional intercellular communication. The data also indicate that the compounds may interfere with the promotive function of TPA, at least in part, by the destruction of oxidants within the cells. Xanthine oxidase was excluded as a major source of such intracellular oxidants because allopurinol (50 microM) did not significantly affect either the accumulation of oxidants in the cells or the downregulation of gap junctional communication in response to TPA. Taken together, these data also suggest that TPA-induced oxidants play a role in the translocation of PKC to cellular membranes and it is at this level where the antioxidants may interfere in TPA-induced downregulation of gap junctional function. PMID:7503766

  12. Co-targeting Deoxyribonucleic Acid–Dependent Protein Kinase and Poly(Adenosine Diphosphate-Ribose) Polymerase-1 Promotes Accelerated Senescence of Irradiated Cancer Cells

    SciTech Connect

    Azad, Arun; Bukczynska, Patricia; Jackson, Susan; Haput, Ygal; Cullinane, Carleen; McArthur, Grant A.; Solomon, Benjamin

    2014-02-01

    Purpose: To examine the effects of combined blockade of DNA-dependent protein kinase (DNA-PK) and poly(adenosine diphosphate-ribose) polymerase-1 (PARP-1) on accelerated senescence in irradiated H460 and A549 non-small cell lung cancer cells. Methods and Materials: The effects of KU5788 and AG014699 (inhibitors of DNA-PK and PARP-1, respectively) on clonogenic survival, DNA double-strand breaks (DSBs), apoptosis, mitotic catastrophe, and accelerated senescence in irradiated cells were examined in vitro. For in vivo experiments, H460 xenografts established in athymic nude mice were treated with BEZ235 (a DNA-PK, ATM, and phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor) and AG014699 to determine effects on proliferation, DNA DSBs, and accelerated senescence after radiation. Results: Compared with either inhibitor alone, combination treatment with KU57788 and AG014699 reduced postradiation clonogenic survival and significantly increased persistence of Gamma-H2AX (γH2AX) foci in irradiated H460 and A549 cells. Notably, these effects coincided with the induction of accelerated senescence in irradiated cells as reflected by positive β-galactosidase staining, G2-M cell-cycle arrest, enlarged and flattened cellular morphology, increased p21 expression, and senescence-associated cytokine secretion. In irradiated H460 xenografts, concurrent therapy with BEZ235 and AG014699 resulted in sustained Gamma-H2AX (γH2AX) staining and prominent β-galactosidase activity. Conclusion: Combined DNA-PK and PARP-1 blockade increased tumor cell radiosensitivity and enhanced the prosenescent properties of ionizing radiation in vitro and in vivo. These data provide a rationale for further preclinical and clinical testing of this therapeutic combination.

  13. Locally accelerated growth is part of the innate immune response and repair mechanisms in reef-building corals as detected by green fluorescent protein (GFP)-like pigments

    NASA Astrophysics Data System (ADS)

    D'Angelo, C.; Smith, E. G.; Oswald, F.; Burt, J.; Tchernov, D.; Wiedenmann, J.

    2012-12-01

    Homologs of the green fluorescent protein (GFP) are a prevalent group of host pigments responsible for the green, red and purple-blue colours of many reef-building corals. They have been suggested to contribute to the striking coloration changes of different corals species in response to wounding and infestation with epibionts/parasites. In order to elucidate the physiological processes underlying the potentially disease-related colour changes, we have analysed spatial and temporal expression patterns of GFP-like proteins and other biomarkers in corals from the Red Sea, the Arabian/Persian Gulf and Fiji both in their natural habitat and under specific laboratory conditions. The expression of distinct GFP-like proteins and the growth marker proliferating cell nuclear antigen was upregulated in growing branch tips and margins of healthy coral colonies as well as in disturbed colony parts. Furthermore, phenoloxidase activity increased in these proliferating tissues. It is thus demonstrated that locally accelerated growth is part of the innate immune response and repair mechanisms in reef-building corals and, moreover, these processes can be detected utilizing the excellent biomarker properties of GFP-like proteins. Finally, the results of this work suggest an additional vulnerability of corals in predicted future scenarios of increased ocean acidification, warming and eutrophication that are anticipated to reduce coral growth capacity.

  14. Homer proteins accelerate Ca2+ clearance mediated by the plasma membrane Ca2+ pump in hippocampal neurons.

    PubMed

    Salm, Elizabeth J; Thayer, Stanley A

    2012-07-20

    The plasma membrane Ca(2+) ATPase (PMCA) is responsible for maintaining basal intracellular Ca(2+) concentration ([Ca(2+)](i)) and returning small increases in [Ca(2+)](i) back to resting levels. The carboxyl terminus of some PMCA splice variants bind Homer proteins; how binding affects PMCA function is unknown. Here, we examined the effects of altered expression of Homer proteins on PMCA-mediated Ca(2+) clearance from rat hippocampal neurons in culture. The kinetics of PMCA-mediated recovery from the [Ca(2+)](i) increase evoked by a brief train of action potentials was determined in the soma of single neurons using indo-1-based photometry. Exogenous expression of Homer 1a, Homer 1c or Homer 2a did not affect PMCA function. However, shRNA mediated knockdown of Homer 1 slowed PMCA mediated Ca(2+) clearance by 28% relative to cells expressing non-silencing shRNA. The slowed recovery rate in cells expressing Homer 1 shRNA was reversed by expression of a short Homer 2 truncation mutant. These results indicate that constitutively expressed Homer proteins tonically stimulate PMCA function in hippocampal neurons. We propose a model in which binding of short or long Homer proteins to the carboxyl terminus of the PMCA stimulates Ca(2+) clearance rate. PMCA-mediated Ca(2+) clearance may be stimulated following incorporation of the pump into Homer organized signaling domains and following induction of the Homer 1a immediate early gene. PMID:22732411

  15. Increased levels of p21ras-GTP and enhanced DNA synthesis accompany elevated tyrosyl phosphorylation of GAP-associated proteins, p190 and p62, in c-src overexpressors.

    PubMed

    Chang, J H; Wilson, L K; Moyers, J S; Zhang, K; Parsons, S J

    1993-04-01

    While examining the role of pp60c-src in cellular proliferation, we found that overexpression of c-src in C3H10T1/2 murine fibroblasts results in an augmented mitogenic response to epidermal growth factor (EGF) [Luttrell, D.K., Luttrell, L.M. & Parsons, S.J. (1988). Mol. Cell. Biol., 8, 497-501; Wilson, L.K., Luttrell, D.K., Parsons, S.J. (1989). Mol. Cell. Biol., 9, 1536-1544] and enhanced tyrosyl phosphorylation of specific cellular proteins [Wilson, L.K. & Parsons, S.J. (1990). 5, 1471-1480]. Here we identify two of these proteins as the GAP (GTPase-activating protein of p21ras)-associated proteins, p190 and p62. Evidence is presented to support the notion that, in 10T1/2 fibroblasts, p190 is a preferred substrate of pp60c-src, while p62 is preferentially phosphorylated by the EGF receptor. First, the phosphotyrosine content of p190 in quiescent cells is three- to fivefold higher in c-src overexpressors than in control cells and is not altered by growth factor treatment. In contrast, tyrosyl phosphorylation of p62 is undetectable in quiescent cells and transiently observable upon EGF addition. Second, the phosphotyrosine content of p190 in cells overexpressing defective pp60c-src is reduced in comparison with wild-type (wt) c-src overexpressors, while that of p62 is significantly less affected. Further studies revealed that tyrosyl phosphorylation of p190 and p62 is not required for GAP complex formation, as equal amounts of p190 and p62 proteins could be detected in GAP complexes from wt and variant c-src overexpressors both before and after EGF stimulation. However, analysis of GTP-bound p21ras revealed higher basal and EGF-stimulated levels in c-src overexpressors than in control cells. Taken together, these results suggest that one mechanism by which pp60c-src may contribute to early events in the EGF-induced mitogenic pathway in 10T1/2 fibroblasts is by increasing the level of GAP-associated p190 and p62 tyrosyl phosphorylation, which in turn results in

  16. Strong-light photoinhibition treatment accelerates the changes of protein secondary structures in triton-treated photosystem I and photosystem II complexes.

    PubMed

    Ruan, X; Xu, Q; Mao, H B; Li, G F; Wei, J; Gong, Y D; Kuang, T Y; Zhao, N M

    2001-04-01

    Changes in the protein secondary structure and electron transport activity of the Triton X-100-treated photosystem I (PSI) and photosystem II (PSII) complexes after strong illumination treatment were studied using Fourier transform-infrared (FT-IR) spectroscopy and an oxygen electrode. Short periods of photoinhibitory treatment led to obvious decreases in the rates of PSI-mediated electron transport activity and PSII-mediated oxygen evolution in the native or Triton-treated PSI and PSII complexes. In the native PSI and PSII complexes, the protein secondary structures had little changes after the photoinhibitory treatment. However, in both Triton-treated PSI and PSII complexes, short photoinhibition times caused significant loss of alpha-helical content and increase of beta-sheet structure, similar to the conformational changes in samples of Triton-treated PSI and PSII complexes after long periods of dark incubation. Our results demonstrate that strong-light treatment to the Triton-treated PSI and PSII complexes accelerates destruction of the transmembrane structure of proteins in the two photosynthetic membranes. PMID:11565905

  17. Acceleration of Lung Regeneration by Platelet-Rich Plasma Extract through the Low-Density Lipoprotein Receptor-Related Protein 5-Tie2 Pathway.

    PubMed

    Mammoto, Tadanori; Chen, Zhao; Jiang, Amanda; Jiang, Elisabeth; Ingber, Donald E; Mammoto, Akiko

    2016-01-01

    Angiogenesis, the growth of new blood vessels, plays a key role in organ development, homeostasis, and regeneration. The cooperation of multiple angiogenic factors, rather than a single factor, is required for physiological angiogenesis. Recently, we have reported that soluble platelet-rich plasma (PRP) extract, which contains abundant angiopoietin-1 and multiple other angiogenic factors, stimulates angiogenesis and maintains vascular integrity in vitro and in vivo. In this report, we have demonstrated that mouse PRP extract increases phosphorylation levels of the Wnt coreceptor low-density lipoprotein receptor-related protein 5 (LRP5) and thereby activates angiogenic factor receptor Tie2 in endothelial cells (ECs) and accelerates EC sprouting and lung epithelial cell budding in vitro. PRP extract also increases phosphorylation levels of Tie2 in the mouse lungs and accelerates compensatory lung growth and recovery of exercise capacity after unilateral pneumonectomy in mice, whereas soluble Tie2 receptor or Lrp5 knockdown attenuates the effects of PRP extract. Because human PRP extract is generated from autologous peripheral blood and can be stored at -80°C, our findings may lead to the development of novel therapeutic interventions for various angiogenesis-related lung diseases and to the improvement of strategies for lung regeneration. PMID:26091161

  18. Plasma accelerators

    SciTech Connect

    Ruth, R.D.; Chen, P.

    1986-03-01

    In this paper we discuss plasma accelerators which might provide high gradient accelerating fields suitable for TeV linear colliders. In particular we discuss two types of plasma accelerators which have been proposed, the Plasma Beat Wave Accelerator and the Plasma Wake Field Accelerator. We show that the electric fields in the plasma for both schemes are very similar, and thus the dynamics of the driven beams are very similar. The differences appear in the parameters associated with the driving beams. In particular to obtain a given accelerating gradient, the Plasma Wake Field Accelerator has a higher efficiency and a lower total energy for the driving beam. Finally, we show for the Plasma Wake Field Accelerator that one can accelerate high quality low emittance beams and, in principle, obtain efficiencies and energy spreads comparable to those obtained with conventional techniques.

  19. E9-Im9 Colicin DNase−Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study

    PubMed Central

    2008-01-01

    Protein−protein transient and dynamic interactions underlie all biological processes. The molecular dynamics (MD) of the E9 colicin DNase protein, its Im9 inhibitor protein, and their E9-Im9 recognition complex are investigated by combining multiple-copy (MC) MD and accelerated MD (aMD) explicit-solvent simulation approaches, after validation with crystalline-phase and solution experiments. Im9 shows higher flexibility than its E9 counterpart. Im9 displays a significant reduction of backbone flexibility and a remarkable increase in motional correlation upon E9 association. Im9 loops 23−31 and 54−64 open with respect to the E9-Im9 X-ray structure and show high conformational diversity. Upon association a large fraction (∼20 nm2) of E9 and Im9 protein surfaces become inaccessible to water. Numerous salt bridges transiently occurring throughout our six 50 ns long MC-MD simulations are not present in the X-ray model. Among these Im9 Glu31−E9 Arg96 and Im9 Glu41−Lys89 involve interface interactions. Through the use of 10 ns of Im9 aMD simulation, we reconcile the largest thermodynamic impact measured for Asp51Ala mutation with Im9 structure and dynamics. Lys57 acts as an essential molecular switch to shift Im9 surface loop towards an ideal configuration for E9 inhibition. This is achieved by switching Asp60−Lys57 and Asp62−Lys57 hydrogen bonds to Asp51−Lys57 salt bridge. E9-Im9 recognition involves shifts of conformational distributions, reorganization of intramolecular hydrogen bond patterns, and formation of new inter- and intramolecular interactions. The description of key transient biological interactions can be significantly enriched by the dynamic and atomic-level information provided by computer simulations. PMID:19053689

  20. Overexpression of AtGRDP2, a novel glycine-rich domain protein, accelerates plant growth and improves stress tolerance

    PubMed Central

    Ortega-Amaro, María A.; Rodríguez-Hernández, Aída A.; Rodríguez-Kessler, Margarita; Hernández-Lucero, Eloísa; Rosales-Mendoza, Sergio; Ibáñez-Salazar, Alejandro; Delgado-Sánchez, Pablo; Jiménez-Bremont, Juan F.

    2015-01-01

    Proteins with glycine-rich signatures have been reported in a wide variety of organisms including plants, mammalians, fungi, and bacteria. Plant glycine-rich protein genes exhibit developmental and tissue-specific expression patterns. Herein, we present the characterization of the AtGRDP2 gene using Arabidopsis null and knockdown mutants and, Arabidopsis and lettuce over-expression lines. AtGRDP2 encodes a short glycine-rich domain protein, containing a DUF1399 domain and a putative RNA recognition motif (RRM). AtGRDP2 transcript is mainly expressed in Arabidopsis floral organs, and its deregulation in Arabidopsis Atgrdp2 mutants and 35S::AtGRDP2 over-expression lines produces alterations in development. The 35S::AtGRDP2 over-expression lines grow faster than the WT, while the Atgrdp2 mutants have a delay in growth and development. The over-expression lines accumulate higher levels of indole-3-acetic acid and, have alterations in the expression pattern of ARF6, ARF8, and miR167 regulators of floral development and auxin signaling. Under salt stress conditions, 35S::AtGRDP2 over-expression lines displayed higher tolerance and increased expression of stress marker genes. Likewise, transgenic lettuce plants over-expressing the AtGRDP2 gene manifest increased growth rate and early flowering time. Our data reveal an important role for AtGRDP2 in Arabidopsis development and stress response, and suggest a connection between AtGRDP2 and auxin signaling. PMID:25653657

  1. The senescence-accelerated prone mouse (SAMP8): a model of age-related cognitive decline with relevance to alterations of the gene expression and protein abnormalities in Alzheimer's disease.

    PubMed

    Butterfield, D Allan; Poon, H Fai

    2005-10-01

    The senescence-accelerated mouse (SAM) is an accelerated aging model that was established through phenotypic selection from a common genetic pool of AKR/J strain of mice. The SAM model was established in 1981, including nine major senescence-accelerated mouse prone (SAMP) substrains and three major senescence-accelerated mouse resistant (SAMR) substrains, each of which exhibits characteristic disorders. Recently, SAMP8 have drawn attention in gerontological research due to its characteristic learning and memory deficits at old age. Many recent reports provide insight into mechanisms of the cognitive impairment and pathological changes in SAMP8. Therefore, this mini review examines the recent findings of SAMP8 mice abnormalities at the gene and protein levels. The genes and proteins described in this review are functionally categorized into neuroprotection, signal transduction, protein folding/degradation, cytoskeleton/transport, immune response and reactive oxygen species (ROS) production. All of these processes are involved in learning and memory. Although these studies provide insight into the mechanisms that contribute to the learning and memory decline in aged SAMP8 mice, higher throughput techniques of proteomics and genomics are necessary to study the alterations of gene expression and protein abnormalities in SAMP8 mice brain in order to more completely understand the central nervous system dysfunction in this mouse model. The SAMP8 is a good animal model to investigate the fundamental mechanisms of age-related learning and memory deficits at the gene and protein levels. PMID:16026957

  2. Kinase programs spatiotemporally regulate gap junction assembly and disassembly: Effects on wound repair.

    PubMed

    Solan, Joell L; Lampe, Paul D

    2016-02-01

    Gap junctions are highly ordered plasma membrane domains that are constantly assembled, remodeled and turned over due to the short half-life of connexins, the integral membrane proteins that form gap junctions. Connexin 43 (Cx43), by far the most widely expressed connexin, is phosphorylated at multiple serine residues in the cytoplasmic, C-terminal region allowing for exquisite cellular control over gap junctional communication. This is evident during epidermal wounding where spatiotemporal changes in connexin expression occur as cells are instructed whether to die, proliferate or migrate to promote repair. Early gap junctional communication is required for initiation of keratinocyte migration, but accelerated Cx43 turnover is also critical for proper wound healing at later stages. These events are controlled via a "kinase program" where sequential phosphorylation of Cx43 leads to reductions in Cx43's half-life and significant depletion of gap junctions from the plasma membrane within several hours. The complex regulation of gap junction assembly and turnover affords several steps where intervention might speed wound healing. PMID:26706150

  3. Upregulated expression of polycomb protein Ring1 contributes to poor prognosis and accelerated proliferation in human hepatocellular carcinoma.

    PubMed

    Xiong, Yicheng; Hu, Baoying; Wei, Lixian; Jiang, Dawei; Zhu, Mingyan

    2015-12-01

    Ring finger protein 1 (Ring1) have recently been reported to be closely related to aggressive tumor features in multiple cancer types, including prostate cancer, non-small-cell lung cancer, and bladder cancer. However, the role of Ring1 in human hepatocarcinogenesis remains unclear. In this study, we aimed at investigating the latent role of Ring1 in hepatocellular carcinoma (HCC) development. The expression of Ring1 was evaluated using Western blot analysis in 8 paired fresh HCC tissues and immunohistochemistry on 98 paraffin-embedded sections from 2005 to 2008. Moreover, RNA interference, CCK-8, colony formation, and flow-cytometry analyses were performed to investigate the role of Ring1 in the regulation of HCC cell proliferation. Compared with adjacent normal tissues, the level of Ring1 was significantly increased in HCC specimens. High expression of Ring1 was associated with histological grade (P = 0.011) and tumor size (P = 0.004), and Ring1 expression was positively related with the proliferation marker Ki-67 (P < 0.001). Moreover, knocking down Ring1 induced growth impairment and G1/S cell cycle arrest in HCC cells. Kaplan-Meier survival curves showed that high expression of Ring1 indicated poor prognosis of HCC (P = 0.03). On the basis of these results, we proposed that the expression of Ring1 protein may be a novel indicator of HCC prognosis. PMID:26141041

  4. GAP Activity, but Not Subcellular Targeting, Is Required for Arabidopsis RanGAP Cellular and Developmental Functions[OPEN

    PubMed Central

    Boruc, Joanna; Griffis, Anna H.N.; Rodrigo-Peiris, Thushani; Zhou, Xiao; Tilford, Bailey; Van Damme, Daniël; Meier, Iris

    2015-01-01

    The Ran GTPase activating protein (RanGAP) is important to Ran signaling involved in nucleocytoplasmic transport, spindle organization, and postmitotic nuclear assembly. Unlike vertebrate and yeast RanGAP, plant RanGAP has an N-terminal WPP domain, required for nuclear envelope association and several mitotic locations of Arabidopsis thaliana RanGAP1. A double null mutant of the two Arabidopsis RanGAP homologs is gametophyte lethal. Here, we created a series of mutants with various reductions in RanGAP levels by combining a RanGAP1 null allele with different RanGAP2 alleles. As RanGAP level decreases, the severity of developmental phenotypes increases, but nuclear import is unaffected. To dissect whether the GAP activity and/or the subcellular localization of RanGAP are responsible for the observed phenotypes, this series of rangap mutants were transformed with RanGAP1 variants carrying point mutations abolishing the GAP activity and/or the WPP-dependent subcellular localization. The data show that plant development is differentially affected by RanGAP mutant allele combinations of increasing severity and requires the GAP activity of RanGAP, while the subcellular positioning of RanGAP is dispensable. In addition, our results indicate that nucleocytoplasmic trafficking can tolerate both partial depletion of RanGAP and delocalization of RanGAP from the nuclear envelope. PMID:26091693

  5. Increase in presenilin 1 (PS1) levels in senescence-accelerated mice (SAMP8) may indirectly impair memory by affecting amyloid precursor protein (APP) processing.

    PubMed

    Kumar, Vijaya B; Franko, Mark; Banks, William A; Kasinadhuni, Pranav; Farr, Susan A; Vyas, Kamlesh; Choudhuri, Veena; Morley, John E

    2009-02-01

    Senescence-accelerated mice (SAMP8) serve as a model for Alzheimer's disease (AD) as they exhibit early loss of memory and increased amyloid precursor protein (APP) expression. APP is a ubiquitous membrane protein that is physiologically processed by site-specific proteolysis firstly by alpha- or beta-secretases, releasing a large fragment called APP(S) that contains most of the extracellular sequences of APP, a small extracellular stub, the transmembrane region and the cytoplasmic tail of APP (;AICD'-APP intracellular domain). These are subsequently cleaved by gamma-secretase at multiple sites in the transmembrane region, releasing small peptides, Abeta(1-40) and Abeta(1-42), the major components of AD-associated amyloid fibrils. gamma-secretase is a high-molecular-mass complex composed of presenilin-1 (PS1), nicastrin, APH-1 and Pen-2. As PS1 has been shown to play a critical role in facilitating gamma-secretase activity, and mutations in this protein are associated with familial AD (FAD), we have cloned it from SAMP8 mouse hippocampus and compared its sequence with those of other species. Furthermore, changes in the expression of PS1 with age in the hippocampal tissue of SAMP8 were studied. The results showed that the SAMP8 PS1 cDNA sequence is identical to that of normal mice. However, its expression in the hippocampus of SAMP8 exhibited an increase, while CD-1 mice, a strain that does not exhibit premature memory loss, showed no change with age. An increased amount or mutation(s) in PS1, which alters the stoichiometric balance of the gamma-secretase complex, may be the cause of aberrant or increased processing of APP, resulting in Abeta accumulation leading to loss of memory. PMID:19181896

  6. Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent.

    PubMed

    Peter, Emanuel K; Shea, Joan-Emma; Pivkin, Igor V

    2016-05-14

    In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC). The new development significantly can reduce the amount of replicas and the computational cost needed to enhance sampling in protein simulations. We introduce 2 different methods which primarily differ in the exchange scheme between the parallel ensembles. We apply this approach on folding of 2 different β-stranded peptides: the C-terminal β-hairpin fragment of GB1 and TrpZip4. Additionally, we use the new simulation technique to study the folding of TrpCage, a small fast folding α-helical peptide. Subsequently, we apply the new methodology on conformation changes in signaling of the light-oxygen voltage (LOV) sensitive domain from Avena sativa (AsLOV2). Our results agree well with data reported in the literature. In simulations of dialanine, we compare the statistical sampling of the 2 techniques with conventional REMD and analyze their performance. The new techniques can reduce the computational cost of REMD significantly and can be used in enhanced sampling simulations of biomolecules. PMID:27111190

  7. Macromolecular Composition Dictates Receptor and G Protein Selectivity of Regulator of G Protein Signaling (RGS) 7 and 9-2 Protein Complexes in Living Cells*

    PubMed Central

    Masuho, Ikuo; Xie, Keqiang; Martemyanov, Kirill A.

    2013-01-01

    Regulator of G protein signaling (RGS) proteins play essential roles in the regulation of signaling via G protein-coupled receptors (GPCRs). With hundreds of GPCRs and dozens of G proteins, it is important to understand how RGS regulates selective GPCR-G protein signaling. In neurons of the striatum, two RGS proteins, RGS7 and RGS9-2, regulate signaling by μ-opioid receptor (MOR) and dopamine D2 receptor (D2R) and are implicated in drug addiction, movement disorders, and nociception. Both proteins form trimeric complexes with the atypical G protein β subunit Gβ5 and a membrane anchor, R7BP. In this study, we examined GTPase-accelerating protein (GAP) activity as well as Gα and GPCR selectivity of RGS7 and RGS9-2 complexes in live cells using a bioluminescence resonance energy transfer-based assay that monitors dissociation of G protein subunits. We showed that RGS9-2/Gβ5 regulated both Gi and Go with a bias toward Go, but RGS7/Gβ5 could serve as a GAP only for Go. Interestingly, R7BP enhanced GAP activity of RGS7 and RGS9-2 toward Go and Gi and enabled RGS7 to regulate Gi signaling. Neither RGS7 nor RGS9-2 had any activity toward Gz, Gs, or Gq in the absence or presence of R7BP. We also observed no effect of GPCRs (MOR and D2R) on the G protein bias of R7 RGS proteins. However, the GAP activity of RGS9-2 showed a strong receptor preference for D2R over MOR. Finally, RGS7 displayed an four times greater GAP activity relative to RGS9-2. These findings illustrate the principles involved in establishing G protein and GPCR selectivity of striatal RGS proteins. PMID:23857581

  8. NATIONAL GAP ANALYSIS PROGRAM

    EPA Science Inventory

    GAP Analysis is a rapid conservation evaluation method for assessing the current status of biodiversity at large spatial scales. GAP Analysis provides a systematic approach for evaluating the protection afforded biodiversity in given areas. It uses Geographic Information System (...

  9. Overactivation of the protein kinase C-signaling pathway suppresses the defects of cells lacking the Rho3/Rho4-GAP Rgd1p in Saccharomyces cerevisiae.

    PubMed Central

    de Bettignies, G; Thoraval, D; Morel, C; Peypouquet, M F; Crouzet, M

    2001-01-01

    The nonessential RGD1 gene encodes a Rho-GTPase activating protein for the Rho3 and Rho4 proteins in Saccharomyces cerevisiae. Previous studies have revealed genetic interactions between RGD1 and the SLG1 and MID2 genes, encoding two putative sensors for cell integrity signaling, and VRP1 encoding an actin and myosin interacting protein involved in polarized growth. To better understand the role of Rgd1p, we isolated multicopy suppressor genes of the cell lethality of the double mutant rgd1Delta mid2Delta. RHO1 and RHO2 encoding two small GTPases, MKK1 encoding one of the MAP-kinase kinases in the protein kinase C (PKC) pathway, and MTL1, a MID2-homolog, were shown to suppress the rgd1Delta defects strengthening the functional links between RGD1 and the cell integrity pathway. Study of the transcriptional activity of Rlm1p, which is under the control of Mpk1p, the last kinase of the PKC pathway, and follow-up of the PST1 transcription, which is positively regulated by Rlm1p, indicate that the lack of RGD1 function diminishes the PKC pathway activity. We hypothesize that the rgd1Delta inactivation, at least through the hyperactivation of the small GTPases Rho3p and Rho4p, alters the secretory pathway and/or the actin cytoskeleton and decreases activity of the PKC pathway. PMID:11779787

  10. Practice Gaps in Pruritus.

    PubMed

    Silverberg, Jonathan I

    2016-07-01

    There are several practice gaps in the evaluation and management of itch. These gaps include a dearth of objective measures of itch, infrequent use of validated patient-reported outcomes for itch, non-evidence-based treatment, and lack of consensus about the ideal workup for generalized itch. The present article reviews these gaps and presents potential solutions. PMID:27363881

  11. Behind the Pay Gap

    ERIC Educational Resources Information Center

    Dey, Judy Goldberg; Hill, Catherine

    2007-01-01

    Women have made remarkable gains in education during the past three decades, yet these achievements have resulted in only modest improvements in pay equity. The gender pay gap has become a fixture of the U.S. workplace and is so ubiquitous that many simply view it as normal. "Behind the Pay Gap" examines the gender pay gap for college graduates.…

  12. Funding Gap Study.

    ERIC Educational Resources Information Center

    Newmyer, Joe; McIntyre, Chuck

    The "funding gap" in public higher education in California represents the difference between state appropriations and the amount needed to fully support each segment's educational mission. This report identifies and defines the funding gap for the California Community Colleges (CCC); measures the consequences of this gap on program quality and…

  13. An Immunomodulatory Protein (Ling Zhi-8) from a Ganoderma lucidum Induced Acceleration of Wound Healing in Rat Liver Tissues after Monopolar Electrosurgery

    PubMed Central

    Lin, Hao-Jan; Chang, Yushan-Sophie; Lin, Li-Hsiang; Haung, Chiung-Fang; Wu, Chia-Yu; Ou, Keng-Liang

    2014-01-01

    The purpose of this study was to investigate the effect of an immunomodulatory protein (Ling Zhi-8, LZ-8) on wound healing in rat liver tissues after monopolar electrosurgery. Animals were sacrificed for evaluations at 0, 3, 7, and 28 days postoperatively. It was found that the wound with the LZ-8 treatment significantly increases wound healing. Western blot analysis clearly indicated that the expression of NF-κB was decreased at 3, 7, and 28 days when liver tissues were treated with LZ-8. Moreover, caspase-3 activity of the liver tissue also significantly decreases at 7 and 28 days, respectively. DAPI staining and TUNEL assays revealed that only a minimal dispersion of NF-κB was found on the liver tissue treated with LZ-8 at day 7 as compared with day 3 and tissues without LZ-8 treatment. Similarly, apoptosis was decreased on liver tissues treated with LZ-8 at 7 days when compared to the control (monopolar electrosurgery) tissues. Therefore, the analytical results demonstrated that LZ-8 induced acceleration of wound healing in rat liver tissues after monopolar electrosurgery. PMID:24883073

  14. Accelerated Reader.

    ERIC Educational Resources Information Center

    Education Commission of the States, Denver, CO.

    This paper provides an overview of Accelerated Reader, a system of computerized testing and record-keeping that supplements the regular classroom reading program. Accelerated Reader's primary goal is to increase literature-based reading practice. The program offers a computer-aided reading comprehension and management program intended to motivate…

  15. Accelerated, Spleen-Based Titration of Variant Creutzfeldt-Jakob Disease Infectivity in Transgenic Mice Expressing Human Prion Protein with Sensitivity Comparable to That of Survival Time Bioassay

    PubMed Central

    Halliez, Sophie; Reine, Fabienne; Herzog, Laetitia; Jaumain, Emilie; Haïk, Stéphane; Rezaei, Human; Vilotte, Jean-Luc; Laude, Hubert

    2014-01-01

    ABSTRACT The dietary exposure of the human population to the prions responsible for the bovine spongiform encephalopathy (BSE) epizooty has led to the emergence of variant Creutzfeldt-Jakob disease (vCJD). This fatal, untreatable neurodegenerative disorder is a growing public health concern because the prevalence of the infection seems much greater than the disease incidence and because secondary transmission of vCJD by blood transfusion or use of blood products has occurred. A current limitation in variant CJD risk assessment is the lack of quantitative information on the infectivity of contaminated tissues. To address this limitation, we tested the potential of a transgenic mouse line overexpressing human prion protein (PrP), which was previously reported to propagate vCJD prions. Endpoint titration of vCJD infectivity in different tissues was evaluated by two different methods: (i) the “classical” bioassay, based on the appearance of clinical symptoms and the detection of pathological prion protein in tissues of the inoculated mouse, and (ii) a shortened bioassay based on the detection of the protein in the mouse spleen at defined time points. The two methods proved equally sensitive in quantifying infectivity, even after very-low-dose inoculation of infected material, but the time schedule was shortened from ∼2.5 years to ∼1 year with the spleen bioassay. Compared to the “gold-standard” RIII model routinely used for endpoint titration of vCJD/BSE prions, either method improved the sensitivity by >2 orders of magnitude and allowed reevaluating the infectious titer of spleen from a vCJD individual at disease end stage to >1,000-fold-higher values. IMPORTANCE Here, we provide key reevaluation of the infectious titer of variant CJD brain and spleen tissues. The highly sensitive, accelerated spleen-based assay should thus constitute a key advance for variant CJD epidemiological and risk assessment purposes and should greatly facilitate future titration

  16. Antideuteron sensitivity for the GAPS experiment

    NASA Astrophysics Data System (ADS)

    Aramaki, T.; Hailey, C. J.; Boggs, S. E.; von Doetinchem, P.; Fuke, H.; Mognet, S. I.; Ong, R. A.; Perez, K.; Zweerink, J.

    2016-02-01

    The General Antiparticle Spectrometer (GAPS) is a novel approach for indirect dark matter searches that exploits cosmic antiparticles, especially antideuterons. The GAPS antideuteron measurement utilizes distinctive detection methods using atomic X-rays and charged particles from the decay of exotic atoms as well as the timing and stopping range of the incoming particle, which together provide excellent antideuteron identification. Prior to the future balloon experiment, an accelerator test and a prototype flight were successfully conducted in 2005 and 2012 respectively, in order to verify the GAPS detection concept. This paper describes how the sensitivity of GAPS to antideuterons was estimated using a Monte Carlo simulation along with the atomic cascade model and the Intra-Nuclear Cascade model. The sensitivity for the GAPS antideuteron search obtained using this method is 2.0 ×10-6 [m-2s-1sr-1(GeV/n)-1] for the proposed long duration balloon program (LDB, 35 days × 3 flights), indicating that GAPS has a strong potential to probe a wide variety of dark matter annihilation and decay models through antideuteron measurements. GAPS is proposed to fly from Antarctica in the austral summer of 2019-2020.

  17. Pado, a fluorescent protein with proton channel activity can optically monitor membrane potential, intracellular pH, and map gap junctions

    PubMed Central

    Kang, Bok Eum; Baker, Bradley J.

    2016-01-01

    An in silico search strategy was developed to identify potential voltage-sensing domains (VSD) for the development of genetically encoded voltage indicators (GEVIs). Using a conserved charge distribution in the S2 α-helix, a single in silico search yielded most voltage-sensing proteins including voltage-gated potassium channels, voltage-gated calcium channels, voltage-gated sodium channels, voltage-gated proton channels, and voltage-sensing phosphatases from organisms ranging from mammals to bacteria and plants. A GEVI utilizing the VSD from a voltage-gated proton channel identified from that search was able to optically report changes in membrane potential. In addition this sensor was capable of manipulating the internal pH while simultaneously reporting that change optically since it maintains the voltage-gated proton channel activity of the VSD. Biophysical characterization of this GEVI, Pado, demonstrated that the voltage-dependent signal was distinct from the pH-dependent signal and was dependent on the movement of the S4 α-helix. Further investigation into the mechanism of the voltage-dependent optical signal revealed that inhibiting the dimerization of the fluorescent protein greatly reduced the optical signal. Dimerization of the FP thereby enabled the movement of the S4 α-helix to mediate a fluorescent response. PMID:27040905

  18. Pado, a fluorescent protein with proton channel activity can optically monitor membrane potential, intracellular pH, and map gap junctions.

    PubMed

    Kang, Bok Eum; Baker, Bradley J

    2016-01-01

    An in silico search strategy was developed to identify potential voltage-sensing domains (VSD) for the development of genetically encoded voltage indicators (GEVIs). Using a conserved charge distribution in the S2 α-helix, a single in silico search yielded most voltage-sensing proteins including voltage-gated potassium channels, voltage-gated calcium channels, voltage-gated sodium channels, voltage-gated proton channels, and voltage-sensing phosphatases from organisms ranging from mammals to bacteria and plants. A GEVI utilizing the VSD from a voltage-gated proton channel identified from that search was able to optically report changes in membrane potential. In addition this sensor was capable of manipulating the internal pH while simultaneously reporting that change optically since it maintains the voltage-gated proton channel activity of the VSD. Biophysical characterization of this GEVI, Pado, demonstrated that the voltage-dependent signal was distinct from the pH-dependent signal and was dependent on the movement of the S4 α-helix. Further investigation into the mechanism of the voltage-dependent optical signal revealed that inhibiting the dimerization of the fluorescent protein greatly reduced the optical signal. Dimerization of the FP thereby enabled the movement of the S4 α-helix to mediate a fluorescent response. PMID:27040905

  19. Reduced expression of adherens and gap junction proteins can have a fundamental role in the development of heart failure following cardiac hypertrophy in rats.

    PubMed

    dos Santos, Daniele O; Blefari, Valdecir; Prado, Fernanda P; Silva, Carlos A; Fazan, Rubens; Salgado, Helio C; Ramos, Simone G; Prado, Cibele M

    2016-02-01

    Hypertension causes cardiac hypertrophy, cardiac dysfunction and heart failure (HF). The mechanisms implicated in the transition from compensated to decompensated cardiac hypertrophy are not fully understood. This study was aimed to investigate whether alterations in the expression of intercalated disk proteins could contribute to the transition of compensated cardiac hypertrophy to dilated heart development that culminates in HF. Male rats were submitted to abdominal aortic constriction and at 90 days post surgery (dps), three groups were observed: sham-operated animals (controls), animals with hypertrophic hearts (HH) and animals with hypertrophic + dilated hearts (HD). Blood pressure was evaluated. The hearts were collected and Western blot and immunofluorescence were performed to desmoglein-2, desmocollin-2, N-cadherin, plakoglobin, Bcatenin, and connexin-43. Cardiac systolic function was evaluated using the Vevo 2100 ultrasound system. Data were considered significant when p b 0.05. Seventy percent of the animals presented with HH and 30% were HD at 90 dps. The blood pressure increased in both groups. The amount of desmoglein-2 and desmocollin-2 expression was increased in both groups and no difference was observed in either group. The expression of N-cadherin, plakoglobin and B-catenin increased in the HHgroup and decreased in the HDgroup; and connexin-43 decreased only in theHDgroup. Therewas no difference between the ejection fraction and fractional shortening at 30 and 60 dps; however, they were decreased in the HD group at 90 dps. We found that while some proteins have increased expression accompanied by the increase in the cell volume associated with preserved systolic cardiac function in theHHgroup, these same proteins had decreased expression evenwithout significant reduction in the cell volume associated with decreased systolic cardiac function in HD group. The increased expression of desmoglein-2 and desmocollin-2 in both the HH and HD groups could

  20. ETA-II accelerator upgrades

    SciTech Connect

    Nilson, D.G.; Deadrick, F.J.; Hibbs, S.M.; Sampayan, S.E.; Petersen, D.E.

    1991-09-01

    We discuss recent improvements to the ETA-II linear induction electron accelerator. The accelerator`s cells have been carefully reconditioned to raise the maximum accelerating gap voltage from approximately 100 kV to 125 kV. Insulators of Rexolite plastic in a new ``zero-gap`` arrangement replaced the alumina originals after several alternative materials were investigated. A new multi-cable current feed system will be used to eliminate pulse reflection interactions encountered in earlier experiments. Improved alignment fixtures have been installed to help minimize beam perturbation due to poorly aligned intercell magnets between 10-cell groups. A stretched wire alignment technique (SWAT) has been utilized to enhance overall magnetic alignment, and to characterize irreducible alignment errors. These changes are in conjunction with an expansion of the accelerator from a 20-cell to a 60-cell configuration. When completed, the upgraded accelerator is expected to deliver 2.5 kA of electron beam current at 7.5 MeV in bursts of up to fifty 70-ns pulses at a 5-kHz repetition rate. A 5.5-meter-long wiggler will convert the energy into 3-GW microwave pulses at 140 GHz for plasma heating experiments in the Microwave Tokamak Experiment (MTX).

  1. LINEAR ACCELERATOR

    DOEpatents

    Colgate, S.A.

    1958-05-27

    An improvement is presented in linear accelerators for charged particles with respect to the stable focusing of the particle beam. The improvement consists of providing a radial electric field transverse to the accelerating electric fields and angularly introducing the beam of particles in the field. The results of the foregoing is to achieve a beam which spirals about the axis of the acceleration path. The combination of the electric fields and angular motion of the particles cooperate to provide a stable and focused particle beam.

  2. Hydrogen supplemented air inhalation reduces changes of prooxidant enzyme and gap junction protein levels after transient global cerebral ischemia in the rat hippocampus.

    PubMed

    Hugyecz, Marietta; Mracskó, Eva; Hertelendy, Péter; Farkas, Eszter; Domoki, Ferenc; Bari, Ferenc

    2011-08-01

    Transient global cerebral ischemia (TGCI) occurs during acute severe hypotension depriving the brain of oxygen and glucose for a short period of time. During reperfusion, several mechanisms can induce secondary neuronal damage, including the increased production of reactive oxygen species (ROS). Hydrogen gas-enriched air inhalation is a neuroprotective approach with proven antioxidant potential, which has not yet been examined in TGCI. Accordingly, we set out to describe the effect of inhalation of 2.1% hydrogen supplemented room air (H(2)-RA) in comparison with a well studied neuroprotective agent, rosiglitazone (RSG) in a TGCI rat model. Male Wistar rats were exposed to TGCI (n=26) or sham operation (n=26), while a third group served as intact control (naive, n=5). The operated groups were further divided into non-treated, H(2)-RA, RSG (6 mg/kg i.v.) and vehicle treated animals. Tissue samples from the hippocampus and frontal cortex were taken 3 days following surgery. Western blot analysis was applied to determine the expressions of cyclooxygenase-2 (COX-2), neuronal and endothelial nitric oxide synthase (nNOS and eNOS, respectively), manganese superoxide dismutase (MnSOD) and glial connexin proteins: connexin 30 and connexin 43. The expressions of COX-2, and connexin proteins were upregulated, while nNOS was downregulated 3 days after TGCI. Both RSG and H(2)-RA prevented the changes of enzyme and connexin levels. Considering the lack of harmful side effects, inhalation of H(2)-RA can be a promising approach to reduce neuronal damage after TGCI. PMID:21718970

  3. The gap gene network

    PubMed Central

    2010-01-01

    Gap genes are involved in segment determination during the early development of the fruit fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize the current knowledge of the gap gene network through a comprehensive survey of the experimental literature. I focus on genetic and molecular evidence, which provides us with an almost-complete picture of the regulatory interactions responsible for trunk gap gene expression. I discuss the regulatory mechanisms involved, and highlight the remaining ambiguities and gaps in the evidence. This is followed by a brief discussion of molecular regulatory mechanisms for transcriptional regulation, as well as precision and size-regulation provided by the system. Finally, I discuss evidence on the evolution of gap gene expression from species other than Drosophila. My survey concludes that studies of the gap gene system continue to reveal interesting and important new insights into the role of gene regulatory networks in development and evolution. PMID:20927566

  4. Three-dimensional polycaprolactone scaffold-conjugated bone morphogenetic protein-2 promotes cartilage regeneration from primary chondrocytes in vitro and in vivo without accelerated endochondral ossification.

    PubMed

    Jeong, Claire G; Zhang, Huina; Hollister, Scott J

    2012-08-01

    As articular cartilage is avascular, and mature chondrocytes do not proliferate, cartilage lesions have a limited capacity for regeneration after severe damage. The treatment of such damage has been challenging due to the limited availability of autologous healthy cartilage and lengthy and expensive cell isolation and expansion procedures. Hence, the use of bone morphogenetic protein-2 (BMP-2), a potent regulator of chondrogenic expression, has received considerable attention in cartilage and osteochondral tissue engineering. However, the exact role of BMP-2 in cartilage repair has been postulated to promote both cartilage formation and subsequent cartilage degradation through hypertrophy and endochondral ossification. Furthermore, it is likely that the manner in which BMP-2 is presented to chondrocytes will influence the physiologic pathway (repair vs. degeneration). This study investigates the relative influence of BMP-2 on cartilage matrix and potential subsequent bone matrix production using primary chondrocytes seeded on designed 3D polycaprolactone (PCL) scaffolds with chemically conjugated BMP-2. The results show that chemically conjugated BMP-2 PCL scaffolds can promote significantly greater cartilage regeneration from seeded chondrocytes both in vitro and in vivo compared with untreated scaffolds. Furthermore, our results demonstrate that the conjugated BMP-2 does not particularly accelerate endochondral ossification even in a readily permissible and highly vascular in vivo environment compared with untreated PCL scaffolds. This study not only reveals the potential use of the BMP-2 conjugation delivery method for enhanced cartilage tissue formation but also gives new insights for the effects of conjugated BMP-2 on cartilage regeneration and osteochondral ossification. PMID:22615065

  5. Acceleration switch

    DOEpatents

    Abbin, J.P. Jr.; Devaney, H.F.; Hake, L.W.

    1979-08-29

    The disclosure relates to an improved integrating acceleration switch of the type having a mass suspended within a fluid filled chamber, with the motion of the mass initially opposed by a spring and subsequently not so opposed.

  6. Acceleration switch

    DOEpatents

    Abbin, Jr., Joseph P.; Devaney, Howard F.; Hake, Lewis W.

    1982-08-17

    The disclosure relates to an improved integrating acceleration switch of the type having a mass suspended within a fluid filled chamber, with the motion of the mass initially opposed by a spring and subsequently not so opposed.

  7. ION ACCELERATOR

    DOEpatents

    Bell, J.S.

    1959-09-15

    An arrangement for the drift tubes in a linear accelerator is described whereby each drift tube acts to shield the particles from the influence of the accelerating field and focuses the particles passing through the tube. In one embodiment the drift tube is splii longitudinally into quadrants supported along the axis of the accelerator by webs from a yoke, the quadrants. webs, and yoke being of magnetic material. A magnetic focusing action is produced by energizing a winding on each web to set up a magnetic field between adjacent quadrants. In the other embodiment the quadrants are electrically insulated from each other and have opposite polarity voltages on adjacent quadrants to provide an electric focusing fleld for the particles, with the quadrants spaced sufficienily close enough to shield the particles within the tube from the accelerating electric field.

  8. High-powered pulsed-ion-beam acceleration and transport

    SciTech Connect

    Humphries, S. Jr.; Lockner, T.R.

    1981-11-01

    The state of research on intense ion beam acceleration and transport is reviewed. The limitations imposed on ion beam transport by space charge effects and methods available for neutralization are summarized. The general problem of ion beam neutralization in regions free of applied electric fields is treated. The physics of acceleration gaps is described. Finally, experiments on multi-stage ion acceleration are summarized.

  9. The National "Expertise Gap"

    ERIC Educational Resources Information Center

    Hamilton, Kendra

    2005-01-01

    This article discusses the Woodrow Wilson National Fellowship Foundation's report, "Diversity and the Ph.D.," released in May, which documents in troubling detail the exact dimensions of what the foundation's president, Dr. Robert Weisbuch, is calling the national "expertise gap." Weisbuch states that the expertise gap extends beyond the…

  10. Confronting the Achievement Gap

    ERIC Educational Resources Information Center

    Gardner, David

    2007-01-01

    This article talks about the large achievement gap between children of color and their white peers. The reasons for the achievement gap are varied. First, many urban minorities come from a background of poverty. One of the detrimental effects of growing up in poverty is receiving inadequate nourishment at a time when bodies and brains are rapidly…

  11. States Address Achievement Gaps.

    ERIC Educational Resources Information Center

    Christie, Kathy

    2002-01-01

    Summarizes 2 state initiatives to address the achievement gap: North Carolina's report by the Advisory Commission on Raising Achievement and Closing Gaps, containing an 11-point strategy, and Kentucky's legislation putting in place 10 specific processes. The North Carolina report is available at www.dpi.state.nc.us.closingthegap; Kentucky's…

  12. The Parenting Gap

    ERIC Educational Resources Information Center

    Reeves, Richard V.; Howard, Kimberly

    2013-01-01

    The parenting gap is a big factor in the opportunity gap. The chances of upward social mobility are lower for children with parents struggling to do a good job--in terms of creating a supportive and stimulating home environment. Children lucky enough to have strong parents are more likely to succeed at all the critical life stages, which means…

  13. Narrowing Participation Gaps

    ERIC Educational Resources Information Center

    Hand, Victoria; Kirtley, Karmen; Matassa, Michael

    2015-01-01

    Shrinking the achievement gap in mathematics is a tall order. One way to approach this challenge is to think about how the achievement gap manifests itself in the classroom and take concrete action. For example, opportunities to participate in activities that involve mathematical reasoning and argumentation in a safe and supportive manner are…

  14. Bridging the Gap: Linking Simulation and Testing

    SciTech Connect

    Krajewski, Paul E.; Carsley, John; Stoudt, Mark R.; Hovanski, Yuri

    2012-09-01

    The Materials Genome Initiative (MGI) which is a key enabler for the Advanced Manufacturing Partnership, announced in 2011 by U.S. President Barack Obama, was established to accelerate the development and deployment of advanced materials. The MGI is driven by the need to "bridge the gap" between (I) experimental results and computational analysis to enable the rapid development and validation of new mateirals, and (II) the processes required to convert these materials into useable goods.

  15. ETA-II accelerator upgrades

    SciTech Connect

    Nilson, D.G.; Deadrick, F.J.; Hibbs, S.M.; Sampayan, S.E.; Petersen, D.E.

    1991-09-01

    We discuss recent improvements to the ETA-II linear induction electron accelerator. The accelerator's cells have been carefully reconditioned to raise the maximum accelerating gap voltage from approximately 100 kV to 125 kV. Insulators of Rexolite plastic in a new zero-gap'' arrangement replaced the alumina originals after several alternative materials were investigated. A new multi-cable current feed system will be used to eliminate pulse reflection interactions encountered in earlier experiments. Improved alignment fixtures have been installed to help minimize beam perturbation due to poorly aligned intercell magnets between 10-cell groups. A stretched wire alignment technique (SWAT) has been utilized to enhance overall magnetic alignment, and to characterize irreducible alignment errors. These changes are in conjunction with an expansion of the accelerator from a 20-cell to a 60-cell configuration. When completed, the upgraded accelerator is expected to deliver 2.5 kA of electron beam current at 7.5 MeV in bursts of up to fifty 70-ns pulses at a 5-kHz repetition rate. A 5.5-meter-long wiggler will convert the energy into 3-GW microwave pulses at 140 GHz for plasma heating experiments in the Microwave Tokamak Experiment (MTX).

  16. Multi-beam linear accelerator EVT

    NASA Astrophysics Data System (ADS)

    Teryaev, Vladimir E.; Kazakov, Sergey Yu.; Hirshfield, Jay L.

    2016-09-01

    A novel electron multi-beam accelerator is presented. The accelerator, short-named EVT (Electron Voltage Transformer) belongs to the class of two-beam accelerators. It combines an RF generator and essentially an accelerator within the same vacuum envelope. Drive beam-lets and an accelerated beam are modulated in RF modulators and then bunches pass into an accelerating structure, comprising uncoupled with each other and inductive tuned cavities, where the energy transfer from the drive beams to the accelerated beam occurs. A phasing of bunches is solved by choice correspond distances between gaps of the adjacent cavities. Preliminary results of numerical simulations and the initial specification of EVT operating in S-band, with a 60 kV gun and generating a 2.7 A, 1.1 MV beam at its output is presented. A relatively high efficiency of 67% and high design average power suggest that EVT can find its use in industrial applications.

  17. Protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Proteins are the major structural and functional components of all cells in the body. They are macromolecules that comprise 1 or more chains of amino acids that vary in their sequence and length and are folded into specific 3-dimensional structures. The sizes and conformations of proteins, therefor...

  18. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  19. Acceleration Studies

    NASA Technical Reports Server (NTRS)

    Rogers, Melissa J. B.

    1993-01-01

    Work to support the NASA MSFC Acceleration Characterization and Analysis Project (ACAP) was performed. Four tasks (analysis development, analysis research, analysis documentation, and acceleration analysis) were addressed by parallel projects. Work concentrated on preparation for and implementation of near real-time SAMS data analysis during the USMP-1 mission. User support documents and case specific software documentation and tutorials were developed. Information and results were presented to microgravity users. ACAP computer facilities need to be fully implemented and networked, data resources must be cataloged and accessible, future microgravity missions must be coordinated, and continued Orbiter characterization is necessary.

  20. GAP-43 gene expression regulates information storage.

    PubMed

    Holahan, Matthew R; Honegger, Kyle S; Tabatadze, Nino; Routtenberg, Aryeh

    2007-06-01

    Previous reports have shown that overexpression of the growth- and plasticity-associated protein GAP-43 improves memory. However, the relation between the levels of this protein to memory enhancement remains unknown. Here, we studied this issue in transgenic mice (G-Phos) overexpressing native, chick GAP-43. These G-Phos mice could be divided at the behavioral level into "spatial bright" and "spatial dull" groups based on their performance on two hidden platform water maze tasks. G-Phos dull mice showed both acquisition and retention deficits on the fixed hidden platform task, but were able to learn a visible platform task. G-Phos bright mice showed memory enhancement relative to wild type on the more difficult movable hidden platform spatial memory task. In the hippocampus, the G-Phos dull group showed a 50% greater transgenic GAP-43 protein level and a twofold elevated transgenic GAP-43 mRNA level than that measured in the G-Phos bright group. Unexpectedly, the dull group also showed an 80% reduction in hippocampal Tau1 staining. The high levels of GAP-43 seen here leading to memory impairment find its histochemical and behavioral parallel in the observation of Rekart et al. (Neuroscience 126: 579-584) who described elevated levels of GAP-43 protein in the hippocampus of Alzheimer's patients. The present data suggest that moderate overexpression of a phosphorylatable plasticity-related protein can enhance memory, while excessive overexpression may produce a "neuroplasticity burden" leading to degenerative and hypertrophic events culminating in memory dysfunction. PMID:17554085

  1. SPARK GAP SWITCH

    DOEpatents

    Neal, R.B.

    1957-12-17

    An improved triggered spark gap switch is described, capable of precisely controllable firing time while switching very large amounts of power. The invention in general comprises three electrodes adjustably spaced and adapted to have a large potential impressed between the outer electrodes. The central electrode includes two separate elements electrically connected togetaer and spaced apart to define a pair of spark gaps between the end electrodes. Means are provided to cause the gas flow in the switch to pass towards the central electrode, through a passage in each separate element, and out an exit disposed between the two separate central electrode elements in order to withdraw ions from the spark gap.

  2. Plasma accelerator

    DOEpatents

    Wang, Zhehui; Barnes, Cris W.

    2002-01-01

    There has been invented an apparatus for acceleration of a plasma having coaxially positioned, constant diameter, cylindrical electrodes which are modified to converge (for a positive polarity inner electrode and a negatively charged outer electrode) at the plasma output end of the annulus between the electrodes to achieve improved particle flux per unit of power.

  3. Accelerated Achievement

    ERIC Educational Resources Information Center

    Ford, William J.

    2010-01-01

    This article focuses on the accelerated associate degree program at Ivy Tech Community College (Indiana) in which low-income students will receive an associate degree in one year. The three-year pilot program is funded by a $2.3 million grant from the Lumina Foundation for Education in Indianapolis and a $270,000 grant from the Indiana Commission…

  4. Particle acceleration

    NASA Technical Reports Server (NTRS)

    Vlahos, L.; Machado, M. E.; Ramaty, R.; Murphy, R. J.; Alissandrakis, C.; Bai, T.; Batchelor, D.; Benz, A. O.; Chupp, E.; Ellison, D.

    1986-01-01

    Data is compiled from Solar Maximum Mission and Hinothori satellites, particle detectors in several satellites, ground based instruments, and balloon flights in order to answer fundamental questions relating to: (1) the requirements for the coronal magnetic field structure in the vicinity of the energization source; (2) the height (above the photosphere) of the energization source; (3) the time of energization; (4) transistion between coronal heating and flares; (5) evidence for purely thermal, purely nonthermal and hybrid type flares; (6) the time characteristics of the energization source; (7) whether every flare accelerates protons; (8) the location of the interaction site of the ions and relativistic electrons; (9) the energy spectra for ions and relativistic electrons; (10) the relationship between particles at the Sun and interplanetary space; (11) evidence for more than one acceleration mechanism; (12) whether there is single mechanism that will accelerate particles to all energies and also heat the plasma; and (13) how fast the existing mechanisms accelerate electrons up to several MeV and ions to 1 GeV.

  5. Medium Beta Superconducting Accelerating Structures

    SciTech Connect

    Jean Delayen

    2001-09-01

    While, originally, the development of superconducting structures was cleanly divided between low-beta resonators for heavy ions and beta=1 resonators for electrons, recent interest in protons accelerators (high and low current, pulsed and cw) has necessitated the development of structures that bridge the gap between the two. These activities have resulted both in new geometries and in the adaptation of well-known geometries optimized to this intermediate velocity range. Their characteristics and properties are reviewed.

  6. Photonic band gap materials

    SciTech Connect

    Soukoulis, C.M. |

    1993-12-31

    An overview of the theoretical and experimental efforts in obtaining a photonic band gap, a frequency band in three-dimensional dielectric structures in which electromagnetic waves are forbidden, is presented.

  7. Fiber optic gap gauge

    DOEpatents

    Wood, Billy E.; Groves, Scott E.; Larsen, Greg J.; Sanchez, Roberto J.

    2006-11-14

    A lightweight, small size, high sensitivity gauge for indirectly measuring displacement or absolute gap width by measuring axial strain in an orthogonal direction to the displacement/gap width. The gap gauge includes a preferably titanium base having a central tension bar with springs connecting opposite ends of the tension bar to a pair of end connector bars, and an elongated bow spring connected to the end connector bars with a middle section bowed away from the base to define a gap. The bow spring is capable of producing an axial strain in the base proportional to a displacement of the middle section in a direction orthogonal to the base. And a strain sensor, such as a Fabry-Perot interferometer strain sensor, is connected to measure the axial strain in the base, so that the displacement of the middle section may be indirectly determined from the measurement of the axial strain in the base.

  8. Gaps in Oncology

    Cancer.gov

    The first plenary of the EPEC-O (Education in Palliative and End-of-Life Care for Oncology) Self-Study Original Version provides background for the curriculum and identifies gaps in current and desired comprehensive cancer care.

  9. Association with the Plasma Membrane Is Sufficient for Potentiating Catalytic Activity of Regulators of G Protein Signaling (RGS) Proteins of the R7 Subfamily.

    PubMed

    Muntean, Brian S; Martemyanov, Kirill A

    2016-03-25

    Regulators of G protein Signaling (RGS) promote deactivation of heterotrimeric G proteins thus controlling the magnitude and kinetics of responses mediated by G protein-coupled receptors (GPCR). In the nervous system, RGS7 and RGS9-2 play essential role in vision, reward processing, and movement control. Both RGS7 and RGS9-2 belong to the R7 subfamily of RGS proteins that form macromolecular complexes with R7-binding protein (R7BP). R7BP targets RGS proteins to the plasma membrane and augments their GTPase-accelerating protein (GAP) activity, ultimately accelerating deactivation of G protein signaling. However, it remains unclear if R7BP serves exclusively as a membrane anchoring subunit or further modulates RGS proteins to increase their GAP activity. To directly answer this question, we utilized a rapidly reversible chemically induced protein dimerization system that enabled us to control RGS localization independent from R7BP in living cells. To monitor kinetics of Gα deactivation, we coupled this strategy with measuring changes in the GAP activity by bioluminescence resonance energy transfer-based assay in a cellular system containing μ-opioid receptor. This approach was used to correlate changes in RGS localization and activity in the presence or absence of R7BP. Strikingly, we observed that RGS activity is augmented by membrane recruitment, in an orientation independent manner with no additional contributions provided by R7BP. These findings argue that the association of R7 RGS proteins with the membrane environment provides a major direct contribution to modulation of their GAP activity. PMID:26811338

  10. Robotic Tube-Gap Inspector

    NASA Technical Reports Server (NTRS)

    Gilbert, Jeffrey L.; Gutow, David A.; Maslakowski, John E.

    1993-01-01

    Robotic vision system measures small gaps between nearly parallel tubes. Robot-held video camera examines closely spaced tubes while computer determines gaps between tubes. Video monitor simultaneously displays data on gaps.

  11. Compact accelerator

    DOEpatents

    Caporaso, George J.; Sampayan, Stephen E.; Kirbie, Hugh C.

    2007-02-06

    A compact linear accelerator having at least one strip-shaped Blumlein module which guides a propagating wavefront between first and second ends and controls the output pulse at the second end. Each Blumlein module has first, second, and third planar conductor strips, with a first dielectric strip between the first and second conductor strips, and a second dielectric strip between the second and third conductor strips. Additionally, the compact linear accelerator includes a high voltage power supply connected to charge the second conductor strip to a high potential, and a switch for switching the high potential in the second conductor strip to at least one of the first and third conductor strips so as to initiate a propagating reverse polarity wavefront(s) in the corresponding dielectric strip(s).

  12. BICEP's acceleration

    SciTech Connect

    Contaldi, Carlo R.

    2014-10-01

    The recent Bicep2 [1] detection of, what is claimed to be primordial B-modes, opens up the possibility of constraining not only the energy scale of inflation but also the detailed acceleration history that occurred during inflation. In turn this can be used to determine the shape of the inflaton potential V(φ) for the first time — if a single, scalar inflaton is assumed to be driving the acceleration. We carry out a Monte Carlo exploration of inflationary trajectories given the current data. Using this method we obtain a posterior distribution of possible acceleration profiles ε(N) as a function of e-fold N and derived posterior distributions of the primordial power spectrum P(k) and potential V(φ). We find that the Bicep2 result, in combination with Planck measurements of total intensity Cosmic Microwave Background (CMB) anisotropies, induces a significant feature in the scalar primordial spectrum at scales k∼ 10{sup -3} Mpc {sup -1}. This is in agreement with a previous detection of a suppression in the scalar power [2].

  13. Current Status and Future Plans for the General Antiparticle Spectrometer (GAPS)

    SciTech Connect

    Fabris, Lorenzo; Koglin, Johnathon D; Craig, Teresa M; Mori, Ken-Ichi; Ziock, Klaus-Peter

    2012-01-01

    We discuss current progress and future plans for the general antiparticle spectrometer experiment (GAPS). GAPS detects antideuterons through the X-rays and pions emitted during the deexcitation of exotic atoms formed when the antideuterons are slowed down and stopped in targets. GAPS provides an exceptionally sensitive means to detect cosmic-ray antideuterons. Cosmic-ray antideuterons can provide indirect evidence for the existence of dark matter in such form as neutralinos or Kaluza-Klein particles. We describe results of accelerator testing of GAPS prototypes, tentative design concepts for a flight GAPS detector, and near-term plans for flying a GAPS prototype on a balloon.

  14. Gap Cycling for SWIFT

    PubMed Central

    Corum, Curtis A.; Idiyatullin, Djaudat; Snyder, Carl J.; Garwood, Michael

    2014-01-01

    Purpose SWIFT (SWeep Imaging with Fourier Transformation) is a non-Cartesian MRI method with unique features and capabilities. In SWIFT, radiofrequency (RF) excitation and reception are performed nearly simultaneously, by rapidly switching between transmit and receive during a frequency-swept RF pulse. Because both the transmitted pulse and data acquisition are simultaneously amplitude-modulated in SWIFT (in contrast to continuous RF excitation and uninterrupted data acquisition in more familiar MRI sequences), crosstalk between different frequency bands occurs in the data. This crosstalk leads to a “bulls-eye” artifact in SWIFT images. We present a method to cancel this inter-band crosstalk by cycling the pulse and receive gap positions relative to the un-gapped pulse shape. We call this strategy “gap cycling.” Methods We carry out theoretical analysis, simulation and experiments to characterize the signal chain, resulting artifacts, and their elimination for SWIFT. Results Theoretical analysis reveals the mechanism for gap-cycling’s effectiveness in canceling inter-band crosstalk in the received data. We show phantom and in-vivo results demonstrating bulls-eye artifact free images. Conclusion Gap cycling is an effective method to remove bulls-eye artifact resulting from inter-band crosstalk in SWIFT data. PMID:24604286

  15. Supersize me: Cronobacter sakazakii phage GAP32

    SciTech Connect

    Abbasifar, Reza; Griffiths, Mansel W.; Sabour, Parviz M.; Ackermann, Hans-Wolfgang; Vandersteegen, Katrien; Lavigne, Rob; Noben, Jean-Paul; Alanis Villa, Argentina; Abbasifar, Arash; Nash, John H.E.; Kropinski, Andrew M.

    2014-07-15

    Cronobacter sakazakii is a Gram-negative pathogen found in milk-based formulae that causes infant meningitis. Bacteriophages have been proposed to control bacterial pathogens; however, comprehensive knowledge about a phage is required to ensure its safety before clinical application. We have characterized C. sakazakii phage vB{sub C}saM{sub G}AP32 (GAP32), which possesses the second largest sequenced phage genome (358,663 bp). A total of 571 genes including 545 protein coding sequences and 26 tRNAs were identified, thus more genes than in the smallest bacterium, Mycoplasma genitalium G37. BLASTP and HHpred searches, together with proteomic analyses reveal that only 23.9% of the putative proteins have defined functions. Some of the unique features of this phage include: a chromosome condensation protein, two copies of the large subunit terminase, a predicted signal-arrest-release lysin; and an RpoD-like protein, which is possibly involved in the switch from immediate early to delayed early transcription. Its closest relatives are all extremely large myoviruses, namely coliphage PBECO4 and Klebsiella phage vB{sub K}leM-RaK2, with whom it shares approximately 44% homologous proteins. Since the homologs are not evenly distributed, we propose that these three phages belong to a new subfamily. - Highlights: • Cronobacter sakazakii phage vB{sub C}saM{sub G}AP32 has a genome of 358,663 bp. • It encodes 545 proteins which is more than Mycoplasma genitalium G37. • It is a member of the Myoviridae. • It is peripherally related to coliphage PBECO4 and Klebsiella phage vB{sub K}leM-RaK2. • GAP32 encodes a chromosome condensation protein.

  16. Advanced concepts for acceleration

    SciTech Connect

    Keefe, D.

    1986-07-01

    Selected examples of advanced accelerator concepts are reviewed. Such plasma accelerators as plasma beat wave accelerator, plasma wake field accelerator, and plasma grating accelerator are discussed particularly as examples of concepts for accelerating relativistic electrons or positrons. Also covered are the pulsed electron-beam, pulsed laser accelerator, inverse Cherenkov accelerator, inverse free-electron laser, switched radial-line accelerators, and two-beam accelerator. Advanced concepts for ion acceleration discussed include the electron ring accelerator, excitation of waves on intense electron beams, and two-wave combinations. (LEW)

  17. SUMO-SIM Interactions Regulate the Activity of RGSZ2 Proteins

    PubMed Central

    Garzón, Javier; Rodríguez-Muñoz, María; Vicente-Sánchez, Ana; García-López, María Ángeles; Martínez-Murillo, Ricardo; Fischer, Thierry; Sánchez-Blázquez, Pilar

    2011-01-01

    The RGSZ2 gene, a regulator of G protein signaling, has been implicated in cognition, Alzheimer's disease, panic disorder, schizophrenia and several human cancers. This 210 amino acid protein is a GTPase accelerating protein (GAP) on Gαi/o/z subunits, binds to the N terminal of neural nitric oxide synthase (nNOS) negatively regulating the production of nitric oxide, and binds to the histidine triad nucleotide-binding protein 1 at the C terminus of different G protein-coupled receptors (GPCRs). We now describe a novel regulatory mechanism of RGS GAP function through the covalent incorporation of Small Ubiquitin-like MOdifiers (SUMO) into RGSZ2 RGS box (RH) and the SUMO non covalent binding with SUMO-interacting motifs (SIM): one upstream of the RH and a second within this region. The covalent attachment of SUMO does not affect RGSZ2 binding to GPCR-activated GαGTP subunits but abolishes its GAP activity. By contrast, non-covalent binding of SUMO with RH SIM impedes RGSZ2 from interacting with GαGTP subunits. Binding of SUMO to the RGSZ2 SIM that lies outside the RH does not affect GαGTP binding or GAP activity, but it could lead to regulatory interactions with sumoylated proteins. Thus, sumoylation and SUMO-SIM interactions constitute a new regulatory mechanism of RGS GAP function and therefore of GPCR cell signaling as well. PMID:22163035

  18. Precision gap particle separator

    DOEpatents

    Benett, William J.; Miles, Robin; Jones, II., Leslie M.; Stockton, Cheryl

    2004-06-08

    A system for separating particles entrained in a fluid includes a base with a first channel and a second channel. A precision gap connects the first channel and the second channel. The precision gap is of a size that allows small particles to pass from the first channel into the second channel and prevents large particles from the first channel into the second channel. A cover is positioned over the base unit, the first channel, the precision gap, and the second channel. An port directs the fluid containing the entrained particles into the first channel. An output port directs the large particles out of the first channel. A port connected to the second channel directs the small particles out of the second channel.

  19. MULTIPLE SPARK GAP SWITCH

    DOEpatents

    Schofield, A.E.

    1958-07-22

    A multiple spark gap switch of unique construction is described which will permit controlled, simultaneous discharge of several capacitors into a load. The switch construction includes a disc electrode with a plurality of protuberances of generally convex shape on one surface. A firing electrode is insulatingly supponted In each of the electrode protuberances and extends substantially to the apex thereof. Individual electrodes are disposed on an insulating plate parallel with the disc electrode to form a number of spark gaps with the protuberances. These electrodes are each connected to a separate charged capacitor and when a voltage ls applied simultaneously between the trigger electrodes and the dlsc electrode, each spark gap fires to connect its capacitor to the disc electrode and a subsequent load.

  20. Accelerators and the Accelerator Community

    SciTech Connect

    Malamud, Ernest; Sessler, Andrew

    2008-06-01

    In this paper, standing back--looking from afar--and adopting a historical perspective, the field of accelerator science is examined. How it grew, what are the forces that made it what it is, where it is now, and what it is likely to be in the future are the subjects explored. Clearly, a great deal of personal opinion is invoked in this process.

  1. Effect of IL-6 and IL-8 on the expression of the complement activation inhibitors MAC-inhibitory protein and decay-accelerating factor in ovarian cancer A2780 cells

    PubMed Central

    Kapka-Skrzypczak, Lucyna; Popek, Sylwia; Sawicki, Krzysztof; Wolińska, Ewa; Czajka, Magdalena; Skrzypczak, Maciej

    2016-01-01

    The aim of the present study was to evaluate the role of interleukin (IL)-6 and IL-8 on the expression of the membrane-bound complement inhibitors membrane attack complex-inhibitory protein (CD59) and decay-accelerating factor (CD55), in the human ovarian carcinoma A2780 cell line, which is a non-producing IL-6 cell line that does exhibit IL-6 responsiveness, due to the presence of IL-6 receptors. Extracellular levels of complement system inhibitors were evaluated by western blotting and reverse transcription-quantitative polymerase chain reaction. Cellular localization of CD55 and CD59 in the ovarian cancer cells was assessed by immunofluorescence. The detection of a soluble form of CD55 and CD59 released by the A2780 cells following stimulation with IL-6 and IL-8 was detected by enzyme-linked immunosorbent assay. The present data revealed that A2780 cells express CD55 and CD59 at the mRNA and protein level, but do not secrete these proteins to the culture medium. Results of western blotting demonstrated that the protein level of CD59 was regulated by IL-6 and IL-8 in a dose-dependent manner. Immunofluorescence analysis revealed that the ovarian cancer A2780 cell line expresses the membrane bound form of CD55 protein. The present results indicate that CD55 and CD59 may affect the efficiency of complement-mediated immunotherapies. PMID:27446461

  2. Pulsar Polar Cap and Slot Gap Models: Confronting Fermi Data

    NASA Technical Reports Server (NTRS)

    Harding, Alice K.

    2012-01-01

    Rotation-powered pulsars are excellent laboratories for studying particle acceleration as well as fundamental physics of strong gravity, strong magnetic fields and relativity. I will review acceleration and gamma-ray emission from the pulsar polar cap and slot gap. Predictions of these models can be tested with the data set on pulsars collected by the Large Area Telescope on the Fermi Gamma-Ray Telescope over the last four years, using both detailed light curve fitting and population synthesis.

  3. Bridging NCL research gaps.

    PubMed

    Stehr, Frank; van der Putten, Herman

    2015-10-01

    The neuronal ceroid lipofuscinoses, collectively called NCLs, are rare and fatal lysosomal storage diseases that mainly affect children. Due to the fact that NCLs are both rare and heterogeneous (mutations in thirteen different genes) significant gaps exist in both preclinical and clinical research. Altogether, these gaps are major hurdles to bring therapies to patients while the need for new therapies is urgent to help them and their families. To define gaps and discuss solutions, a round table discussion involving teams and different stake holders took place during the 14th International Conference on Neuronal Ceroid Lipofuscinoses (Batten Disease) in Cordóba, Argentina. Topics covered by the teams and their leaders (in parentheses) included basic and translational research gaps with regard to large animal models (I. Tammen, D.N. Palmer), human NCL pathology and access to human tissue (J.D. Cooper, H.H. Goebel), rare NCLs (S. Hofman, I. Noher), links of NCLs to other diseases (F.M. Platt), gaps between clinic and clinical trials (H. Adams, A. Schulz), international collaborative efforts working towards a cure (S.E. Mole, H. Band) perspectives on palliative care from patient organizations (M. Frazier, A. West), and issues NCL researchers face when progressing to independent career in academia (M. Bond). Thoughts presented by the team leaders include previously unpublished opinions and information on the lack of understanding of disease pathomechanisms, gene function, assays for drug discovery and target validation, natural history of disease, and biomarkers for monitoring disease progression and treatment effects. This article is not intended to review the NCL literature. It includes personal opinions of the authors and it provides the reader with a summary of gaps discussed and solutions proposed by the teams. This article is part of a Special Issue entitled: Current Research on the Neuronal Ceroid Lipofuscinoses (Batten Disease). PMID:26056946

  4. Spark gap electrode erosion

    NASA Astrophysics Data System (ADS)

    Krompholz, H.; Kristiansen, M.

    1984-12-01

    The results of a one-year contract on electrode erosion phenomena are summarized. The arc voltage drop in a spark gap was measured for various electrode, gas, and pressure combinations. A previously developed model of self breakdown voltage distribution was extended. A jet model for electrode erosion was proposed and an experimental arrangement for testing the model was constructed. The effects of inhomogeneities and impurities in the electrodes were investigated. Some of the work described here is scheduled for completion in 1985 under a current grant (AFOSR 84-0032). The areas of investigation described here include: (1) Self breakdown voltage distributions; (2) Electrode erosion; (3) Spark gap voltage recovery.

  5. Development of Bipolar Pulse Accelerator for Pulsed Ion Beam Implantation to Semiconductor

    NASA Astrophysics Data System (ADS)

    Masugata, Katsumi; Kawahara, Yoshihiro; Mitsui, Chihiro; Kitamura, Iwao; Takahashi, Takakazu; Tanaka, Yasunori; Tanoue, Hisao; Arai, Kazuo

    2002-12-01

    To improve the purity of the ion beams new type of pulsed power ion accelerator named "bipolar pulse accelerator" was proposed. The accelerator consists of two acceleration gaps (an ion source gap and a post acceleration gap) and a drift tube, and a bipolar pulse is applied to the drift tube to accelerate the beam. In the accelerator intended ions are selectively accelerated and the purity of the ion beam is enhanced. As the first step of the development of the accelerator, a Br-type magnetically insulated acceleration gap is developed. The gap has an ion source of coaxial gas puff plasma gun on the grounded anode and a negative pulse is applied to the cathode to accelerate the ion beam. By using the plasma gun, ion source plasma (nitrogen) of current density around 100 A/cm2 is obtained. In the paper, the experimental results of the evaluation of the ion beam and the characteristics of the gap are shown with the principle and the design concept of the proposed accelerator.

  6. Assessment of Protein Binding of 5-Hydroxythalidomide Bioactivated in Humanized Mice with Human P450 3A-Chromosome or Hepatocytes by Two-Dimensional Electrophoresis/Accelerator Mass Spectrometry.

    PubMed

    Yamazaki, Hiroshi; Suemizu, Hiroshi; Kazuki, Yasuhiro; Oofusa, Ken; Kuribayashi, Shunji; Shimizu, Makiko; Ninomiya, Shinichi; Horie, Toru; Shibata, Norio; Guengerich, F Peter

    2016-08-15

    Bioactivation of 5-hydroxy-[carbonyl-(14)C]thalidomide, a known metabolite of thalidomide, by human artificial or native cytochrome P450 3A enzymes, and nonspecific binding in livers of mice was assessed using two-dimensional electrophoresis combined with accelerator mass spectrometry. The apparent major target proteins were liver microsomal cytochrome c oxidase subunit 6B1 and ATP synthase subunit α in mice containing humanized P450 3A genes or transplanted humanized liver. Liver cytosolic retinal dehydrogenase 1 and glutathione transferase A1 were targets in humanized mice with P450 3A and hepatocytes, respectively. 5-Hydroxythalidomide is bioactivated by human P450 3A enzymes and trapped with proteins nonspecifically in humanized mice. PMID:27464947

  7. Closing the Performance Gap.

    ERIC Educational Resources Information Center

    Riggins, Cheryl G.

    2002-01-01

    Describes how the principal of a K-2, 400-student suburban elementary school near Flint, Michigan, worked with her staff and superintendent to develop and implement a strategic plan to close the student achievement gap. Reports significant improvement in reading and math scores after 1 year. (PKP)

  8. The Academic Generation Gap

    ERIC Educational Resources Information Center

    Dronzek, Anna

    2008-01-01

    The current generation gap in academia is different--fundamentally shaped by the structural problems of academic employment. The job market has especially exacerbated tensions between senior and junior faculty by ratcheting up expectations and requirements at every stage of the academic career. The disparities have been mentioned often enough to…

  9. Multiple gap photovoltaic device

    DOEpatents

    Dalal, Vikram L.

    1981-01-01

    A multiple gap photovoltaic device having a transparent electrical contact adjacent a first cell which in turn is adjacent a second cell on an opaque electrical contact, includes utilizing an amorphous semiconductor as the first cell and a crystalline semiconductor as the second cell.

  10. STEMMING the Gap

    ERIC Educational Resources Information Center

    Kahler, Jim; Valentine, Nancy

    2011-01-01

    America has a gap when it comes to youth pursuing science and technology careers. In an effort to improve the knowledge and application of science, technology, engineering, and math (STEM), after-school programs can work in conjunction with formal in-school curriculum to improve science education. One organization that actively addresses this…

  11. Bridge the Gap.

    ERIC Educational Resources Information Center

    Klein, Mel; Cufaude, Jeffrey B.

    1989-01-01

    This document consists of two paired articles: the first, "Preparing Faculty Out of Class Experiences," by Mel Klein, and the second, "Help Advisers Be More Than Ghost Signatures," by Jeffrey B. Calfaude. Each article shares insights on how faculty advisers "bridge the gap" between students and faculty. When faculty members are asked to advise…

  12. Estimating Gender Wage Gaps

    ERIC Educational Resources Information Center

    McDonald, Judith A.; Thornton, Robert J.

    2011-01-01

    Course research projects that use easy-to-access real-world data and that generate findings with which undergraduate students can readily identify are hard to find. The authors describe a project that requires students to estimate the current female-male earnings gap for new college graduates. The project also enables students to see to what…

  13. Gaining on the Gap

    ERIC Educational Resources Information Center

    Smith, Robert G.

    2010-01-01

    About three-quarters of the 2009 graduates of the highly diverse Arlington, Virginia, Public Schools completed one or more Advanced Placement or International Baccalaureate courses during their high school careers. That figure serves as one indicator of a decade-long initiative to eliminate achievement gaps while raising achievement for all…

  14. Crystal Structures of Human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating Protein (RabGAP) Domains Reveal Critical Elements for GLUT4 Translocation

    SciTech Connect

    S Park; W Jin; S Shoelson

    2011-12-31

    We have solved the x-ray crystal structures of the RabGAP domains of human TBC1D1 and human TBC1D4 (AS160), at 2.2 and 3.5 {angstrom} resolution, respectively. Like the yeast Gyp1p RabGAP domain, whose structure was solved previously in complex with mouse Rab33B, the human TBC1D1 and TBC1D4 domains both have 16 {alpha}-helices and no {beta}-sheet elements. We expected the yeast Gyp1p RabGAP/mouse Rab33B structure to predict the corresponding interfaces between cognate mammalian RabGAPs and Rabs, but found that residues were poorly conserved. We further tested the relevance of this model by Ala-scanning mutagenesis, but only one of five substitutions within the inferred binding site of the TBC1D1 RabGAP significantly perturbed catalytic efficiency. In addition, substitution of TBC1D1 residues with corresponding residues from Gyp1p did not enhance catalytic efficiency. We hypothesized that biologically relevant RabGAP/Rab partners utilize additional contacts not described in the yeast Gyp1p/mouse Rab33B structure, which we predicted using our two new human TBC1D1 and TBC1D4 structures. Ala substitution of TBC1D1 Met{sup 930}, corresponding to a residue outside of the Gyp1p/Rab33B contact, substantially reduced catalytic activity. GLUT4 translocation assays confirmed the biological relevance of our findings. Substitutions with lowest RabGAP activity, including catalytically dead RK and Met{sup 930} and Leu{sup 1019} predicted to perturb Rab binding, confirmed that biological activity requires contacts between cognate RabGAPs and Rabs beyond those in the yeast Gyp1p RabGAP/mouse Rab33B structure.

  15. Accelerator system and method of accelerating particles

    NASA Technical Reports Server (NTRS)

    Wirz, Richard E. (Inventor)

    2010-01-01

    An accelerator system and method that utilize dust as the primary mass flux for generating thrust are provided. The accelerator system can include an accelerator capable of operating in a self-neutralizing mode and having a discharge chamber and at least one ionizer capable of charging dust particles. The system can also include a dust particle feeder that is capable of introducing the dust particles into the accelerator. By applying a pulsed positive and negative charge voltage to the accelerator, the charged dust particles can be accelerated thereby generating thrust and neutralizing the accelerator system.

  16. Attention's Accelerator.

    PubMed

    Reinhart, Robert M G; McClenahan, Laura J; Woodman, Geoffrey F

    2016-06-01

    How do people get attention to operate at peak efficiency in high-pressure situations? We tested the hypothesis that the general mechanism that allows this is the maintenance of multiple target representations in working and long-term memory. We recorded subjects' event-related potentials (ERPs) indexing the working memory and long-term memory representations used to control attention while performing visual search. We found that subjects used both types of memories to control attention when they performed the visual search task with a large reward at stake, or when they were cued to respond as fast as possible. However, under normal circumstances, one type of target memory was sufficient for slower task performance. The use of multiple types of memory representations appears to provide converging top-down control of attention, allowing people to step on the attentional accelerator in a variety of high-pressure situations. PMID:27056975

  17. Oxidative Stress, Lens Gap Junctions, and Cataracts

    PubMed Central

    Beyer, Eric C.

    2009-01-01

    Abstract The eye lens is constantly subjected to oxidative stress from radiation and other sources. The lens has several mechanisms to protect its components from oxidative stress and to maintain its redox state, including enzymatic pathways and high concentrations of ascorbate and reduced glutathione. With aging, accumulation of oxidized lens components and decreased efficiency of repair mechanisms can contribute to the development of lens opacities or cataracts. Maintenance of transparency and homeostasis of the avascular lens depend on an extensive network of gap junctions. Communication through gap junction channels allows intercellular passage of molecules (up to 1 kDa) including antioxidants. Lens gap junctions and their constituent proteins, connexins (Cx43, Cx46, and Cx50), are also subject to the effects of oxidative stress. These observations suggest that oxidative stress-induced damage to connexins (and consequent altered intercellular communication) may contribute to cataract formation. Antioxid. Redox Signal. 11, 339–353. PMID:18831679

  18. Stemming the Gap

    ERIC Educational Resources Information Center

    Kahler, Jim; Valentine, Nancy

    2011-01-01

    In years past, strong analytical, creative, and communication skills were enough to prepare students for successful careers, but as technological change accelerates, so must innovation in science education. Unfortunately, American students today are lacking exposure to the programs and curriculum that teach these technical skills. Only 32.4% of…

  19. Deterministic multidimensional nonuniform gap sampling

    NASA Astrophysics Data System (ADS)

    Worley, Bradley; Powers, Robert

    2015-12-01

    Born from empirical observations in nonuniformly sampled multidimensional NMR data relating to gaps between sampled points, the Poisson-gap sampling method has enjoyed widespread use in biomolecular NMR. While the majority of nonuniform sampling schemes are fully randomly drawn from probability densities that vary over a Nyquist grid, the Poisson-gap scheme employs constrained random deviates to minimize the gaps between sampled grid points. We describe a deterministic gap sampling method, based on the average behavior of Poisson-gap sampling, which performs comparably to its random counterpart with the additional benefit of completely deterministic behavior. We also introduce a general algorithm for multidimensional nonuniform sampling based on a gap equation, and apply it to yield a deterministic sampling scheme that combines burst-mode sampling features with those of Poisson-gap schemes. Finally, we derive a relationship between stochastic gap equations and the expectation value of their sampling probability densities.

  20. RF-Based Accelerators for HEDP Research

    SciTech Connect

    Staples, John W.; Sessler, Andrew; Keller, Roderich; Ostroumov,Petr; Chou, Weiren

    2005-05-09

    Accelerator-driven High-Energy Density Physics (HEDP) experiments require typically 1 nanosecond, 1 microcoulomb pulses of mass 20 ions accelerated to several MeV to produce eV-level excitations in thin targets, the warm dense matter regime. Traditionally the province of induction linacs, RF-based acceleration may be a viable alternative with recent breakthroughs in accelerating structures and high-field compact superconducting solenoids. A reference design for an RF-based accelerator for HEDP research is presented using 15 T solenoids and multiple-gap RF structures configured with multiple parallel beams combined at the target. The beam is ballistically compressed with an induction linac core providing the necessary energy sweep and injected into a plasma-neutralized drift compression channel resulting in a 1 mm radius beam spot 1 nanosecond long at a thin foil or low-density target.

  1. Mapping of four mouse genes encoding eye lens-specific structural, gap junction, and integral membrane proteins: Cryba1 (crystallin{beta}A3/A1), Crybb2 (crystallin{beta}B2), Gja8 (MP70), and Lim2 (MP19)

    SciTech Connect

    Kerscher, S.; Boyd, Y.; Lyon, M.F.

    1995-09-20

    Four genes encoding eye lens-specific proteins, potential candidate genes for congenital cataract (CC) mutations, were mapped in the mouse genome using a panel of somatic cell hybrids and DNAs from the EUCIB (European Collaborative Interspecific Backcross). Two of them are lens fiber cell structural proteins: the Cryba1 locus encoding crystallin{beta}A3/A1 maps to chromosome 11, 2.5 {+-} 2.5 cM distal to D11Mit31, and the Crybb2 locus encoding crystallin{beta}B2 maps to chromosome 5, 9.1 {+-} 4.3 cM distal to D5Mit88. The other two genes encode lens-specific gap junction and integral membrane proteins, respectively: the Gja8 locus encoding gap junction membrane channel protein {alpha}8, also called connexin50 or MP70, maps to chromosome 3, 11.9 {+-} 5.0 cM distal to D3Mit22, and the Lim2 locus encoding lens intrinsic membrane protein 2, also call MP19, maps to chromosome 7, 2.5 {+-} 2.5 cM proximal to Ngfg. All four map positions, when compared with the corresponding positions in human, lie within known regions of conserved synteny between mouse and human chromosomes. 43 refs., 2 figs., 1 tab.

  2. Determinants of Small Ubiquitin-like Modifier 1 (SUMO1) Protein Specificity, E3 Ligase, and SUMO-RanGAP1 Binding Activities of Nucleoporin RanBP2

    SciTech Connect

    Gareau, Jaclyn R.; Reverter, David; Lima, Christopher D.

    2012-02-16

    The RanBP2 nucleoporin contains an internal repeat domain (IR1-M-IR2) that catalyzes E3 ligase activity and forms a stable complex with SUMO-modified RanGAP1 and UBC9 at the nuclear pore complex. RanBP2 exhibits specificity for SUMO1 as RanGAP1-SUMO1/UBC9 forms a more stable complex with RanBP2 compared with RanGAP1-SUMO2 that results in greater protection of RanGAP-SUMO1 from proteases. The IR1-M-IR2 SUMO E3 ligase activity also shows a similar preference for SUMO1. We utilized deletions and domain swap constructs in protease protection assays and automodification assays to define RanBP2 domains responsible for RanGAP1-SUMO1 protection and SUMO1-specific E3 ligase activity. Our data suggest that elements in both IR1 and IR2 exhibit specificity for SUMO1. IR1 protects RanGAP1-SUMO1/UBC9 and functions as the primary E3 ligase of RanBP2, whereas IR2 retains the ability to interact with SUMO1 to promote SUMO1-specific E3 ligase activity. To determine the structural basis for SUMO1 specificity, a hybrid IR1 construct and IR1 were used to determine three new structures for complexes containing UBC9 with RanGAP1-SUMO1/2. These structures show more extensive contacts among SUMO, UBC9, and RanBP2 in complexes containing SUMO1 compared with SUMO2 and suggest that differences in SUMO specificity may be achieved through these subtle conformational differences.

  3. Acceleration modules in linear induction accelerators

    NASA Astrophysics Data System (ADS)

    Wang, Shao-Heng; Deng, Jian-Jun

    2014-05-01

    The Linear Induction Accelerator (LIA) is a unique type of accelerator that is capable of accelerating kilo-Ampere charged particle current to tens of MeV energy. The present development of LIA in MHz bursting mode and the successful application into a synchrotron have broadened LIA's usage scope. Although the transformer model is widely used to explain the acceleration mechanism of LIAs, it is not appropriate to consider the induction electric field as the field which accelerates charged particles for many modern LIAs. We have examined the transition of the magnetic cores' functions during the LIA acceleration modules' evolution, distinguished transformer type and transmission line type LIA acceleration modules, and re-considered several related issues based on transmission line type LIA acceleration module. This clarified understanding should help in the further development and design of LIA acceleration modules.

  4. GapBlaster—A Graphical Gap Filler for Prokaryote Genomes

    PubMed Central

    Veras, Adonney; de Melo, Diego Magalhães; Soares, Siomar; Pinheiro, Kenny; Guimarães, Luis; Azevedo, Vasco; Silva, Artur; Ramos, Rommel T. J.

    2016-01-01

    The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer. PMID:27171416

  5. GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.

    PubMed

    de Sá, Pablo H C G; Miranda, Fábio; Veras, Adonney; de Melo, Diego Magalhães; Soares, Siomar; Pinheiro, Kenny; Guimarães, Luis; Azevedo, Vasco; Silva, Artur; Ramos, Rommel T J

    2016-01-01

    The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer. PMID:27171416

  6. How empty are disk gaps opened by giant planets?

    SciTech Connect

    Fung, Jeffrey; Shi, Ji-Ming; Chiang, Eugene

    2014-02-20

    Gap clearing by giant planets has been proposed to explain the optically thin cavities observed in many protoplanetary disks. How much material remains in the gap determines not only how detectable young planets are in their birth environments, but also how strong co-rotation torques are, which impacts how planets can survive fast orbital migration. We determine numerically how the average surface density inside the gap, Σ{sub gap}, depends on planet-to-star mass ratio q, Shakura-Sunyaev viscosity parameter α, and disk height-to-radius aspect ratio h/r. Our results are derived from our new graphics processing unit accelerated Lagrangian hydrodynamical code PEnGUIn and are verified by independent simulations with ZEUS90. For Jupiter-like planets, we find Σ{sub gap}∝q {sup –2.2}α{sup 1.4}(h/r){sup 6.6}, and for near brown dwarf masses, Σ{sub gap}∝q {sup –1}α{sup 1.3}(h/r){sup 6.1}. Surface density contrasts inside and outside gaps can be as large as 10{sup 4}, even when the planet does not accrete. We derive a simple analytic scaling, Σ{sub gap}∝q {sup –2}α{sup 1}(h/r){sup 5}, that compares reasonably well to empirical results, especially at low Neptune-like masses, and use discrepancies to highlight areas for progress.

  7. The Pathogenic Mutation T182A Converts the Prion Protein into a Molten Globule-like Conformation Whose Misfolding to Oligomers but Not to Fibrils Is Drastically Accelerated.

    PubMed

    Singh, Jogender; Udgaonkar, Jayant B

    2016-01-26

    Delineation of the effects of pathogenic mutations linked with familial prion diseases on the structure and misfolding of prion protein (PrP) will be useful in understanding the molecular mechanism of PrP misfolding. Here, it has been shown that the pathogenic mutation T182A causes a drastic reduction in the apparent cooperativity and enthalpy of unfolding of the mouse prion protein (moPrP) under misfolding-prone conditions by converting the protein into a molten globule (MG)-like conformation. Hydrogen-deuterium exchange studies in conjunction with mass spectrometry indicate that the T182A mutation disrupts the core of the protein, thereby increasing overall structural dynamics. T182A moPrP is shown to misfold to oligomers very much faster than does wild-type (wt) moPrP but to misfold to fibrils at a rate similar to that of wt moPrP. This observation suggests that oligomers are unlikely to play a productive role in the direct pathway of aggregation from monomer to fibrils. The observation that fully folded T182A moPrP has a MG-like structure, and that it misfolds to oligomers much faster than does wt moPrP, suggests that a MG-like intermediate, whose structure resembles that of fully folded T182A moPrP, might be populated early on the pathway of misfolding of wt moPrP to oligomers. PMID:26713717

  8. Light-dependent degradation of the D1 protein in photosystem II is accelerated after inhibition of the water splitting reaction

    SciTech Connect

    Jegerschoeld, C.V.; Virgin, I.; Styring, S. )

    1990-07-03

    Strong illumination of oxygen-evolving organisms inhibits the electron transport through photosystem II (photoinhibition). In addition the illumination leads to a rapid turnover of the D1 protein in the reaction center of photosystem II. In this study the light-dependent degradation of the D1 reaction center protein and the light-dependent inhibition of electron-transport reactions have been studied in thylakoid membranes in which the oxygen evolution has been reversibly inhibited by Cl- depletion. The results show that Cl(-)-depleted thylakoid membranes are very vulnerable to damage induced by illumination. Both the D1 protein and the inhibition of the oxygen evolution are 15-20 times more sensitive to illumination than in control thylakoid membranes. The presence, during the illumination, of the herbicide 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) prevented both the light-dependent degradation of the D1 protein and the inhibition of the electron transport. The protection exerted by DCMU is seen only in Cl(-)-depleted thylakoid membranes. These observations lead to the proposal that continuous illumination of Cl(-)-depleted thylakoid membranes generates anomalously long-lived, highly oxidizing radicals on the oxidizing side of photosystem II, which are responsible for the light-induced protein damage and inhibition. The presence of DCMU during the illumination prevents the formation of these radicals, which explains the protective effects of the herbicide. It is also observed that in Cl(-)-depleted thylakoid membranes, oxygen evolution (measured after the readdition of Cl-) is inhibited before electron transfer from diphenylcarbazide to dichlorophenolindophenol.

  9. Msb3/Gyp3 GAP selectively opposes Rab5 signaling at endolysosomal organelles

    PubMed Central

    Nickerson, Daniel P.; Chapin, Hannah C.; Milnes, Joshua; Merz, Alexey J.

    2014-01-01

    Traffic through endosomes and lysosomes is controlled by small G-proteins of the Rab5 and Rab7 families. Like humans, Saccharomyces cerevisiae has three Rab5s (Vps21, Ypt52, and Ypt53), and one Rab7 (Ypt7). Here, we elucidate the functional roles and regulation of the yeast Rab5s. Using GFP-tagged cargoes, a novel quantitative multivesicular body (MVB) sorting assay, and electron microscopy, we show that MVB biogenesis and cargo sorting are severely impaired in vps21Δ ypt52Δ double mutants. Ypt53, the third Rab5 paralog, is hardly expressed during normal growth but its transcription is strongly induced by cellular stress through the calcineurin-Crz1 pathway. The requirement for Rab5 activity in stress tolerance facilitated identification of Msb3/Gyp3 as the principal Rab5 GAP (GTPase accelerating protein), and in vitro GAP assays verified that Vps21 is a preferred Gyp3 target. Finally, we demonstrate that Gyp3 spatially restricts active Vps21 to intermediate endosomal compartments by preventing Vps21 accumulation on lysosomal vacuoles. Gyp3 therefore operates as a compartmental insulator that enforces the boundary between penultimate and terminal compartments of the endolysosomal pathway. PMID:22748138

  10. Progress on plasma accelerators

    SciTech Connect

    Chen, P.

    1986-05-01

    Several plasma accelerator concepts are reviewed, with emphasis on the Plasma Beat Wave Accelerator (PBWA) and the Plasma Wake Field Accelerator (PWFA). Various accelerator physics issues regarding these schemes are discussed, and numerical examples on laboratory scale experiments are given. The efficiency of plasma accelerators is then revealed with suggestions on improvements. Sources that cause emittance growth are discussed briefly.

  11. Skills Gaps in Australian Firms

    ERIC Educational Resources Information Center

    Lindorff, Margaret

    2011-01-01

    This paper reports the results of a survey of more than 2000 managers examining perceptions of skills gaps in a range of Australian firms. It finds that three quarters report a skills gap, and almost one third report skills gaps across the whole organisation. Firm size and industry differences exist in perceptions of the effect of the skills gap…

  12. SOUTHWEST REGIONAL GAP LAND COVER

    EPA Science Inventory

    The Gap Analysis Program is a national inter-agency program that maps the distribution

    of plant communities and selected animal species and compares these distributions with land

    stewardship to identify gaps in biodiversity protection. GAP uses remote satellite imag...

  13. Multiwavelength Emission From Pulsar Slot Gaps

    NASA Technical Reports Server (NTRS)

    Harding, Alice K.; Stern, Julie; Dyks, Jarek

    2008-01-01

    We present results of a 3D model of optical to gamma-ray emission from the slot gap accelerator of a rotation-powered pulsar. Primary electrons accelerating to high altitude in the pulsar magnetosphere at the outer edge of the open field volume, as well as electron-positron pairs on field line interior to the slot gap, radiate curvature, inverse Compton and synchrotron radiation. Both primaries and pairs undergo cyclotron resonant absorption of radio photons, allowing them to maintain significant pitch angles and to produce a broad spectrum of emission from infra-red to GeV energies. Synchrotron radiation from pairs with a power-law energy spectrum dominate the spectrum up to 10 MeV. Synchrotron and curvature radiation of primaries dominates from 10 MeV up to a few GeV. The high-energy pulse profiles are dominated by caustics on trailing field lines. In the case of the Crab pulsar, the radio conal emission may also form caustics in phase with the high-energy peaks. If resonant absorption of radio emission produces high-energy synchroti-on radiation, emission below 200 Mev is expected to exhibit correlations in time and phase with the radio emission.

  14. Recent results of studies of acceleration of compact toroids

    NASA Astrophysics Data System (ADS)

    Hammer, J. H.; Hartmen, C. W.; Eddleman, J.

    1984-03-01

    The observed gross stability and self-contained structure of compact toroids (CT's) give rise to the possibility, unique among magnetically confined plasmas, of translating CT's from their point of origin over distances many times their own length. This feature has led us to consider magnetic acceleration of CT's to directed kinetic energies much greater than their stored magnetic and thermal energies. A CT accelerator falls in the very broad gap between traditional particle accelerators at one extreme, which are limited in the number of particles per bunch by electrostatic repulsive forces, and mass accelerators such as rail guns at the other extreme, which accelerate many particles but are forced by the stress limitations of solids to far smaller accelerations. A typical CT has about a Coulomb of particles, weighs 10 micrograms and can be accelerated by magnetic forces of several tons, leading to an acceleration on the order of 10(11) gravities.

  15. The connexin43 mimetic peptide Gap19 inhibits hemichannels without altering gap junctional communication in astrocytes

    PubMed Central

    Abudara, Verónica; Bechberger, John; Freitas-Andrade, Moises; De Bock, Marijke; Wang, Nan; Bultynck, Geert; Naus, Christian C.; Leybaert, Luc; Giaume, Christian

    2014-01-01

    In the brain, astrocytes represent the cellular population that expresses the highest amount of connexins (Cxs). This family of membrane proteins is the molecular constituent of gap junction channels and hemichannels that provide pathways for direct cytoplasm-to-cytoplasm and inside-out exchange, respectively. Both types of Cx channels are permeable to ions and small signaling molecules allowing astrocytes to establish dynamic interactions with neurons. So far, most pharmacological approaches currently available do not distinguish between these two channel functions, stressing the need to develop new specific molecular tools. In astrocytes two major Cxs are expressed, Cx43 and Cx30, and there is now evidence indicating that at least Cx43 operates as a gap junction channel as well as a hemichannel in these cells. Based on studies in primary cultures as well as in acute hippocampal slices, we report here that Gap19, a nonapeptide derived from the cytoplasmic loop of Cx43, inhibits astroglial Cx43 hemichannels in a dose-dependent manner, without affecting gap junction channels. This peptide, which not only selectively inhibits hemichannels but is also specific for Cx43, can be delivered in vivo in mice as TAT-Gap19, and displays penetration into the brain parenchyma. As a result, Gap19 combined with other tools opens up new avenues to decipher the role of Cx43 hemichannels in interactions between astrocytes and neurons in physiological as well as pathological situations. PMID:25374505

  16. A spatial focusing model for G protein signals. Regulator of G protein signaling (RGS) protien-mediated kinetic scaffolding.

    PubMed

    Zhong, Huailing; Wade, Susan M; Woolf, Peter J; Linderman, Jennifer J; Traynor, John R; Neubig, Richard R

    2003-02-28

    Regulators of G protein signaling (RGS) are GTPase-accelerating proteins (GAPs), which can inhibit heterotrimeric G protein pathways. In this study, we provide experimental and theoretical evidence that high concentrations of receptors (as at a synapse) can lead to saturation of GDP-GTP exchange making GTP hydrolysis rate-limiting. This results in local depletion of inactive heterotrimeric G-GDP, which is reversed by RGS GAP activity. Thus, RGS enhances receptor-mediated G protein activation even as it deactivates the G protein. Evidence supporting this model includes a GTP-dependent enhancement of guanosine 5'-3-O-(thio)triphosphate (GTPgammaS) binding to G(i) by RGS. The RGS domain of RGS4 is sufficient for this, not requiring the NH(2)- or COOH-terminal extensions. Furthermore, a kinetic model including only the GAP activity of RGS replicates the GTP-dependent enhancement of GTPgammaS binding observed experimentally. Finally in a Monte Carlo model, this mechanism results in a dramatic "spatial focusing" of active G protein. Near the receptor, G protein activity is maintained even with RGS due to the ability of RGS to reduce depletion of local Galpha-GDP levels permitting rapid recoupling to receptor and maintained G protein activation near the receptor. In contrast, distant signals are suppressed by the RGS, since Galpha-GDP is not depleted there. Thus, a novel RGS-mediated "kinetic scaffolding" mechanism is proposed which narrows the spatial range of active G protein around a cluster of receptors limiting the spill-over of G protein signals to more distant effector molecules, thus enhancing the specificity of G(i) protein signals. PMID:12446706

  17. Accelerator development for the NRL (Naval Research Laboratory) free-electron-laser program. Final report, July 1981-April 1986

    SciTech Connect

    Lucey, R.; Putnam, S.

    1988-06-01

    Included in the report are descriptions of the final assembly and operation of the Linear Induction Accelerator(LIA), installation and testing of a new accelerating gap in the five-core stage of the accelerator to operate at 150 kV, and the moving of and modifications of the charging and firing controls for remote operation of the accelerator.

  18. Arabidopsis accelerated-cell-death11, ACD11, is a ceramide-1-phosphate transfer protein and intermediary regulator of phytoceramide levels

    PubMed Central

    Simanshu, Dhirendra K.; Zhai, Xiuhong; Munch, David; Hofius, Daniel; Markham, Jonathan E.; Bielawski, Jacek; Bielawska, Alicja; Malinina, Lucy; Molotkovsky, Julian G.; Mundy, John W.; Patel, Dinshaw J.; Brown, Rhoderick E.

    2014-01-01

    SUMMARY The accelerated-cell-death11 (acd11) mutant of Arabidopsis provides a genetic model for studying immune response activation and localized cellular suicide that halts pathogen spread during infection in plants. Here, we elucidate ACD11 structure/function and show that acd11 disruption dramatically alters the in vivo balance of sphingolipid mediators that regulate eukaryotic programmed cell death. In acd11 mutants, normally low ceramide-1-phosphate (C1P) levels become elevated, but the relatively abundant cell death inducer, phytoceramide, rises acutely. ACD11 exhibits selective intermembrane transfer of C1P and phyto-C1P. Crystal structures establish C1P binding via a surface-localized, phosphate headgroup recognition center connected to an interior hydrophobic pocket that adaptively ensheaths lipid chains via a cleft-like gating mechanism. Point mutation mapping confirms functional involvement of binding-site residues. A π-helix (π-bulge) near the lipid-binding cleft distinguishes apo-ACD11 from other GLTP-folds. The global two-layer, α-helically-dominated, ‘sandwich’ topology displaying C1P-selective binding identifies ACD11 as the plant prototype of a new GLTP-fold subfamily. PMID:24412362

  19. The Small C-terminal Domain Phosphatase 1 Inhibits Cancer Cell Migration and Invasion by Dephosphorylating Ser(P)68-Twist1 to Accelerate Twist1 Protein Degradation.

    PubMed

    Sun, Tong; Fu, Junjiang; Shen, Tao; Lin, Xia; Liao, Lan; Feng, Xin-Hua; Xu, Jianming

    2016-05-27

    Twist1 is a basic helix-loop-helix transcription factor that strongly promotes epithelial-to-mesenchymal transition, migration, invasion, and metastasis of cancer cells. The MAPK-phosphorylated Twist1 on its serine 68 (Ser(P)(68)-Twist1) has a significantly enhanced stability and function to drive cancer cell invasion and metastasis. However, the phosphatase that dephosphorylates Ser(P)(68)-Twist1 and destabilizes Twist1 has not been identified and characterized. In this study, we screened a serine/threonine phosphatase cDNA expression library in HEK293T cells with ectopically coexpressed Twist1. We found that the small C-terminal domain phosphatase 1 (SCP1) specifically dephosphorylates Ser(P)(68)-Twist1 in both cell-free reactions and living cells. SCP1 uses its amino acid residues 43-63 to interact with the N terminus of Twist1. Increased SCP1 expression in cells decreased Ser(P)(68)-Twist1 and total Twist1 proteins, whereas knockdown of SCP1 increased Ser(P)(68)-Twist1 and total Twist1 proteins. Furthermore, the levels of SCP1 are negatively correlated with Twist1 protein levels in several cancer cell lines. SCP1-dephosphorylated Twist1 undergoes fast degradation via the ubiquitin-proteasome pathway. Importantly, an increase in SCP1 expression in breast cancer cells with either endogenous or ectopically expressed Twist1 largely inhibits the Twist1-induced epithelial-to-mesenchymal transition phenotype and the migration and invasion capabilities of these cells. These results indicate that SCP1 is the phosphatase that counterregulates the MAPK-mediated phosphorylation of Ser(68)-Twist1. Thus, an increase in SCP1 expression and activity may be a useful strategy for eliminating the detrimental roles of Twist1 in cancer cells. PMID:26975371

  20. GAP Final Technical Report 12-14-04

    SciTech Connect

    Andrew J. Bordner, PhD, Senior Research Scientist

    2004-12-14

    The Genomics Annotation Platform (GAP) was designed to develop new tools for high throughput functional annotation and characterization of protein sequences and structures resulting from genomics and structural proteomics, benchmarking and application of those tools. Furthermore, this platform integrated the genomic scale sequence and structural analysis and prediction tools with the advanced structure prediction and bioinformatics environment of ICM. The development of GAP was primarily oriented towards the annotation of new biomolecular structures using both structural and sequence data. Even though the amount of protein X-ray crystal data is growing exponentially, the volume of sequence data is growing even more rapidly. This trend was exploited by leveraging the wealth of sequence data to provide functional annotation for protein structures. The additional information provided by GAP is expected to assist the majority of the commercial users of ICM, who are involved in drug discovery, in identifying promising drug targets as well in devising strategies for the rational design of therapeutics directed at the protein of interest. The GAP also provided valuable tools for biochemistry education, and structural genomics centers. In addition, GAP incorporates many novel prediction and analysis methods not available in other molecular modeling packages. This development led to signing the first Molsoft agreement in the structural genomics annotation area with the University of oxford Structural Genomics Center. This commercial agreement validated the Molsoft efforts under the GAP project and provided the basis for further development of the large scale functional annotation platform.

  1. DEATH LINE OF GAMMA-RAY PULSARS WITH OUTER GAPS

    SciTech Connect

    Wang, Ren-Bo; Hirotani, Kouichi E-mail: hirotani@tiara.sinica.edu.tw

    2011-08-01

    We analytically investigate the condition for a particle accelerator to be active in the outer magnetosphere of a rotation-powered pulsar. Within the accelerator (or the gap), the magnetic-field-aligned electric field accelerates electrons and positrons, which emit copious gamma-rays via the curvature process. If one of the gamma-rays emitted by a single pair materializes as a new pair on average, the gap is self-sustained. However, if the neutron-star spin-down rate decreases below a certain limit, the gap becomes no longer self-sustained and the gamma-ray emission ceases. We explicitly compute the multiplicity of cascading pairs and find that the obtained limit corresponds to a modification of the previously derived outer-gap death line. In addition to this traditional death line, we find another death line, which becomes important for millisecond pulsars, by separately considering the threshold of photon-photon pair production. Combining these traditional and new death lines, we give predictions on the detectability of gamma-ray pulsars with Fermi and AGILE. An implication for X-ray observations of heated polar-cap emission is also discussed.

  2. The Slot Gap Model for Pulsar High-Energy Emission

    NASA Technical Reports Server (NTRS)

    Harding, Alice K.; Muslimov, Alexander

    2004-01-01

    A new picture of pulsar high-energy emission is proposed that is different from both the traditional polar cap and outer gap models, but combines elements of each. The slot gap model is based on electron acceleration along the edge of the open field region from the neutron star surface to near the light cylinder. Along the last open field line, the pair formation front rises to very high altitude forming a slot gap, where the accelerating electric field is unscreened by pairs. Electrons continue to accelerate to high altitudes in the slot gap, reaching a radiation reaction-limited energy of several TeV. The resulting radiation pattern features sharp caustics on the trailing edge of the open field region, allowing for the possibility of double-peaked pulse profiles very similar to those observed in gamma-ray pulsars. Since emission from a large range of altitudes arrives in phase, this model very naturally explains the phase alignment of radiation at all wavelengths from the Crab pulsar.

  3. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System

    PubMed Central

    Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

    2015-01-01

    The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively. PMID:26568953

  4. Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System.

    PubMed

    Liu, Yu; Hong, Yang; Lin, Chun-Yuan; Hung, Che-Lun

    2015-01-01

    The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively. PMID:26568953

  5. Beta amyloid-induced upregulation of death receptor 6 accelerates the toxic effect of N-terminal fragment of amyloid precursor protein.

    PubMed

    Xu, Yuxia; Wang, Dandan; Luo, Ying; Li, Wei; Shan, Ye; Tan, Xiangshi; Zhu, Cuiqing

    2015-01-01

    Amyloid precursor protein (APP) plays essential roles in the development of the Alzheimer's disease. Although full-length APP has been thoroughly studied, the role of the cleavage fragments especially the N-terminal fragments (N-APPs) in Alzheimer's disease pathogenesis was still elusive. In this study, we demonstrated that application of recombinant APP₁₈₋₂₈₆ could enhance beta amyloid (Aβ)-induced neuronal injuries which were related to the activation of apoptosis proteins. Aβ treatment could induce a slight increase of N-APPs release. In addition, expression of death receptor 6 (DR6) was increased in Aβ-treated neurons and APP transgenic mice. Moreover, the effect of APP₁₈₋₂₈₆ on Aβ-induced injuries could be suppressed by the application of recombinant DR6₄₁₋₃₄₁ and DR6 antibody. Furthermore, pull-down assay revealed that APP₁₈₋₂₈₆ could bind both exogenous and endogenous DR6. Aβ promoted APP₁₈₋₂₈₆ targeting to neuron which was accompanied with the increase of DR6 expression, whereas downregulation of DR6 by interference RNA could alleviate the binding of N-APPs to neuron and also suppressed Aβ-dependent toxic effect with N-APPs. These results suggested that APP N-terminal fragments might play neurotoxic roles in Aβ-induced neuronal injuries through cell surface DR6. PMID:25150572

  6. Filling the launch gap

    NASA Astrophysics Data System (ADS)

    Hoeser, S.

    1986-05-01

    Vehicles proposed to fill the gap in the U.S. space program's space transport needs for the next decade resulting from the January Challenger disaster, are discussed. Prior to the accident, the Air Force planned to purchase a Complementary Expendable Launch Vehicle system consisting of 10 single-use Titan-34D7 rockets. Another heavy lift booster now considered is the Phoenix H. Commercial launch vehicle systems projected to be available in the necessary time frame include the 215,000-pound thrust 4000-pound LEO payload capacity NASA Delta, the 11,300-pound LEO payload capacity Atlas Centaur the first ICBM, and the all-solid propellant expendable 2000-pound LEO payload Conestoga rocket. Also considered is the man-rated fully reusable Phoenix vertical take-off and vertical-landing launch vehicle.

  7. The Gap-Tpc

    NASA Astrophysics Data System (ADS)

    Rossi, B.; Anastasio, A.; Boiano, A.; Catalanotti, S.; Cocco, A. G.; Covone, G.; Di Meo, P.; Longo, G.; Vanzanella, A.; Walker, S.; Wang, H.; Wang, Y.; Fiorillo, G.

    2016-02-01

    Several experiments have been conducted worldwide, with the goal of observing low-energy nuclear recoils induced by WIMPs scattering off target nuclei in ultra-sensitive, low-background detectors. In the last few decades noble liquid detectors designed to search for dark matter in the form of WIMPs have been extremely successful in improving their sensitivities and setting the best limits. One of the crucial problems to be faced for the development of large size (multi ton-scale) liquid argon experiments is the lack of reliable and low background cryogenic PMTs: their intrinsic radioactivity, cost, and borderline performance at 87 K rule them out as a possible candidate for photosensors. We propose a brand new concept of liquid argon-based detector for direct dark matter search: the Geiger-mode Avalanche Photodiode Time Projection Chamber (GAP-TPC) optimized in terms of residual radioactivity of the photosensors, energy and spatial resolution, light and charge collection efficiency.

  8. Photonic Crystal Laser Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M

    2003-05-21

    Photonic crystals have great potential for use as laser-driven accelerator structures. A photonic crystal is a dielectric structure arranged in a periodic geometry. Like a crystalline solid with its electronic band structure, the modes of a photonic crystal lie in a set of allowed photonic bands. Similarly, it is possible for a photonic crystal to exhibit one or more photonic band gaps, with frequencies in the gap unable to propagate in the crystal. Thus photonic crystals can confine an optical mode in an all-dielectric structure, eliminating the need for metals and their characteristic losses at optical frequencies. We discuss several geometries of photonic crystal accelerator structures. Photonic crystal fibers (PCFs) are optical fibers which can confine a speed-of-light optical mode in vacuum. Planar structures, both two- and three-dimensional, can also confine such a mode, and have the additional advantage that they can be manufactured using common microfabrication techniques such as those used for integrated circuits. This allows for a variety of possible materials, so that dielectrics with desirable optical and radiation-hardness properties can be chosen. We discuss examples of simulated photonic crystal structures to demonstrate the scaling laws and trade-offs involved, and touch on potential fabrication processes.

  9. Undecidability of the spectral gap.

    PubMed

    Cubitt, Toby S; Perez-Garcia, David; Wolf, Michael M

    2015-12-10

    The spectral gap--the energy difference between the ground state and first excited state of a system--is central to quantum many-body physics. Many challenging open problems, such as the Haldane conjecture, the question of the existence of gapped topological spin liquid phases, and the Yang-Mills gap conjecture, concern spectral gaps. These and other problems are particular cases of the general spectral gap problem: given the Hamiltonian of a quantum many-body system, is it gapped or gapless? Here we prove that this is an undecidable problem. Specifically, we construct families of quantum spin systems on a two-dimensional lattice with translationally invariant, nearest-neighbour interactions, for which the spectral gap problem is undecidable. This result extends to undecidability of other low-energy properties, such as the existence of algebraically decaying ground-state correlations. The proof combines Hamiltonian complexity techniques with aperiodic tilings, to construct a Hamiltonian whose ground state encodes the evolution of a quantum phase-estimation algorithm followed by a universal Turing machine. The spectral gap depends on the outcome of the corresponding 'halting problem'. Our result implies that there exists no algorithm to determine whether an arbitrary model is gapped or gapless, and that there exist models for which the presence or absence of a spectral gap is independent of the axioms of mathematics. PMID:26659181

  10. Preparation of Gap Junctions in Membrane Microdomains for Immunoprecipitation and Mass Spectrometry Interactome Analysis.

    PubMed

    Fowler, Stephanie; Akins, Mark; Bennett, Steffany A L

    2016-01-01

    Protein interaction networks at gap junction plaques are increasingly implicated in a variety of intracellular signaling cascades. Identifying protein interactions of integral membrane proteins is a valuable tool for determining channel function. However, several technical challenges exist. Subcellular fractionation of the bait protein matrix is usually required to identify less abundant proteins in complex homogenates. Sufficient solvation of the lipid environment without perturbation of the protein interactome must also be achieved. The present chapter describes the flotation of light and heavy liver tissue membrane microdomains to facilitate the identification and analysis of endogenous gap junction proteins and includes technical notes for translation to other integral membrane proteins, tissues, or cell culture models. These procedures are valuable tools for the enrichment of gap junction membrane compartments and for the identification of gap junction signaling interactomes. PMID:27207290

  11. Introducing Defects in Photonic Band-Gap (PBG) Crystals

    SciTech Connect

    Johnson, Elliott C.; /North Dakota State U. /SLAC

    2007-11-07

    Photonic Band-Gap (PBG) fibers are a periodic array of optical materials arranged in a lattice called a photonic crystal. The use of PBG fibers for particle acceleration is being studied by the Advanced Accelerator Research Department (AARD) at SLAC. By introducing defects in such fibers, e.g. removing one or more capillaries from a hexagonal lattice, spatially confined modes suitable for particle acceleration may be created. The AARD has acquired several test samples of PBG fiber arrays with varying refractive index, capillary size, and length from an external vendor for testing. The PBGs were inspected with a microscope and characteristics of the capillaries including radii, spacing, and errors in construction were determined. Transmission tests were performed on these samples using a broad-range spectrophotometer. In addition, detailed E-field simulations of different PBG configurations were done using the CUDOS and RSOFT codes. Several accelerating modes for different configurations were found and studied in detail.

  12. TGF-β3 and TNFα perturb blood-testis barrier (BTB) dynamics by accelerating the clathrin-mediated endocytosis of integral membrane proteins: A new concept of BTB regulation during spermatogenesis*

    PubMed Central

    Xia, Weiliang; Wong, Elissa W. P.; Mruk, Dolores D.; Cheng, C. Yan

    2008-01-01

    In adult mammals such as rats, the blood-testis barrier (BTB) conferred by adjacent Sertoli cells in the seminiferous epithelium segregates post-meiotic germ cell development from the systemic circulation and is one of the tightest blood-tissue barriers. Yet it must “open” transiently at stage VIII of the epithelial cycle to accommodate the migration of preleptotene/leptotene spermatocytes. While this is a vital event of spermatogenesis, the mechanism(s) that regulates BTB dynamics is virtually unknown. Recent studies have suggested that transforming growth factor-β3 (TGF-β3) and tumor necrosis factor α (TNFα) secreted by Sertoli and germ cells into the microenvironment of the BTB are capable of inducing reversible BTB disruption in vivo, apparently by reducing the steady-state levels of occludin and zonula occludens-1 (ZO-1) at the BTB via the p38 mitogen activated protein (MAP) kinase signaling pathway. In this study, local administration of TGF-β3 (200 ng/testis) to the testis reversibly perturbed the BTB integrity in vivo. We next sought to delineate the mechanism by which these cytokines maintain the steady-state level of integral membrane proteins: occludin, junctional adhesion molecule-A (JAM-A) and N-cadherin at the BTB. Primary Sertoli cells cultured in vitro were shown to establish intact tight junctions and functional BTB within two days when assessed by transepithelial electrical resistance (TER) measurement across the cell epithelium. Sertoli cell integral membrane protein internalization at the BTB was assessed by biotinylation of cell surface proteins, to be followed by tracking the endocytosed/biotinylated proteins by using specific antibodies. Both TGF-β3 (3 ng/ml) and TNFα (10 ng/ml) were shown to significantly accelerate the kinetics of internalization of JAM-A, N-cadherin, and occludin versus controls. Treatment of cells with phenylarsine oxide (PAO) at 10 μM that blocks clathrin-mediated endocytosis was shown to inhibit the TGF-β3

  13. High expression of vacuolar protein sorting 4B (VPS4B) is associated with accelerated cell proliferation and poor prognosis in human hepatocellular carcinoma.

    PubMed

    Jiang, Dawei; Hu, Baoying; Wei, Lixian; Xiong, Yicheng; Wang, Gang; Ni, Tingting; Zong, Chunyan; Ni, Runzhou; Lu, Cuihua

    2015-03-01

    Vacuolar protein sorting 4B (VPS4B) is a member of ATPase family proteins that have been shown to play important roles in the formation of MVBs, virus budding and abscission of cytokinesis. In this study, we investigated the prognostic role of VPS4B in human hepatocellular carcinoma (HCC) and its effect on the growth of HCC cells. Western blot and immunohistochemistrical analyses revealed that VPS4B was significantly upregulated in 98 HCC tissues, compared with adjacent nontumorous samples. Meanwhile, clinicopathological variables and univariate and multivariate survival analyses showed that high VPS4B expression was correlated with multiple clinicopathological factors, including AJCC stage, microvascular invasion, Ki-67 and a poor prognosis. More importantly, univariate and multivariate survival analyses demonstrated that VPS4B served as an independent prognostic factor for survival in HCC patients. Furthermore, we found that VPS4B was lowly expressed in serum-starved Huh7 and HepG2 HCC cells, and was progressively increased after serum-refeeding. To study whether VPS4B could regulate the proliferation of HCC cells, VPS4B was knocked down in both Huh7 and HepG2 cells through the transfection of VPS4B-siRNA oligos. Flow cytometry and CCK-8 assay results indicated that interference of VPS4B led to cell cycle arrest and reduced cell proliferation of HCC cells. Taken together, our results implied that VPS4B could be a candidate prognostic biomarker as well as a potential therapeutical target of HCC. PMID:25547899

  14. Special purpose modes in photonic band gap fibers

    SciTech Connect

    Spencer, James; Noble, Robert; Campbell, Sara

    2013-04-02

    Photonic band gap fibers are described having one or more defects suitable for the acceleration of electrons or other charged particles. Methods and devices are described for exciting special purpose modes in the defects including laser coupling schemes as well as various fiber designs and components for facilitating excitation of desired modes. Results are also presented showing effects on modes due to modes in other defects within the fiber and due to the proximity of defects to the fiber edge. Techniques and devices are described for controlling electrons within the defect(s). Various applications for electrons or other energetic charged particles produced by such photonic band gap fibers are also described.

  15. Laser driven ion accelerator

    DOEpatents

    Tajima, Toshiki

    2006-04-18

    A system and method of accelerating ions in an accelerator to optimize the energy produced by a light source. Several parameters may be controlled in constructing a target used in the accelerator system to adjust performance of the accelerator system. These parameters include the material, thickness, geometry and surface of the target.

  16. Laser driven ion accelerator

    DOEpatents

    Tajima, Toshiki

    2005-06-14

    A system and method of accelerating ions in an accelerator to optimize the energy produced by a light source. Several parameters may be controlled in constructing a target used in the accelerator system to adjust performance of the accelerator system. These parameters include the material, thickness, geometry and surface of the target.

  17. A C-terminal domain of GAP is sufficient to stimulate ras p21 GTPase activity.

    PubMed Central

    Marshall, M S; Hill, W S; Ng, A S; Vogel, U S; Schaber, M D; Scolnick, E M; Dixon, R A; Sigal, I S; Gibbs, J B

    1989-01-01

    The cDNA for bovine ras p21 GTPase activating protein (GAP) has been cloned and the 1044 amino acid polypeptide encoded by the clone has been shown to bind the GTP complexes of both normal and oncogenic Harvey (Ha) ras p21. To identify the regions of GAP critical for the catalytic stimulation of ras p21 GTPase activity, a series of truncated forms of GAP protein were expressed in Escherichia coli. The C-terminal 343 amino acids of GAP (residues 702-1044) were observed to bind Ha ras p21-GTP and stimulate Ha ras p21 GTPase activity with the same efficiency (kcat/KM congruent to 1 x 10(6) M-1 s-1 at 24 degrees C) as GAP purified from bovine brain or full-length GAP expressed in E. coli. Deletion of the final 61 amino acid residues of GAP (residues 986-1044) rendered the protein insoluble upon expression in E. coli. These results define a distinct catalytic domain at the C terminus of GAP. In addition, GAP contains amino acid similarity with the B and C box domains conserved among phospholipase C-II, the crk oncogene product, and the non-receptor tyrosine kinase oncogene products. This homologous region is located in the N-terminal half of GAP outside of the catalytic domain that stimulates ras p21 GTPase activity and may constitute a distinct structural or functional domain within the GAP protein. Images PMID:2545441

  18. Matrix-assisted laser desorption/ionization coupled with quadrupole/orthogonal acceleration time-of-flight mass spectrometry for protein discovery, identification, and structural analysis.

    PubMed

    Baldwin, M A; Medzihradszky, K F; Lock, C M; Fisher, B; Settineri, T A; Burlingame, A L

    2001-04-15

    The design and operation of a novel UV-MALDI ionization source on a commercial QqoaTOF mass spectrometer (Applied Biosystem/MDS Sciex QSTAR Pulsar) is described. Samples are loaded on a 96-well target plate, the movement of which is under software control and can be readily automated. Unlike conventional high-energy MALDI-TOF, the ions are produced with low energies (5-10 eV) in a region of relatively low vacuum (8 mTorr). Thus, they are cooled by extensive low-energy collisions before selection in the quadrupole mass analyzer (Q1), potentially giving a quasi-continuous ion beam ideally suited to the oaTOF used for mass analysis of the fragment ions, although ion yields from individual laser shots may vary widely. Ion dissociation is induced by collisions with argon in an rf-only quadrupole cell, giving typical low-energy CID spectra for protonated peptide ions. Ions separated in the oaTOF are registered by a four-anode detector and time-to-digital converter and accumulated in "bins" that are 625 ps wide. Peak shapes depend upon the number of ion counts in adjacent bins. As expected, the accuracy of mass measurement is shown to be dependent upon the number of ions recorded for a particular peak. With internal calibration, mass accuracy better than 10 ppm is attainable for peaks that contain sufficient ions to give well-defined Gaussian profiles. By virtue of its high resolution, capability for accurate mass measurements, and sensitivity in the low-femotomole range, this instrument is ideally suited to protein identification for proteomic applications by generation of peptide tags, manual sequence interpretation, identification of modifications such as phosphorylation, and protein structural elucidation. Unlike the multiply charged ions typical of electrospray ionization, the singly charged MALDI-generated peptide ions show a linear dependence of optimal collision energy upon molecular mass, which is advantageous for automated operation. It is shown that the novel

  19. Undecidability of the spectral gap

    NASA Astrophysics Data System (ADS)

    Cubitt, Toby S.; Perez-Garcia, David; Wolf, Michael M.

    2015-12-01

    The spectral gap—the energy difference between the ground state and first excited state of a system—is central to quantum many-body physics. Many challenging open problems, such as the Haldane conjecture, the question of the existence of gapped topological spin liquid phases, and the Yang-Mills gap conjecture, concern spectral gaps. These and other problems are particular cases of the general spectral gap problem: given the Hamiltonian of a quantum many-body system, is it gapped or gapless? Here we prove that this is an undecidable problem. Specifically, we construct families of quantum spin systems on a two-dimensional lattice with translationally invariant, nearest-neighbour interactions, for which the spectral gap problem is undecidable. This result extends to undecidability of other low-energy properties, such as the existence of algebraically decaying ground-state correlations. The proof combines Hamiltonian complexity techniques with aperiodic tilings, to construct a Hamiltonian whose ground state encodes the evolution of a quantum phase-estimation algorithm followed by a universal Turing machine. The spectral gap depends on the outcome of the corresponding ‘halting problem’. Our result implies that there exists no algorithm to determine whether an arbitrary model is gapped or gapless, and that there exist models for which the presence or absence of a spectral gap is independent of the axioms of mathematics.

  20. Axial gap rotating electrical machine

    DOEpatents

    None

    2016-02-23

    Direct drive rotating electrical machines with axial air gaps are disclosed. In these machines, a rotor ring and stator ring define an axial air gap between them. Sets of gap-maintaining rolling supports bear between the rotor ring and the stator ring at their peripheries to maintain the axial air gap. Also disclosed are wind turbines using these generators, and structures and methods for mounting direct drive rotating electrical generators to the hubs of wind turbines. In particular, the rotor ring of the generator may be carried directly by the hub of a wind turbine to rotate relative to a shaft without being mounted directly to the shaft.

  1. Gap and stripline combined monitor

    DOEpatents

    Yin, Y.

    1984-02-16

    A combined gap and stripline monitor device for measuring the intensity and position of a charged particle beam bunch in a beam pipe of a synchrotron radiation facility. The monitor has first and second beam pipe portions with an axial gap therebetween. An outer pipe cooperates with the first beam pipe portion to form a gap enclosure, while inner strips cooperate with the first beam pipe portion to form a stripline monitor, with the stripline length being the same as the gap enclosure length.

  2. Gap and stripline combined monitor

    DOEpatents

    Yin, Yan

    1986-01-01

    A combined gap and stripline monitor device (10) for measuring the intensity and position of a charged particle beam bunch in a beam pipe of a synchotron radiation facility. The monitor has first and second beam pipe portions (11a, 11b) with an axial gap (12) therebetween. An outer pipe (14) cooperates with the first beam pipe portion (11a) to form a gap enclosure, while inner strips (23a-d) cooperate with the first beam pipe portion (11a) to form a stripline monitor, with the stripline length being the same as the gap enclosure length.

  3. Study of Gap Junctions in Human Embryonic Stem Cells.

    PubMed

    Pébay, Alice; Wong, Raymond C B

    2016-01-01

    Gap junctional intercellular communication (GJIC) has been described in different cell types including stem cells and has been involved in different biological events. GJIC is required for mouse embryonic stem cell maintenance and proliferation and various studies suggest that functional GJIC is a common characteristic of human embryonic stem cells (hESC) maintained in different culture conditions. This chapter introduces methods to study gap junctions in hESC, from expression of gap junction proteins to functional study of GJIC in hESC proliferation, apoptosis, colony growth, and pluripotency. PMID:24859928

  4. Heat shock protein hsp70 accelerates the recovery of heat-shocked mammalian cells through its modulation of heat shock transcription factor HSF1.

    PubMed Central

    Kim, D; Ouyang, H; Li, G C

    1995-01-01

    The role of mammalian 70-kDa heat shock protein (hsp70) in regulating cellular response to heat shock was examined by using three closely related rat cells: control Rat-1 cells, thermotolerant Rat-1 (TT Rat-1) cells, and heat-resistant M21 cells, a derivative of Rat-1 cells that constitutively overexpress human hsp70. In all these cells, after a prescribed heat shock, the level of the phosphorylated form of heat shock transcription factor HSF1 and that of HSF1 capable of binding to its cognitive DNA sequence heat shock element (HSE) exhibit similar time dependence. The amount of a constitutive HSE-binding activity (CHBA), on the other hand, inversely correlates with those of the two aforementioned forms of HSF1. The recovery kinetics from heat shock are different for the three cell lines, with the thermal-resistant TT Rat-1 and M21 cells showing faster recovery in terms of the state of phosphorylation of HSF1 and its ability to bind HSE or in terms of the reappearance of CHBA. Treatment with okadaic acid, a serine/threonine phosphatase inhibitor, delays the recovery kinetics of Rat-1 cells but not that of thermal-resistant M21 cells. These results are interpreted in terms of a role for hsp70 in the recovery of heat-shocked mammalian cells. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:7892235

  5. BBU design of linear induction accelerator cells for radiography application

    SciTech Connect

    Shang, C.C.; Chen, Y.J.; Gaporaso, G.J.; Houck, T.L.; Molau, N.E.; Focklen, J.; Gregory, S.

    1997-05-06

    There is an ongoing effort to develop accelerating modules for high-current electron accelerators for advanced radiography application. Accelerating modules with low beam-cavity coupling impedances along with gap designs with acceptable field stresses comprise a set of fundamental design criteria. We examine improved cell designs which have been developed for accelerator application in several radiographic operating regimes. We evaluate interaction impedances, analyze the effects of beam structure coupling on beam dynamics (beam break-up instability and corkscrew motion). We also provide estimates of coupling through interesting new high-gradient insulators and evaluate their potential future application in induction cells.

  6. Loss of Ypk1, the yeast homolog to the human serum- and glucocorticoid-induced protein kinase, accelerates phospholipase B1-mediated phosphatidylcholine deacylation.

    PubMed

    Surlow, Beth A; Cooley, Benjamin M; Needham, Patrick G; Brodsky, Jeffrey L; Patton-Vogt, Jana

    2014-11-01

    Ypk1, the yeast homolog of the human serum- and glucocorticoid-induced kinase (Sgk1), affects diverse cellular activities, including sphingolipid homeostasis. We now report that Ypk1 also impacts the turnover of the major phospholipid, phosphatidylcholine (PC). Pulse-chase radiolabeling reveals that a ypk1Δ mutant exhibits increased PC deacylation and glycerophosphocholine production compared with wild type yeast. Deletion of PLB1, a gene encoding a B-type phospholipase that hydrolyzes PC, in a ypk1Δ mutant curtails the increased PC deacylation. In contrast to previous data, we find that Plb1 resides in the ER and in the medium. Consistent with a link between Ypk1 and Plb1, the levels of both Plb1 protein and PLB1 message are elevated in a ypk1Δ strain compared with wild type yeast. Furthermore, deletion of PLB1 in a ypk1Δ mutant exacerbates phenotypes associated with loss of YPK1, including slowed growth and sensitivity to cell wall perturbation, suggesting that increased Plb1 activity buffers against the loss of Ypk1. Because Plb1 lacks a consensus phosphorylation site for Ypk1, we probed other processes under the control of Ypk1 that might be linked to PC turnover. Inhibition of sphingolipid biosynthesis by the drug myriocin or through utilization of a lcb1-100 mutant results in increased PLB1 expression. Furthermore, we discovered that the increase in PLB1 expression observed upon inhibition of sphingolipid synthesis or loss of Ypk1 is under the control of the Crz1 transcription factor. Taken together, these results suggest a functional interaction between Ypk1 and Plb1 in which altered sphingolipid metabolism up-regulates PLB1 expression via Crz1. PMID:25258318

  7. Bioinorganic Chemistry Special Feature: Gapped DNA is anisotropically bent

    NASA Astrophysics Data System (ADS)

    Guo, Hong; Tullius, Thomas D.

    2003-04-01

    Ionizing radiation damages DNA in several ways, including through formation of a single-nucleoside gap in one DNA strand. We have developed a two-dimensional gel electrophoresis method to investigate the effect of a strand gap on DNA structure. We generate a library of gapped DNA molecules by treating a DNA restriction fragment with the hydroxyl radical, generated by the reaction of Fe(II) EDTA with hydrogen peroxide. The DNA molecule studied contains a fixed bend produced by a set of phased adenine tracts. The A-tract bend serves as a reference bend for investigating the conformational nature of a strand gap. In the first electrophoretic dimension, a bent DNA molecule that has been treated with the hydroxyl radical is electrophoresed on a native gel. Smearing of the band on the native gel indicates that the library of gapped DNA molecules contains a variety of DNA conformations. In the second electrophoretic dimension, gapped DNA molecules having different native gel mobilities are electrophoresed on separate lanes of a denaturing gel to reveal how each strand gap affects the native gel mobility (and thus shape) of the DNA. Our results demonstrate that a single-nucleoside gap in a DNA duplex leads to an anisotropic, directional bend in the DNA helix axis. The implications of our findings for recognition of this lesion by DNA repair proteins are discussed.

  8. The N-terminal region of GAP regulates cytoskeletal structure and cell adhesion.

    PubMed Central

    McGlade, J; Brunkhorst, B; Anderson, D; Mbamalu, G; Settleman, J; Dedhar, S; Rozakis-Adcock, M; Chen, L B; Pawson, T

    1993-01-01

    Ras GTPase activating protein (GAP) possesses a C-terminal domain that interacts with GTP-bound Ras, and an N-terminal region containing two SH2 domains and an SH3 domain. In addition to its association with Ras, GAP binds stably to autophosphorylated beta PDGF receptors, and to two cytoplasmic phosphoproteins: p62, an RNA binding protein, and p190, which possesses GAP activity towards small guanine nucleotide binding proteins in the Rho/Rac family. To define the region of GAP that mediates these interactions with cellular phosphoproteins, and to investigate the biological significance of these complexes, a truncated GAP polypeptide (GAP-N) containing residues 1-445 was stably expressed in Rat-2 fibroblasts. GAP-N contains the SH2 and SH3 domains, but lacks the Ras GTPase activating domain. Stimulation of cells expressing GAP-N with PDGF induced association of GAP-N with the beta PDGF receptor, and phosphorylation of GAP-N on tyrosine, consistent with the notion that GAP SH2 domains direct binding to the autophosphorylated beta PDGF receptor in vivo. GAP-N bound constitutively to p190 in both serum-deprived and growth factor-stimulated cells. This GAP-N-p190 complex had Rho GAP activity in vitro. The expression of GAP-N in Rat-2 cells correlated with changes in the cytoskeleton and in cell adhesion, typified by the disruption of action stress fibres, a reduction in focal contacts, and an impaired ability to adhere to fibronectin. These results suggest that the N-terminal domain of GAP can direct interactions with cellular phosphoproteins in vivo, and thereby exert an effector function which modulates the cytoskeleton and cell adhesion.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:8344248

  9. Measuring the Gap

    PubMed Central

    She, Xinshu; Zhao, Deqing; Scholnick, Jenna

    2016-01-01

    China is a large country where rapid development is accompanied by growing inequalities. How economic inequalities translate to health inequalities is unknown. Baseline health assessment is lacking among rural Chinese children. We aimed at assessing baseline student health of rural Chinese children and comparing them with those of urban children of similar ages. A cross-sectional study was conducted using the 2003 Global School-Based Student Health Survey among 100 students Grade 4 to 6 from rural Guizhou, China. Results were summarized and compared with public data from urban Beijing using multivariate logistic regression models. Rural children are more likely to not wash their hands before a meal (odds ratio [OR] = 5.71, P < .01) and after using the toilet (OR = 5.41, P < .01). They are more likely to feel sick or to get into trouble after drinking (OR = 7.28, P < .01). They are more likely to have used drugs (OR = 8.54, P < .01) and to have no close friends (OR = 8.23, P < .01). An alarming percentage of rural (8.22%) and urban (14.22%) children have had suicidal ideation in the past year (OR = 0.68, P > .05). Rural parents are more likely to not know their children’s whereabouts (OR = 1.81, P < .05). Rural children are more than 4 times likely to have serious injuries (OR = 4.64, P < .01) and to be bullied (OR = 4.01, P < .01). In conclusion, school-age rural Chinese children exhibit more health risk behaviors and fewer protective factors at baseline compared to their urban counterparts. Any intervention aimed at improving child health should take this distributive gap into consideration. PMID:27335999

  10. Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies

    PubMed Central

    Kamerlin, Shina C. L.; Haranczyk, Maciej

    2009-01-01

    Hybrid quantum mechanical / molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting here different types of QM/MM calculations of electrostatic energies (and related properties), our focus will be on pKa calculations. This reflects the fact that pKa of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to large discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor, as well as a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that by using this approach, we are able to reproduce the relevant sidechain pKas with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide

  11. Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies

    SciTech Connect

    Kamerlin, Shina C. L.; Haranczyk, Maciej; Warshel, Arieh

    2009-03-01

    Hybrid quantum mechanical / molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for propercomputational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting here different types of QM/MM calculations of electrostatic energies (and related properties), our focus will be on pKa calculations. This reflects the fact that pKa of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to large discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor, as well as a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that by using this approach, we are able to reproduce the relevant sidechain pKas with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an

  12. GAP Analysis Bulletin Number 15

    USGS Publications Warehouse

    Maxwell, Jill, (Edited By); Gergely, Kevin; Aycrigg, Jocelyn; Canonico, Gabrielle; Davidson, Anne; Coffey, Nicole

    2008-01-01

    The Mission of the Gap Analysis Program (GAP) is to promote conservation by providing broad geographic information on biological diversity to resource managers, planners, and policy makers who can use the information to make informed decisions. As part of the National Biological Information Infrastructure (NBII) ?a collaborative program to provide increased access to data and information on the nation?s biological resources--GAP data and analytical tools have been used in hundreds of applications: from basic research to comprehensive state wildlife plans; from educational projects in schools to ecoregional assessments of biodiversity. The challenge: keeping common species common means protecting them BEFORE they become threatened. To do this on a state or regional basis requires key information such as land cover descriptions, predicted distribution maps for native animals, and an assessment of the level of protection currently given to those plants and animals. GAP works cooperatively with Federal, state, and local natural resource professionals and academics to provide this kind of information. GAP activities focus on the creation of state and regional databases and maps that depict patterns of land management, land cover, and biodiversity. These data can be used to identify ?gaps? in conservation--instances where an animal or plant community is not adequately represented on the existing network of conservation lands. GAP is administered through the U.S. Geological Survey. Through building partnerships among disparate groups, GAP hopes to foster the kind of collaboration that is needed to address conservation issues on a broad scale. For more information, contact: John Mosesso National GAP Director 703-648-4079 Kevin Gergely National GAP Operations Manager 208-885-3565

  13. The direction of acceleration

    NASA Astrophysics Data System (ADS)

    Wilhelm, Thomas; Burde, Jan-Philipp; Lück, Stephan

    2015-11-01

    Acceleration is a physical quantity that is difficult to understand and hence its complexity is often erroneously simplified. Many students think of acceleration as equivalent to velocity, a ˜ v. For others, acceleration is a scalar quantity, which describes the change in speed Δ|v| or Δ|v|/Δt (as opposed to the change in velocity). The main difficulty with the concept of acceleration therefore lies in developing a correct understanding of its direction. The free iOS app AccelVisu supports students in acquiring a correct conception of acceleration by showing acceleration arrows directly at moving objects.

  14. TURBULENT SHEAR ACCELERATION

    SciTech Connect

    Ohira, Yutaka

    2013-04-10

    We consider particle acceleration by large-scale incompressible turbulence with a length scale larger than the particle mean free path. We derive an ensemble-averaged transport equation of energetic charged particles from an extended transport equation that contains the shear acceleration. The ensemble-averaged transport equation describes particle acceleration by incompressible turbulence (turbulent shear acceleration). We find that for Kolmogorov turbulence, the turbulent shear acceleration becomes important on small scales. Moreover, using Monte Carlo simulations, we confirm that the ensemble-averaged transport equation describes the turbulent shear acceleration.

  15. Grid Gap Measurement for an NSTAR Ion Thruster

    NASA Technical Reports Server (NTRS)

    Diaz, Esther M.; Soulas, George C.

    2006-01-01

    The change in gap between the screen and accelerator grids of an engineering model NSTAR ion optics assembly was measured during thruster operation with beam extraction. The molybdenum ion optics assembly was mounted onto an engineering model NSTAR ion thruster. The measurement technique consisted of measuring the difference in height of an alumina pin relative to the downstream accelerator grid surface. The alumina pin was mechanically attached to the center aperture of the screen grid and protruded through the center aperture of the accelerator grid. The change in pin height was monitored using a long distance microscope coupled to a digital imaging system. Transient and steady-state hot grid gaps were measured at three power levels: 0.5, 1.5 and 2.3 kW. Also, the change in grid gap was measured during the transition between power levels, and during the startup with high voltage applied just prior to discharge ignition. Performance measurements, such as perveance, electron backstreaming limit and screen grid ion transparency, were also made to confirm that this ion optics assembly performed similarly to past testing. Results are compared to a prior test of 30 cm titanium ion optics.

  16. CONTINUOUS ABORT GAP CLEANING AT RHIC.

    SciTech Connect

    DREES,A.FLILLER,R.III.FU,W.MICHNOFF,R.

    2004-07-05

    Since the RHIC Au-Au run in the year 2001 the 200 MHz cavity system was used at storage and a 28 MHz system during injection and acceleration. The rebucketing procedure potentially causes a higher debunching rate of heavy ion beams in addition to amplifying debunching due to other mechanisms. At the end of a four hour store, debunched beam can easily account for more than 50% of the total beam intensity. This effect is even stronger with the achieved high intensities of the RHIC Au-Au run in 2004. A beam abort at the presence of a lot of debunched beam bears the risk of magnet quenching and experimental detector damage due to uncontrolled beam losses. Thus it is desirable to avoid any accumulation of debunched beam from the beginning of each store, in particular to anticipate cases of unscheduled beam aborts due to a system failure. A combination of a fast transverse kickers and the new 2-stage copper collimator system are used to clean the abort gap continuously throughout the store with a repetition rate of 1 Hz. This report gives. an overview of the new gap cleaning procedure and the achieved performance.

  17. Pneumatic gap sensor and method

    DOEpatents

    Bagdal, Karl T.; King, Edward L.; Follstaedt, Donald W.

    1992-01-01

    An apparatus and method for monitoring and maintaining a predetermined width in the gap between a casting nozzle and a casting wheel, wherein the gap is monitored by means of at least one pneumatic gap sensor. The pneumatic gap sensor is mounted on the casting nozzle in proximity to the casting surface and is connected by means of a tube to a regulator and a transducer. The regulator provides a flow of gas through a restictor to the pneumatic gap sensor, and the transducer translates the changes in the gas pressure caused by the proximity of the casting wheel to the pneumatic gap sensor outlet into a signal intelligible to a control device. The relative positions of the casting nozzle and casting wheel can thereby be selectively adjusted to continually maintain a predetermined distance between their adjacent surfaces. The apparatus and method enables accurate monitoring of the actual casting gap in a simple and reliable manner resistant to the extreme temperatures and otherwise hostile casting environment.

  18. Pneumatic gap sensor and method

    DOEpatents

    Bagdal, K.T.; King, E.L.; Follstaedt, D.W.

    1992-03-03

    An apparatus and method for monitoring and maintaining a predetermined width in the gap between a casting nozzle and a casting wheel, wherein the gap is monitored by means of at least one pneumatic gap sensor. The pneumatic gap sensor is mounted on the casting nozzle in proximity to the casting surface and is connected by means of a tube to a regulator and a transducer. The regulator provides a flow of gas through a restictor to the pneumatic gap sensor, and the transducer translates the changes in the gas pressure caused by the proximity of the casting wheel to the pneumatic gap sensor outlet into a signal intelligible to a control device. The relative positions of the casting nozzle and casting wheel can thereby be selectively adjusted to continually maintain a predetermined distance between their adjacent surfaces. The apparatus and method enables accurate monitoring of the actual casting gap in a simple and reliable manner resistant to the extreme temperatures and otherwise hostile casting environment. 6 figs.

  19. Accelerating Particles with Plasma

    SciTech Connect

    Litos, Michael; Hogan, Mark

    2014-11-05

    Researchers at SLAC explain how they use plasma wakefields to accelerate bunches of electrons to very high energies over only a short distance. Their experiments offer a possible path for the future of particle accelerators.

  20. Improved plasma accelerator

    NASA Technical Reports Server (NTRS)

    Cheng, D. Y.

    1971-01-01

    Converging, coaxial accelerator electrode configuration operates in vacuum as plasma gun. Plasma forms by periodic injections of high pressure gas that is ionized by electrical discharges. Deflagration mode of discharge provides acceleration, and converging contours of plasma gun provide focusing.

  1. Gene Circuit Analysis of the Terminal Gap Gene huckebein

    PubMed Central

    Ashyraliyev, Maksat; Siggens, Ken; Janssens, Hilde; Blom, Joke; Akam, Michael; Jaeger, Johannes

    2009-01-01

    The early embryo of Drosophila melanogaster provides a powerful model system to study the role of genes in pattern formation. The gap gene network constitutes the first zygotic regulatory tier in the hierarchy of the segmentation genes involved in specifying the position of body segments. Here, we use an integrative, systems-level approach to investigate the regulatory effect of the terminal gap gene huckebein (hkb) on gap gene expression. We present quantitative expression data for the Hkb protein, which enable us to include hkb in gap gene circuit models. Gap gene circuits are mathematical models of gene networks used as computational tools to extract regulatory information from spatial expression data. This is achieved by fitting the model to gap gene expression patterns, in order to obtain estimates for regulatory parameters which predict a specific network topology. We show how considering variability in the data combined with analysis of parameter determinability significantly improves the biological relevance and consistency of the approach. Our models are in agreement with earlier results, which they extend in two important respects: First, we show that Hkb is involved in the regulation of the posterior hunchback (hb) domain, but does not have any other essential function. Specifically, Hkb is required for the anterior shift in the posterior border of this domain, which is now reproduced correctly in our models. Second, gap gene circuits presented here are able to reproduce mutants of terminal gap genes, while previously published models were unable to reproduce any null mutants correctly. As a consequence, our models now capture the expression dynamics of all posterior gap genes and some variational properties of the system correctly. This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network. PMID:19876378

  2. The Nature of Accelerating Modes in PBG Fibers

    SciTech Connect

    Noble, TRobert J.; /SLAC

    2011-05-19

    Transverse magnetic (TM) modes with phase velocities at or just below the speed of light, c, are intended to accelerate relativistic particles in hollow-core, photonic band gap (PBG) fibers. These are so-called 'surface defect modes', being lattice modes perturbed by the defect to have their frequencies shifted into the band gap, and they can have any phase velocity. PBG fibers also support so-called 'core defect modes' which are characterized as having phase velocities always greater than c and never cross the light line. In this paper we explore the nature of these two classes of accelerating modes and compare their properties.

  3. Acceleration gradient of a plasma wakefield accelerator

    SciTech Connect

    Uhm, Han S.

    2008-02-25

    The phase velocity of the wakefield waves is identical to the electron beam velocity. A theoretical analysis indicates that the acceleration gradient of the wakefield accelerator normalized by the wave breaking amplitude is K{sub 0}({xi})/K{sub 1}({xi}), where K{sub 0}({xi}) and K{sub 1}({xi}) are the modified Bessel functions of the second kind of order zero and one, respectively and {xi} is the beam parameter representing the beam intensity. It is also shown that the beam density must be considerably higher than the diffuse plasma density for the large radial velocity of plasma electrons that are required for a high acceleration gradient.

  4. Far field acceleration

    SciTech Connect

    Fernow, R.C.

    1995-07-01

    Far fields are propagating electromagnetic waves far from their source, boundary surfaces, and free charges. The general principles governing the acceleration of charged particles by far fields are reviewed. A survey of proposed field configurations is given. The two most important schemes, Inverse Cerenkov acceleration and Inverse free electron laser acceleration, are discussed in detail.

  5. Angular Acceleration Without Torque?

    NASA Astrophysics Data System (ADS)

    Kaufman, Richard D.

    2012-01-01

    Hardly. Just as Robert Johns qualitatively describes angular acceleration by an internal force in his article "Acceleration Without Force?" here we will extend the discussion to consider angular acceleration by an internal torque. As we will see, this internal torque is due to an internal force acting at a distance from an instantaneous center.2

  6. Sustained linear acceleration

    NASA Technical Reports Server (NTRS)

    Fraser, T. M.

    1973-01-01

    The subjective effects of sustained acceleration are discussed, including positive, negative, forward, backward, and lateral acceleration effects. Physiological effects, such as retinal and visual response, unconsciousness and cerebral function, pulmonary response, and renal output, are studied. Human tolerance and performance under sustained acceleration are ascertained.

  7. Angular Acceleration without Torque?

    ERIC Educational Resources Information Center

    Kaufman, Richard D.

    2012-01-01

    Hardly. Just as Robert Johns qualitatively describes angular acceleration by an internal force in his article "Acceleration Without Force?" here we will extend the discussion to consider angular acceleration by an internal torque. As we will see, this internal torque is due to an internal force acting at a distance from an instantaneous center.

  8. Acceleration: It's Elementary

    ERIC Educational Resources Information Center

    Willis, Mariam

    2012-01-01

    Acceleration is one tool for providing high-ability students the opportunity to learn something new every day. Some people talk about acceleration as taking a student out of step. In actuality, what one is doing is putting a student in step with the right curriculum. Whole-grade acceleration, also called grade-skipping, usually happens between…

  9. Advanced Test Accelerator (ATA) injector

    SciTech Connect

    Jackson, C.H.; Bubp, D.G.; Fessenden, T.J.; Hester, R.E.; Neil, V.K.; Paul, A.C.; Prono, D.S.

    1983-03-09

    The ATA injector, developed from experience gained from the Experimental Test Accelerator (ETA) linac, has recently been completed. The injector consists of ten 0.25 MV cells that are used to develop 2.5 MV across a single diode gap. The 10 kA beam is extracted from a 500 cm/sup 2/ plasma cathode at average rates of up to 5 Hz and burst rates to 1 kHz. Pulsed power from 20 water filled blumleins is divided and introduced symmetrically through four ports on each cell. All major insulators are fabricated from filled epoxy castings. With these improvements, the ATA injector is smaller than the ETA injector; has a faster pulse response; has lower voltage stress on insulators and higher ultimate performance. Injector characterization tests began in October 1982. These tests include beam current, energy, and emittance measurements.

  10. Annular arc accelerator shock tube

    NASA Technical Reports Server (NTRS)

    Leibowitz, L. P. (Inventor)

    1976-01-01

    An annular arc accelerator shock tube employs a cold gas driver to flow a stream of gas from an expansion section through a high voltage electrode section to a test section, thus driving a shock wave in front of it. A glow discharge detects the shock wave and actuates a trigger generator which in turn fires spark-gap switches to discharge a bank of capacitors across a centered cathode and an annular anode in tandem electrode sections. The initial shock wave passes through the anode section from the cathode section thereby depositing energy into the flow gas without the necessity of any diaphragm opening in the gas flow from the expansion section through the electrode sections.

  11. Pallidal gap junctions-triggers of synchrony in Parkinson's disease?

    PubMed Central

    Schwab, Bettina C; Heida, Tjitske; Zhao, Yan; van Gils, Stephan A; van Wezel, Richard J A

    2014-01-01

    Although increased synchrony of the neural activity in the basal ganglia may underlie the motor deficiencies exhibited in Parkinson's disease (PD), how this synchrony arises, propagates through the basal ganglia, and changes under dopamine replacement remains unknown. Gap junctions could play a major role in modifying this synchrony, because they show functional plasticity under the influence of dopamine and after neural injury. In this study, confocal imaging was used to detect connexin-36, the major neural gap junction protein, in postmortem tissues of PD patients and control subjects in the putamen, subthalamic nucleus (STN), and external and internal globus pallidus (GPe and GPi, respectively). Moreover, we quantified how gap junctions affect synchrony in an existing computational model of the basal ganglia. We detected connexin-36 in the human putamen, GPe, and GPi, but not in the STN. Furthermore, we found that the number of connexin-36 spots in PD tissues increased by 50% in the putamen, 43% in the GPe, and 109% in the GPi compared with controls. In the computational model, gap junctions in the GPe and GPi strongly influenced synchrony. The basal ganglia became especially susceptible to synchronize with input from the cortex when gap junctions were numerous and high in conductance. In conclusion, connexin-36 expression in the human GPe and GPi suggests that gap junctional coupling exists within these nuclei. In PD, neural injury and dopamine depletion could increase this coupling. Therefore, we propose that gap junctions act as a powerful modulator of synchrony in the basal ganglia. PMID:25124148

  12. Pallidal gap junctions-triggers of synchrony in Parkinson's disease?

    PubMed

    Schwab, Bettina C; Heida, Tjitske; Zhao, Yan; van Gils, Stephan A; van Wezel, Richard J A

    2014-10-01

    Although increased synchrony of the neural activity in the basal ganglia may underlie the motor deficiencies exhibited in Parkinson's disease (PD), how this synchrony arises, propagates through the basal ganglia, and changes under dopamine replacement remains unknown. Gap junctions could play a major role in modifying this synchrony, because they show functional plasticity under the influence of dopamine and after neural injury. In this study, confocal imaging was used to detect connexin-36, the major neural gap junction protein, in postmortem tissues of PD patients and control subjects in the putamen, subthalamic nucleus (STN), and external and internal globus pallidus (GPe and GPi, respectively). Moreover, we quantified how gap junctions affect synchrony in an existing computational model of the basal ganglia. We detected connexin-36 in the human putamen, GPe, and GPi, but not in the STN. Furthermore, we found that the number of connexin-36 spots in PD tissues increased by 50% in the putamen, 43% in the GPe, and 109% in the GPi compared with controls. In the computational model, gap junctions in the GPe and GPi strongly influenced synchrony. The basal ganglia became especially susceptible to synchronize with input from the cortex when gap junctions were numerous and high in conductance. In conclusion, connexin-36 expression in the human GPe and GPi suggests that gap junctional coupling exists within these nuclei. In PD, neural injury and dopamine depletion could increase this coupling. Therefore, we propose that gap junctions act as a powerful modulator of synchrony in the basal ganglia. PMID:25124148

  13. Studies on the cell biology of interendothelial cell gaps

    PubMed Central

    Ochoa, Cristhiaan D.

    2012-01-01

    Pain, redness, heat, and swelling are hallmarks of inflammation that were recognized as early as the first century AD. Despite these early observations, the mechanisms responsible for swelling, in particular, remained an enigma for nearly two millennia. Only in the past century have scientists and physicians gained an appreciation for the role that vascular endothelium plays in controlling the exudation that is responsible for swelling. One of these mechanisms is the formation of transient gaps between adjacent endothelial cell borders. Inflammatory mediators act on endothelium to reorganize the cytoskeleton, decrease the strength of proteins that connect cells together, and induce transient gaps between endothelial cells. These gaps form a paracellular route responsible for exudation. The discovery that interendothelial cell gaps are causally linked to exudation began in the 1960s and was accompanied by significant controversy. Today, the role of gap formation in tissue edema is accepted by many, and significant scientific effort is dedicated toward developing therapeutic strategies that will prevent or reverse the endothelial cell gaps that are present during the course of inflammatory illness. Given the importance of this field in endothelial cell biology and inflammatory disease, this focused review catalogs key historical advances that contributed to our modern-day understanding of the cell biology of interendothelial gap formation. PMID:21964402

  14. Project acceleration : making the leap from pilot to commercialization.

    SciTech Connect

    Borneo, Daniel R.

    2010-05-01

    Since the energy storage technology market is in a relatively emergent phase, narrowing the gap between pilot project status and commercialization is fundamental to the accelerating of this innovative market space. This session will explore regional market design factors to facilitate the storage enterprise. You will also hear about: quantifying transmission and generation efficiency enhancements; resource planning for storage; and assessing market mechanisms to accelerate storage adoption regionally.

  15. GAP junctional communication in brain secondary organizers.

    PubMed

    Bosone, Camilla; Andreu, Abraham; Echevarria, Diego

    2016-06-01

    Gap junctions (GJs) are integral membrane proteins that enable the direct cytoplasmic exchange of ions and low molecular weight metabolites between adjacent cells. They are formed by the apposition of two connexons belonging to adjacent cells. Each connexon is formed by six proteins, named connexins (Cxs). Current evidence suggests that gap junctions play an important part in ensuring normal embryo development. Mutations in connexin genes have been linked to a variety of human diseases, although the precise role and the cell biological mechanisms of their action remain almost unknown. Among the big family of Cxs, several are expressed in nervous tissue but just a few are expressed in the anterior neural tube of vertebrates. Many efforts have been made to elucidate the molecular bases of Cxs cell biology and how they influence the morphogenetic signal activity produced by brain signaling centers. These centers, orchestrated by transcription factors and morphogenes determine the axial patterning of the mammalian brain during its specification and regionalization. The present review revisits the findings of GJ composed by Cx43 and Cx36 in neural tube patterning and discuss Cx43 putative enrollment in the control of Fgf8 signal activity coming from the well known secondary organizer, the isthmic organizer. PMID:27273333

  16. Structural determinants of G-protein alpha subunit selectivity by regulator of G-protein signaling 2 (RGS2).

    PubMed

    Kimple, Adam J; Soundararajan, Meera; Hutsell, Stephanie Q; Roos, Annette K; Urban, Daniel J; Setola, Vincent; Temple, Brenda R S; Roth, Bryan L; Knapp, Stefan; Willard, Francis S; Siderovski, David P

    2009-07-17

    "Regulator of G-protein signaling" (RGS) proteins facilitate the termination of G protein-coupled receptor (GPCR) signaling via their ability to increase the intrinsic GTP hydrolysis rate of Galpha subunits (known as GTPase-accelerating protein or "GAP" activity). RGS2 is unique in its in vitro potency and selectivity as a GAP for Galpha(q) subunits. As many vasoconstrictive hormones signal via G(q) heterotrimer-coupled receptors, it is perhaps not surprising that RGS2-deficient mice exhibit constitutive hypertension. However, to date the particular structural features within RGS2 determining its selectivity for Galpha(q) over Galpha(i/o) substrates have not been completely characterized. Here, we examine a trio of point mutations to RGS2 that elicits Galpha(i)-directed binding and GAP activities without perturbing its association with Galpha(q). Using x-ray crystallography, we determined a model of the triple mutant RGS2 in complex with a transition state mimetic form of Galpha(i) at 2.8-A resolution. Structural comparison with unliganded, wild type RGS2 and of other RGS domain/Galpha complexes highlighted the roles of these residues in wild type RGS2 that weaken Galpha(i) subunit association. Moreover, these three amino acids are seen to be evolutionarily conserved among organisms with modern cardiovascular systems, suggesting that RGS2 arose from the R4-subfamily of RGS proteins to have specialized activity as a potent and selective Galpha(q) GAP that modulates cardiovascular function. PMID:19478087

  17. Eight electrode optical readout gap

    DOEpatents

    Boettcher, Gordon E.; Crain, Robert W.

    1985-01-01

    A protective device for a plurality of electrical circuits includes a pluity of isolated electrodes forming a gap with a common electrode. An output signal, electrically isolated from the circuits being monitored, is obtained by a photosensor viewing the discharge gap through an optical window. Radioactive stabilization of discharge characteristics is provided for slowly changing voltages and carbon tipped dynamic starters provide desirable discharge characteristics for rapidly varying voltages. A hydrogen permeation barrier is provided on external surfaces of the device.

  18. Compact Plasma Accelerator

    NASA Technical Reports Server (NTRS)

    Foster, John E.

    2004-01-01

    A plasma accelerator has been conceived for both material-processing and spacecraft-propulsion applications. This accelerator generates and accelerates ions within a very small volume. Because of its compactness, this accelerator could be nearly ideal for primary or station-keeping propulsion for spacecraft having masses between 1 and 20 kg. Because this accelerator is designed to generate beams of ions having energies between 50 and 200 eV, it could also be used for surface modification or activation of thin films.

  19. Application of stochastic automata networks for creation of continuous time Markov chain models of voltage gating of gap junction channels.

    PubMed

    Snipas, Mindaugas; Pranevicius, Henrikas; Pranevicius, Mindaugas; Pranevicius, Osvaldas; Paulauskas, Nerijus; Bukauskas, Feliksas F

    2015-01-01

    The primary goal of this work was to study advantages of numerical methods used for the creation of continuous time Markov chain models (CTMC) of voltage gating of gap junction (GJ) channels composed of connexin protein. This task was accomplished by describing gating of GJs using the formalism of the stochastic automata networks (SANs), which allowed for very efficient building and storing of infinitesimal generator of the CTMC that allowed to produce matrices of the models containing a distinct block structure. All of that allowed us to develop efficient numerical methods for a steady-state solution of CTMC models. This allowed us to accelerate CPU time, which is necessary to solve CTMC models, ~20 times. PMID:25705700

  20. High brightness electron accelerator

    DOEpatents

    Sheffield, Richard L.; Carlsten, Bruce E.; Young, Lloyd M.

    1994-01-01

    A compact high brightness linear accelerator is provided for use, e.g., in a free electron laser. The accelerator has a first plurality of acclerating cavities having end walls with four coupling slots for accelerating electrons to high velocities in the absence of quadrupole fields. A second plurality of cavities receives the high velocity electrons for further acceleration, where each of the second cavities has end walls with two coupling slots for acceleration in the absence of dipole fields. The accelerator also includes a first cavity with an extended length to provide for phase matching the electron beam along the accelerating cavities. A solenoid is provided about the photocathode that emits the electons, where the solenoid is configured to provide a substantially uniform magnetic field over the photocathode surface to minimize emittance of the electons as the electrons enter the first cavity.

  1. Acceleration in astrophysics

    SciTech Connect

    Colgate, S.A.

    1993-12-31

    The origin of cosmic rays and applicable laboratory experiments are discussed. Some of the problems of shock acceleration for the production of cosmic rays are discussed in the context of astrophysical conditions. These are: The presumed unique explanation of the power law spectrum is shown instead to be a universal property of all lossy accelerators; the extraordinary isotropy of cosmic rays and the limited diffusion distances implied by supernova induced shock acceleration requires a more frequent and space-filling source than supernovae; the near perfect adiabaticity of strong hydromagnetic turbulence necessary for reflecting the accelerated particles each doubling in energy roughly 10{sup 5} to {sup 6} scatterings with negligible energy loss seems most unlikely; the evidence for acceleration due to quasi-parallel heliosphere shocks is weak. There is small evidence for the expected strong hydromagnetic turbulence, and instead, only a small number of particles accelerate after only a few shock traversals; the acceleration of electrons in the same collisionless shock that accelerates ions is difficult to reconcile with the theoretical picture of strong hydromagnetic turbulence that reflects the ions. The hydromagnetic turbulence will appear adiabatic to the electrons at their much higher Larmor frequency and so the electrons should not be scattered incoherently as they must be for acceleration. Therefore the electrons must be accelerated by a different mechanism. This is unsatisfactory, because wherever electrons are accelerated these sites, observed in radio emission, may accelerate ions more favorably. The acceleration is coherent provided the reconnection is coherent, in which case the total flux, as for example of collimated radio sources, predicts single charge accelerated energies much greater than observed.

  2. High-fat Diet Accelerates Intestinal Tumorigenesis Through Disrupting Intestinal Cell Membrane Integrity

    PubMed Central

    Park, Mi-Young; Kim, Min Young; Seo, Young Rok; Kim, Jong-Sang; Sung, Mi-Kyung

    2016-01-01

    Background: Excess energy supply induces chronic low-grade inflammation in association with oxidative stress in various tissues including intestinal epithelium. The objective of this study was to investigate the effect of high-fat diet (HFD) on intestinal cell membrane integrity and intestinal tumorigenesis in ApcMin/+ mice. Methods: Mice were fed with either normal diet (ND) or HFD for 12 weeks. The number of intestinal tumors were counted and biomarkers of endotoxemia, oxidative stress, and inflammation were determined. Changes in intestinal integrity was measured by fluorescein isothiocyanate (FITC)-dextran penetration and membrane gap junction protein expression. Results: HFD group had significantly higher number of tumors compared to ND group (P < 0.05). Blood total antioxidant capacity was lower in HFD group, while colonic 8-hydroxy-2′-deoxyguanosine level, a marker of oxidative damage, was higher in HFD group compared to that of ND group (P < 0.05). The penetration of FITC-dextran was substantially increased in HFD group (P < 0.05) while the expressions of membrane gap junction proteins including zonula occludens-1, claudin-1, and occludin were lower in HFD group (P < 0.05) compared to those in ND group. Serum concentration of lipopolysaccharide (LPS) receptor (CD14) and colonic toll-like receptor 4 (a LPS receptor) mRNA expression were significantly higher in HFD group than in ND group (P < 0.05), suggesting that significant endotoxemia may occur in HFD group due to the increased membrane permeability. Serum interleukin-6 concentration and myeloperoxidase activity were also higher in HFD group compared to those of ND group (P < 0.05). Conclusions: HFD increases oxidative stress disrupting intestinal gap junction proteins, thereby accelerating membrane permeability endotoxemia, inflammation, and intestinal tumorigenesis. PMID:27390738

  3. Gap Filling in Road Extraction Using Radon Transformation

    NASA Astrophysics Data System (ADS)

    Matkan, A. A.; Hajeb, M.; Eslami, M.; Pourali, H.; Sadeghian, S.

    2012-07-01

    Road information has a key role in many applications such as transportation, automatic navigation, traffic management, crisis management, and also to facilitate and accelerate updating databases in a GIS. Therefore in the past two decades, automatic road extraction has become an important issue in remote sensing, photogrammetry and computer vision. An essential challenge in road extraction process is filling the gaps which have appeared due to getting placed under trees, tunnels or any other reason. Connection of roads is a momentous topological property that is necessity to perform most of the spatial analyses. Hence, Gap filling is an important post-process. The main aim of this paper is to provide a method which is applicable in road extraction algorithms to automatic fill the gaps. The proposed algorithm is based on Radon transformation and has four stags. In the first stage, detected road are thinned insofar as one pixel width is achieved. Then endpoints are detected. In the second stage, regarding to some constraints those endpoints which do not belong to any gaps are identified and deleted from endpoints list. In the third stage, the real gaps are found using the road direction computed by used of Radon technique. In fourth stage, the selected endpoints are connected together using Spline interpolation. This algorithm is applied on several datasets and also on a real detected road. The experimental results show that the proposed algorithm has good performance on straight roads but it does not work well in intersections, due to being direction-oriented.

  4. Plasma inverse transition acceleration

    SciTech Connect

    Xie, Ming

    2001-06-18

    It can be proved fundamentally from the reciprocity theorem with which the electromagnetism is endowed that corresponding to each spontaneous process of radiation by a charged particle there is an inverse process which defines a unique acceleration mechanism, from Cherenkov radiation to inverse Cherenkov acceleration (ICA) [1], from Smith-Purcell radiation to inverse Smith-Purcell acceleration (ISPA) [2], and from undulator radiation to inverse undulator acceleration (IUA) [3]. There is no exception. Yet, for nearly 30 years after each of the aforementioned inverse processes has been clarified for laser acceleration, inverse transition acceleration (ITA), despite speculation [4], has remained the least understood, and above all, no practical implementation of ITA has been found, until now. Unlike all its counterparts in which phase synchronism is established one way or the other such that a particle can continuously gain energy from an acceleration wave, the ITA to be discussed here, termed plasma inverse transition acceleration (PITA), operates under fundamentally different principle. As a result, the discovery of PITA has been delayed for decades, waiting for a conceptual breakthrough in accelerator physics: the principle of alternating gradient acceleration [5, 6, 7, 8, 9, 10]. In fact, PITA was invented [7, 8] as one of several realizations of the new principle.

  5. TE sub r azimuthal modes for a biconic transmission line in the small-gap limit

    SciTech Connect

    Johnson, W.A.; Mendel, C.W. Jr.; Seidel, D.B. )

    1992-04-15

    Azimuthally asymmetric modes in a biconic transmission line with a small-gap angle may be approximated by transmission-line-like'' modes. It is shown that the errors in these approximations are second order in the gap angle and approximate error bounds are provided. As an example demonstrating the application of this analysis in biconic structures, an analysis to characterize of the electromagnetic waves in the vacuum feed of the Particle Beam Fusion Accelerator II is provided.

  6. Explaining the gender wealth gap.

    PubMed

    Ruel, Erin; Hauser, Robert M

    2013-08-01

    To assess and explain the United States' gender wealth gap, we use the Wisconsin Longitudinal Study to examine wealth accumulated by a single cohort over 50 years by gender, by marital status, and limited to the respondents who are their family's best financial reporters. We find large gender wealth gaps between currently married men and women, and between never-married men and women. The never-married accumulate less wealth than the currently married, and there is a marital disruption cost to wealth accumulation. The status-attainment model shows the most power in explaining gender wealth gaps between these groups explaining about one-third to one-half of the gap, followed by the human-capital explanation. In other words, a lifetime of lower earnings for women translates into greatly reduced wealth accumulation. After controlling for the full model, we find that a gender wealth gap remains between married men and women that we speculate may be related to gender differences in investment strategies and selection effects. PMID:23264038

  7. Field induced gap infrared detector

    NASA Technical Reports Server (NTRS)

    Elliott, C. Thomas (Inventor)

    1990-01-01

    A tunable infrared detector which employs a vanishing band gap semimetal material provided with an induced band gap by a magnetic field to allow intrinsic semiconductor type infrared detection capabilities is disclosed. The semimetal material may thus operate as a semiconductor type detector with a wavelength sensitivity corresponding to the induced band gap in a preferred embodiment of a diode structure. Preferred semimetal materials include Hg(1-x)Cd(x)Te, x is less than 0.15, HgCdSe, BiSb, alpha-Sn, HgMgTe, HgMnTe, HgZnTe, HgMnSe, HgMgSe, and HgZnSe. The magnetic field induces a band gap in the semimetal material proportional to the strength of the magnetic field allowing tunable detection cutoff wavelengths. For an applied magnetic field from 5 to 10 tesla, the wavelength detection cutoff will be in the range of 20 to 50 micrometers for Hg(1-x)Cd(x)Te alloys with x about 0.15. A similar approach may also be employed to generate infrared energy in a desired band gap and then operating the structure in a light emitting diode or semiconductor laser type of configuration.

  8. The Dielectric Wall Accelerator

    SciTech Connect

    Caporaso, George J.; Chen, Yu-Jiuan; Sampayan, Stephen E.

    2009-01-01

    The Dielectric Wall Accelerator (DWA), a class of induction accelerators, employs a novel insulating beam tube to impress a longitudinal electric field on a bunch of charged particles. The surface flashover characteristics of this tube may permit the attainment of accelerating gradients on the order of 100 MV/m for accelerating pulses on the order of a nanosecond in duration. A virtual traveling wave of excitation along the tube is produced at any desired speed by controlling the timing of pulse generating modules that supply a tangential electric field to the tube wall. Because of the ability to control the speed of this virtual wave, the accelerator is capable of handling any charge to mass ratio particle; hence it can be used for electrons, protons and any ion. The accelerator architectures, key technologies and development challenges will be described.

  9. Accelerating molecular docking calculations using graphics processing units.

    PubMed

    Korb, Oliver; Stützle, Thomas; Exner, Thomas E

    2011-04-25

    The generation of molecular conformations and the evaluation of interaction potentials are common tasks in molecular modeling applications, particularly in protein-ligand or protein-protein docking programs. In this work, we present a GPU-accelerated approach capable of speeding up these tasks considerably. For the evaluation of interaction potentials in the context of rigid protein-protein docking, the GPU-accelerated approach reached speedup factors of up to over 50 compared to an optimized CPU-based implementation. Treating the ligand and donor groups in the protein binding site as flexible, speedup factors of up to 16 can be observed in the evaluation of protein-ligand interaction potentials. Additionally, we introduce a parallel version of our protein-ligand docking algorithm PLANTS that can take advantage of this GPU-accelerated scoring function evaluation. We compared the GPU-accelerated parallel version to the same algorithm running on the CPU and also to the highly optimized sequential CPU-based version. In terms of dependence of the ligand size and the number of rotatable bonds, speedup factors of up to 10 and 7, respectively, can be observed. Finally, a fitness landscape analysis in the context of rigid protein-protein docking was performed. Using a systematic grid-based search methodology, the GPU-accelerated version outperformed the CPU-based version with speedup factors of up to 60. PMID:21434638

  10. Role of GapC in the pathogenesis of Staphylococcus aureus.

    PubMed

    Kerro-Dego, Oudessa; Prysliak, Tracy; Perez-Casal, Jose; Potter, Andrew A

    2012-05-01

    Staphylococcus aureus is recognized worldwide as a major pathogen causing clinical or subclinical intramammary infections in lactating cows, sheep and goats. S. aureus produces a wide arsenal of cell surface and extracellular proteins involved in virulence. Among these are two conserved proteins with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity named glyceraldehyde-3-phosphate dehydrogenase-B (GapB) and -C (GapC). In this study, we used the S. aureus wild type strain RN6390 and its isogenic gapC mutant H330 in in vitro and in vivo studies and determined that the S. aureus GapC protein plays a role on adherence to and internalization into bovine mammary epithelial (MAC-T) cells. In addition, we found that S. aureus H330 did not caused mastitis after an experimental infection of ovine mammary glands. Together, these results show that GapC is important in the pathogenesis of S. aureus mastitis. PMID:22176759

  11. Fermilab tevatron high level RF accelerating systems

    SciTech Connect

    Kerns, Q.; Kerns, C.; Miller, H.; Reid, J.; Tawzer, S.; Webber, R.; Wildman, D.

    1985-10-01

    Eight tuned rf cavities have been installed and operated in the F0 straight section of the Tevatron. Their mechanical placement along the beam line enables them to be operated for colliding beams as two independent groups of four cavities, group 1-4 accelerating antiprotons and group 5-8 accelerating protons. The only difference is that the spacing between cavities 4 and 5 was increased to stay clear of the F0 colliding point. The cavities can easily be rephased by switching cables in a low-level distribution system (fan-out) so that the full accelerating capability of all eight cavities can be used during fixed target operations. Likewise, the cables from capacitive probes on each cavity gap can be switched to proper lengths and summed in a fan-back system to give an rf signal representing the amplitude and phase as ''seen by the beam,'' separately for protons and antiprotons. Such signals have been used to phase lock the Tevatron to the Main Ring for synchronous transfer. A cavity consists of two quarter-wave resonators placed back to back with a coaxial drift tube separating the two accelerating gaps by ..pi.. radians. The cavities are very similar to the prototype which has been previously described/sup 3/ and is operating as Station 8 in the Tevatron. Only additional water cooling around the high current region of the drift tube supports and a double loop used to monitor the unbalance current through the Hipernom mode damping resistor have been added. Each cavity has a Q of about7100, a shunt impedance of 1.2 M..cap omega.., and is capable of running cw with a peak accelerating voltage of 360

  12. ACCELERATION RESPONSIVE SWITCH

    DOEpatents

    Chabrek, A.F.; Maxwell, R.L.

    1963-07-01

    An acceleration-responsive device with dual channel capabilities whereby a first circuit is actuated upon attainment of a predetermined maximum acceleration level and when the acceleration drops to a predetermined minimum acceleriltion level another circuit is actuated is described. A fluid-damped sensing mass slidably mounted in a relatively frictionless manner on a shaft through the intermediation of a ball bushing and biased by an adjustable compression spring provides inertially operated means for actuating the circuits. (AEC)

  13. Space Acceleration Measurement System

    NASA Technical Reports Server (NTRS)

    1993-01-01

    This training video, presented by the Lewis Research Center's Space Experiments Division, gives a background and detailed instructions for preparing the space acceleration measurement system (SAMS) for use. The SAMS measures, conditions, and records forces of low gravity accelerations, and is used to determine the effect of these forces on various experiments performed in microgravity. Inertial sensors are used to measure positive and negative acceleration over a specified frequency range. The video documents the SAMS' uses in different configurations during shuttle missions.

  14. Wake field accelerators

    SciTech Connect

    Wilson, P.B.

    1986-02-01

    In a wake field accelerator a high current driving bunch injected into a structure or plasma produces intense induced fields, which are in turn used to accelerate a trailing charge or bunch. The basic concepts of wake field acceleration are described. Wake potentials for closed cavities and periodic structures are derived, as are wake potentials on a collinear path with a charge distribution. Cylindrically symmetric structures excited by a beam in the form of a ring are considered. (LEW)

  15. Accelerating into the future

    NASA Astrophysics Data System (ADS)

    Murray, Cherry

    2009-05-01

    Accelerator science has traditionally been associated with high-energy physics and nuclear physics. But the use of accelerators in other areas of science, as well as in medicine and industry, is steadily growing. Accelerators are now, for example, used to treat cancer using proton therapy, which can deposit radiation onto a tumour while causing much less damage to surrounding healthy tissue than with other treatment techniques.

  16. Optically pulsed electron accelerator

    DOEpatents

    Fraser, J.S.; Sheffield, R.L.

    1985-05-20

    An optically pulsed electron accelerator can be used as an injector for a free electron laser and comprises a pulsed light source, such as a laser, for providing discrete incident light pulses. A photoemissive electron source emits electron bursts having the same duration as the incident light pulses when impinged upon by same. The photoemissive electron source is located on an inside wall of a radiofrequency-powered accelerator cell which accelerates the electron burst emitted by the photoemissive electron source.

  17. Optically pulsed electron accelerator

    DOEpatents

    Fraser, John S.; Sheffield, Richard L.

    1987-01-01

    An optically pulsed electron accelerator can be used as an injector for a free electron laser and comprises a pulsed light source, such as a laser, for providing discrete incident light pulses. A photoemissive electron source emits electron bursts having the same duration as the incident light pulses when impinged upon by same. The photoemissive electron source is located on an inside wall of a radio frequency powered accelerator cell which accelerates the electron burst emitted by the photoemissive electron source.

  18. Miniaturization Techniques for Accelerators

    SciTech Connect

    Spencer, James E.

    2003-05-27

    The possibility of laser driven accelerators [1] suggests the need for new structures based on micromachining and integrated circuit technology because of the comparable scales. Thus, we are exploring fully integrated structures including sources, optics (for both light and particle) and acceleration in a common format--an accelerator-on-chip (AOC). Tests suggest a number of preferred materials and techniques but no technical or fundamental roadblocks at scales of order 1 {micro}m or larger.

  19. RhoGAPs and Rho GTPases in platelets.

    PubMed

    Elvers, Margitta

    2016-08-01

    Platelet cytoskeletal reorganization is essential for platelet adhesion and thrombus formation in hemostasis and thrombosis. The Rho GTPases RhoA, Rac1 and Cdc42 are the main players in cytoskeletal dynamics of platelets responsible for the formation of filopodia and lamellipodia to strongly increase the platelet surface upon activation. They are involved in platelet activation and aggregate formation including platelet secretion, integrin activation and arterial thrombus formation. The activity of Rho GTPases is tightly controlled by different proteins such as GTPase-activating proteins (GAPs). GAPs stimulate GTP hydrolysis to terminate Rho signaling. The role and impact of GAPs in platelets is not well-defined and many of the RhoGAPs identified are not known to be present in platelets or to have any function in platelets. The recently identified RhoGAPs Oligophrenin1 (OPHN1) and Nadrin regulate the activity of RhoA, Rac1 and Cdc42 and subsequent platelet cytoskeletal reorganization, platelet activation and thrombus formation. In the last years, the analysis of genetically modified mice helped to gain the understanding of Rho GTPases and their regulators in cytoskeletal rearrangements and other Rho mediated cellular processes in platelets. PMID:25639730

  20. ABORT GAP CLEANING IN RHIC.

    SciTech Connect

    DREES,A.; AHRENS,L.; III FLILLER,R.; GASSNER,D.; MCINTYRE,G.T.; MICHNOFF,R.; TRBOJEVIC,D.

    2002-06-03

    During the RHIC Au-run in 2001 the 200 MHz storage cavity system was used for the first time. The rebucketing procedure caused significant beam debunching in addition to amplifying debunching due to other mechanisms. At the end of a four hour store, debunched beam could account for approximately 30%-40% of the total beam intensity. Some of it will be in the abort gap. In order to minimize the risk of magnet quenching due to uncontrolled beam losses at the time of a beam dump, a combination of a fast transverse kicker and copper collimators were used to clean the abort gap. This report gives an overview of the gap cleaning procedure and the achieved performance.

  1. Particle acceleration in flares

    NASA Technical Reports Server (NTRS)

    Benz, Arnold O.; Kosugi, Takeo; Aschwanden, Markus J.; Benka, Steve G.; Chupp, Edward L.; Enome, Shinzo; Garcia, Howard; Holman, Gordon D.; Kurt, Victoria G.; Sakao, Taro

    1994-01-01

    Particle acceleration is intrinsic to the primary energy release in the impulsive phase of solar flares, and we cannot understand flares without understanding acceleration. New observations in soft and hard X-rays, gamma-rays and coherent radio emissions are presented, suggesting flare fragmentation in time and space. X-ray and radio measurements exhibit at least five different time scales in flares. In addition, some new observations of delayed acceleration signatures are also presented. The theory of acceleration by parallel electric fields is used to model the spectral shape and evolution of hard X-rays. The possibility of the appearance of double layers is further investigated.

  2. Charged particle accelerator grating

    DOEpatents

    Palmer, Robert B.

    1986-09-02

    A readily disposable and replaceable accelerator grating for a relativistic particle accelerator. The grating is formed for a plurality of liquid droplets that are directed in precisely positioned jet streams to periodically dispose rows of droplets along the borders of a predetermined particle beam path. A plurality of lasers are used to direct laser beams into the droplets, at predetermined angles, thereby to excite the droplets to support electromagnetic accelerating resonances on their surfaces. Those resonances operate to accelerate and focus particles moving along the beam path. As the droplets are distorted or destroyed by the incoming radiation, they are replaced at a predetermined frequency by other droplets supplied through the jet streams.

  3. Accelerator-based BNCT.

    PubMed

    Kreiner, A J; Baldo, M; Bergueiro, J R; Cartelli, D; Castell, W; Thatar Vento, V; Gomez Asoia, J; Mercuri, D; Padulo, J; Suarez Sandin, J C; Erhardt, J; Kesque, J M; Valda, A A; Debray, M E; Somacal, H R; Igarzabal, M; Minsky, D M; Herrera, M S; Capoulat, M E; Gonzalez, S J; del Grosso, M F; Gagetti, L; Suarez Anzorena, M; Gun, M; Carranza, O

    2014-06-01

    The activity in accelerator development for accelerator-based BNCT (AB-BNCT) both worldwide and in Argentina is described. Projects in Russia, UK, Italy, Japan, Israel, and Argentina to develop AB-BNCT around different types of accelerators are briefly presented. In particular, the present status and recent progress of the Argentine project will be reviewed. The topics will cover: intense ion sources, accelerator tubes, transport of intense beams, beam diagnostics, the (9)Be(d,n) reaction as a possible neutron source, Beam Shaping Assemblies (BSA), a treatment room, and treatment planning in realistic cases. PMID:24365468

  4. Acceleration of polarized protons in circular accelerators

    SciTech Connect

    Courant, E.D.; Ruth, R.D.

    1980-09-12

    The theory of depolarization in circular accelerators is presented. The spin equation is first expressed in terms of the particle orbit and then converted to the equivalent spinor equation. The spinor equation is then solved for three different situations: (1) a beam on a flat top near a resonance, (2) uniform acceleration through an isolated resonance, and (3) a model of a fast resonance jump. Finally, the depolarization coefficient, epsilon, is calculated in terms of properties of the particle orbit and the results are applied to a calculation of depolarization in the AGS.

  5. Want to Close the Achievement Gap? Close the Teaching Gap

    ERIC Educational Resources Information Center

    Darling-Hammond, Linda

    2015-01-01

    For years now, educators have looked to international tests as a yardstick to measure how well students from the United States are learning compared with their peers. The answer has been: not so well. The United States has been falling further behind other nations and has struggled with a large achievement gap. Federal policy under No Child Left…

  6. Minority Gaps Smaller in Some Pentagon Schools. The Achievement Gap.

    ERIC Educational Resources Information Center

    Viadero, Debra

    2000-01-01

    This third in a four-part series on why academic achievement gaps exist explains how U.S. Department of Defense schools for children of military families offer lessons on how to raise academic achievement among minority students. Minority students in these schools do better than their counterparts almost anywhere in the United States on…

  7. Folk Belief Theory, the Rigor Gap, and the Achievement Gap

    ERIC Educational Resources Information Center

    Torff, Bruce

    2014-01-01

    Folk belief theory is suggested as a primary cause for the persistence of the achievement gap. In this research-supported theory, culturally specified folk beliefs about learning and teaching prompt educators to direct more rigorous curriculum to high-advantage students but not to low-advantage students, resulting in impoverished pedagogy in…

  8. Advanced simulation study on bunch gap transient effect

    NASA Astrophysics Data System (ADS)

    Kobayashi, Tetsuya; Akai, Kazunori

    2016-06-01

    Bunch phase shift along the train due to a bunch gap transient is a concern in high-current colliders. In KEKB operation, the measured phase shift along the train agreed well with a simulation and a simple analytical form in most part of the train. However, a rapid phase change was observed at the leading part of the train, which was not predicted by the simulation or by the analytical form. In order to understand the cause of this observation, we have developed an advanced simulation, which treats the transient loading in each of the cavities of the three-cavity system of the accelerator resonantly coupled with energy storage (ARES) instead of the equivalent single cavities used in the previous simulation, operating in the accelerating mode. In this paper, we show that the new simulation reproduces the observation, and clarify that the rapid phase change at the leading part of the train is caused by a transient loading in the three-cavity system of ARES. KEKB is being upgraded to SuperKEKB, which is aiming at 40 times higher luminosity than KEKB. The gap transient in SuperKEKB is investigated using the new simulation, and the result shows that the rapid phase change at the leading part of the train is much larger due to higher beam currents. We will also present measures to mitigate possible luminosity reduction or beam performance deterioration due to the rapid phase change caused by the gap transient.

  9. Advanced Accelerating Structures and Their Interaction with Electron Beams

    SciTech Connect

    Gai Wei

    2009-01-22

    In this paper, we give a brief description of several advanced accelerating structures, such as dielectric loaded waveguides, photonic band gap, metamaterials and improved iris-loaded cavities. We describe wakefields generated by passing high current electron beams through these structures, and applications of wakefields to advanced accelerator schemes. One of the keys to success for high gradient wakefield acceleration is to develop high current drive beam sources. As an example, the high current RF photo injector at the Argonne Wakefield Accelerator, passed a {approx}80 nC electron beam through a high gradient dielectric loaded structure to achieve a 100 MV/m gradient. We will summarize recent related experiments on beam-structure interactions and also discuss high current electron beam generation and propagation and their applications to wakefield acceleration.

  10. Advanced accelerating structures and their interaction with electron beams.

    SciTech Connect

    Gai, W.; High Energy Physics

    2008-01-01

    In this paper, we give a brief description of several advanced accelerating structures, such as dielectric loaded waveguides, photonic band gap, metamaterials and improved iris-loaded cavities. We describe wakefields generated by passing high current electron beams through these structures, and applications of wakefields to advanced accelerator schemes. One of the keys to success for high gradient wakefield acceleration is to develop high current drive beam sources. As an example, the high current RF photo injector at the Argonne Wakefield Accelerator, passed a {approx}80 nC electron beam through a high gradient dielectric loaded structure to achieve a 100 MV/m gradient. We will summarize recent related experiments on beam-structure interactions and also discuss high current electron beam generation and propagation and their applications to wakefield acceleration.

  11. Molecular and Behavioral Changes Associated with Adult Hippocampus-Specific SynGAP1 Knockout

    ERIC Educational Resources Information Center

    Muhia, Mary; Willadt, Silvia; Yee, Benjamin K.; Feldon, Joram; Paterna, Jean-Charles; Schwendener, Severin; Vogt, Kaspar; Kennedy, Mary B.; Knuesel, Irene

    2012-01-01

    The synaptic Ras/Rap-GTPase-activating protein (SynGAP1) plays a unique role in regulating specific downstream intracellular events in response to N-methyl-D-aspartate receptor (NMDAR) activation. Constitutive heterozygous loss of SynGAP1 disrupts NMDAR-mediated physiological and behavioral processes, but the disruptions might be of developmental…

  12. Longitudinal Bunch Position Control for the Super-B Accelerator

    SciTech Connect

    Bertsche, Kirk; Rivetta, Claudio; Sullivam, Michael K.; Drago, Alessandro; /Frascati

    2009-05-15

    The use of normal conducting cavities and an ion-clearing gap will cause a significant RF accelerating voltage gap transient and longitudinal phase shift of the individual bunches along the bunch train in both rings of the SuperB accelerator. Small relative centroid position shifts between bunches of the colliding beams will have a large adverse impact on the luminosity due to the small {beta}*{sub y} at the interaction point (IP). We investigate the possibility of minimizing the relative longitudinal position shift between bunches by reducing the gap transient in each ring and matching the longitudinal bunch positions of the two rings at the IP using feedback/feedforward techniques in the LLRF. The analysis is conducted assuming maximum use of the klystron power installed in the system.

  13. Scaling FFAG accelerator for muon acceleration

    SciTech Connect

    Lagrange, JB.; Planche, T.; Mori, Y.

    2011-10-06

    Recent developments in scaling fixed field alternating gradient (FFAG) accelerators have opened new ways for lattice design, with straight sections, and insertions like dispersion suppressors. Such principles and matching issues are detailed in this paper. An application of these new concepts is presented to overcome problems in the PRISM project.

  14. Angular velocities, angular accelerations, and coriolis accelerations

    NASA Technical Reports Server (NTRS)

    Graybiel, A.

    1975-01-01

    Weightlessness, rotating environment, and mathematical analysis of Coriolis acceleration is described for man's biological effective force environments. Effects on the vestibular system are summarized, including the end organs, functional neurology, and input-output relations. Ground-based studies in preparation for space missions are examined, including functional tests, provocative tests, adaptive capacity tests, simulation studies, and antimotion sickness.

  15. GAP JUNCTION FUNCTION AND CANCER

    EPA Science Inventory

    Gap Junctions (GJs) provide cell-to-cell communication (GJIC) of essential metabolites and ions. Js allow tissues to average responses, clear waste products, and minimize the effects of xenobiotics by dilution and allowing steady-state catabolism. any chemicals can adversely affe...

  16. The Racial Academic Achievement Gap

    ERIC Educational Resources Information Center

    Green, Toneka M.

    2008-01-01

    Closing the racial academic achievement gap is a problem that must be solved in order for future society to properly function. Minorities including African-American and Latino students' standardized test scores are much lower than white students. By the end of fourth grade, African American, Latino, and poor students of all races are two years…

  17. Gap Balanced Total Knee Arthroplasty

    MedlinePlus

    Gap Balanced Total Knee Arthroplasty – SIGMA® with AOX™ You must have Javascript enabled in your web browser. View Program Transcript Click Here to view the OR-Live, Inc. Privacy Policy and Legal Notice © 2010 OR-Live, Inc. All rights reserved.

  18. Literary Gaps Invite Creative Interaction.

    ERIC Educational Resources Information Center

    Watson, Jerry J.

    Literary gaps were identified by Wolfgang Iser in 1974 as "vacant pages" that invite the reader to reflect and enter into the text thereby motivating students to experience the text as reality. Arthur Applebee, in 1979, identified three categories to distinguish children's types of interaction with stories: (1) the complexity of literary and…

  19. Multiple input electrode gap controller

    DOEpatents

    Hysinger, C.L.; Beaman, J.J.; Melgaard, D.K.; Williamson, R.L.

    1999-07-27

    A method and apparatus for controlling vacuum arc remelting (VAR) furnaces by estimation of electrode gap based on a plurality of secondary estimates derived from furnace outputs. The estimation is preferably performed by Kalman filter. Adaptive gain techniques may be employed, as well as detection of process anomalies such as glows. 17 figs.

  20. Multiple input electrode gap controller

    DOEpatents

    Hysinger, Christopher L.; Beaman, Joseph J.; Melgaard, David K.; Williamson, Rodney L.

    1999-01-01

    A method and apparatus for controlling vacuum arc remelting (VAR) furnaces by estimation of electrode gap based on a plurality of secondary estimates derived from furnace outputs. The estimation is preferably performed by Kalman filter. Adaptive gain techniques may be employed, as well as detection of process anomalies such as glows.

  1. Brain Responses to Filled Gaps

    ERIC Educational Resources Information Center

    Hestvik, Arild; Maxfield, Nathan; Schwartz, Richard G.; Shafer, Valerie

    2007-01-01

    An unresolved issue in the study of sentence comprehension is whether the process of gap-filling is mediated by the construction of empty categories (traces), or whether the parser relates fillers directly to the associated verb's argument structure. We conducted an event-related potentials (ERP) study that used the violation paradigm to examine…

  2. The Culture Gap among Educators.

    ERIC Educational Resources Information Center

    Kilian, Crawford

    1996-01-01

    Addresses the cultural gap between teachers who are computer literate and those who are not. Highlights include traditional teaching methods; surface reasons for not using computers, including high cost, complexity, hostile interface, and rapid obsolescence; the opportunity for students to become independent lifelong learners with the Internet;…

  3. Large gap magnetic suspension system

    NASA Technical Reports Server (NTRS)

    Abdelsalam, Moustafa K.; Eyssa, Y. M.

    1991-01-01

    The design of a large gap magnetic suspension system is discussed. Some of the topics covered include: the system configuration, permanent magnet material, levitation magnet system, superconducting magnets, resistive magnets, superconducting levitation coils, resistive levitation coils, levitation magnet system, and the nitrogen cooled magnet system.

  4. Closing the Gaps. Research Brief

    ERIC Educational Resources Information Center

    Johnston, Howard

    2011-01-01

    Achievement gaps between groups of students (minority and white, rich and poor, English speakers and English language learners) are complex and intractable. Increasingly, they are being seen as a result of disparities between opportunities for learning available to different groups. By changing the opportunity structures of schools and…

  5. Closing the Teacher Quality Gap

    ERIC Educational Resources Information Center

    Haycock, Kati; Crawford, Candace

    2008-01-01

    Schools and districts rarely have a fair distribution of teacher talent. Poor children and black children are less likely to be taught by the strongest teachers and more likely to be taught by the weakest. Several districts have implemented programs to reduce the teacher quality gap. Hamilton County, Tennessee, launched an initiative that included…

  6. The Widening Income Achievement Gap

    ERIC Educational Resources Information Center

    Reardon, Sean F.

    2013-01-01

    Has the academic achievement gap between high-income and low-income students changed over the last few decades? If so, why? And what can schools do about it? Researcher Sean F. Reardon conducted a comprehensive analysis of research to answer these questions and came up with some striking findings. In this article, he shows that income-related…

  7. Accelerators (4/5)

    ScienceCinema

    None

    2011-10-06

    1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.

  8. J-PARC Accelerator

    SciTech Connect

    Yamazaki, Yoshishige

    2008-02-21

    The Japan Proton Accelerator Research Complex (J-PARC) is under construction in Tokai site. The linac beam commissioning started last fall, while the beam commissioning of the 3-GeV Rapid-Cycling Synchrotron (RCS) will start this fall. The status of the J-PARC accelerator is reported with emphasis on the technical development accomplished for the J-PARC.

  9. Particle Acceleration in Jets

    NASA Technical Reports Server (NTRS)

    Nishikawa, Ken-Ichi

    2005-01-01

    Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., active galactic nuclei (AGNs), gamma ray burst (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Fermi acceleration is the mechanism usually assumed for the acceleration of particles in astrophysical environments.

  10. Diagnostics for induction accelerators

    SciTech Connect

    Fessenden, T.J.

    1996-04-01

    The induction accelerator was conceived by N. C. Christofilos and first realized as the Astron accelerator that operated at LLNL from the early 1960`s to the end of 1975. This accelerator generated electron beams at energies near 6 MeV with typical currents of 600 Amperes in 400 ns pulses. The Advanced Test Accelerator (ATA) built at Livermore`s Site 300 produced 10,000 Ampere beams with pulse widths of 70 ns at energies approaching 50 MeV. Several other electron and ion induction accelerators have been fabricated at LLNL and LBNL. This paper reviews the principal diagnostics developed through efforts by scientists at both laboratories for measuring the current, position, energy, and emittance of beams generated by these high current, short pulse accelerators. Many of these diagnostics are closely related to those developed for other accelerators. However, the very fast and intense current pulses often require special diagnostic techniques and considerations. The physics and design of the more unique diagnostics developed for electron induction accelerators are presented and discussed in detail.

  11. Accelerators Beyond The Tevatron?

    SciTech Connect

    Lach, Joseph

    2010-07-01

    Following the successful operation of the Fermilab superconducting accelerator three new higher energy accelerators were planned. They were the UNK in the Soviet Union, the LHC in Europe, and the SSC in the United States. All were expected to start producing physics about 1995. They did not. Why?

  12. Microscale acceleration history discriminators

    DOEpatents

    Polosky, Marc A.; Plummer, David W.

    2002-01-01

    A new class of micromechanical acceleration history discriminators is claimed. These discriminators allow the precise differentiation of a wide range of acceleration-time histories, thereby allowing adaptive events to be triggered in response to the severity (or lack thereof) of an external environment. Such devices have applications in airbag activation, and other safety and surety applications.

  13. KEK digital accelerator

    NASA Astrophysics Data System (ADS)

    Iwashita, T.; Adachi, T.; Takayama, K.; Leo, K. W.; Arai, T.; Arakida, Y.; Hashimoto, M.; Kadokura, E.; Kawai, M.; Kawakubo, T.; Kubo, Tomio; Koyama, K.; Nakanishi, H.; Okazaki, K.; Okamura, K.; Someya, H.; Takagi, A.; Tokuchi, A.; Wake, M.

    2011-07-01

    The High Energy Accelerator Research Organization KEK digital accelerator (KEK-DA) is a renovation of the KEK 500 MeV booster proton synchrotron, which was shut down in 2006. The existing 40 MeV drift tube linac and rf cavities have been replaced by an electron cyclotron resonance (ECR) ion source embedded in a 200 kV high-voltage terminal and induction acceleration cells, respectively. A DA is, in principle, capable of accelerating any species of ion in all possible charge states. The KEK-DA is characterized by specific accelerator components such as a permanent magnet X-band ECR ion source, a low-energy transport line, an electrostatic injection kicker, an extraction septum magnet operated in air, combined-function main magnets, and an induction acceleration system. The induction acceleration method, integrating modern pulse power technology and state-of-art digital control, is crucial for the rapid-cycle KEK-DA. The key issues of beam dynamics associated with low-energy injection of heavy ions are beam loss caused by electron capture and stripping as results of the interaction with residual gas molecules and the closed orbit distortion resulting from relatively high remanent fields in the bending magnets. Attractive applications of this accelerator in materials and biological sciences are discussed.

  14. Accelerators (5/5)

    ScienceCinema

    None

    2011-10-06

    1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.

  15. Accelerating global forest mortality

    NASA Astrophysics Data System (ADS)

    McDowell, N. G.

    2014-12-01

    Forest mortality is apparently accelerating globally. The evidence supporting this contention is now substantial, as is the evidence suggesting the acceleration has just begun and will become progressively worse in upcoming decades. I will review the data and models used to make these contentions.

  16. Accelerators (3/5)

    ScienceCinema

    None

    2011-10-06

    1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.

  17. Accelerators, Beams And Physical Review Special Topics - Accelerators And Beams

    SciTech Connect

    Siemann, R.H.; /SLAC

    2011-10-24

    Accelerator science and technology have evolved as accelerators became larger and important to a broad range of science. Physical Review Special Topics - Accelerators and Beams was established to serve the accelerator community as a timely, widely circulated, international journal covering the full breadth of accelerators and beams. The history of the journal and the innovations associated with it are reviewed.

  18. Cascaded radiation pressure acceleration

    SciTech Connect

    Pei, Zhikun; Shen, Baifei E-mail: zhxm@siom.ac.cn; Zhang, Xiaomei E-mail: zhxm@siom.ac.cn; Wang, Wenpeng; Zhang, Lingang; Yi, Longqing; Shi, Yin; Xu, Zhizhan

    2015-07-15

    A cascaded radiation-pressure acceleration scheme is proposed. When an energetic proton beam is injected into an electrostatic field moving at light speed in a foil accelerated by light pressure, protons can be re-accelerated to much higher energy. An initial 3-GeV proton beam can be re-accelerated to 7 GeV while its energy spread is narrowed significantly, indicating a 4-GeV energy gain for one acceleration stage, as shown in one-dimensional simulations and analytical results. The validity of the method is further confirmed by two-dimensional simulations. This scheme provides a way to scale proton energy at the GeV level linearly with laser energy and is promising to obtain proton bunches at tens of gigaelectron-volts.

  19. Gaps"

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2013

    2013-01-01

    This study investigated the effect of daily quizzes on the performance of college students. Students in an introductory psychology course used their own wireless-enabled devices to take short Internet-based quizzes at the beginning of every class. The quiz items were drawn approximately equally from material covered in the readings and the…

  20. The Rho-GAP Bem2p plays a GAP-independent role in the morphogenesis checkpoint

    PubMed Central

    Marquitz, Aron R.; Harrison, Jacob C.; Bose, Indrani; Zyla, Trevin R.; McMillan, John N.; Lew, Daniel J.

    2002-01-01

    The Saccharomyces cerevisiae morphogenesis checkpoint delays mitosis in response to insults that impair actin organization and/or bud formation. The delay is due to accumulation of the inhibitory kinase Swe1p, which phosphorylates the cyclin-dependent kinase Cdc28p. Having screened through a panel of yeast mutants with defects in cell morphogenesis, we report here that the polarity establishment protein Bem2p is required for the checkpoint response. Bem2p is a Rho-GTPase activating protein (GAP) previously shown to act on Rho1p, and we now show that it also acts on Cdc42p, the GTPase primarily responsible for establishment of cell polarity in yeast. Whereas the morphogenesis role of Bem2p required GAP activity, the checkpoint role of Bem2p did not. Instead, this function required an N-terminal Bem2p domain. Thus, this single protein has a GAP-dependent role in promoting cell polarity and a GAP-independent role in responding to defects in cell polarity by enacting the checkpoint. Surprisingly, Swe1p accumulation occurred normally in bem2 cells, but they were nevertheless unable to promote Cdc28p phosphorylation. Therefore, Bem2p defines a novel pathway in the morphogenesis checkpoint. PMID:12145202

  1. Accelerated luminophore discovery through combinatorial synthesis.

    PubMed

    Lowry, Michael S; Hudson, William R; Pascal, Robert A; Bernhard, Stefan

    2004-11-01

    A method for accelerating the discovery of ionic luminophores using combinatorial techniques is reported. The photophysical properties of the resulting transition-metal-based chromophores were compared against a series of analogous, traditionally prepared species. The strong overlap between these two sets confirms the identity of the parallel synthesis products and supports the truthfulness of the combinatorial results. Further support for the combinatorial method comes from the adherence of these complexes to the energy gap law. The relationship between the structure of a complex and its photophysical properties was also considered, and static DFT calculations were used to assess whether it is feasible to predict the luminescent behavior of novel materials. PMID:15506778

  2. Radio frequency focused interdigital linear accelerator

    DOEpatents

    Swenson, Donald A.; Starling, W. Joel

    2006-08-29

    An interdigital (Wideroe) linear accelerator employing drift tubes, and associated support stems that couple to both the longitudinal and support stem electromagnetic fields of the linac, creating rf quadrupole fields along the axis of the linac to provide transverse focusing for the particle beam. Each drift tube comprises two separate electrodes operating at different electrical potentials as determined by cavity rf fields. Each electrode supports two fingers, pointing towards the opposite end of the drift tube, forming a four-finger geometry that produces an rf quadrupole field distribution along its axis. The fundamental periodicity of the structure is equal to one half of the particle wavelength .beta..lamda., where .beta. is the particle velocity in units of the velocity of light and .lamda. is the free space wavelength of the rf. Particles are accelerated in the gaps between drift tubes. The particle beam is focused in regions inside the drift tubes.

  3. Analyzing radial acceleration with a smartphone acceleration sensor

    NASA Astrophysics Data System (ADS)

    Vogt, Patrik; Kuhn, Jochen

    2013-03-01

    This paper continues the sequence of experiments using the acceleration sensor of smartphones (for description of the function and the use of the acceleration sensor, see Ref. 1) within this column, in this case for analyzing the radial acceleration.

  4. The (Non-)Existence of Gapping in Chinese and Its Implications for the Theory of Gapping.

    ERIC Educational Resources Information Center

    Tang, Sze-Wing

    2001-01-01

    Shows that there are at least two types of gapping in natural languages: canonical gapping and LPD. Argues that Chinese has some gapping sentences that result from ATB movement from V to "v." Data from Chinese affirm Johnson's (1994) theory of gapping that gapping occurs in those languages only with verb movement. (Author/VWL)

  5. Emplacement Gantry Gap Analysis Study

    SciTech Connect

    R. Thornley

    2005-05-27

    To date, the project has established important to safety (ITS) performance requirements for structures, systems, and components (SSCs) based on the identification and categorization of event sequences that may result in a radiological release. These performance requirements are defined within the ''Nuclear Safety Design Bases for License Application'' (NSDB) (BSC 2005 [DIRS 171512], Table A-11). Further, SSCs credited with performing safety functions are classified as ITS. In turn, assurance that these SSCs will perform as required is sought through the use of consensus codes and standards. This gap analysis is based on the design completed for license application only. Accordingly, identification of ITS SSCs beyond those defined within the NSDB are based on designs that may be subject to further development during detail design. Furthermore, several design alternatives may still be under consideration to satisfy certain safety functions, and final selection will not be determined until further design development has occurred. Therefore, for completeness, alternative designs currently under consideration will be discussed throughout this study. This gap analysis will evaluate each code and standard identified within the ''Emplacement Gantry ITS Standards Identification Study'' (BSC 2005 [DIRS 173586]) to ensure each ITS performance requirement is fully satisfied. When a performance requirement is not fully satisfied, a gap is highlighted. This study will identify requirements to supplement or augment the code or standard to meet performance requirements. Further, this gap analysis will identify nonstandard areas of the design that will be subject to a design development plan. Nonstandard components and nonstandard design configurations are defined as areas of the design that do not follow standard industry practices or codes and standards. Whereby, assurance that an SSC will perform as required may not be readily sought though the use of consensus standards. This

  6. Gap Test Calibrations and Their Scaling

    NASA Astrophysics Data System (ADS)

    Sandusky, Harold

    2011-06-01

    Common tests for measuring the threshold for shock initiation are the NOL large scale gap test (LSGT) with a 50.8-mm diameter donor/gap and the expanded large scale gap test (ELSGT) with a 95.3-mm diameter donor/gap. Despite the same specifications for the explosive donor and polymethyl methacrylate (PMMA) gap in both tests, calibration of shock pressure in the gap versus distance from the donor scales by a factor of 1.75, not the 1.875 difference in their sizes. Recently reported model calculations suggest that the scaling discrepancy results from the viscoelastic properties of PMMA in combination with different methods for obtaining shock pressure. This is supported by the consistent scaling of these donors when calibrated in water-filled aquariums. Calibrations with water gaps will be provided and compared with PMMA gaps. Scaling for other donor systems will also be provided. Shock initiation data with water gaps will be reviewed.

  7. Air Gap Effects in LX-17

    SciTech Connect

    Souers, P C; Ault, S; Avara, R; Bahl, K L; Boat, R; Cunningham, B; Gidding, D; Janzen, J; Kuklo, D; Lee, R; Lauderbach, L; Weingart, W C; Wu, B; Winer, K

    2005-09-26

    Three experiments done over twenty years on gaps in LX-17 are reported. For the detonation front moving parallel to the gaps, jets of gas products were seen coming from the gaps at velocities greater than the detonation velocity. A case can be made that the jet velocity increased with gap thickness but the data is scattered. For the detonation front moving transverse to the gap, time delays were seen. The delays roughly increase with gap width, going from 0-70 ns at 'zero gap' to around 300 ns at 0.5-1 mm gap. Larger gaps of up to 6 mm width almost certainly stopped the detonation, but this was not proved. Real-time resolution of the parallel jets and determination of the actual re-detonation or failure in the transverse case needs to be done in future experiments.

  8. Vacuum system for Advanced Test Accelerator

    SciTech Connect

    Denhoy, B.S.

    1981-09-03

    The Advanced Test Accelerator (ATA) is a pulsed linear electron beam accelerator designed to study charged particle beam propagation. ATA is designed to produce a 10,000 amp 50 MeV, 70 ns electron beam. The electron beam acceleration is accomplished in ferrite loaded cells. Each cell is capable of maintaining a 70 ns 250 kV voltage pulse across a 1 inch gap. The electron beam is contained in a 5 inch diameter, 300 foot long tube. Cryopumps turbomolecular pumps, and mechanical pumps are used to maintain a base pressure of 2 x 10/sup -6/ torr in the beam tube. The accelerator will be installed in an underground tunnel. Due to the radiation environment in the tunnel, the controlling and monitoring of the vacuum equipment, pressures and temperatures will be done from the control room through a computer interface. This paper describes the vacuum system design, the type of vacuum pumps specified, the reasons behind the selection of the pumps and the techniques used for computer interfacing.

  9. Ion beam accelerator system

    NASA Technical Reports Server (NTRS)

    Aston, Graeme (Inventor)

    1984-01-01

    A system is described that combines geometrical and electrostatic focusing to provide high ion extraction efficiency and good focusing of an accelerated ion beam. The apparatus includes a pair of curved extraction grids (16, 18) with multiple pairs of aligned holes positioned to direct a group of beamlets (20) along converging paths. The extraction grids are closely spaced and maintained at a moderate potential to efficiently extract beamlets of ions and allow them to combine into a single beam (14). An accelerator electrode device (22) downstream from the extraction grids, is at a much lower potential than the grids to accelerate the combined beam.

  10. Ion beam accelerator system

    NASA Technical Reports Server (NTRS)

    Aston, G. (Inventor)

    1981-01-01

    A system is described that combines geometrical and electrostatic focusing to provide high ion extraction efficiency and good focusing of an accelerated ion beam. The apparatus includes a pair of curved extraction grids with multiple pairs of aligned holes positioned to direct a group of beamlets along converging paths. The extraction grids are closely spaced and maintained at a moderate potential to efficiently extract beamlets of ions and allow them to combine into a single beam. An accelerator electrode device downstream from the extraction grids is at a much lower potential than the grids to accelerate the combined beam. The application of the system to ion implantation is mentioned.

  11. The MESA accelerator

    SciTech Connect

    Aulenbacher, Kurt

    2013-11-07

    The MESA accelerator will operate for particle and nuclear physics experiments in two different modes. A first option is conventional c.w. acceleration yielding 150-200MeV spin-polarized external beam. Second, MESA will be operated as a superconducting multi-turn energy recovery linac (ERL), opening the opportunity to perform experiments with a windowless target with beam current of up to 10 mA. The perspectives for innovative experiments with such a machine are discussed together with a sketch of the accelerator physics issues that have to be solved.

  12. Accelerator Toolbox for MATLAB

    SciTech Connect

    Terebilo, Andrei

    2001-05-29

    This paper introduces Accelerator Toolbox (AT)--a collection of tools to model particle accelerators and beam transport lines in the MATLAB environment. At SSRL, it has become the modeling code of choice for the ongoing design and future operation of the SPEAR 3 synchrotron light source. AT was designed to take advantage of power and simplicity of MATLAB--commercially developed environment for technical computing and visualization. Many examples in this paper illustrate the advantages of the AT approach and contrast it with existing accelerator code frameworks.

  13. Twisted waveguide accelerating structure.

    SciTech Connect

    Kang, Y. W.

    2000-08-15

    A hollow waveguide with a uniform cross section may be used for accelerating charged particles if the phase velocity of an accelerating mode is equal to or less than the free space speed of light. Regular straight hollow waveguides have phase velocities of propagating electromagnetic waves greater than the free-space speed of light. if the waveguide is twisted, the phase velocities of the waveguide modes become slower. The twisted waveguide structure has been modeled and computer simulated in 3-D electromagnetic solvers to show the slow-wave properties for the accelerating mode.

  14. Roles of gap junctions, connexins, and pannexins in epilepsy

    PubMed Central

    Mylvaganam, Shanthini; Ramani, Meera; Krawczyk, Michal; Carlen, Peter L.

    2014-01-01

    Enhanced gap junctional communication (GJC) between neurons is considered a major factor underlying the neuronal synchrony driving seizure activity. In addition, the hippocampal sharp wave ripple complexes, associated with learning and seizures, are diminished by GJC blocking agents. Although gap junctional blocking drugs inhibit experimental seizures, they all have other non-specific actions. Besides interneuronal GJC between dendrites, inter-axonal and inter-glial GJC is also considered important for seizure generation. Interestingly, in most studies of cerebral tissue from animal seizure models and from human patients with epilepsy, there is up-regulation of glial, but not neuronal gap junctional mRNA and protein. Significant changes in the expression and post-translational modification of the astrocytic connexin Cx43, and Panx1 were observed in an in vitro Co++ seizure model, further supporting a role for glia in seizure-genesis, although the reasons for this remain unclear. Further suggesting an involvement of astrocytic GJC in epilepsy, is the fact that the expression of astrocytic Cx mRNAs (Cxs 30 and 43) is several fold higher than that of neuronal Cx mRNAs (Cxs 36 and 45), and the number of glial cells outnumber neuronal cells in mammalian hippocampal and cortical tissue. Pannexin expression is also increased in both animal and human epileptic tissues. Specific Cx43 mimetic peptides, Gap 27 and SLS, inhibit the docking of astrocytic connexin Cx43 proteins from forming intercellular gap junctions (GJs), diminishing spontaneous seizures. Besides GJs, Cx membrane hemichannels in glia and Panx membrane channels in neurons and glia are also inhibited by traditional gap junctional pharmacological blockers. Although there is no doubt that connexin-based GJs and hemichannels, and pannexin-based membrane channels are related to epilepsy, the specific details of how they are involved and how we can modulate their function for therapeutic purposes remain to be

  15. Electronic gap sensor and method

    DOEpatents

    Williams, Robert S.; King, Edward L.; Campbell, Steven L.

    1991-01-01

    An apparatus and method for regulating the gap between a casting nozzle and a casting wheel in which the gap between the casting nozzle and the casting wheel is monitored by means of at least one sensing element protruding from the face of the casting nozzle. The sensing element is preferably connected to a voltage source and the casting wheel grounded. When the sensing element contacts the casting wheel, an electric circuit is completed. The completion of the circuit can be registered by an indicator, and the presence or absence of a completed circuit indicates the relative position of the casting nozzle to the casting wheel. The relative positions of the casting nozzle and casting wheel can thereby be selectively adjusted to continually maintain a predetermined distance between their adjacent surfaces.

  16. Gap junctions as electrical synapses.

    PubMed

    Bennett, M V

    1997-06-01

    Gap junctions are the morphological substrate of one class of electrical synapse. The history of the debate on electrical vs. chemical transmission is instructive. One lesson is that Occam's razor sometimes cuts too deep; the nervous system does its operations in a number of different ways and a unitarian approach can lead one astray. Electrical synapses can do many things that chemical synapses can do, and do them just as slowly. More intriguing are the modulatory actions that chemical synapses can have on electrical synapses. Voltage dependence provides an important window on structure function relations of the connexins, even where the dependence may have no physiological role. The new molecular approaches will greatly advance our knowledge of where gap junctions occur and permit experimental manipulation with high specificity. PMID:9278865

  17. Interplay between phosphorylation and palmitoylation mediates plasma membrane targeting and sorting of GAP43

    PubMed Central

    Gauthier-Kemper, Anne; Igaev, Maxim; Sündermann, Frederik; Janning, Dennis; Brühmann, Jörg; Moschner, Katharina; Reyher, Hans-Jürgen; Junge, Wolfgang; Glebov, Konstantin; Walter, Jochen; Bakota, Lidia; Brandt, Roland

    2014-01-01

    Phosphorylation and lipidation provide posttranslational mechanisms that contribute to the distribution of cytosolic proteins in growing nerve cells. The growth-associated protein GAP43 is susceptible to both phosphorylation and S-palmitoylation and is enriched in the tips of extending neurites. However, how phosphorylation and lipidation interplay to mediate sorting of GAP43 is unclear. Using a combination of biochemical, genetic, and imaging approaches, we show that palmitoylation is required for membrane association and that phosphorylation at Ser-41 directs palmitoylated GAP43 to the plasma membrane. Plasma membrane association decreased the diffusion constant fourfold in neuritic shafts. Sorting to the neuritic tip required palmitoylation and active transport and was increased by phosphorylation-mediated plasma membrane interaction. Vesicle tracking revealed transient association of a fraction of GAP43 with exocytic vesicles and motion at a fast axonal transport rate. Simulations confirmed that a combination of diffusion, dynamic plasma membrane interaction and active transport of a small fraction of GAP43 suffices for efficient sorting to growth cones. Our data demonstrate a complex interplay between phosphorylation and lipidation in mediating the localization of GAP43 in neuronal cells. Palmitoylation tags GAP43 for global sorting by piggybacking on exocytic vesicles, whereas phosphorylation locally regulates protein mobility and plasma membrane targeting of palmitoylated GAP43. PMID:25165142

  18. Psoriasis Trends and Practice Gaps.

    PubMed

    Gottlieb, Alice B; Greb, Jacqueline E; Goldminz, Ari M

    2016-07-01

    The present article addresses several high-impact practice gaps affecting psoriatic patients, current practices, the barriers that prevent the delivery of optimal care, and recommendations to improve patient outcomes. Discussions of treatment, cardiovascular risk factor screening, psoriatic arthritis screening, and biologics are included. Finally, an overview of current resident exposure to psoriatic care and recommendations for improvements in resident education are made. PMID:27363878

  19. Randomized gap and amplitude estimation

    NASA Astrophysics Data System (ADS)

    Zintchenko, Ilia; Wiebe, Nathan

    2016-06-01

    We provide a method for estimating spectral gaps in low-dimensional systems. Unlike traditional phase estimation, our approach does not require ancillary qubits nor does it require well-characterized gates. Instead, it only requires the ability to perform approximate Haar random unitary operations, applying the unitary whose eigenspectrum is sought and performing measurements in the computational basis. We discuss application of these ideas to in-place amplitude estimation and quantum device calibration.

  20. A contoured gap coaxial plasma gun with injected plasma armature

    NASA Astrophysics Data System (ADS)

    Witherspoon, F. Douglas; Case, Andrew; Messer, Sarah J.; Bomgardner, Richard; Phillips, Michael W.; Brockington, Samuel; Elton, Raymond

    2009-08-01

    A new coaxial plasma gun is described. The long term objective is to accelerate 100-200 μg of plasma with density above 1017 cm-3 to greater than 200 km/s with a Mach number above 10. Such high velocity dense plasma jets have a number of potential fusion applications, including plasma refueling, magnetized target fusion, injection of angular momentum into centrifugally confined mirrors, high energy density plasmas, and others. The approach uses symmetric injection of high density plasma into a coaxial electromagnetic accelerator having an annular gap geometry tailored to prevent formation of the blow-by instability. The injected plasma is generated by numerous (currently 32) radially oriented capillary discharges arranged uniformly around the circumference of the angled annular injection region of the accelerator. Magnetohydrodynamic modeling identified electrode profiles that can achieve the desired plasma jet parameters. The experimental hardware is described along with initial experimental results in which approximately 200 μg has been accelerated to 100 km/s in a half-scale prototype gun. Initial observations of 64 merging injector jets in a planar cylindrical testing array are presented. Density and velocity are presently limited by available peak current and injection sources. Steps to increase both the drive current and the injected plasma mass are described for next generation experiments.

  1. A contoured gap coaxial plasma gun with injected plasma armature.

    PubMed

    Witherspoon, F Douglas; Case, Andrew; Messer, Sarah J; Bomgardner, Richard; Phillips, Michael W; Brockington, Samuel; Elton, Raymond

    2009-08-01

    A new coaxial plasma gun is described. The long term objective is to accelerate 100-200 microg of plasma with density above 10(17) cm(-3) to greater than 200 km/s with a Mach number above 10. Such high velocity dense plasma jets have a number of potential fusion applications, including plasma refueling, magnetized target fusion, injection of angular momentum into centrifugally confined mirrors, high energy density plasmas, and others. The approach uses symmetric injection of high density plasma into a coaxial electromagnetic accelerator having an annular gap geometry tailored to prevent formation of the blow-by instability. The injected plasma is generated by numerous (currently 32) radially oriented capillary discharges arranged uniformly around the circumference of the angled annular injection region of the accelerator. Magnetohydrodynamic modeling identified electrode profiles that can achieve the desired plasma jet parameters. The experimental hardware is described along with initial experimental results in which approximately 200 microg has been accelerated to 100 km/s in a half-scale prototype gun. Initial observations of 64 merging injector jets in a planar cylindrical testing array are presented. Density and velocity are presently limited by available peak current and injection sources. Steps to increase both the drive current and the injected plasma mass are described for next generation experiments. PMID:19725654

  2. Induction accelerators for the phase rotator system

    SciTech Connect

    Reginato, Lou; Yu, Simon; Vanecek, Dave

    2001-07-30

    The principle of magnetic induction has been applied to the acceleration of high current beams in betatrons and a variety of induction accelerators. The linear induction accelerator (LIA) consists of a simple nonresonant structure where the drive voltage is applied to an axially symmetric gap that encloses a toroidal ferromagnetic material. The change in flux in the magnetic core induces an axial electric field that provides particle acceleration. This simple nonresonant (low Q) structure acts as a single turn transformer that can accelerate from hundreds of amperes to tens of kiloamperes, basically only limited by the drive impedance. The LIA is typically a low gradient structure that can provide acceleration fields of varying shapes and time durations from tens of nanoseconds to several microseconds. The efficiency of the LIA depends on the beam current and can exceed 50% if the beam current exceeds the magnetization current required by the ferromagnetic material. The acceleration voltage available is simply given by the expression V=A dB/dt. Hence, for a given cross section of material, the beam pulse duration influences the energy gain. Furthermore, a premium is put on minimizing the diameter, which impacts the total weight or cost of the magnetic material. The diameter doubly impacts the cost of the LIA since the power (cost) to drive the cores is proportional to the volume as well. The waveform requirements during the beam pulse makes it necessary to make provisions in the pulsing system to maintain the desired dB/dt during the useful part of the acceleration cycle. This is typically done two ways, by using the final stage of the pulse forming network (PFN) and by the pulse compensation network usually in close proximity of the acceleration cell. The choice of magnetic materials will be made by testing various materials both ferromagnetic and ferrimagnetic. These materials will include the nickel-iron, silicon steel amorphous and various types of ferrites not

  3. CLASHING BEAM PARTICLE ACCELERATOR

    DOEpatents

    Burleigh, R.J.

    1961-04-11

    A charged-particle accelerator of the proton synchrotron class having means for simultaneously accelerating two separate contra-rotating particle beams within a single annular magnet structure is reported. The magnet provides two concentric circular field regions of opposite magnetic polarity with one field region being of slightly less diameter than the other. The accelerator includes a deflector means straddling the two particle orbits and acting to collide the two particle beams after each has been accelerated to a desired energy. The deflector has the further property of returning particles which do not undergo collision to the regular orbits whereby the particles recirculate with the possibility of colliding upon subsequent passages through the deflector.

  4. Accelerator on a Chip

    SciTech Connect

    England, Joel

    2014-06-30

    SLAC's Joel England explains how the same fabrication techniques used for silicon computer microchips allowed their team to create the new laser-driven particle accelerator chips. (SLAC Multimedia Communications)

  5. HEAVY ION LINEAR ACCELERATOR

    DOEpatents

    Van Atta, C.M.; Beringer, R.; Smith, L.

    1959-01-01

    A linear accelerator of heavy ions is described. The basic contributions of the invention consist of a method and apparatus for obtaining high energy particles of an element with an increased charge-to-mass ratio. The method comprises the steps of ionizing the atoms of an element, accelerating the resultant ions to an energy substantially equal to one Mev per nucleon, stripping orbital electrons from the accelerated ions by passing the ions through a curtain of elemental vapor disposed transversely of the path of the ions to provide a second charge-to-mass ratio, and finally accelerating the resultant stripped ions to a final energy of at least ten Mev per nucleon.

  6. Dielectric assist accelerating structure

    NASA Astrophysics Data System (ADS)

    Satoh, D.; Yoshida, M.; Hayashizaki, N.

    2016-01-01

    A higher-order TM02 n mode accelerating structure is proposed based on a novel concept of dielectric loaded rf cavities. This accelerating structure consists of ultralow-loss dielectric cylinders and disks with irises which are periodically arranged in a metallic enclosure. Unlike conventional dielectric loaded accelerating structures, most of the rf power is stored in the vacuum space near the beam axis, leading to a significant reduction of the wall loss, much lower than that of conventional normal-conducting linac structures. This allows us to realize an extremely high quality factor and a very high shunt impedance at room temperature. A simulation of a 5 cell prototype design with an existing alumina ceramic indicates an unloaded quality factor of the accelerating mode over 120 000 and a shunt impedance exceeding 650 M Ω /m at room temperature.

  7. Non-accelerator experiments

    SciTech Connect

    Goldhaber, M.

    1986-01-01

    This report discusses several topics which can be investigated without the use of accelerators. Topics covered are: (1) proton decay, (2) atmospheric neutrinos, (3) neutrino detection, (4) muons from Cygnus X-3, and (5) the double-beta decay.

  8. Principles of Induction Accelerators

    NASA Astrophysics Data System (ADS)

    Briggs*, Richard J.

    The basic concepts involved in induction accelerators are introduced in this chapter. The objective is to provide a foundation for the more detailed coverage of key technology elements and specific applications in the following chapters. A wide variety of induction accelerators are discussed in the following chapters, from the high current linear electron accelerator configurations that have been the main focus of the original developments, to circular configurations like the ion synchrotrons that are the subject of more recent research. The main focus in the present chapter is on the induction module containing the magnetic core that plays the role of a transformer in coupling the pulsed power from the modulator to the charged particle beam. This is the essential common element in all these induction accelerators, and an understanding of the basic processes involved in its operation is the main objective of this chapter. (See [1] for a useful and complementary presentation of the basic principles in induction linacs.)

  9. Accelerator on a Chip

    ScienceCinema

    England, Joel

    2014-07-16

    SLAC's Joel England explains how the same fabrication techniques used for silicon computer microchips allowed their team to create the new laser-driven particle accelerator chips. (SLAC Multimedia Communications)

  10. Rare Isotope Accelerators

    NASA Astrophysics Data System (ADS)

    Savard, Guy

    2002-04-01

    The next frontier for low-energy nuclear physics involves experimentation with accelerated beams of short-lived radioactive isotopes. A new facility, the Rare Isotope Accelerator (RIA), is proposed to produce large amount of these rare isotopes and post-accelerate them to energies relevant for studies in nuclear physics, astrophysics and the study of fundamental interactions at low energy. The basic science motivation for this facility will be introduced. The general facility layout, from the 400 kW heavy-ion superconducting linac used for production of the required isotopes to the novel production and extraction schemes and the highly efficient post-accelerator, will be presented. Special emphasis will be put on a number of technical breakthroughs and recent R&D results that enable this new facility.

  11. Vibration control in accelerators

    SciTech Connect

    Montag, C.

    2011-01-01

    In the vast majority of accelerator applications, ground vibration amplitudes are well below tolerable magnet jitter amplitudes. In these cases, it is necessary and sufficient to design a rigid magnet support structure that does not amplify ground vibration. Since accelerator beam lines are typically installed at an elevation of 1-2m above ground level, special care has to be taken in order to avoid designing a support structure that acts like an inverted pendulum with a low resonance frequency, resulting in untolerable lateral vibration amplitudes of the accelerator components when excited by either ambient ground motion or vibration sources within the accelerator itself, such as cooling water pumps or helium flow in superconducting magnets. In cases where ground motion amplitudes already exceed the required jiter tolerances, for instance in future linear colliders, passive vibration damping or active stabilization may be considered.

  12. Charged particle accelerator grating

    DOEpatents

    Palmer, R.B.

    1985-09-09

    A readily disposable and replaceable accelerator grating for a relativistic particle accelerator is described. The grating is formed for a plurality of liquid droplets that are directed in precisely positioned jet streams to periodically dispose rows of droplets along the borders of a predetermined particle beam path. A plurality of lasers are used to direct laser beams onto the droplets, at predetermined angles, thereby to excite the droplets to support electromagnetic accelerating resonances on their surfaces. Those resonances operate to accelerate and focus particles moving along the beam path. As the droplets are distorted or destroyed by the incoming radiation, they are replaced at a predetermined frequency by other droplets supplied through the jet streams.

  13. Accelerator vibration issues

    SciTech Connect

    Tennant, R.A.

    1985-01-01

    Vibrations induced in accelerator structures can cause particle-beam jitter and alignment difficulties. Sources of these vibrations may include pump oscillations, cooling-water turbulence, and vibrations transmitted through the floor to the accelerator structure. Drift tubes (DT) in a drift tube linac (DTL) are components likely to affect beam jitter and alignment because they normally have a heavy magnet structure on the end of a long and relatively small support stem. The natural vibrational frequencies of a drift tube have been compared with theoretical predictions. In principle, by knowing natural frequencies of accelerator components and system vibrational frequncies, an accelerator can be designed that does not have these frequencies coinciding. 2 refs., 2 figs., 2 tabs.

  14. Amps particle accelerator definition study

    NASA Technical Reports Server (NTRS)

    Sellen, J. M., Jr.

    1975-01-01

    The Particle Accelerator System of the AMPS (Atmospheric, Magnetospheric, and Plasmas in Space) payload is a series of charged particle accelerators to be flown with the Space Transportation System Shuttle on Spacelab missions. In the configuration presented, the total particle accelerator system consists of an energetic electron beam, an energetic ion accelerator, and both low voltage and high voltage plasma acceleration devices. The Orbiter is illustrated with such a particle accelerator system.

  15. FilGAP and its close relatives: a mediator of Rho-Rac antagonism that regulates cell morphology and migration.

    PubMed

    Nakamura, Fumihiko

    2013-07-01

    Cell migration, phagocytosis and cytokinesis are mechanically intensive cellular processes that are mediated by the dynamic assembly and contractility of the actin cytoskeleton. GAPs (GTPase-activating proteins) control activities of the Rho family proteins including Cdc42, Rac1 and RhoA, which are prominent upstream regulators of the actin cytoskeleton. The present review concerns a class of Rho GAPs, FilGAP (ARHGAP24 gene product) and its close relatives (ARHGAP22 and AHRGAP25 gene products). FilGAP is a GAP for Rac1 and a binding partner of FLNa (filamin A), a widely expressed F-actin (filamentous actin)-cross-linking protein that binds many different proteins that are important in cell regulation. Phosphorylation of FilGAP serine/threonine residues and binding to FLNa modulate FilGAP's GAP activity and, as a result, its ability to regulate cell protrusion and spreading. FLNa binds to FilGAP at F-actin-enriched sites, such as at the leading edge of the cell where Rac1 activity is controlled to inhibit actin assembly. FilGAP then dissociates from FLNa in actin networks by myosin-dependent mechanical deformation of FLNa's FilGAP-binding site to relocate at the plasma membrane by binding to polyphosphoinositides. Since actomyosin contraction is activated downstream of RhoA-ROCK (Rho-kinase), RhoA activity regulates Rac1 through FilGAP by signalling to the force-generating system. FilGAP and the ARHGAP22 gene product also act as mediators between RhoA and Rac1 pathways, which lead to amoeboid and mesenchymal modes of cell movements respectively. Therefore FilGAP and its close relatives are key regulators that promote the reciprocal inhibitory relationship between RhoA and Rac1 in cell shape changes and the mesenchymal-amoeboid transition in tumour cells. PMID:23763313

  16. Breakthrough: Fermilab Accelerator Technology

    ScienceCinema

    None

    2014-08-12

    There are more than 30,000 particle accelerators in operation around the world. At Fermilab, scientists are collaborating with other laboratories and industry to optimize the manufacturing processes for a new type of powerful accelerator that uses superconducting niobium cavities. Experimenting with unique polishing materials, a Fermilab team has now developed an efficient and environmentally friendly way of creating cavities that can propel particles with more than 30 million volts per meter.

  17. Rolamite acceleration sensor

    DOEpatents

    Abbin, Joseph P.; Briner, Clifton F.; Martin, Samuel B.

    1993-01-01

    A rolamite acceleration sensor which has a failsafe feature including a housing, a pair of rollers, a tension band wrapped in an S shaped fashion around the rollers, wherein the band has a force-generation cut out and a failsafe cut out or weak portion. The failsafe cut out or weak portion breaks when the sensor is subjected to an excessive acceleration so that the sensor fails in an open circuit (non-conducting) state permanently.

  18. Rolamite acceleration sensor

    DOEpatents

    Abbin, J.P.; Briner, C.F.; Martin, S.B.

    1993-12-21

    A rolamite acceleration sensor is described which has a failsafe feature including a housing, a pair of rollers, a tension band wrapped in an S shaped fashion around the rollers, wherein the band has a force-generation cut out and a failsafe cut out or weak portion. The failsafe cut out or weak portion breaks when the sensor is subjected to an excessive acceleration so that the sensor fails in an open circuit (non-conducting) state permanently. 6 figures.

  19. Microgravity Acceleration Measurement System

    NASA Technical Reports Server (NTRS)

    Foster, William

    2009-01-01

    Microgravity Acceleration Measurement System (MAMS) is an ongoing study of the small forces (vibrations and accelerations) on the ISS that result from the operation of hardware, crew activities, as well as dockings and maneuvering. Results will be used to generalize the types of vibrations affecting vibration-sensitive experiments. Investigators seek to better understand the vibration environment on the space station to enable future research.

  20. Breakthrough: Fermilab Accelerator Technology

    SciTech Connect

    2012-04-23

    There are more than 30,000 particle accelerators in operation around the world. At Fermilab, scientists are collaborating with other laboratories and industry to optimize the manufacturing processes for a new type of powerful accelerator that uses superconducting niobium cavities. Experimenting with unique polishing materials, a Fermilab team has now developed an efficient and environmentally friendly way of creating cavities that can propel particles with more than 30 million volts per meter.