bluuebunny/crossref_metadata_2025 huggingface dataset:
Epoxide reduction with hydrazine on graphene: A first principles study
Authors: Kim Min Chan , Hwang Gyeong S. , Ruoff Rodney S.
Published: August 2009

Mechanisms for epoxide reduction with hydrazine on a single-layer graphene sheet are examined using quantum mechanical calculations within the framework of gradient-corrected spin-polarized density-functional theory. We find that the reduction reaction is mainly governed by epoxide ring opening which is initiated by H transfer from hydrazine or its derivatives. In addition, our calculations suggest that the epoxide reduction by hydrazine may predominantly follow a direct Eley–Rideal mechanism rather than a Langmuir–Hinshelwood mechanism. We also discuss the generation of various hydrazine derivatives during the reduction of graphene oxide with hydrazine and their potential contribution to lowering the barrier height of epoxide ring opening.
Coupled mode effects on energy transfer in weakly coupled, two-temperature plasmas
Authors: Vorberger J. , Gericke D. O.
Published: August 2009

The effects of collective modes on the temperature relaxation in fully ionized, weakly coupled plasmas are investigated. A coupled mode (CM) formula for the electron-ion energy transfer is derived within the random phase approximation and it is shown how it can be evaluated using standard methods. The CM rates are considerably smaller than rates based on Fermi’s golden rule for some parameters and identical for others. It is shown how the CM effects are connected to the occurrence of ion acoustic modes and when they occur. Interestingly, CM effects occur also for plasmas with very high electron temperatures; a regime, where the Landau–Spitzer approach is believed to be accurate.
A model Hamiltonian to simulate the complex photochemistry of benzene II
Authors: Penfold Thomas J. , Worth Graham A.
Published: August 2009

The photophysics and photochemistry of benzene is a classic example of the richness of competing pathways available to a molecule after photoexcitation. Computer simulations are one way to provide a molecular picture for the dynamics behind the experimental observations. In this paper we develop a vibronic coupling Hamiltonian prepared in a previous paper [G. A. Worth, J. Photochem. Photobiol., A 190, 190 (2007)]. Using CASPT2 we add dynamic correlation to the description of the excited states, improving their accuracy dramatically. Seven coupled states and all vibrational modes are included in the model and the parameters are obtained by fitting to points provided by the quantum chemistry calculations. The model is shown to be a good fit of the adiabatic surfaces and its accuracy is demonstrated by the calculation of three absorption bands, which compare favorably with the experimentally obtained spectra.
Electron density measurements in an atmospheric pressure argon discharge by means of plasma radiation
Authors: Qi Bing , Huang Jianjun , Gao Liang , Qiu Yunming
Published: August 2009

A method is developed for measuring the electron density in argon during atmospheric pressure dielectric barrier discharge. The oscillating electromagnetic signal is detected by an antenna at a distance from the plasma source. The electron density is then calculated from the ion oscillation frequency. The results show that the electron density in the plasma after the turnoff of the discharge channel is 2.55×1019 m−3 with an applied voltage of 2.73 kV, and it decays almost exponentially down to 1.00×1019 m−3 over 49.2 ns. The electron density is found to increase linearly with increasing voltage.
Photoelectron spectroscopy of small IBr−(CO2)n (n=–3) cluster anions
Authors: Sheps Leonid , Miller Elisa M. , Lineberger W. Carl
Published: August 2009

We report the photoelectron spectra of small IBr−(CO2)n cluster anions (n=0–3). The vibrational state-resolved spectrum of IBr− permits reliable identification of the origins of the excited A′ Π32 and A Π31 states of neutral IBr through a high-quality Franck–Condon spectral simulation. As a result, we directly determine several important spectroscopic parameters: the adiabatic electron affinity (EA) of IBr, EA=2.512±0.003 eV, the ground electronic state (X Σ+1/22) bond strength of IBr−, D0(IBr−)=0.966±0.003 eV, its equilibrium bond length, ReX(IBr−)=3.01±0.01 Å, and its vibrational frequency, ωe(IBr−)=134±10 cm−1. These values represent a substantial improvement over existing experimental information and are in good agreement with recent theoretical studies. The photoelectron spectra of the first three cluster anions, IBr−(CO2)n (n=1–3), do not exhibit resolved vibrational structure, but the similarity to the IBr− photoelectron spectrum indicates minimal electron delocalization onto the solvent. The cluster anion spectra shift to progressively higher electron binding energies, providing information on the magnitude of the solvent perturbation and estimates of the EA of IBr−(CO2)n.
Efficient exact and K-skip methods for stochastic simulation of coupled chemical reactions
Authors: Cai Xiaodong , Wen Ji
Published: August 2009

Gillespie’s direct method (DM) [D. Gillespie, J. Chem. Phys. 81, 2340 (1977)] for exact stochastic simulation of chemical reaction systems has been widely adopted. It is easy to implement but requires large computation for relatively large systems. Recently, two more efficient methods, next reaction method (NRM) [M. A. Gibson and J. Bruck, J. Phys. Chem. A 105, 1876 (2000)] and optimized DM (ODM) [Y. Cao et al., J. Chem. Phys. 121, 4059 (2004)], have been developed to improve simulation speed. It has been demonstrated that the ODM is the state-of-the-art most efficient method for exact stochastic simulation of most practical reaction systems. In this paper, we first develop an exact stochastic simulation algorithm named ODMK that is more efficient than the ODM. We then develop an approximate method named K-skip method to further accelerate simulation. Using two chemical reaction systems, we demonstrate that our ODMK and K-skip method can save 20%–30% and 70%–80% simulation time, respectively, comparing to the ODM. We also show that our ODMK and K-skip method provide almost the same simulation accuracy as the ODM.
On the use of shifted Jacobi polynomials in accurate evaluation of roots and weights of Rys polynomials
Authors: Flocke N.
Published: August 2009

In this paper it is shown that shifted Jacobi polynomials Gn(p,q,x) can be used in connection with the Gaussian quadrature modified moment technique to greatly enhance the accuracy of evaluation of Rys roots and weights used in Gaussian integral evaluation in quantum chemistry. A general four-term inhomogeneous recurrence relation is derived for the shifted Jacobi polynomial modified moments over the Rys weight function e−Tx/x. It is shown that for q=1/2 this general four-term inhomogeneous recurrence relation reduces to a three-term p-dependent inhomogeneous recurrence relation. Adjusting p to proper values depending on the Rys exponential parameter T, the method is capable of delivering highly accurate results for large number of roots and weights in the most difficult to treat intermediate T range. Examples are shown, and detailed formulas together with practical suggestions for their efficient implementation are also provided.
Growths of staggered InGaN quantum wells light-emitting diodes emitting at 520–525 nm employing graded growth-temperature profile
Authors: Zhao Hongping , Liu Guangyu , Li Xiao-Hang , Huang G. S. , Poplawsky Jonathan D. , Penn S. Tafon , Dierolf Volkmar , Tansu Nelson
Published: August 2009

Three-layer staggered InGaN quantum wells (QWs) light-emitting diodes (LEDs) emitting at 520–525 nm were grown by metal-organic chemical vapor deposition by employing graded growth-temperature profile. The use of staggered InGaN QW, with improved electron-hole wave functions overlap design, leads to an enhancement of its radiative recombination rate. Both cathodoluminescence and electroluminescence measurements of three-layer staggered InGaN QW LED exhibited enhancements by 1.8–2.8 and 2.0–3.5 times, respectively, over those of conventional InGaN QW LED.
Magnetic-field asymmetry of nonlinear transport in narrow channels with asymmetric hybrid confinement
Authors: Brandenstein-Köth Bettina , Worschech Lukas , Forchel Alfred
Published: August 2009

The authors realized narrow constrictions in a two-dimensional electron gas (2DEG) with an in-plane asymmetry by means of a hybrid confinement. Unequal sidewalls of the constrictions were formed by combination of a single etched trench in a modulation doped GaAs/AlGaAs heterostructure which cuts through the 2DEG with an adjacent metallic top-gate, which depletes the underlying 2DEG. The two-terminal conductance was analyzed in magnetic fields applied perpendicular to the sample surface. In nonlinear transport, the conductance shows pronounced differences for an inversion of the magnetic field. The asymmetric conductance is related to scattering asymmetries caused by the different sidewalls in the asymmetric constriction.
A systematic search for minimum structures of small gold clusters Aun (n=2–20) and their electronic properties
Authors: Assadollahzadeh Behnam , Schwerdtfeger Peter
Published: August 2009

A systematic search for global and energetically low-lying minimum structures of neutral gold clusters Aun (n=2–20) is performed within a seeded genetic algorithm technique using density functional theory together with a relativistic pseudopotential. Choosing the energetically lowest lying structures we obtain electronic properties by applying a larger basis set within an energy-consistent relativistic small-core pseudopotential approach. The possibility of extrapolating these properties to the bulk limit for such small cluster sizes is discussed. In contrast to previous calculations on cesium clusters [B. Assadollahzadeh et al., Phys. Rev. B 78, 245423 (2008)] we find a rather slow convergence of any of the properties toward the bulk limit. As a result, we cannot predict the onset of metallic character with increasing cluster size, and much larger clusters need to be considered to obtain any useful information about the bulk limit. Our calculated properties show a large odd-even cluster size oscillation in agreement, for example, with experimental ionization potentials and electron affinities. For the calculated polarizabilities we find a clear transition to lower values at Au14, the first cluster size where the predicted global minimum clearly shows a compact three-dimensional (3D) structure. Hence, the measurement of cluster polarizabilities is ideal to identify the 2D→3D transition at low temperatures for gold. Our genetic algorithm confirms the pyramidal structure for Au20.
Coupled flutter of parallel plates
Authors: Schouveiler Lionel , Eloy Christophe
Published: August 2009

Experimental visualizations of the coupled flutter of an assembly of two, three, and four flexible parallel cantilevered plates immersed in an axial uniform flow are presented. Depending on the flow velocity, on the interplate distance, and on the plate length, different coupled modes are observed. Selected modes and the associated thresholds and frequencies are compared with the results of a linear stability analysis.
Propagation lengths of surface plasmon polaritons on metal films with arrays of subwavelength holes by infrared imaging spectroscopy
Authors: Cilwa Katherine E. , Rodriguez Kenneth R. , Heer Joseph M. , Malone Marvin A. , Corwin Lloyd D. , Coe James V.
Published: August 2009

Metal films with arrays of subwavelength holes (mesh) exhibit extraordinary transmission resonances to which many attribute a role for surface plasmon polaritons (SPPs); others debated this point. Experimental measurements of propagation lengths are presented under conditions that pertain to the use of SPPs for surface spectroscopy. The lateral extent of electromagnetic propagation along the mesh surface is measured by recording absorption spectra of a line of latex microspheres as a function of distance away from the line along the mesh. Measurements reveal an exponential functional form for decay of absorption signal laterally from the absorption source. Results at 697 cm−1, which are closest to the strongest transmission resonance of the mesh, reveal a 1/e propagation distance along the surface of 17.8±2.9 μm. This is 40% larger than the lattice spacing implicating the holes as the SPP damping mechanism, however, this is significantly shorter than smooth metal expectations.
Influence of deviatoric stress on the pressure-induced structural phase transition of ZnO studied by optical second harmonic generation measurements
Authors: Bayarjargal L. , Winkler B. , Haussühl E. , Boehler R.
Published: August 2009

The pressure-induced B4⇆B1 structural phase transition of ZnO has been studied with the second harmonic generation (SHG) technique. Measurements in nonhydrostatic and hydrostatic pressure transmitting media show slightly different transition pressures (9–11 GPa) and a different pressure dependence of the SHG intensities. These observations are consistent with the presence of a tetragonal and hexagonal intermediate phase as a result of hydrostatic and axial compression, respectively. In contrast to earlier work, it is shown that it is not necessary to use nanocrystalline starting material to be able to recover the B1 phase at ambient conditions.
Characteristics of ultraviolet photoluminescence from high quality tin oxide nanowires
Authors: Chen Rui , Xing G. Z. , Gao J. , Zhang Z. , Wu T. , Sun H. D.
Published: August 2009

We investigate the optical properties of ultraviolet range emission from high quality tin oxide nanowires prepared by vapor-liquid-solid growth technique. Temperature dependent photoluminescence (PL) measurement is performed between 10 and 300 K. At low temperatures, the PL originates from radiative recombination of excitons bound to neutral donors, donor-acceptor pair transition and their associated longitudinal optical (LO) phonon replicas. The LO-phonon replicas up to third order with Huang–Rhys factor of 0.34 are observed. Evolution of the peaks and the origin of PL thermal quenching at high temperatures are discussed in detail.
Dip-shaped InGaN/GaN quantum-well light-emitting diodes with high efficiency
Authors: Park Seoung-Hwan , Ahn Doyeol , Koo Bun-Hei , Kim Jong-Wook
Published: August 2009

Optical properties of dip-shaped InGaN/GaN quantum well (QW) light-emitting diodes are investigated using the multiband effective-mass theory. These results are compared with those of conventional and staggered InGaN/GaN QW light-emitting diodes. In the case of a dip-shaped QW structure, the carrier density dependence of the transition wavelength is reduced due to a relatively small internal field effect. Also, we observe that the heavy-hole effective mass around the topmost valence band is greatly reduced with the inclusion of the dip-shaped layer. The spontaneous emission peak of a dip-shaped QW structure is shown to be larger than that of a staggered QW structure or a conventional QW structure. This is mainly due to the fact that a dip-shaped QW structure has larger optical matrix elements produced by Kane’s parameter.
Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB
Authors: Yu Bomina , Hunt John F.
Published: August 2009

Promiscuous substrate recognition, the ability to catalyze transformations of chemically diverse compounds, is an evolutionarily advantageous, but poorly understood phenomenon. The promiscuity of DNA repair enzymes is particularly important, because it enables diverse kinds of damage to different nucleotide bases to be repaired in a metabolically parsimonious manner. We present enzymological and crystallographic studies of the mechanisms underlying promiscuous substrate recognition by
Escherichia coli
AlkB, a DNA repair enzyme that removes methyl adducts and some larger alkylation lesions from endocyclic positions on purine and pyrimidine bases. In vitro Michaelis–Menten analyses on a series of alkylated bases show high activity in repairing N1-methyladenine (m1A) and N3-methylcytosine (m3C), comparatively low activity in repairing 1,
N
6
-ethenoadenine, and no detectable activity in repairing N1-methylguanine or N3-methylthymine. AlkB has a substantially higher
k
cat
and
K
m
for m3C compared with m1A. Therefore, the enzyme maintains similar net activity on the chemically distinct substrates by increasing the turnover rate of the substrate with nominally lower affinity. Cocrystal structures provide insight into the structural basis of this “
k
cat
/
K
m
compensation,” which makes a significant contribution to promiscuous substrate recognition by AlkB. In analyzing a large ensemble of crystal structures solved in the course of these studies, we observed 2 discrete global conformations of AlkB differing in the accessibility of a tunnel hypothesized to control diffusion of the O
2
substrate into the active site. Steric interactions between a series of protein loops control this conformational transition and present a plausible mechanism for preventing O
2
binding before nucleotide substrate binding.
Phosphorylation of CARMA1 by HPK1 is critical for NF-κB activation in T cells
Authors: Brenner Dirk , Brechmann Markus , Röhling Simone , Tapernoux Myriam , Mock Thomas , Winter Dominic , Lehmann Wolf D. , Kiefer Friedemann , Thome Margot , Krammer Peter H. , Arnold Rüdiger
Published: August 2009

Activation of the NF-κB pathway in T cells is required for induction of an adaptive immune response. Hematopoietic progenitor kinase (HPK1) is an important proximal mediator of T-cell receptor (TCR)-induced NF-κB activation. Knock-down of HPK1 abrogates TCR-induced IKKβ and NF-κB activation, whereas active HPK1 leads to increased IKKβ activity in T cells. Yet, the precise molecular mechanism of this process remains elusive. Here, we show that HPK1-mediated NF-κB activation is dependent on the adaptor protein CARMA1. HPK1 interacts with CARMA1 in a TCR stimulation-dependent manner and phosphorylates the linker region of CARMA1. Interestingly, the putative HPK1 phosphorylation sites in CARMA1 are different from known PKCθ consensus sites. Mutations of residues S549, S551, and S552 in CARMA1 abrogated phosphorylation of a CARMA1-linker construct by HPK1 in vitro. In addition, CARMA1 S551A or S5549A/S551A point mutants failed to restore HPK1-mediated and TCR-mediated NF-κB activation and IL-2 expression in CARMA1-deficient T cells. Thus, we identify HPK1 as a kinase specific for CARMA1 and suggest HPK1-mediated phosphorylation of CARMA1 as an additional regulatory mechanism tuning the NF-κB response upon TCR stimulation.
Mouse
prickle1
, the homolog of a PCP gene, is essential for epiblast apical-basal polarity
Authors: Tao Hirotaka , Suzuki Makoto , Kiyonari Hiroshi , Abe Takaya , Sasaoka Toshikuni , Ueno Naoto
Published: August 2009

Planar cell polarity (PCP) genes are essential for establishing planar cell polarity in both invertebrate and vertebrate tissues and are known to regulate cellular morphogenesis and cell movements during development. We focused on Prickle, one of the core components of the PCP pathway, and deleted one of two mouse
prickle
homologous genes,
mpk1
. We found that the deletion of
mpk1
gene resulted in early embryonic lethality, between embryonic day (E)5.5 and E6.5, associated with failure of distal visceral endoderm migration and primitive streak formation. The
mpk1
−/−
epiblast tissue was disorganized, and analyses at the cellular level revealed abnormal cell shapes, mislocalized extracellular matrix (ECM) proteins, and disrupted orientation of mitotic spindles, from which loss of apico-basal (AB) polarity of epiblast cells are suspected. Furthermore, we show
mpk1
genetically interacts with another core PCP gene
Vangl2/stbm
in the epiblast formation, suggesting that PCP components are commonly required for the establishment and/or the maintenance of epiblast AB polarity. This was further supported by our finding that overexpression of ΔPET/LIM (ΔP/L), a dominant-negative Pk construct, in
Xenopus
embryo disrupted uniform localization of an apical marker PKCζ, and expanded the apical domain of ectoderm cells. Our results demonstrate a role for
mpk1
in AB polarity formation rather than expected role as a PCP gene.
Helicobacter pylori
moves through mucus by reducing mucin viscoelasticity
Authors: Celli Jonathan P. , Turner Bradley S. , Afdhal Nezam H. , Keates Sarah , Ghiran Ionita , Kelly Ciaran P. , Ewoldt Randy H. , McKinley Gareth H. , So Peter , Erramilli Shyamsunder , Bansil Rama
Published: August 2009

The ulcer-causing gastric pathogen
Helicobacter pylori
is the only bacterium known to colonize the harsh acidic environment of the human stomach.
H. pylori
survives in acidic conditions by producing urease, which catalyzes hydrolysis of urea to yield ammonia thus elevating the pH of its environment. However, the manner in which
H. pylori
is able to swim through the viscoelastic mucus gel that coats the stomach wall remains poorly understood. Previous rheology studies on gastric mucin, the key viscoelastic component of gastric mucus, indicate that the rheology of this material is pH dependent, transitioning from a viscous solution at neutral pH to a gel in acidic conditions. Bulk rheology measurements on porcine gastric mucin (PGM) show that pH elevation by
H. pylori
induces a dramatic decrease in viscoelastic moduli. Microscopy studies of the motility of
H. pylori
in gastric mucin at acidic and neutral pH in the absence of urea show that the bacteria swim freely at high pH, and are strongly constrained at low pH. By using two-photon fluorescence microscopy to image the bacterial motility in an initially low pH mucin gel with urea present we show that the gain of translational motility by bacteria is directly correlated with a rise in pH indicated by 2′,7′-Bis-(2-Carboxyethyl)-5-(and-6)-carboxyfluorescein (BCECF), a pH sensitive fluorescent dye. This study indicates that the helicoidal-shaped
H. pylori
does not bore its way through the mucus gel like a screw through a cork as has previously been suggested, but instead achieves motility by altering the rheological properties of its environment.
Polo-like kinases mediate cell survival in mitochondrial dysfunction
Authors: Matsumoto Takumi , Wang Ping-yuan , Ma Wenzhe , Sung Ho Joong , Matoba Satoaki , Hwang Paul M.
Published: August 2009

Cancer cells often display defects in mitochondrial respiration, thus the identification of pathways that promote cell survival under this metabolic state may have therapeutic implications. Here, we report that the targeted ablation of mitochondrial respiration markedly increases expression of Polo-like kinase 2 (PLK2) and that it is required for the in vitro growth of these nonrespiring cells. Furthermore, we identify PLK2 as a kinase that phosphorylates Ser-137 of PLK1, which is sufficient to mediate this survival signal. In vivo, knockdown of PLK2 in an isogenic human cell line with a modest defect in mitochondrial respiration eliminates xenograft formation, indicating that PLK2 activity is necessary for growth of cells with compromised respiration. Our findings delineate a mitochondrial dysfunction responsive cell cycle pathway critical for determining cancer cell outcome.
The equivalent of a thallium binding residue from an archeal homolog controls cation interactions in brain glutamate transporters
Authors: Teichman Shlomit , Qu Shaogang , Kanner Baruch I.
Published: August 2009

Glutamate transporters maintain low synaptic concentrations of neurotransmitter by coupling uptake to flux of other ions. Their transport cycle consists of two separate translocation steps, namely cotransport of glutamic acid with three Na
+
followed by countertransport of K
+
. Two Tl
+
binding sites, presumed to serve as sodium sites, were observed in the crystal structure of a related archeal homolog and the side chain of a conserved aspartate residue contributed to one of these sites. We have mutated the corresponding residue of the eukaryotic glutamate transporters GLT-1 and EAAC1 to asparagine, serine, and cysteine. Remarkably, these mutants exhibited significant sodium-dependent radioactive acidic amino acid uptake when expressed in HeLa cells. Reconstitution experiments revealed that net uptake by the mutants in K
+
-loaded liposomes was impaired. However, with Na
+
and unlabeled L-aspartate inside the liposomes, exchange levels were around 50–90% of those by wild-type. In further contrast to wild-type, where either substrate or K
+
stimulated the anion conductance by the transporter, substrate but not K
+
modulated the anion conductance of the mutants expressed in oocytes. Both with wild-type EAAC1 and EAAC1-D455N, not only sodium but also lithium could support radioactive acidic amino acid uptake. In contrast, with D455S and D455C, radioactive uptake was only observed in the presence of sodium. Thus the conserved aspartate is required for transporter-cation interactions in each of the two separate translocation steps and likely participates in an overlapping sodium and potassium binding site.
The XNP remodeler targets dynamic chromatin in Drosophila
Authors: Schneiderman Jonathan I. , Sakai Akiko , Goldstein Sara , Ahmad Kami
Published: August 2009

Heterochromatic gene silencing results from the establishment of a repressive chromatin structure over reporter genes. Gene silencing is often variegated, implying that chromatin may stochastically switch from repressive to permissive structures as cells divide. To identify remodeling enzymes involved in reorganizing heterochromatin, we tested 11 SNF2-type chromatin remodelers in
Drosophila
for effects on gene silencing. Overexpression of five remodelers affects gene silencing, and the most potent de-repressor is the α-thalassaemia mental retardation syndrome X-linked (ATRX) homolog X-linked nuclear protein (XNP). Although the mammalian ATRX protein localizes to heterochromatin,
Drosophila
XNP is not a general component of heterochromatin. Instead, XNP localizes to active genes and to a major focus near the heterochromatin of the X chromosome. The XNP focus corresponds to an unusual decondensed satellite DNA block, and both active genes and the XNP focus are sites of ongoing nucleosome replacement. We suggest that the XNP remodeler modulates nucleosome dynamics at its target sites to limit chromatin accessibility. Although XNP at active genes may contribute to gene silencing, we find that a single focus is present across
Drosophila
species and that perturbation of this site cripples heterochromatic gene silencing. Thus, the XNP focus appears to be a functional genetic element that can contribute to gene silencing throughout the nucleus.
Behavioral tagging is a general mechanism of long-term memory formation
Authors: Ballarini Fabricio , Moncada Diego , Martinez Maria Cecilia , Alen Nadia , Viola Haydée
Published: August 2009

In daily life, memories are intertwined events. Little is known about the mechanisms involved in their interactions. Using two hippocampus-dependent (spatial object recognition and contextual fear conditioning) and one hippocampus-independent (conditioned taste aversion) learning tasks, we show that in rats subjected to weak training protocols that induce solely short term memory (STM), long term memory (LTM) is promoted and formed only if training sessions took place in contingence with a novel, but not familiar, experience occurring during a critical time window around training. This process requires newly synthesized proteins induced by novelty and reveals a general mechanism of LTM formation that begins with the setting of a “learning tag” established by a weak training. These findings represent the first comprehensive set of evidences indicating the existence of a behavioral tagging process that in analogy to the synaptic tagging and capture process, need the creation of a transient, protein synthesis-independent, and input specific tag.
Molecular mechanisms determining conserved properties of short-term synaptic depression revealed in NSF and SNAP-25 conditional mutants
Authors: Kawasaki Fumiko , Ordway Richard W.
Published: August 2009

Current models of synaptic vesicle trafficking implicate a core complex of proteins comprised of
N
-ethylmaleimide-sensitive factor (NSF), soluble NSF attachment proteins (SNAPs), and SNAREs in synaptic vesicle fusion and neurotransmitter release. Despite this progress, major challenges remain in establishing the in vivo functions of these proteins and their roles in determining the physiological properties of synapses. The present study employs glutamatergic adult neuromuscular synapses of
Drosophila
, which exhibit conserved properties of short-term synaptic plasticity with respect to mammalian glutamatergic synapses, to address these issues through genetic analysis. Our findings establish an in vivo role for SNAP-25 in synaptic vesicle priming, and support a zippering model of SNARE function in this process. Moreover, these studies define the contribution of SNAP-25-dependent vesicle priming to the detailed properties of short-term depression elicited by paired-pulse (PP) and train stimulation. In contrast, NSF is shown here not to be required for WT PP depression, but to be critical for maintaining neurotransmitter release during sustained stimulation. In keeping with this role, disruption of NSF function results in activity-dependent redistribution of the t-SNARE proteins, SYNTAXIN and SNAP-25, away from neurotransmitter release sites (active zones). These findings support a role for NSF in replenishing active zone t-SNAREs for subsequent vesicle priming, and provide new insight into the spatial organization of SNARE protein cycling during synaptic activity. Together, the results reported here establish in vivo contributions of SNAP-25 and NSF to synaptic vesicle trafficking and define molecular mechanisms determining conserved functional properties of short-term depression.
Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex
Authors: Seo Hyuk-Soo , Ma Yingli , Debler Erik W. , Wacker Daniel , Kutik Stephan , Blobel Günter , Hoelz André
Published: August 2009

The Nup84 complex constitutes a key building block in the nuclear pore complex (NPC). Here we present the crystal structure of one of its 7 components, Nup120, which reveals a β propeller and an α-helical domain representing a novel fold. We discovered a previously unidentified interaction of Nup120 with Nup133 and confirmed the physiological relevance in vivo. As mapping of the individual components in the Nup84 complex places Nup120 and Nup133 at opposite ends of the heptamer, our findings indicate a head-to-tail arrangement of elongated Nup84 complexes into a ring structure, consistent with a fence-like coat for the nuclear pore membrane. The attachment site for Nup133 lies at the very end of an extended unstructured region, which allows for flexibility in the diameter of the Nup84 complex ring. These results illuminate important roles of terminal unstructured segments in nucleoporins for the architecture, function, and assembly of the NPC.
Identification of a serotonin receptor coupled to adenylyl cyclase involved in learning-related heterosynaptic facilitation inAplysia
Authors: Lee Yong-Seok , Choi Sun-Lim , Lee Seung-Hee , Kim Hyoung , Park Hyungju , Lee Nuribalhae , Lee Sue-Hyun , Chae Yeon-Su , Jang Deok-Jin , Kandel Eric R. , Kaang Bong-Kiun
Published: August 2009

Serotonin (5-HT) plays a critical role in modulating synaptic plasticity in the marine molluscAplysiaand in the mammalian nervous system. InAplysiasensory neurons, 5-HT can activate several signal cascades, including PKA and PKC, presumably via distinct types of G protein-coupled receptors. However, the molecular identities of these receptors have not yet been identified. We here report the cloning and functional characterization of a 5-HT receptor that is positively coupled to adenylyl cyclase inAplysianeurons. The cloned receptor, 5-HTapAC1, stimulates the production of cAMP in HEK293T cells and inXenopusoocytes. Moreover, the knockdown of 5-HTapAC1expression by RNA interference blocked 5-HT-induced cAMP production inAplysiasensory neurons and blocked synaptic facilitation in nondepressed or partially depressed sensory-to-motor neuron synapses. These data implicate 5-HTapAC1as a major modulator of learning related synaptic facilitation in the direct sensory to motor neuron pathway of the gill withdrawal reflex.
Nitric oxide activation of Keap1/Nrf2 signaling in human colon carcinoma cells
Authors: Li Chun-Qi , Kim Min Young , Godoy Luiz C. , Thiantanawat Apinya , Trudel Laura J. , Wogan Gerald N.
Published: August 2009

The transcription factor NF-E2-related nuclear factor 2 (Nrf2) regulates expression of genes that protect cells from oxidative damage. Here, we characterized nitric oxide (•NO)-induced Nrf2–Kelch-like ECH-associated protein 1 (Keap1) signaling and its role in counteracting •NO-induced apoptosis of human colon cancer HCT116 cells. Nrf2 was localized in the cytoplasm in control cells; •NO triggered its rapid nuclear accumulation, transcriptional activation, and up-regulation of HO-1, NQO1, and GCL, but not GST A4 and P1 subunits. Nrf2 accumulation in the nucleus was also associated with enhanced transcription and posttranscriptional modifications. (
S
)-nitrosation of Keap1 may contribute to nuclear accumulation of Nrf2 by facilitating its dissociation from Keap1, thus initiating •NO-mediated Nrf2–Keap1 signaling. •NO-mediated induction of ARE-dependent genes occurred well before apoptosis, as judged by caspase 3 activation. Collectively, these results show that the Nrf2–Keap1 signaling pathway mediates protective cellular responses to mitigate •NO-induced damage and may contribute to the relative resistance of HCT116 to •NO-induced cytotoxicity.
Evidence of carbon monoxide-mediated phase advancement of the yeast metabolic cycle
Authors: Tu Benjamin P. , McKnight Steven L.
Published: August 2009

Prototrophic strains of budding yeast exhibit robust metabolic cycles during continuous growth under nutrient-limiting conditions. Previous studies revealed periodic fluctuations of aminolevulinic acid, a precursor of heme, indicating that heme biosynthesis is temporally regulated during these metabolic cycles. The enzyme that catabolizes heme, heme oxygenase, was found to be expressed in a highly periodic manner at both the mRNA and protein level. Heme oxygenase generates the biological gas, carbon monoxide (CO), as a product of heme catabolism. It is shown that pulsed administration of CO induces a phase advancement into the oxidative, respiratory phase of the metabolic cycles. This CO-mediated phase advancement takes place only if the gas is administered during the temporal window when it is predicted to be generated. It is further shown that a yeast strain bearing a targeted deletion of the gene encoding heme oxygenase displays protracted metabolic cycles. These observations provide evidence that gaseous CO may function as a cellular signaling molecule that helps cue metabolic cycling.
Measurement of amyloid fibril mass-per-length by tilted-beam transmission electron microscopy
Authors: Chen Bo , Thurber Kent R. , Shewmaker Frank , Wickner Reed B. , Tycko Robert
Published: August 2009

We demonstrate that accurate values of mass-per-length (MPL), which serve as strong constraints on molecular structure, can be determined for amyloid fibrils by quantification of intensities in dark-field electron microscope images obtained in the tilted-beam mode of a transmission electron microscope. MPL values for fibrils formed by residues 218–289 of the HET-s fungal prion protein, for 2-fold- and 3-fold-symmetric fibrils formed by the 40-residue β-amyloid peptide, and for fibrils formed by the yeast prion protein Sup35NM are in good agreement with previous results from scanning transmission electron microscopy. Results for fibrils formed by the yeast prion protein Rnq1, for which the MPL value has not been previously reported, support an in-register parallel β-sheet structure, with one Rnq1 molecule per 0.47-nm β-sheet repeat spacing. Since tilted-beam dark-field images can be obtained on many transmission electron microscopes, this work should facilitate MPL determination by a large number of research groups engaged in studies of amyloid fibrils and similar supramolecular assemblies.
Immunological traits have the potential to improve selection of pigs for resistance to clinical and subclinical disease
Authors: Henryon M. , Heegaard P. M. H. , Nielsen J. , Berg P. , Juul-Madsen H. R.
Published: August 2009

It was reasoned that, if we used a large sample of pigs, we could demonstrate that total and differential numbers of leukocytes, expression levels of swine leukocyte antigens (SLA) I and II, and serum concentrations of IgG and haptoglobin show additive genetic variation and are, therefore, potentially useful as criteria to improve selection of pigs for resistance to clinical and subclinical disease. We tested this premise by assessing 4204 male pigs from the Duroc, Landrace, and Yorkshire breeds for total and differential numbers of leukocytes and serum concentrations of IgG and haptoglobin; 1217 of the Duroc and Landrace pigs were also assessed for expression levels of SLA I and II. We estimated the amount of additive genetic variation by fitting linear animal models to the total and differential numbers of leukocytes and serum concentrations of IgG and haptoglobin. We fitted linear sire models to the expression levels of SLA I and II. We detected additive genetic variation for each group of traits. Total and differential numbers of leukocytes were moderately heritable (h2=0·22 to 0·30), expression levels of SLA I and II were moderate-to-highly heritable (h2=0·46 to 1·23), while serum concentrations of IgG and haptoglobin were lowly heritable (h2=0·14 to 0·16). The additive genetic variation shown for the immunological traits is encouraging for pig breeders. It indicates that these traits are potentially useful as criteria to improve selection of pigs for resistance to clinical and subclinical disease.
Associations of PrP genotypes with live weight and slaughter traits in an experimental flock of Swaledale sheep in Great Britain
Authors: Man W. Y. N. , Brotherstone S. , Merrell B. G. , Murray W. A. , Villanueva B.
Published: August 2009

Polymorphisms at codons 136, 154 and 171 of the gene encoding the prion protein (PrP) are associated with susceptibility to classical scrapie in sheep. Genetic selection for scrapie resistance based on PrP genotypes is central to the scrapie eradication programme in Great Britain but there are concerns about how this may affect other economically important traits. The objective of this study was to evaluate associations of PrP genotypes with live weight and slaughter traits in a hill sheep breed in Great Britain. Data used were from an experimental flock of Swaledale sheep in which the alleles ARR, ARQ, AHQ and VRQ were present. About 1450 genotyped lambs with birth, marking and weaning weights, and 620 with slaughter records were used for the study. Mixed models with various fixed effects and random direct genetic and maternal effects were tested to determine the appropriate model to use for each trait. None of the differences in lamb performance between PrP genotypes consistently reached significance. Therefore, this study does not support existence of significant relationships between PrP genotype and lamb performance traits in this breed.
Responses to supplementation by dairy cows given low pasture allowances in different seasons 1. Pasture intake and substitution
Authors: Penno J. W. , Macdonald K. A. , Holmes C. W. , Davis S. R. , Wilson G. F. , Brookes I. M. , Thom E. R.
Published: August 2009

Two factorial experiments were designed to determine the effects of stage of lactation, and season of the year, on cow responses to supplementary feeding. These experiments were conducted over consecutive years with 128 high genetic merit multiparous Holstein-Friesian cows in early, mid and late lactation in spring, summer, autumn and winter. At each stage of lactation, and in each season of the year, cows were offered a restricted pasture allowance (25 to 35 kg dry matter (DM) per cow per day), either unsupplemented (control) or supplemented with 50 MJ metabolizable energy (ME) per cow per day in experiment 1 and 80 MJ ME per cow per day in experiment 2. Two different supplements were offered, namely, rolled maize grain (MG) and a mixture of foods (BR) formulated to nutritionally balance the diet. In experiment 2, a fourth treatment consisting solely of a generous pasture allowance (60 to 75 kg DM per cow per day, AP) was introduced. Offering MG and BR increased DM intake (DMI). At the restricted pasture allowance, increasing total ME allowance (MEA) by offering supplementary foods increased ME intake (MEI) by 0·68 (s.e. 0·047) MJ per extra MJ ME offered. This highly significant (P<0·001) linear relationship was consistent across seasons, and did not diminish at higher MEA. In experiment 2, cows in early lactation had lower substitution rates than mid and late lactation cows irrespective of season. Substitution rate was higher when higher pasture allowance or quality of pasture on offer enabled the unsupplemented cows to achieve higher DMI from pasture than at other times of the year. These results suggest that one of the key factors determining the intake response to supplementary foods is pasture allowance. Within spring calving dairying systems, the largest increases in total DMI per kg of supplement offered is likely when offering supplements to early lactation cows grazing restricted allowances of high quality pasture.
Responses to supplementation by dairy cows given low pasture allowances in different seasons 2. Milk production
Authors: Penno J. W. , Macdonald K. A. , Holmes C. W. , Davis S. R. , Wilson G. F. , Brookes I. M. , Thom E. R.
Published: August 2009

Two factorial experiments were designed to determine the effects of stage of lactation, and season of the year, on cow responses to supplementary feeding. These experiments were conducted over consecutive years with 128 high genetic merit multiparous Holstein-Friesian cows in early, mid and late lactation in spring, summer, autumn and winter. At each stage of lactation, and in each season of the year, cows were offered a restricted pasture allowance (25 to 35 kg dry matter (DM) per cow per day), either unsupplemented (control) or with supplement at 50 MJ metabolizable energy (ME) per cow per day in experiment 1 and 80 MJ ME per cow per day in experiment 2. The two supplements given in both years were rolled maize grain (MG) and a mixture of foods formulated to nutritionally balance the diet (BR). In experiment 2, another treatment, of a generous pasture allowance (60 to 75 kg DM per cow per day) (AP), was imposed on an additional group of early lactation cows during each season. Direct milk solids (MS) (milk fat plus milk protein) responses in experiment 1 to MG were 169, 279, 195 and 251 g MS per cow per day in spring, summer, autumn and winter, respectively, while those to BR were 107, 250, 192, 289 g MS per cow per day. In experiment 2, however, milk solids responses to both supplements during spring were slightly below the control treatment, with values similar to those in experiment 1 in summer and autumn for cows on the BR but not the MG supplement. Milk solids responses to supplementary foods were largest during seasons of the year when the quantity and quality of pasture on offer resulted in the lowest milk solids yield from unsupplemented cows. When carry-over effects of feeding MG and BR on milk solids production were detected, they were only about half the magnitude of the direct effects. Serum urea concentrations were higher in control cows than those offered MG with a similar effect for BR in all but summer in experiment 1, while serum glucose concentrations were highest in winter and lowest in summer. The most important factor influencing milk solids responses was the relative food deficit (RFD) represented by the decline in milk solids yield of the respective control groups after changing from a generous pasture allowance to restricted allowance when the feeding treatments were imposed. Total milk solids responses (direct and carry-over) to supplements were greatest when severe food restrictions, relative to the cows' current food demand, resulted in large reductions in milk solids yield of the control groups. The RFD was the best predictor of milk solids response to supplementary foods. Therefore, it is likely that cows are most responsive to supplementary foods during or immediately after the imposition of a severe food restriction.
Response of growing pigs toPeniophora lycii- andEscherichia coli-derived phytases or varying ratios of calcium to total phosphorus
Authors: Adeola O. , Olukosi O. A. , Jendza J. A. , Dilger R. N. , Bedford M. R.
Published: August 2009

Two experiments were conducted to study the effects of phytase derived fromEscherichia coli(ECP) andPeniophora lycii(PLP) on performance, nutrient digestibility, and phosphorus (P) equivalency values of young pigs; and the influence of varying ratios of calcium (Ca) to total phosphorus (Ca:tP) with or without ECP on growth performance of pigs. In each experiment, 48 10-kg pigs were housed in individual pens for 28 days. Experiment 1 was designed to study the efficacy of ECP and PLP in improving growth performance and bone mineralization of young pigs given a low inorganic P (iP) diet. In the experiment, pigs were blocked by weight and sex and randomly allocated to eight dietary treatments. Each treatment had six replicates. The treatments were a positive control with adequate iP (PC); a low iP negative control (NC) diet; NC with supplemental iP in the form of monosodium phosphate added to provide 0·75 or 1·50 g iP per kg diet (as-fed basis); NC with ECP or PLP added at 500 or 1000 FTU per kg (as-fed basis; one phytase unit or FTU is defined as the quantity of enzyme required to liberate 1 μmol of iP per min, at pH 5·5, from an excess of 15 μmol/l sodium phytate at 37°C). In experiment 2, the objective was to study the effect of varying Ca:tP ratio with or without ECP on growth performance of growing pigs. Pigs (eight replicates) were blocked by weight and sex and randomly assigned to six dietary treatments in a 3×2 factorial arrangement of Ca:tP ratios at 1·2, 1·5, or 1·8; and ECP at 0 or 1000 FTU per kg (as-fed basis). In experiment 1, ECP (P<0·001) and PLP (P<0·05) linearly increased daily gain. There was a positive linear (P<0·05) response to the supplementation of the NC diet with ECP or PLP in the mineralization of the third and fourth metacarpal bones. Phosphorus equivalency values for 500 FTU of ECP or PLP based on mineralization of the third metacarpal bone were 0·77 g or 0·572 g, respectively. There were linear (P<0·001) and quadratic (P<0·05) responses to ECP, and linear (P<0·01) response to PLP in P digestibility. Neither iP supplementation nor either of the two phytases had significant effects on digestibility of dry matter, protein or energy. In experiment 2, reducing Ca:tP ratio linearly improved (P<0·05) daily gain, food intake, and food efficiency in pigs regardless of phytase supplementation. There was an enzyme by Ca:tP interaction on food intake. These studies in young pigs showed that ECP and PLP were efficacious in improving the growth performance and bone mineralization and that reducing the Ca:tP ratio enhanced performance response to phytase supplementation.