bluuebunny/crossref_metadata_2025 huggingface dataset:
Elucidation of the mechanism of mitochondrial iron loading in Friedreich's ataxia by analysis of a mouse mutant
Authors: Huang Michael Li-Hsuan , Becker Erika M. , Whitnall Megan , Rahmanto Yohan Suryo , Ponka Prem , Richardson Des R.
Published: September 2009

We used the muscle creatine kinase (MCK) conditional frataxin knockout mouse to elucidate how frataxin deficiency alters iron metabolism. This is of significance because frataxin deficiency leads to Friedreich's ataxia, a disease marked by neurologic and cardiologic degeneration. Using cardiac tissues, we demonstrate that frataxin deficiency leads to down-regulation of key molecules involved in 3 mitochondrial utilization pathways: iron-sulfur cluster (ISC) synthesis (iron-sulfur cluster scaffold protein1/2 and the cysteine desulferase Nfs1), mitochondrial iron storage (mitochondrial ferritin), and heme synthesis (5-aminolevulinate dehydratase, coproporphyrinogen oxidase, hydroxymethylbilane synthase, uroporphyrinogen III synthase, and ferrochelatase). This marked decrease in mitochondrial iron utilization and resultant reduced release of heme and ISC from the mitochondrion could contribute to the excessive mitochondrial iron observed. This effect is compounded by increased iron availability for mitochondrial uptake through (i) transferrin receptor1 up-regulation, increasing iron uptake from transferrin; (ii) decreased ferroportin1 expression, limiting iron export; (iii) increased expression of the heme catabolism enzyme heme oxygenase1 and down-regulation of ferritin-H and -L, both likely leading to increased “free iron” for mitochondrial uptake; and (iv) increased expression of the mammalian exocyst protein Sec15l1 and the mitochondrial iron importer mitoferrin-2 (Mfrn2), which facilitate cellular iron uptake and mitochondrial iron influx, respectively. Our results enable the construction of a model explaining the cytosolic iron deficiency and mitochondrial iron loading in the absence of frataxin, which is important for understanding the pathogenesis of Friedreich's ataxia.
Genetic perturbation of postsynaptic activity regulates synapse elimination in developing cerebellum
Authors: Lorenzetto Erika , Caselli Luana , Feng Guoping , Yuan Weilong , Nerbonne Jeanne M. , Sanes Joshua R. , Buffelli Mario
Published: September 2009

In many parts of the vertebrate nervous system, synaptic connections are remodeled during early postnatal life. Neural activity plays an important role in regulating one such rearrangement, synapse elimination, in the developing neuromuscular system, but there is little direct evidence on roles of pre- or postsynaptic activity in regulating synapse elimination in the developing brain. To address this issue, we expressed a chloride channel-yellow fluorescent protein fusion in cerebellar Purkinje cells (PCs) of transgenic mice to decrease their excitability. We then assessed elimination of supernumerary climbing fiber inputs to PCs. Individual PCs are innervated by multiple climbing fibers at birth; all but one are eliminated during the first three postnatal weeks in wild-type mice, but multiple innervation persists for at least three months in the transgenic mice. The normal redistribution of climbing fiber synapses from PC somata to proximal dendrites was also blunted in transgenics. These results show that normal electrical activity of the postsynaptic cell is required for it to attain a mature innervation pattern.
Chemoenzymatic synthesis of GDP-
l
-fucose and the Lewis X glycan derivatives
Authors: Wang Wei , Hu Tianshun , Frantom Patrick A. , Zheng Tianqing , Gerwe Brian , del Amo David Soriano , Garret Sarah , Seidel Ronald D. , Wu Peng
Published: September 2009

Lewis X (Le
x
)-containing glycans play important roles in numerous cellular processes. However, the absence of robust, facile, and cost-effective methods for the synthesis of Le
x
and its structurally related analogs has severely hampered the elucidation of the specific functions of these glycan epitopes. Here we demonstrate that chemically defined guanidine 5′-diphosphate-β-
l
-fucose (GDP-fucose), the universal fucosyl donor, the Le
x
trisaccharide, and their C-5 substituted derivatives can be synthesized on preparative scales, using a chemoenzymatic approach. This method exploits
l
-fucokinase/GDP-fucose pyrophosphorylase (FKP), a bifunctional enzyme isolated from
Bacteroides fragilis
9343, which converts
l
-fucose into GDP-fucose via a fucose-1-phosphate (Fuc-1-P) intermediate. Combining the activities of FKP and a
Helicobacter pylori
α1,3 fucosyltransferase, we prepared a library of Le
x
trisaccharide glycans bearing a wide variety of functional groups at the fucose C-5 position. These neoglycoconjugates will be invaluable tools for studying Le
x
-mediated biological processes.
An Armadillo motif in Ufd3 interacts with Cdc48 and is involved in ubiquitin homeostasis and protein degradation
Authors: Zhao Gang , Li Guangtao , Schindelin Hermann , Lennarz William J.
Published: September 2009

The yeast AAA-ATPase Cdc48 and the ubiquitin fusion degradation (UFD) proteins play important, evolutionarily conserved roles in ubiquitin dependent protein degradation. The N-terminal domain of Cdc48 interacts with substrate-recruiting cofactors, whereas the C terminus of Cdc48 binds to proteins such as Ufd3 that process substrates. Ufd3 is essential for efficient protein degradation and for maintaining cellular ubiquitin levels. This protein contains an N-terminal WD40 domain, a central ubiquitin-binding domain, and a C-terminal Cdc48-binding PUL domain. The crystal structure of the PUL domain reveals an Armadillo repeat with high structural similarity to importin-α, and the Cdc48-binding site could be mapped to the concave surface of the PUL domain by biochemical studies. Alterations of the Cdc48 binding site of Ufd3 by site-directed mutagenesis resulted in a depletion of cellular ubiquitin pools and reduced activity of the ubiquitin fusion degradation pathway. Therefore, our data provide direct evidence that the functions of Ufd3 in ubiquitin homeostasis and protein degradation depend on its interaction with the C terminus of Cdc48.
Limited terminal transferase in human DNA polymerase μ defines the required balance between accuracy and efficiency in NHEJ
Authors: Andrade Paula , Martín María José , Juárez Raquel , López de Saro Francisco , Blanco Luis
Published: September 2009

DNA polymerase mu (Polμ) is a family X member implicated in DNA repair, with template-directed and terminal transferase (template-independent) activities. It has been proposed that the terminal transferase activity of Polμ can be specifically required during non-homologous end joining (NHEJ) to create or increase complementarity of DNA ends. By site-directed mutagenesis in human Polμ, we have identified a specific DNA ligand residue (Arg
387
) that is responsible for its limited terminal transferase activity compared to that of human TdT, its closest homologue (42% amino acid identity). Polμ mutant R387K (mimicking TdT) displayed a large increase in terminal transferase activity, but a weakened interaction with ssDNA. That paradox can be explained by the regulatory role of Arg
387
in the translocation of the primer from a non-productive E:DNA complex to a productive E:DNA:dNTP complex in the absence of a templating base, which is probably the rate limiting step during template-independent synthesis. Further, we show that the Polμ switch from terminal transferase to templated insertions in NHEJ reactions is triggered by recognition of a 5′-P at a second DNA end, whose 3′-protrusion could provide a templating base to facilitate such a special “pre-catalytic translocation step.” These studies shed light on the mechanism by which a rate-limited terminal transferase activity in Polμ could regulate the balance between accuracy and necessary efficiency, providing some variability during NHEJ.
Metalloproteinase MT5-MMP is an essential modulator of neuro-immune interactions in thermal pain stimulation
Authors: Folgueras Alicia R. , Valdés-Sánchez Teresa , Llano Elena , Menéndez Luis , Baamonde Ana , Denlinger Bristol L. , Belmonte Carlos , Juárez Lucía , Lastra Ana , García-Suárez Olivia , Astudillo Aurora , Kirstein Martina , Pendás Alberto M. , Fariñas Isabel , López-Otín Carlos
Published: September 2009

Peripheral interactions between nociceptive fibers and mast cells contribute to inflammatory pain, but little is known about mechanisms mediating neuro-immune communication. Here we show that metalloproteinase MT5-MMP (MMP-24) is an essential mediator of peripheral thermal nociception and inflammatory hyperalgesia. We report that MT5-MMP is expressed by CGRP-containing peptidergic nociceptors in dorsal root ganglia and that Mmp24-deficient mice display enhanced sensitivity to noxious thermal stimuli under basal conditions. Consistently, mutant peptidergic sensory neurons hyperinnervate the skin, a phenotype that correlates with changes in the regulated cleavage of the cell-cell adhesion molecule N-cadherin. In contrast to basal nociception, Mmp24
−/−
mice do not develop thermal hyperalgesia during inflammation, a phenotype that appears associated with alterations in N-cadherin-mediated cell-cell interactions between mast cells and sensory fibers. Collectively, our findings demonstrate an essential role of MT5-MMP in the development of dermal neuro-immune synapses and suggest that this metalloproteinase may be a target for pain control.
Phosphoinositides and SNARE chaperones synergistically assemble and remodel SNARE complexes for membrane fusion
Authors: Mima Joji , Wickner William
Published: September 2009

Yeast vacuole fusion requires 4 SNAREs, 2 SNARE chaperone systems (Sec17p/Sec18p/ATP and the HOPS complex), and 2 phosphoinositides, phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P
2
]. By reconstituting proteoliposomal fusion with purified components, we now show that phosphoinositides have 4 distinct roles: PI(3)P is recognized by the PX domain of the SNARE Vam7p; PI(3)P enhances the capacity of membrane-bound SNAREs to drive fusion in the absence of SNARE chaperones; either PI(3)P or PI(4,5)P
2
can activate SNARE chaperones for the recruitment of Vam7p into fusion-competent SNARE complexes; and either PI(3)P or PI(4,5)P
2
strikingly promotes synergistic SNARE complex remodeling by Sec17p/Sec18p/ATP and HOPS. This ternary synergy of phosphoinositides and 2 SNARE chaperone systems is required for rapid fusion.
Differential but convergent functions of Ca
2+
binding to synaptotagmin-1 C
2
domains mediate neurotransmitter release
Authors: Shin Ok-Ho , Xu Jun , Rizo Josep , Südhof Thomas C.
Published: September 2009

Neurotransmitter release is triggered by cooperative Ca
2+
-binding to the Ca
2+
-sensor protein synaptotagmin-1. Synaptotagmin-1 contains two C2 domains, referred to as the C2A and C2B domains, that bind Ca
2+
with similar properties and affinities. However, Ca
2+
binding to the C2A domain is not required for release, whereas Ca
2+
binding to the C2B domain is essential for release. We now demonstrate that despite its expendability, Ca
2+
-binding to the C2A domain significantly contributes to the overall triggering of neurotransmitter release, and determines its Ca
2+
cooperativity. Biochemically, Ca
2+
induces more tight binding of the isolated C2A domain than of the isolated C2B domain to standard liposomes composed of phosphatidylcholine and phosphatidylserine. However, here we show that surprisingly, the opposite holds true when the double C2A/B-domain fragment of synaptotagmin-1 is used instead of isolated C2 domains, and when liposomes containing a physiological lipid composition are used. Under these conditions, Ca
2+
binding to the C2B domain but not the C2A domain becomes the primary determinant of phospholipid binding. Thus, the unique requirement for Ca
2+
binding to the C2B domain for synaptotagmin-1 in Ca
2+
-triggered neurotransmitter release may be accounted for, at least in part, by the unusual phospholipid-binding properties of its double C2A/B-domain fragment.
Louis Reichardt: The long climb to science's summits
Authors: LeBrasseur Nicole
Published: September 2009

From the highest mountains to biology's own Everest—the brain—Reichardt tackles the biggest challenges of climbing and biology.
Paraspeckles: nuclear bodies built on long noncoding RNA
Authors: Bond Charles S. , Fox Archa H.
Published: September 2009

Paraspeckles are ribonucleoprotein bodies found in the interchromatin space of mammalian cell nuclei. These structures play a role in regulating the expression of certain genes in differentiated cells by nuclear retention of RNA. The core paraspeckle proteins (PSF/SFPQ, P54NRB/NONO, and PSPC1 [paraspeckle protein 1]) are members of the DBHS (Drosophila melanogaster behavior, human splicing) family. These proteins, together with the long nonprotein-coding RNA NEAT1 (MEN-ε/β), associate to form paraspeckles and maintain their integrity. Given the large numbers of long noncoding transcripts currently being discovered through whole transcriptome analysis, paraspeckles may be a paradigm for a class of subnuclear bodies formed around long noncoding RNA.
Minority heating by ICRH: a tool for investigating burning plasma physics in FAST
Authors: Cardinali A. , Briguglio S. , Calabrò G. , Crisanti F. , Di Troia C. , Fogaccia G. , Marinucci M. , Vlad G. , Zonca F.
Published: September 2009

A combined Fokker–Planck numerical analysis of the quasi-linear plasma–ion-cyclotron (IC) wave interaction and collisional relaxation of minority ion tails created by IC absorption was performed in order to determine the characteristic fast-ion parameters that are necessary for addressing some of the main ITER burning plasma physics issues, e.g. fast-ion transport due to collective mode excitations, cross-scale couplings of micro-turbulence with meso-scale fluctuations due to energetic particles, etc. These investigations refer to actual scenarios of the Fusion Advanced Studies Torus (FAST), a conceptual tokamak design operating with deuterium plasmas in a dimensionless parameter range similar to that of ITER and equipped with IC resonance heating (ICRH) as a main heating scheme. The destabilization and saturation of fast-ion driven Alfvénic modes below and above the energetic particle modes stability threshold are investigated by numerical simulations with the HMGC code, which assumes the anisotropic energetic particle distribution function accelerated by ICRH as input. The results of this study, obtained by integration of different numerical simulation analyses aimed at investigating the various relevant physics, are presented and discussed.
Numerical simulations of fast ion loss measurements induced by magnetic islands in the ASDEX Upgrade tokamak
Authors: Gobbin M. , Marrelli L. , Fahrbach H.U. , Garcia-Muñoz M. , Günter S. , Martin P. , White R.B.
Published: September 2009

A test particle approach, implemented with the Hamiltonian code ORBIT, is used to simulate measurements of fast ion losses induced by magnetic islands in the ASDEX Upgrade tokamak. In particular, the numerical simulations reproduce the toroidal localization of losses and the lost ions pitch angle and energy distribution experimentally measured with the fast ion losses detector (FILD) in the presence of a neoclassical tearing mode (NTM). The simulated NTM induced losses occurring on time scales longer than 100 µs are composed of mainly trapped or barely passing particles, consistently with the slow decay of the experimental signal from one FILD channel after the beam switch-off. The numerical simulations have been performed by taking into account the D-shaped plasma geometry, the collision mechanisms, the losses due to ripple effects and the rotation of the mode. The radial profile of the magnetic perturbation is adjusted in order to match ECE measurements. While statistical properties of FILD measurements are rather well reproduced, the simulated total amount of losses is found to be significantly affected by edge details of the magnetic perturbation as it determines the loss mechanism.
In-vessel surface layer evolution during plasma–wall interaction in the Globus-M spherical tokamak
Authors: Gusev V.K. , Alimov V.Kh. , Arkhipov I.I. , Ber B.Ya. , Gorodetsky A.E. , Khromov N.A. , Kurdumov A.A. , Lebedev V.M. , Litunovsky N.V. , Mazul I.V. , Nikolaev Yu.A. , Novokhatsky A.N. , Petrov Yu.V. , Sakharov N.V. , Terukov E.I. , Trapeznikova I.N. , Zakharov A.P. , Zalavutdinov R.Kh.
Published: September 2009

The composition, morphology and structure of the mixed layers deposited onto the surface (deposits) after a preliminary carboboronization procedure (B/C : H layers deposition) and subsequent plasma–wall interaction in the different areas of the Globus-M spherical tokamak have been analysed. Globus-M is almost completely covered by recrystallized graphite protection tiles (currently about 90% of its inner vessel area facing to plasma). The deposit properties were examined by different diagnostic techniques (electron probe microanalysis, scanning electron microscope, x-ray diffraction, nuclear resonance reactions, thermal desorption spectroscopy, infrared Raman scattering and secondary ion mass spectroscopy) after sample exposure to plasma during 3000–10000 tokamak pulses. It was found that deposits existed even in high flux regions (separatrix strike points). The initial composition of the protective layers formed during boronization is dramatically modified during long-term plasma–wall interaction and resulted in significant intermixing of its components with materials of the vessel interior. The properties of the layers deposited onto the surfaces intensively interacting with plasma, as well as the composition of the layers deposited in the ‘shadowed’ zones are discussed. Deuterium retention in Globus-M was estimated relying upon the data on deuterium concentrations in the deposits that were measured by different methods. It is revealed that deuterium was absorbed only in the deposits and its concentration vanished in the bulk of the tiles. Conditions of deuterium desorption are analysed and the merits of recrystallized graphite are discussed.
Nonlinear dynamics of a collapse phenomenon in heliotron plasma with large pressure gradient
Authors: Mizuguchi N. , Suzuki Y. , Ohyabu N.
Published: September 2009

We have executed nonlinear magnetohydrodynamic simulations in a heliotron-type configuration with a large pressure gradient to reveal the nonlinear dynamics of a collapse phenomenon. The simulation results reproduce the qualitative characteristics of the experimental observation on the so-called core density collapse events in the Large Helical Device plasma with the super-dense core profile. A long-term nonlinear behaviour on the event, including the flushing mechanism of the core pressure, is clarified. The simulation result shows the linear growth of the ballooning-like resistive instability modes with the intermediate poloidal wavenumbers. The growth of the modes are eventually saturated, and the system experiences the energy relaxation in about 1 ms. It should be noted that the linear mode structures are localized in the edge region, whereas the core pressure rapidly falls as the system reaches the relaxed state. Such coexistence of the edge perturbation and the core collapse is consistent with the experimental observations. The lost pressure forms a wide base in the peripheral region. The core pressure is, on the other hand, remarkably reduced at a certain period, although it had well withstood the disturbance before it. The most salient feature on this period is the disordering of the magnetic field structure. The system keeps the nested-flux-surface structure well at the beginning, whereas part of them are abruptly lost in this period. Such a situation can induce a flattening of the pressure profile along the reconnected field lines. By checking the place where the plasma loss due to this mechanism occurs, such plasma outlets are found to be located mainly on the disordered region. Thus, one can conclude that the core collapse can be caused by the disturbance of the magnetic field.
Dynamics of ion internal transport barrier in LHD heliotron and JT-60U tokamak plasmas
Authors: Ida K. , Sakamoto Y. , Yoshinuma M. , Takenaga H. , Nagaoka K. , Hayashi N. , Oyama N. , Osakabe M. , Yokoyama M. , Funaba H. , Tamura N. , Tanaka K. , Takeiri Y. , Ikeda K. , Tsumori K. , Kaneko O. , Itoh K. , Inagaki S. , Kobuchi T. , Isayama A. , Suzuki T. , Fujita T. , Matsunaga G. , Shinohara K. , Koide Y. , Yoshida M. , Ide S. , Kamada Y.
Published: September 2009

Dynamics of ion internal transport barrier (ITB) formation and impurity transport both in the Large Helical Device (LHD) heliotron and in the JT-60U tokamak are described. Significant differences between heliotron and tokamak plasmas are observed. The location of the ITB moves outwards during the ITB formation regardless of the sign of magnetic shear in JT-60U, and the ITB becomes more localized in plasmas with negative magnetic shear. In LHD, a low T
e/T
i ratio (<1) of the target plasma with high power heating is found to be necessary to achieve the ITB plasma and the ITB location tends to expand outwards or inwards depending on the condition of the target plasmas. Associated with the formation of the ITB, the carbon density tends to be peaked due to inward convection in JT-60U while the carbon density becomes hollow due to outward convection in LHD. The outward convection observed in LHD contradicts the prediction by neoclassical theory.
Limitations, insights and improvements to gyrokinetics
Authors: Catto Peter J. , Parra Felix I. , Kagan Grigory , Simakov Andrei N.
Published: September 2009

We first consider gyrokinetic quasineutrality limitations when evaluating the axisymmetric radial electric field in a non-turbulent tokamak by an improved examination of intrinsic ambipolarity. We next prove that the background ions in a pedestal of poloidal ion gyroradius scale must be Maxwellian and nearly isothermal in Pfirsch–Schlüter and banana regime tokamak plasmas, and then consider zonal flow behaviour in a pedestal. Finally, we focus on a simplifying procedure for our transport time scale hybrid gyrokinetic-fluid treatment that removes the limitations of gyrokinetic quasineutrality and remains valid in the pedestal.
Investigation of electron Bernstein wave (EBW) coupling and its critical dependence on EBW collisional loss in high-β, H-mode ST plasmas
Authors: Diem S.J. , Taylor G. , Caughman J.B. , Efthimion P.C. , Kugel H. , LeBlanc B.P. , Phillips C.K. , Preinhaelter J. , Sabbagh S.A. , Urban J. , Wilgen J.B.
Published: September 2009

High-β spherical tokamak (ST) plasma conditions cut off propagation of electron cyclotron (EC) waves used for heating and current drive in conventional aspect ratio tokamaks. The electron Bernstein wave (EBW) has no density cutoff and is strongly absorbed and emitted at the EC harmonics, allowing EBWs to be used for heating and current drive in STs. However, this application requires efficient EBW coupling in the high-β, H-mode ST plasma regime. EBW emission (EBE) diagnostics and modelling have been employed on the National Spherical Torus Experiment (NSTX) to study oblique EBW to O-mode (B–X–O) coupling and propagation in H-mode plasmas. Efficient EBW coupling was measured before the L–H transition, but rapidly decayed thereafter. EBE simulations show that EBW collisional damping prior to mode conversion (MC) in the plasma scrape off reduces the coupling efficiency during the H-mode phase when the electron temperature is less than 30 eV inside the MC layer. Lithium evaporation during H-mode plasmas was successfully used to reduce this EBW collisional damping by reducing the electron density and increase the electron temperature in the plasma scrape off. Lithium conditioning increased the measured B–X–O coupling efficiency from less than 10% to 60%, consistent with EBE simulations.
Fabrication of aerogel capsule, bromine-doped capsule, and modified gold cone in modified target for the Fast Ignition Realization Experiment (FIREX) Project
Authors: Nagai Keiji , Yang H. , Norimatsu T. , Azechi H. , Belkada F. , Fujimoto Y. , Fujimura T. , Fujioka K. , Fujioka S. , Homma H. , Ito F. , Iwamoto A. , Jitsuno T. , Kaneyasu Y. , Nakai M. , Nemoto N. , Saika H. , Shimoyama T. , Suzuki Y. , Yamanaka K. , Mima K.
Published: September 2009

The development of target fabrication for the Fast Ignition Realization EXperiment (FIREX) Project is described in this paper. For the first stage of the FIREX Project (FIREX-I), the previously designed target has been modified by using a bromine-doped ablator and coating the inner gold cone with a low-density material. A high-quality bromine-doped capsule without vacuoles was fabricated from bromine-doped deuterated polystyrene. The gold surface was coated with a low-density material by electrochemical plating. For the cryogenic fuel target, a brand new type of aerogel material, phloroglucinol/formaldehyde (PF), was investigated and encapsulated to meet the specifications of 500 µm diameter and 20 µm thickness, with 30 nm nanopores. Polystyrene-based low-density materials were investigated and the relationship between the crosslinker content and the nanopore structure was observed.
In vivo quantitation of metabolites with an incomplete model function
Authors: Popa E , Capobianco E , de Beer R , van Ormondt D , Graveron-Demilly D
Published: September 2009

Metabolites can serve as biomarkers. Estimation of metabolite concentrations from an in vivo magnetic resonance spectroscopy (MRS) signal often uses a reference signal to estimate a model function of the spectral lineshape. When no reference signal is available, the a priori unknown in vivo lineshape must be inferred from the data at hand. This makes quantitation of metabolites from in vivo MRS signals a semi-parametric estimation problem which, in turn, implies setting of hyper-parameters by users of the software involved. Estimation of metabolite concentrations is usually done by nonlinear least-squares (NLLS) fitting of a physical model function based on minimizing the residue. In this work, the semi-parametric task is handled by complementing the usual criterion of minimal residue with a second criterion acting in tandem with it. This second criterion is derived from the general physical knowledge that the width of the line is limited. The limit on the width is a hyper-parameter; its setting appeared not critical so far. The only other hyper-parameter is the relative weight of the two criteria. But its setting too is not critical. Attendant estimation errors, obtained from a Monte Carlo calculation, show that the two-criterion NLLS approach successfully handles the semi-parametric aspect of metabolite quantitation.
Synchrotron-Radiation Photoemission Study of Growth and Stability of Au Clusters on Rutile TiO2(110)-1 1
Authors: Yu Xin , Xu Ling-shun , Zhang Wen-hua , Jiang Zhi-quan , Zhu Jun-fa , Huang Wei-xin
Published: September 2009

The growth and thermal stability of Au clusters on a partially-reduced rutile TiO2(110)-1 1 surface were investigated by high-resolution photoelectron spectroscopy using synchrotron-radiation-light. The valence-band photoelectron spectroscopy results demonstrate that the Ti3+3d feature attenuates quickly with the initial deposition of Au clusters, implying that Au clusters nucleate at the oxygen vacancy sites. The Au4f core-level photoelectron spectroscopy results directly prove the existence of charge transfer from oxygen vacancies to Au clusters. The thermal stability of Au clusters on the partially-reduced and stoichiometric TiO2(110) surfaces was also comparatively investigated by the annealing experiments. With the same film thickness, Au clusters are more thermally stable on the partially-reduced TiO2(110) surface than on the stoichiometric TiO2(110) surface. Meanwhile, large Au nanoparticles are more thermally stable than fine Au nanoparticles.
Resonance Raman Study of AggregatedMeso-tetra(4-pyridinium)porphyrin Diacid
Authors: Li Zun-yun , Lu Tong-tong , He Tian-jing , Liu Fan-chen , Chen Dong-ming
Published: September 2009

Resonance Raman spectra of aggregated meso-tetra(4-pyridinium)porphyrin diacid (H8TPyP6+) were studied with excitation near the exciton absorption bands of 470 nm. The UV-Vis absorption and resonance light scattering spectra of H8TPyP6+ monomers and aggregates were also measured. The observed Raman bands of monomeric and aggregated H8TPyP6+ were assigned on the basis of the observed deuteration shifts and by comparing with the Raman spectra of analogous porphyrin diacids. Aggregation causes moderate downshifts (26 cm1) for high-frequency modes involving the in-plane CC/CN stretches of the porphyrin core and a dramatic upshift (12 cm1) for the out-of-plane saddling mode of the porphyrin ring. The structural changes induced by aggregation and the possible hydrogen bonding interaction between the H8TPyP6+ molecules in the aggregate are discussed based on the spectral observations.
Raman Spectroscopy of Nitrogen Clathrate Hydrates
Authors: Liu Chang-ling , Lu Hai-long , Ye Yu-guang
Published: September 2009

Nitrogen hydrate samples were synthesized using liquid nitrogen and powder ice at 16 MPa and 253 K. Confocal laser Raman spectroscopy was used to investigate the characteristics of nitrogen clathrate hydrates. The results show that the Raman peaks of NN and OH stretching vibration in nitrogen hydrates are observed at 2322.4 and 3092.1 cm1, respectively, which are very similar to those in natural air clathrate hydrates. For comparison, we measured the Raman peaks of NN stretching vibration both in liquid nitrogen and nitrogen molecules saturated water, which appear at 2326.6 and 2325.0 cm1, respectively. The Raman spectroscopic observations on the dissociation process suggest that nitrogen molecules occupy both the large and small cages in nitrogen clathrate hydrates. However, only one Raman peak is observed for NN stretching vibration because the difference of the environment of nitrogen molecules between large and small cages is too small to be differentiated by Raman spectroscopy.
Fluctuation Resonance of Feed Forward Loops in Gene Regulatory Networks
Authors: Dong Yi , Hou Zhong-huai , Xin Hou-wen
Published: September 2009

The feed forward loop (FFL), wherein a gene X can regulate target gene Z alone or cooperatively with gene Y, is one of the most important motifs in gene regulatory networks. Gene expression often involves a small number of reactant molecules and thus internal molecular fluctuation is considerable. Here we studied how an FFL responds to small external signal inputs at gene X, with particular attention paid to the fluctuation resonance (FR) phenomenon of gene Z. We found that for all coherent FFLs, where the sign of the direct regulation path from X to Z is the same as the overall sign of the indirect path via Y, the FR shows a regular single peak, while for incoherent FFLs, the FR exhibits distinct bimodal shapes. The results indicate that one could use small external signals to help identify the regulatory structure of an unknown FFL in complex gene networks.
Effect of Excited-state Substituent Constant on the UV Spectra of 1,4-disubstituted Benzenes
Authors: Chen Guan-fan , Cao Chen-zhong
Published: September 2009

A correlation equation between the UV absorption wavenumbers of 1,4-disubstituted benzenes and the excited-state substituent constant was obtained. For 80 sorts of 1,4-disubstituted benzenes, the correlation coefficient was 0.9805, and the standard deviation was only 672.27 cm1. The results imply that the excited-state substituent constant can be used productively for research on UV energy of 1,4-disubstituted benzenes. The present method provides a new avenue to study the UV absorption spectra of aromatic systems with the excited-state substituent constant, and it is helpful to understand the effect of substituent electrostatic effects on the chemical and physical properties of conjugated compounds with multiple substituents in excited state.
Density Functional Study on Relative Energies, Structures, and Bonding of Low-lying Electronic States of Lutetium Dimer
Authors: Xia Qiong-qiong , Xiao Wei , Zhang Yong-fan , Ning Li-xin , Cui Zhi-feng
Published: September 2009

Low-lying electronic states of the lutetium dimer (Lu2) were studied based on density functional theory (DFT) using ten different density functionals together with three different relativistic effective core pseudopotentials (RECPs). Relative state energies, equilibrium bond lengths, vibrational frequencies, and ground-state dissociation energies were evaluated. It was found that the ground state is a triplet state irrespective of the type of functional and RECP used. This result is in contrast with a previous DFT calculation which gave a singlet ground state for Lu2. By comparing with the high-level ab initio and available experimental results, it is evident that the hybrid-GGA functionals combined with the Stuttgart small-core RECP yield the best overall agreement for the properties under study. The effects of HartreeFock exchange in B3LYP functional on the calculated bond length and dissociation energy of the ground state were examined, and rationalized in terms of 5d participation in LuLu covalent bonding.
Density Functional Study of Physical and Chemical Properties of Nano Size Boron Clusters: Bn(n= 1320)
Authors: Atis Murat , Ozdosan Cem , B. Guvenc Ziya
Published: September 2009

Boron is an element that has ability to build strong and highly directional bonds with boron itself. As a result, boron atoms form diverse structural motifs, ultimately can yield distinct nano structures, such as planar, quasi-planar, convex, cage, open-cage, tubular, spherical, ring, dome-like, shell, capsule, and so on, i.e., it can take almost any shape. Therefore, a deep understanding of the physical and chemical properties becomes important in boron cluster chemistry. Electronic and geometric structures, total and binding energies, harmonic frequencies, point symmetries, charge distributions, dipole moments, chemical bondings and the highest occupied molecular orbitallowest unoccupied molecular orbital energy gaps of neutral Bn (n = 1320) clusters have been investigated by density functional theory (DFT), B3LYP with 6311+ + G(d,p) basis set. Furthermore, the first and the second energy differences are used to obtain the most stable sizes. We have observed that almost all physical properties are size dependent, and double-ring tubular form of B20 has the highest binding energy per atom. The icosahedral structure with an inside atom is found as impossible as a stable structure for the size thirteen. This structure transforms to an open-cage form. The structural transition from two-dimensional to three-dimensional is found at the size of 20 and consistent with the literature. The calculated charges by the Mulliken analysis show that there is a symmetry pattern with respect to the x-z and y-z planes for the charge distributions. The unusual planar stability of the boron clusters may be explained by the delocalized and bonding characteristic together with the existence of the multicentered bonding. The results have been compared to available studies in the literature.
Optical Properties of Neutral and Charged Low Band Gap Alternating Copolyfluorenes: TD-DFT Investigation
Authors: Ding Yong , Zhao Jun-feng , Wang Xiang-si , Liu Sha-sha , Ma Feng-cai
Published: September 2009

Electronic structure and optical properties of neutral and charged low band gap alternating copolyfluorenes (Green 1, which is based on alternating repeating units consisting of alkyl-substituted fluorene and a thiophene-[1,2,5]thiadiazolo-[3,4]quinoxaline-thiophene (T-TDQ-T) unit were investigated theoretically with time-dependent density functional theory (TD-DFT) method, and their excited state properties were further analyzed with 2D site and 3D cube representations. For neutral Green 1, the band gap, binding energy, exciton binding energy, and nuclear relaxation energy were obtained. The transition dipole moments of neutral and charged Green 1 are compared using 3D transition density, which reveals the orientation and strength of transition dipole moments. The charge redistribution of neutral and charged Green 1 upon excitation are displayed and compared with 3D charge difference density. The electron-hole coherences of neutral and charged Green 1 upon excitation are investigated with 2D site representation (transition density matrix). The excited state properties of neutral Green 1 calculated with TD-DFT method are compared with that calculated with ZINDO method, which reveals the importance of electron-electron interaction (in TD-DFT) in the excited state properties.
Density Functional Study on Structures and Relative Stability of Gd(H2O)n3+ (n= 8,9)
Authors: Xiao Wei , Xia Qiong-qiong , Zhang Yong-fan , Ning Li-xin , Cui Zhi-feng
Published: September 2009

Density functional theory calculations were performed to study the structures and relative stability of the gadolinium complexes, Gd(H2O)n3+ (n = 8,9), in vacuo and in aqueous solution. The polarizable continuum model with various radii for the solute cavity was used to study the relative stability in aqueous solution. The calculated molecular geometries for n = 8 and 9 obtained in vacuo are consistent with those observed in experiments. It was found that while the nona-aqua complex is favored in the gas phase, in aqueous solution the octa-aqua conformation is preferred. This result, independent of the types of cavities employed, is in agreement with the experimental observation. The reliability of the present calculation was also addressed by comparing the calculated and experimental free energy of hydration, which revealed that the UA0, UAHF, and UAKS cavities are most appropriate when only the first solvation shell is treated explicitly.
Symmetry Analysis of an X-palindrome in Human and Chimpanzee
Authors: Qi Yan-jiao , Qiu Wen-yuan
Published: September 2009

We analyze for the first time the rules of breaking in an X-palindrome between human and chimpanzee. Results indicate that although the overall changes that occurred in the human X-palindrome are fewer than in the chimpanzee, mutations occurring between the left arm and right arm were nearly equivalent both in human and chimpanzee when compared with orangutan, which implies evolutionary synchronization. However, there are many more A/TG/C changes than G/CA/T in a single arm, which would lead to an increasing trend in GC content and suggest that the composition is not at equilibrium. In addition, it is remarkable to find that there are much more asymmetrical nucleotide changes between the two arms of the human palindrome than that of the chimpanzee palindrome, and these mutations are prone to occur between bases with similar chemical structures. The symmetry seems higher in the chimpanzee palindrome than in the human X-palindrome.
Electronic Transport and Magnetic Properties in Ferroelectric-Ferromagnetic Composites La5/8Ca3/8MnO3:ErMnO3
Authors: Wang Yong-feng , Han Yun-xin , Zhu Chang-fei
Published: September 2009

The crystal structures and electronic transport properties of composites, xLa5/8Ca3/8MnO3: (1 x)ErMnO3 (x = 0, 0.2, 0.4, 0.5, 0.6, 0.8, 1), where ErMnO3 is the insulating ferroelectric and La5/8Ca3/8MnO3 is the metallic ferromagnetic component, were studied. The magnetization of samples (x = 0, 0.5, 1) were also measured as a function of temperature from 4 K to 300 K. The X-ray diffraction data show La5/8Ca3/8MnO3 and ErMnO3 are almost complete immiscible, originating from the significant difference in their crystal structures. All the composites show a metal-insulator transition when the molar fraction of xLa5/8Ca3/8MnO3 component x0.4 and the electronic transport behaviors follow the classical percolation theory model very well. Magnetization of the mixture with x = 0.5 is unique and enhanced greatly compared with that of pure ErMnO3. Comprehensive analysis of the electronic transport and magnetic results suggests that this material system is a new kind of multiferroic with stronger magnetism in a wider temperature range compared with the single phase multiferroic ErMnO3.
Composition Dependent Magnetic Properties of Ni-Co-P Coated Carbon Nanotubes
Authors: Ye Min , Xie Ting , He Bao-lin , Wu Yu-cheng , Meng Guo-wen , Zhang Li-de
Published: September 2009

Carbon nanotubes were coated with a layer of nickel-cobalt-phosphorus (Ni-Co-P) alloy with different compositions of Ni/Co through electroless plating. The effects of the concentration ratio of Co2+ to Ni2+, bath temperature, and pH on deposition rate are discussed. The prepared carbon nanotubes covered with Ni-Co-P were characterized and analyzed by field-emission scanning electron microscopy, transmission electron microscopy, X-ray diffraction, energy dispersive spectroscopy, and a vibrating sample magnetometer. The results show that the deposition rate reached the maximum when the concentration ratio of Co2+ to Ni2+ is 1 and the pH is 9; the deposition rate increases with the increase of bath temperature. The measurements of the magnetic properties of the obtained carbon nanotubes covered with Ni-Co-P indicate that the magnetic properties greatly depend on the concentration ratio of Co2+ to Ni2+, and the magnetic saturation reaches the maximum value when the Co2+ to Ni2+ ratio is 1. In addition, there are two peaks in the coercivity curve at Co2+ to Ni2+ ratios of 1/2 and 4/1, while the two peaks in the magnetic conductivity curve are located at Co2+ to Ni2+ ratios of 1/4 and 4/1.
Preparation and Characterization of Storage and Emission Functional Material of Chlorine Anion: [Ca24Al28O64]4+ (Cl)3.80(O2)0.10
Authors: Sun Jian-qiu , Song Chong-fu , Ning Shen , Lin Shao-bin , Li Quan-xin
Published: September 2009

A storage and emission functional material of [Ca24Al28O64]4+(Cl)3.80(O2)0.10 (C12A7-Cl), was prepared by the solid-state reactions of CaCO3, -Al2O3, and CaCl2 in Cl2/Ar mixture atmosphere. The anionic species stored in the C12A7-Cl material were dominated by Cl, about (2.210.24) 1021 cm3, accompanied by a small amount of O2, O, and O2, measured via ion chromatography, electron paramagnetic resonance, and raman spectra measurements. These results also corroborate identification of time-of-flight mass spectroscopythe anionic species emitted from the C12A7-Cl surface were dominated by the Cl (about 90%) together with a small amount of O and electrons. The structure and morphological alterations of the material were investigated via X-ray diffraction and field emission scanning electron microscope, respectively.
Photocatalytic Degradation of Phenol over MWCNTs-TiO2 Composite Catalysts with Different Diameters
Authors: Li Chen , Wang Wen-dong
Published: September 2009

Titania-based composite catalysts were prepared through a sol-gel route employing multi-walled carbon nanotubes with different diameters. The materials were characterized using thermogravimetric analysis, nitrogen adsorption-desorption isotherm, powder X-ray diffraction, scanning electron microscopy, and diffuse reflectance UV-Vis absorption spectra. The application of the catalysts to photocatalytic degradation of phenol was tested under UV-Vis irradiation. A synergetic effect on phenol removal was observed in case of composite catalysts, which was evaluated in terms of apparent rate constant, total organic carbon removal and photonic efficiency.
Samaria-doped Ceria Modified Ni/YSZ Anode for Direct Methane Fuel in Tubular Solid Oxide Fuel Cells by Impregnation Method
Authors: Zhang Long-shan , Gao Jian-feng , Tian Rui-fen , Xia Chang-rong
Published: September 2009

A porous NiO/yttria-stabilized zirconia anode substrate for tubular solid oxide fuel cells was prepared by gel casting technique. Nano-scale samaria-doped ceria (SDC) particles were formed onto the anode substrate to modify the anode microstructure by the impregnation of solution of Sm(NO3)3 and Ce(NO3)3. Electrochemical impedance spectroscopy, current-voltage and current-powder curves of the cells were measured using an electrochemical workstation. Scanning electron microcopy was used to observe the microstructure. The results indicate that the stability of the performance of the cell operated on humidified methane can be significantly improved by incorporating the nano-structured SDC particles, compared with the unmodified cell. This verifies that the coated SDC electrodes are very effective in suppressing catalytic carbon formation by blocking methane from approaching the Ni, which is catalytically active towards methane pyrolysis. In addition, it was found that a small amount of deposited carbon is beneficial to the performance of the anode. The cell showed a peak power density of 225 mW/cm2 when it was fed with H2 fuel at 700 C, but the power density increased to 400 mW/cm2 when the fuel was switched from hydrogen to methane at the same flow rate. Methane conversion achieved about 90%, measured by gas chromatogram with a 10.0 mL/min flow rate of fuel at 700 C. Although the carbon deposition was not suppressed absolutely, some deposited carbon was beneficial for performance improvement.
Surface Enhanced Raman Scattering on Self-assembled Nano Silver Film Prepared by Electrolysis Method
Authors: Kang Yi-pu , Liu Ren-ming , Si Min-zhen
Published: September 2009

We demonstrate surface enhanced Raman scattering (SERS) detection of self-assembled nano silver film using a low-cost electrolysis strategy at a proper voltage and silver nitrate concentration in electrolyte. The concentration dependence of SERS from crystal violet (CV) molecules adsorbed to silver film was systematically studied. Importantly, the SERS surface enhancement factor of such nano silver film was 603, which was measured by a portable Raman spectrometer. The minimum concentration of detectable CV molecules can be as low as 1011 mol/L. The nano silver film prepared by this electrolysis method is an active, stable, cost-effective, and reusable SERS substrate.
Shape-Controlled Synthesis of Palladium Nanoparticles and Their SPR/SERS Properties
Authors: Shen Xiao-shuang , Wang Guan-zhong , Hong Xun , Zhu Wei
Published: September 2009

Morphological evolution of Pd nanoparticles was studied in a solution-phase synthesis using cetyltrimethylammonium bromide (CTAB) and CTAB/sodium citrate mixture as capping agents, respectively. The morphological diversity of Pd nanoparticles is the combined effect of different Pd twinned seeds formed in the nucleation stage and selectively enlarging one set of crystallographic facets in the growth stage, both of which can be affected by the concentrations of CTAB. Through changing the concentrations of CTAB and sodium ascorbate, Pd nanoparticles with different shapes were obtained. When citrate ions were introduced to manipulate the nucleation and growth process, star-shaped icosahedra and nanorods with pentagram cross-sections were obtained. Pd nanoparticles with different shapes have quite different surface plasmon resonance and surface-enhanced Raman scattering properties.
Saint: a lightweight integration environment for model annotation
Authors: Lister Allyson L. , Pocock Matthew , Taschuk Morgan , Wipat Anil
Published: September 2009

Summary: Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources.

Availability and Implementation: Saint is freely available for use on the web at http://www.cisban.ac.uk/saint. The web application is implemented in Google Web Toolkit and Tomcat, with all major browsers supported. The Java source code is freely available for download at http://saint-annotate.sourceforge.net. The Saint web server requires an installation of libSBML and has been tested on Linux (32-bit Ubuntu 8.10 and 9.04).

Contact:  helpdesk@cisban.ac.uk; a.l.lister@ncl.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.