bluuebunny/crossref_metadata_2025 huggingface dataset:
Purification and biochemical characterization of native ERp29 from rat liver
Authors: HUBBARD Michael J. , MANGUM Jonathan E. , McHUGH Nicola J.
Published: October 2004

ERp29 is a recently characterized resident of the ER (endoplasmic reticulum) lumen that has broad biological significance, being expressed ubiquitously and abundantly in animal cells. As an apparent housekeeper, ERp29 is thought to be a general folding assistant for secretory proteins and to probably function as a PDI (protein disulphide isomerase)-like molecular chaperone. In the present paper, we report the first purification to homogeneity and direct functional analysis of native ERp29, which has led to the unexpected finding that ERp29 lacks PDI-like folding activities. ERp29 was purified 4800-fold in non-denaturing conditions exploiting an unusual affinity for heparin. Two additional biochemical hallmarks that will assist the classification of ERp29 homologues were identified, namely the idiosyncratic behaviours of ERp29 on size-exclusion chromatography (Mrmonomeric mass). In contrast with PDI and parallel-purified co-residents (calreticulin, ERp60), native ERp29 lacked classical chaperone, disulphide reductase and isomerase, and calcium-binding activities. In the chaperone assays, ERp29 neither protected substrate proteins against thermal aggregation nor interacted stably with chemically denatured proteins as detected by cross-linking. ERp29 also did not exhibit helper activity toward calreticulin (chaperone) or PDI and ERp60 (disulphide reductase). By refuting long-standing predictions about chaperone activity, these results expose ERp29 as a functionally distinct member of the ER machinery and prompt a revised hypothesis that ERp29 acts as a non-classical folding assistant. The native preparation and biochemical hallmarks established here provide a useful foundation for ongoing efforts to resolve the functional orphan status of ERp29.
Alternative translation initiation generates a novel isoform of insulin-degrading enzyme targeted to mitochondria
Authors: LEISSRING Malcolm A. , FARRIS Wesley , WU Xining , CHRISTODOULOU Danos C. , HAIGIS Marcia C. , GUARENTE Leonard , SELKOE Dennis J.
Published: October 2004

IDE (insulin-degrading enzyme) is a widely expressed zinc-metallopeptidase that has been shown to regulate both cerebral amyloid β-peptide and plasma insulin levels in vivo. Genetic linkage and allelic association have been reported between the IDE gene locus and both late-onset Alzheimer's disease and Type II diabetes mellitus, suggesting that altered IDE function may contribute to some cases of these highly prevalent disorders. Despite the potentially great importance of this peptidase to health and disease, many fundamental aspects of IDE biology remain unresolved. Here we identify a previously undescribed mitochondrial isoform of IDE generated by translation at an in-frame initiation codon 123 nucleotides upstream of the canonical translation start site, which results in the addition of a 41-amino-acid N-terminal mitochondrial targeting sequence. Fusion of this sequence to the N-terminus of green fluorescent protein directed this normally cytosolic protein to mitochondria, and full-length IDE constructs containing this sequence were also directed to mitochondria, as revealed by immuno-electron microscopy. Endogenous IDE protein was detected in purified mitochondria, where it was protected from digestion by trypsin and migrated at a size consistent with the predicted removal of the N-terminal targeting sequence upon transport into the mitochondrion. Functionally, we provide evidence that IDE can degrade cleaved mitochondrial targeting sequences. Our results identify new mechanisms regulating the subcellular localization of IDE and suggest previously unrecognized roles for IDE within mitochondria.
Significance of the endothelin ETA receptor in the haemodynamic and inotropic effects of endothelin-1 in rats
Authors: BEYER Martin E. , HÖVELBORN Tobias , DELABAR Ursula , HOFFMEISTER Hans Martin
Published: October 2004

The main aim of the present study was to investigate the direct inotropic effects of stimulation of the endothelin (ET) receptor ETA under in vivo conditions. It is well known that ETA receptor stimulation causes pronounced vasoconstriction. The ET-1-induced coronary vasoconstriction may lead to myocardial ischaemia and, consequently, to cardiodepressor effects that may mask the direct positive inotropic effect of ETA receptor stimulation. Thus, in the present study, steps were taken to avoid this possibility. In anaesthetized open-chest rats the haemodynamic and inotropic effects of ETA receptor stimulation were studied by monitoring responses evoked by ET-1 (1 nmol/kg of body weight) after ETB receptor blockade with BQ 788 (0.5 μmol/kg of body weight); these responses were compared with saline controls (after ETB receptor blockade). To avoid vasoconstrictor effects induced by ETA receptor stimulation, additional experiments were performed in the presence of the vasodilator adenosine (2.0 mg·kg−1 of body weight·min−1). Myocardial function was also examined during aortic clamping so as to circumvent the effect of changes in afterload. We studied further the effect of ETA receptor stimulation on myocardial energy metabolism. ETA receptor stimulation reduced cardiac output (−49% compared with control), raised total peripheral resistance (+173%) and reduced myocardial ATP content (−23%). Aortic clamping did not reveal a positive inotropic effect of ETA receptor stimulation. Furthermore, even though adenosine attenuated the decrease in cardiac output (−21%), the increase of total peripheral resistance (+48%) and prevented the fall of myocardial ATP content (+6%), this did not unmask a positive inotropic effect of ETA receptor stimulation. Thus we conclude that ETA receptor stimulation causes vasoconstriction and myocardial ischaemia, but has no positive inotropic effects in rats.
Modeling steps and kinks on the surface of calcite
Authors: Kristensen Rune , Stipp S. L. S. , Refson Keith
Published: October 2004

This work presents modeling results on the cleavage face of calcite as well as on steps and isolated kinks on this face. We used static lattice energy minimization and interatomic potentials fitted to bulk properties. The energy needed to cleave a bulk calcite crystal along the {1 0 1̄ 4} plane was calculated to be 0.59 J m−2 in agreement with previous studies using the same potentials. The perfect surface reconstructs in the top few atomic layers, but its symmetry corresponds to the bulk termination. By contrast, the (1 0 1̄ 4) surface with cleavage steps present reconstructs to form a (2×1) super cell. This may help explain experimental observations of (2×1) symmetry on calcite surfaces. The energy required to form a monatomic obtuse step is calculated to be 1.3×10−10 J m−1 and for the acute step, 2.4×10−10 J m−1, suggesting that obtuse steps dominate on cleaved surfaces. Along the two types of steps, a total of 16 kink geometries exist. We calculated kink defect energy with two different approaches: one where kink pairs were added onto infinitely long steps and one where kinks were placed inside pits on a cleavage surface. Calculations on infintely long steps show that for vacuum conditions, kink pairs possess roughly identical formation energy, about 1.2–2.2 eV, so based on energetics one cannot expect significant differences in kink site frequency.
Simple DFT model of clusters embedded in rare gas matrix: Trapping sites and spectroscopic properties of Na embedded in Ar
Authors: Gervais B. , Giglio E. , Jacquet E. , Ipatov A. , Reinhard P.-G. , Suraud E.
Published: October 2004

We present a theoretical model to study the dynamics of metallic clusters embedded in a rare gas matrix. We describe the active electrons of the embedded cluster using time dependent density functional theory, while the surrounding matrix is described in terms of classical molecular dynamics of polarizable atoms. The coupling between the cluster and the rare gas atoms is deduced from the work of Groß and Spiegelmann [J. Chem. Phys. 108, 4148 (1998)] and reformulated explicitly in a simple and efficient density functional form. The electron rare gas interaction takes the form of an averaged dipole fluctuation term, which retains the van der Waals long range interaction, and a short range repulsive pseudopotential, which accounts for the Pauli repulsion of the electron by the rare gas atom. We applied our model to Na clusters embedded in Ar matrix. For the latter we developed an efficient local pseudopotential, which allows studying systems containing more than 103 Ar atoms. We show that large systems are indeed necessary to account properly for long range polarization of the matrix, that competes with the matrix confinement effect. We focus our study on Na2, Na4, and Na8. For each system, we have determined the geometry of the most favorable trapping site by means of damped molecular dynamics. We present the effect of matrix embedding on the optical absorption spectrum. For Na2, the trapping site can be unambiguously identified by comparison of the absorption spectrum with experiment. For Na4 the spectrum of the embedded cluster is significantly different from the free cluster spectrum, while for Na8 differences are less pronounced.
A simple method for the preparation of pseudopure states in nuclear magnetic resonance quantum information processing
Authors: Fung B. M. , Ermakov Vladimir L.
Published: October 2004

The use of nuclear magnetic resonance (NMR) to carry out quantum information processing (QIP) often requires the preparation, transformation, and detection of pseudopure states. In our previous work, it was shown that the use of pairs of pseudopure states (POPS) as a basis for QIP is very convenient because of the simplicity in experimental execution. It is now further demonstrated that the product of the NMR spectra corresponding to two sets of POPS that share a common pseudopure state has the same peak frequencies as those of the common (single) pseudopure state. Examples of applying two different quantum logic gates to a 5-qubit system are given.
An Anderson impurity model for efficient sampling of adiabatic potential energy surfaces of transition metal complexes
Authors: LaBute M. X. , Endres R. G. , Cox D. L.
Published: October 2004

We present a model intended for rapid sampling of ground and excited state potential energy surfaces for first-row transition metal active sites. The method is computationally inexpensive and is suited for dynamics simulations where (1) adiabatic states are required “on-the-fly” and (2) the primary source of the electronic coupling between the diabatic states is the perturbative spin-orbit interaction among the 3d electrons. The model Hamiltonian we develop is a variant of the Anderson impurity model and achieves efficiency through a physically motivated basis set reduction based on the large value of the d-d Coulomb interaction Ud and a Lánczos matrix diagonalization routine to solve for eigenvalues. The model parameters are constrained by fits to the partial density of states obtained from ab initio density functional theory calculations. For a particular application of our model we focus on electron transfer occurring between cobalt ions solvated by ammonium, incorporating configuration interaction between multiplet states for both metal ions. We demonstrate the capability of the method to efficiently calculate adiabatic potential energy surfaces and the electronic coupling factor we have calculated compares well to previous calculations and experiment.
Infrared depletion spectra of 2-aminopyridine⋅2-pyridone, a Watson–Crick mimic of adenine⋅uracil
Authors: Frey Jann A. , Müller Andreas , Frey Hans-Martin , Leutwyler Samuel
Published: October 2004

The 2-aminopyridine⋅2-pyridone (2AP⋅2PY) dimer is linked by N–H⋯O=C and N–H⋯N hydrogen bonds, providing a model for the Watson–Crick hydrogen bond configuration of the adenine⋅thymine and adenine⋅uracil nucleobase pairs. Mass-specific infrared spectra of 2AP⋅2PY and its seven N–H deuterated isotopomers have been measured between 2550 and 3650 cm−1 by IR laser depletion combined with UV two-color resonant two-photon ionization. The 2PY amide N–H stretch is a very intense band spread over the range 2700–3000 cm−1 due to large anharmonic couplings. It is shifted to lower frequency by 710 cm−1 or ≈20% upon H bonding to 2AP. On the 2AP moiety, the “bound” amino N–H stretch gives rise to a sharp band at 3140 cm−1, which is downshifted by 354 cm−1 or ≈10% upon H bonding to 2PY. The amino group “free” N–H stretch and the H–N–H bend overtone are sharp bands at ≈3530 cm−1 and 3320 cm−1. Ab initio structures and harmonic vibrations were calculated at the Hartree–Fock level and with the PW91 and B3LYP density functionals. The PW91/6-311++G(d,p) method provides excellent predictions for the frequencies and IR intensities of all the isotopomers.
Molecular dynamics of transient oil flows in nanopores I: Imbibition speeds for single wall carbon nanotubes
Authors: Supple S. , Quirke N.
Published: October 2004

The way fluids flow into and fill nanotubes is of wide interest; however, there are currently no experimental data or validated theoretical models for this nanoscale process. We have carried out molecular dynamics simulations of carbon nanotubes imbibing oil at an oil/vapor interface at 300 K. We find that the smallest (7,7) nanotubes imbibe extremely rapidly (⩽800 m/s) along the inner tube surface with the penetration length L a linear function of time. We derive expressions for the penetration length L and the velocity of the imbibing oil and relate both to the solid-fluid surface tensions and interfacial friction. The imbibition of oil by nanotubes is contrasted with the wetting of their external surfaces and that of planar surfaces. In all cases the appropriate surface tensions can be correlated with the minimum of the oil-molecule wall potential providing a means of predicting the internal and external wetting behavior of nanotubes.
Normal Auger spectra of Br in alkali bromide molecules
Authors: Hu Zhengfa , Caló Antonio , Nikkinen Juha , Matila Tommi , Kukk Edwin , Aksela Helena , Aksela Seppo
Published: October 2004

Molecular Auger electron spectra following the bromine 3d ionization in gas-phase alkali bromides and in HBr were studied both experimentally and theoretically. The AES for HBr and CsBr were measured using photoexcitation, and for LiBr, NaBr, and KBr by using electron impact. These results are compared with the theoretical spectra from nonrelativistic ab initio calculations and one-center approximation and with the spectra of Br−, computed with the multiconfiguration Dirac–Fock method.
On the mechanical properties and phase behavior of silica: A simple model based on low coordination and strong association
Authors: Ford Matthew H. , Auerbach Scott M. , Monson P. A.
Published: October 2004

We present a simple and computationally efficient classical atomistic model of silica in which the silicon and oxygen are simulated as hard spheres with four and two association sites, respectively. We have performed isobaric-isothermal Monte Carlo simulations to study the mechanical and phase behavior of this model. We have investigated solid phase structures of the model corresponding to quartz, cristobalite, and coesite, as well as some zeolite structures. For the model these phases are mechanically stable and highly incompressible. Ratios of zero-pressure bulk moduli and thermal expansion coefficients for α quartz, α cristobalite, and coesite are in quite good agreement with experimental values. The pressure-temperature phase diagram was constructed and shows three solid phases corresponding to cristobalite, quartz, and coesite, as well as a fluid or glass phase, behavior qualitatively similar to that seen for silica experimentally.
Dynamics of polymer packaging
Authors: Ali I. , Marenduzzo D. , Yeomans J. M.
Published: October 2004

We use the stochastic rotation dynamics algorithm to investigate the packaging of flexible and semiflexible polymers into a capsid that is permeable to solvent molecules. The model takes into account hydrodynamic interactions arising due to local flow. The flexible chain maintains a random configuration as it is being fed into the capsid, in contrast to the semiflexible chain, whose configuration is initially spool-like, becoming more random at high packing. We measure the packing rate, which is found to decrease with the percentage of the chain packed and highlight the difference between the flexible and semiflexible chains. Reflecting experiments, we find pauses in the packing process for individual chains as the motor loses grip of the fluctuating beads. We also find that hydrodynamics is important, in that the packaging rate is faster when flow is included.
Simulation of electric double layers with multivalent counterions: Ion size effect
Authors: Quesada-Pérez M. , Martı́n-Molina A. , Hidalgo-Álvarez R.
Published: October 2004

In this paper, the structure of the electric double layer in the presence of (mostly) multivalent counterions is investigated through Monte Carlo simulations. Unlike previous similar studies addressing this matter, the difference of this study lies in the use of realistic hydrated ion sizes. Additionally, two different methods for calculating energies in the Metropolis algorithm are applied. The obtained results show that the conclusions of preceding papers must be revised. In particular, our simulations suggest the existence of certain ion layering effects at high surface charge densities, which are not accounted for by integral equation theories in the case of divalent counterions. These layering effects could justify why the overcharging phenomena due to ion size correlations are hardly observable in real colloids with divalent counterions. The existence of charge inversion due to ion size correlations (and without requiring specific counterion adsorption) is probed for trivalent counterions. Moreover, the hypernetted-chain/mean-spherical-approximation is tested under conditions not studied yet.
Icosahedral gold cage clusters: M@Au12− (M=V, Nb, and Ta)
Authors: Zhai Hua-Jin , Li Jun , Wang Lai-Sheng
Published: October 2004

We report the observation and characterization of a series of stable bimetallic 18-valence-electron clusters containing a highly symmetric 12-atom icosahedral Au cage with an encapsulated central heteroatom of Group VB transition metals, M@Au12− (M=V,Nb,Ta). Electronic and structural properties of these clusters were probed by anion photoelectron spectroscopy and theoretical calculations. Characteristics of the M@Au12− species include their remarkably high binding energies and relatively simple spectral features, which reflect their high symmetry and stability. The adiabatic electronic binding energies of M@Au12− were measured to be 3.70±0.03, 3.77±0.03, and 3.76±0.03 eV for M=V, Nb, and Ta, respectively. Comparison of density-functional calculations with experimental data established the highly symmetric icosahedral structures for the 18-electron cluster anions, which may be promising building blocks for cluster-assembled nanomaterials in the form of stoichiometric [M@Au12−]X+ salts.
Organo-noble-gas hydride compounds HKrCCH, HXeCCH, HXeCC, and HXeCCXeH: Formation mechanisms and effect of C13 isotope substitution on the vibrational properties
Authors: Tanskanen Hanna , Khriachtchev Leonid , Lundell Jan , Räsänen Markku
Published: October 2004

We investigate the formation mechanism of HXeCCXeH in a Xe matrix. Our experimental results show that the HXeCCXeH molecules are formed in the secondary reactions involving HXeCC radicals. The experimental data on the formation of HXeCCXeH is fully explained based on the model involving the HXeCC+Xe+H→HXeCCXeH reaction. This reaction is the first case when a noble-gas hydride molecule is formed from another noble-gas molecule. In addition, we investigate the C12/C13 isotope effect on the vibrational properties of organo-noble-gas hydrides (HKrCCH, HXeCCH, HXeCC, and HXeCCXeH) in noble-gas matrixes. The present experimental results and ab initio calculations on carbon isotope shifts of the vibrational modes support the previous assignments of these molecules. Upon C12 to C13 isotope substitution, we observed a pronounced effect on the H-Kr stretching mode of HKrCCH (downshift of 1.0–3.6 cm−1, depending on the matrix site) and a small anomalous shift (+0.1 cm−1) of the H-Xe stretching mode of HXeCCH and HXeCCXeH.
Influence of a depletion interaction on dynamical heterogeneity in a dense quasi-two-dimensional colloid liquid
Authors: Ho Hau My , Cui Bianxiao , Repel Stephen , Lin Binhua , Rice Stuart A.
Published: October 2004

We report the results of digital video microscopy studies of the large particle displacements in a quasi-two-dimensional binary mixture of large (L) and small (S) colloid particles with diameter ratio σL/σS=4.65, as a function of the large and small colloid particle densities. As in the case of the one-component quasi-two-dimensional colloid system, the binary mixtures exhibit structural and dynamical heterogeneity. The distribution of large particle displacements over the time scale examined provides evidence for (at least) two different mechanisms of motion, one associated with particles in locally ordered regions and the other associated with particles in locally disordered regions. When ρL*=NπσL2/4A⩽0.35, the addition of small colloid particles leads to a monotonic decrease in the large particle diffusion coefficient with increasing small particle volume fraction. When ρL*⩾0.35 the addition of small colloid particles to a dense system of large colloid particles at first leads to an increase in the large particle diffusion coefficient, which is then followed by the expected decrease of the large particle diffusion coefficient with increasing small colloid particle volume fraction. The mode coupling theory of the ideal glass transition in three-dimensional systems makes a qualitative prediction that agrees with the initial increase in the large particle diffusion coefficient with increasing small particle density. Nevertheless, because the structural and dynamical heterogeneities of the quasi-two-dimensional colloid liquid occur within the field of equilibrium states, and the fluctuations generate locally ordered domains rather than just disordered regions of higher and lower density, it is suggested that mode coupling theory does not account for all classes of relevant fluctuations in a quasi-two-dimensional liquid.
Tests for thermodynamic state of water’s high-density amorph
Authors: Johari G. P.
Published: October 2004

Analysis of the density and ultrasonic velocity data for water’s high-density amorph (HDA) far from its formation conditions shows that HDA made by pressurizing ice Ih is different from HDA made by pressurizing its low-density amorph (LDA), and the density and ultrasonic velocity of HDA depend upon the pressure and temperature path used to make it from ice Ih. This seems inconsistent with the description of HDA-LDA phase equilibrium. Similar tests may be used to clarify the nature of the nonergodic transitions in GeO2 and SiO2.
On the behavior of the volume viscosity of atom-molecule mixtures
Authors: Ern Alexandre , Dickinson Alan S. , Vesovic Velisa
Published: October 2004

The behavior of the volume viscosity in atom-molecule gas mixtures is investigated in the framework of the first-order Enskog–Chapman expansion when the internal-energy relaxation cross section for atom-molecule collisions is small compared to that for molecule-molecule collisions. Two phenomena are analyzed: first, the sensitivity of the volume viscosity to this particular cross section allows the volume viscosity of the atom-molecule mixture to be significantly larger than that of the pure molecular gas; second, when this cross section is set to zero, the volume viscosity becomes discontinuous at the pure-atom limit.
Observation of Au2H− impurity in pure gold clusters and implications for the anomalous Au-Au distances in gold nanowires
Authors: Zhai Hua-Jin , Kiran Boggavarapu , Wang Lai-Sheng
Published: October 2004

Au 2 H − was recognized and confirmed as a minor contamination to typical photoelectron spectra of Au2−, produced by laser vaporization of a pure Au target using an ultrahigh purity helium carrier gas. The hydrogen source was shown to be from trace H impurities present in the bulk gold target. Carefully designed experiments using H2- and D2-seeded helium carrier gas were used to study the electronic structure of Au2H− and Au2D− using photoelectron spectroscopy and density functional calculations. Well-resolved photoelectron spectra with vibrational resolution were obtained for Au2H− and Au2D−. Two isomers were observed both experimentally and theoretically. The ground state of Au2H− turned out to be linear with a terminal H atom [Au-Au-H]− (1A1,C∞v), whereas a linear [Au-H-Au]− (1A1,D∞h) structure with a bridging H atom was found to be a minor isomer 0.6 eV higher in energy. Calculated electron detachment energies for both isomers agree well with the experimental spectra, confirming their existence in the cluster beam. The observation and confirmation of H impurity in pure gold clusters and the 3.44 Å Au-Au distance in the [Au-H-Au]− isomer presented in the current work provide indirect experimental evidence that the anomalous 3.6 Å Au-Au distances observed in gold nanowires is due to an “invisible” hydrogen impurity atom.
Observation of rotamers of m-aminobenzoic acid: Zero kinetic energy photoelectron and hole-burning resonantly enhanced multiphoton ionization spectroscopy
Authors: He Yonggang , Wu Chengyin , Kong Wei
Published: October 2004

We report studies of supersonically cooled m-aminobenzoic acid using two-color resonantly enhanced multiphoton ionization (REMPI) and two-color zero kinetic energy (ZEKE) photoelectron spectroscopy. Two conformers have been identified and characterized using the hole-burning method in the REMPI experiment. With the aid of ab initio and density functional calculations, vibrational modes of the first electronically excited state (S1) of the neutral species and those of the ground state cation (D0) have been assigned, and the adiabatic ionization potentials have been determined for both conformers. The REMPI spectra are dominated by in-plane motions of the substituents and ring deformation modes. A propensity of Δv=0, where Δv is the change in vibrational quantum number from the S1 to the D0 state, is observed in the ZEKE spectra. The origin of this behavior is discussed in the context of electron back donation from the two substituents in the excited state and in the cationic state. Comparisons of these results with those of p-aminobenzoic acid will be analyzed.
Some issues on the calculation of interfacial properties by molecular simulation
Authors: Duque Daniel , Vega Lourdes F.
Published: October 2004

Some of the pitfalls that may befall molecular simulations of interfaces are discussed. They are all related to the calculation of the pressure tensor profiles, which are needed in order to compute surface tensions. We focus on three controversial points: (1) the calculation of the pressure tensor profiles for polyatomic systems, in particular, when the SHAKE algorithm is employed, (2) the addition of long-range corrections to compensate the truncation of the potential, and (3) the importance of including adequate error intervals with the results. Most of the conclusions are general, but some specifically apply to multiple site molecular-dynamics simulations.
Calculation of single-beam two-photon absorption rate of lanthanides: Effective operator method and perturbative expansion
Authors: Duan Chang-Kui , Ruan Gang , Reid Michael F.
Published: October 2004

Perturbative contributions to single-beam two-photon transition rates may be divided into two types. The first, involving low-energy intermediate states, require a high-order perturbation treatment, or an exact diagonalization. The other, involving high-energy intermediate states, only require a low-order perturbation treatment. We show how to partition the effective transition operator into two terms, corresponding to these two types, in such a way that a many-body perturbation expansion may be generated that obeys the linked cluster theorem and has a simple diagrammatic representation.
Comparison of the dehalogenation of polyhalomethanes and production of strong acids in aqueous and salt (NaCl) water environments: Ultraviolet photolysis of CH2I2
Authors: Guan Xiangguo , Du Yong , Li Yun-Liang , Kwok Wai Ming , Phillips David Lee
Published: October 2004

The ultraviolet photolysis of CH2I2 was studied in water and salt water solutions using photochemistry and picosecond time-resolved resonance Raman spectroscopy. Photolysis in both types of environments produces mainly CH2(OH)2 and HI products. However, photolysis of CH2I2 in salt water leads to the formation of different products/intermediates (CH2ICl and Cl2−) not observed in the absence of salt in aqueous solutions. The amount of CH2(OH)2 and HI products appears to decrease after photolysis of CH2I2 in salt water compared to pure water. We briefly discuss possible implications of these results for photolysis of CH2I2 and other polyhalomethanes in sea water and other salt aqueous environments compared to nonsalt water solvated environments.
Structure, stability, and spectra of C9H3, C11H3, and C13H3 radicals
Authors: Zhang Congjie
Published: October 2004

Density functional theory has been used to investigate the geometries, vibrational frequencies, rotational constants, and dipole moments of the C9H3, C11H3, and C13H3 radicals. Vertical electronic transition energies of C9H3, C11H3, and C13H3 are calculated by the time-dependent density functional theory. Present results show that the most stable arrangements of C9H3, C11H3, and C13H3 are H2C9H, H2C11H, and H2C13H with a C2v symmetry, respectively. Such lowest-energy isomers have an obvious single and triple bond alternation carbon chain. Their isomers HC4(HC)C4H, HC4[C(C2H)]C4H, and C(C4H)3 are predicted to have vibrational frequencies and vertical excitation energies in good agreement with experimental observations. HC4(HC)C4H, HC4[C(C2H)]C4H, and C(C4H)3 have similar trigonal structure, which gives rise to the remarkably similar spectroscopic features as obtained experimentally. On the basis of present calculations, the isomers HC4(HC)C4H, HC4[C(C2H)]C4H, and C(C4H)3 of C9H3, C11H3, and C13H3 radicals are most likely the carriers of the observed spectra.
High density amorphous ices: Disordered water towards close packing
Authors: Saitta A. Marco , Strässle Thierry , Rousse Gwenaëlle , Hamel Gérard , Klotz Stefan , Nelmes Richard J. , Loveday John S.
Published: October 2004

The structure of amorphous ice under pressure has been studied by molecular dynamics at 160 K. The starting low-density phase undergoes significant changes as the density increases, and at ρ=1.51 g/cm3 our calculated gOO(r) is in excellent agreement with in situ neutron diffraction data obtained at 1.8 GPa and 100 K on very high density amorphous ice made at 150 K. As the system is further compressed, in the theoretical simulations, up to ρ=1.90 g/cm3, the structural modifications are continuous up to the highest density. The analysis of orientational distributions reveals that dense amorphous ice is characterized by major distortions of the tetrahedral geometry, and that the pressure structural changes, already observed experimentally at lower densities, can be interpreted as a trend towards a disordered closed-packed structure.
Novel Determination of Elemental Carbon in Sediments by DRIFTS
Authors: Tung Joanne W. T. , Lee Ivan S. C. , Tanner Peter A.
Published: October 2004

Environmental Context. Elemental carbon in anthropogenic pollutants has been linked in a general way to adverse health effects. Carbon may be present in many forms, including charcoal, graphite, organic (such as fuel- and biomass-derived), and inorganic. However, the boundaries between the various forms of carbon are not clearly delineated, which impedes more precise carbon–health linkage. This paper points towards a straightforward, general method for quantifying elemental carbon in environmental samples.
Abstract. A preliminary report is given of a nondestructive diffuse reflectance infrared Fourier transform spectra (DRIFTS) instrumental technique to quantify elemental carbon (EC) in marine sediments. Prolonged ball-milling produces a new IR absorption band at 1590 cm−1, whose intensity correlates well with the mass of EC in the sample.
First Characterization and Dating of East Antarctic Bedrock Inclusions from Subglacial Lake Vostok Accreted Ice
Authors: Delmonte Barbara , Petit Jean R. , Basile-Doelsch Isabelle , Lipenkov Vladimir , Maggi Valter
Published: October 2004

Environmental Context.Lake Vostok is a large subglacial lake trapped below the East Antarctic ice sheet. The meteoric ice from deep Vostok ice cores has been used to document the climatic history of the Earth over hundreds of millennia, while the deeper part of the core preserves some basal rock fragments. These rock fragments represent unique geological samples of the inhospitable, ice-covered East Antarctic Plateau.
Abstract.The Vostok (East Antarctica, 78°S, 106°E) ice core preserves, below the meteoric ice keeping the climatic memory of the last 420 000 years, ice formed by freezing of subglacial Lake Vostok water. This latter contains some bedrock fragments representing unique samples for the geological investigation of the East Antarctic Plateau, covered by ~2–4 km of ice. The first geochemical (87Sr/86Sr versus 143Nd/144Nd) and mineralogical characterization of these inclusions as well as the dating of one of them (Nd model age on whole-rock sample) has given evidence for a Mid-Proterozoic age of the basement lying below the ice sheet, consistent with recent geophysical data. The geochemical characteristics of bedrock inclusions within the accreted ice zone are markedly different from those of the mineral dust of aeolian origin archived in the uppermost part of the Vostok ice core and originating from deflation of the Southern Hemisphere continents, and easily discriminates between the two contributions.
The Use of the 'Ammonium Diffusion' Method for δ15N-NH4+ and δ15N-NO3 - Measurements: Comparison with Other Techniques
Authors: Sebilo Mathieu , Mayer Bernhard , Grably Micheline , Billiou Daniel , Mariotti André
Published: October 2004

Environmental Context.Nitrogen is an essential element for all living organisms, and its biogeochemical cycle is connected to the cycling of carbon, sulfur, phosphorous, oxygen, and trace metals. Measurement of the isotopic composition of ammonium (NH4+) and nitrate (NO3−) containing samples provides a better understanding of the nitrogen cycle. While the established ‘ammonium diffusion’ measurement has many advantages, it is not easy for inexperienced people to prepare samples. This paper shows how the method can be simplified, ideally for samples freshly collected from the field.
Abstract.Several methods have been developed for nitrogen isotope measurements on ammonium (NH4+) and nitrate (NO3−) in solid or aqueous samples. We have tested the accuracy and reproducibility of the ammonium diffusion method for δ15N measurements on NH4+ and NO3− and compared this technique to other established methods. Our results show that the ammonium diffusion technique is capable of generating accurate and reproducible δ15N values for minute quantities of NH4+-N and NO3−-N in aqueous samples, if sufficient care is taken to minimize nitrogen blanks and to optimize the extraction procedure. Hence, the ammonium diffusion method offers an attractive alternative to more labour-intensive and costly methods for determining nitrogen isotope ratios of NH4+ and NO3− in aqueous samples.
Epstein–Barr virus-encoded LMP2A regulates viral and cellular gene expression by modulation of the NF-κB transcription factor pathway
Authors: Stewart Suzanne , Dawson Christopher W. , Takada Kenzo , Curnow John , Moody Cary A. , Sixbey John W. , Young Lawrence S.
Published: October 2004

Epstein–Barr virus (EBV)-associated malignancies display distinct patterns of virus latent gene expression that reflect the complex interplay between the virus and its host cell. In the EBV-associated epithelial tumor nasopharyngeal carcinoma (NPC), the virus-encoded latent membrane protein LMP2A is consistently expressed whereas the oncogenic LMP1 protein appears to be restricted to only a proportion of tumors. In an attempt to understand the contribution of LMP2A to the pathogenesis of NPC, we established carcinoma cell lines stably infected
in vitro
with either a wild-type recombinant EBV (rEBV) or a mutant rEBV in which LMP2A is deleted (rEBV-2A). An NPC-like pattern of EBV gene expression including LMP2A but not LMP1 was consistently observed in carcinoma cells infected with rEBV. However, carcinoma cells infected with rEBV-2A expressed high levels of LMP1 from the signal transducer and activator of transcription (STAT)-regulated L1-TR promoter. Consistent with this effect, basal STAT activity was reduced in rEBV-infected carcinoma cells, and this repression was relieved in the absence of LMP2A. This modulation of STAT activity correlated with the ability of LMP2A to inhibit the autocrine secretion of IL-6 from carcinoma cell lines. Exogenous IL-6 was able to induce expression of LMP1 by means of STAT3 activation both in rEBV-infected carcinoma cell lines and in the EBV-positive C666-1 NPC cell line. The LMP2A-mediated suppression of IL-6 was a consequence of NF-κB inhibition. These data reveal that LMP2A modulates two key transcription factor pathways in carcinoma cells and suggest that this finding may be important in the pathogenesis of EBV-associated tumors.
EosFP, a fluorescent marker protein with UV-inducible green-to-red fluorescence conversion
Authors: Wiedenmann Jörg , Ivanchenko Sergey , Oswald Franz , Schmitt Florian , Röcker Carlheinz , Salih Anya , Spindler Klaus-Dieter , Nienhaus G. Ulrich
Published: October 2004

A gene encoding a fluorescent protein from the stony coral
Lobophyllia hemprichii
has been cloned in
Escherichia coli
and characterized by biochemical and biophysical methods. The protein, which we named EosFP, emits strong green fluorescence (516 nm) that changes to red (581 nm) upon near-UV irradiation at ≈390 nm because of a photo-induced modification involving a break in the peptide backbone next to the chromophore. Single-molecule fluorescence spectroscopy shows that the wild type of EosFP is tetrameric, with strong Förster resonance coupling among the individual fluorophores. We succeeded in breaking up the tetramer into AB and AC subunit dimers by introducing the single point mutations V123T and T158H, respectively, and the combination of both mutations yielded functional monomers. Fusion constructs with a variety of proteins were prepared and expressed in human cells, showing that normal biological functions were retained. The possibility to locally change the emission wavelength by focused UV light makes EosFP a superb marker for experiments aimed at tracking the movements of biomolecules within the living cell.
Innate immunity in
Arabidopsis thaliana
: Lipopolysaccharides activate nitric oxide synthase (NOS) and induce defense genes
Authors: Zeidler Dana , Zähringer Ulrich , Gerber Isak , Dubery Ian , Hartung Thomas , Bors Wolf , Hutzler Peter , Durner Jörg
Published: October 2004

Lipopolysaccharides (LPS) are cell-surface components of Gram-negative bacteria and are microbe-/pathogen-associated molecular patterns in animal pathosystems. As for plants, the molecular mechanisms of signal transduction in response to LPS are not known. Here, we show that
Arabidopsis thaliana
reacts to LPS with a rapid burst of NO, a hallmark of innate immunity in animals. Fifteen LPS preparations (among them
Burkholderia cepacia, Pseudomonas aeruginosa
, and
Erwinia carotovora
) as well as lipoteichoic acid from Gram-positive
Staphylococcus aureus
were found to trigger NO production in suspension-cultured
Arabidopsis
cells as well as in leaves. NO was detected by confocal laser-scanning microscopy in conjunction with the fluorophore 4-amino-5-methylamino-2′,7′-difluorofluorescein diacetate, by electron paramagnetic resonance, and by a NO synthase (NOS) assay. The source of NO was addressed by using T-DNA insertion lines. Interestingly, LPS did not activate the pathogen-inducible
varP
NOS, but
AtNOS1
, a distinct NOS previously associated with hormonal signaling in plants. A prominent feature of LPS treatment was activation of defense genes, which proved to be mediated by NO. Northern analyses and transcription profiling by using DNA microarrays revealed induction of defense-associated genes both locally and systemically. Finally, AtNOS1 mutants showed dramatic susceptibility to the pathogen
Pseudomonas syringae
pv. tomato DC3000. In sum, perception of LPS and induction of NOS contribute toward the activation of plant defense responses.
Variation in sequence and organization of splicing regulatory elements in vertebrate genes
Authors: Yeo Gene , Hoon Shawn , Venkatesh Byrappa , Burge Christopher B.
Published: October 2004

Although core mechanisms and machinery of premRNA splicing are conserved from yeast to human, the details of intron recognition often differ, even between closely related organisms. For example, genes from the pufferfish
Fugu rubripes
generally contain one or more introns that are not properly spliced in mouse cells. Exploiting available genome sequence data, a battery of sequence analysis techniques was used to reach several conclusions about the organization and evolution of splicing regulatory elements in vertebrate genes. The classical splice site and putative branch site signals are completely conserved across the vertebrates studied (human, mouse, pufferfish, and zebrafish), and exonic splicing enhancers also appear broadly conserved in vertebrates. However, another class of splicing regulatory elements, the intronic splicing enhancers, appears to differ substantially between mammals and fish, with G triples (GGG) very abundant in mammalian introns but comparatively rare in fish. Conversely, short repeats of AC and GT are predicted to function as intronic splicing enhancers in fish but are not enriched in mammalian introns. Consistent with this pattern, exonic splicing enhancer-binding SR proteins are highly conserved across all vertebrates, whereas heterogeneous nuclear ribonucleoproteins, which bind many intronic sequences, vary in domain structure and even presence/absence between mammals and fish. Exploiting differences in intronic sequence composition, a statistical model was developed to predict the splicing phenotype of
Fugu
introns in mammalian systems and was used to engineer the spliceability of a
Fugu
intron in human cells by insertion of specific sequences, thereby rescuing splicing in human cells.
Selective interaction between nonribosomal peptide synthetases is facilitated by short communication-mediating domains
Authors: Hahn Martin , Stachelhaus Torsten
Published: October 2004

Nonribosomal peptide synthetases (NRPSs) catalyze the formation of structurally diverse and biologically important peptides. Given their modular organization, NRPSs provide an enormous potential for biocombinatorial approaches to generate novel bioactive compounds. Crucial for the exploitation of this potential is a profound knowledge of the intermolecular communication between partner NRPSs. The overall goal of this study was to understand the basis of protein–protein communication that facilitates the selective interaction in these multienzyme complexes. On this account, we studied the relevance of short regions at the termini of the NRPSs tyrocidine (Tyc) synthetases TycA, TycB, and TycC, constituting the Tyc biosynthetic template.
In vitro
and
in vivo
investigations of C-terminal deletion mutants of the initiation module TycA provided evidence for the existence and impact of short communication-mediating (COM) domains. Their decisive role in protein–protein recognition was subsequently proven by means of COM domain-swapping experiments. Substitution of the terminal COM domains between the donor modules TycA and TycB3, as well as between the acceptor modules TycB1 and TycC1, clearly demonstrated that matching pairs of COM domains are both necessary and sufficient for the establishment of communication between partner NRPSs in trans. These results corroborated the generality of COM domains, which were subsequently exploited to induce crosstalk, even between NRPSs derived from different biosynthetic systems. In conclusion, COM domains represent interesting tools for biocombinatorial approaches, which, for example, could be used for the generation of innovative natural product derivatives.
Correction of ATM gene function by aminoglycoside-induced read-through of premature termination codons
Authors: Lai Chih-Hung , Chun Helen H. , Nahas Shareef A. , Mitui Midori , Gamo Kristin M. , Du Liutao , Gatti Richard A.
Published: October 2004

Approximately 14% of genetic mutations in patients with ataxia-telangiectsia (A-T) are single-nucleotide changes that result in primary premature termination codons (PTCs), either UAA, UAG, or UGA. The purpose of this study was to explore a potential therapeutic approach for this subset of patients by using aminoglycosides to induce PTC read-through, thereby restoring levels of full-length ATM (A-T mutated) protein. In experiments using a modified
in vitro
cDNA coupled transcription/translation protein truncation test, 13 A-T cell lines carrying PTC mutations in different contexts exhibited read-through expression of ATM fragments, with three of four aminoglycosides tested. In
ex vivo
experiments with lymphoblastoid cell lines, we used radiosensitivity, radioresistant DNA synthesis, and irradiation-induced autophosphorylation of ATM Ser-1981 to show that the aminoglycoside-induced full-length ATM protein was functional and corrected, to various extents, the phenotype of A-T cells. These results encourage further testing of other compounds in this class, as well as follow up animal studies. Because some A-T patients with 5–20% of normal levels of ATM protein show slower neurological progression, A-T may prove to be a good model for aminoglycoside-induced read-through therapy.
Conserved residues in the
Plasmodium vivax
Duffy-binding protein ligand domain are critical for erythrocyte receptor recognition
Authors: VanBuskirk Kelley M. , Sevova Elitza , Adams John H.
Published: October 2004

Malaria merozoite invasion of human erythrocytes depends on recognition of specific erythrocyte surface receptors by parasite ligands.
Plasmodium vivax
merozoite invasion is totally dependent on the recognition of the Duffy blood group antigen by the parasite ligand Duffy-binding protein (DBP). Receptor recognition by
P. vivax
relies on a cysteine-rich domain, the DBL domain or region II, at the N terminus of the extracellular portion of DBP. The minimal region of the DBP implicated for receptor recognition lies between cysteines 4 and 8 of the DBL domain, which is a region that also has the highest rate of allelic polymorphisms among parasite isolates. We previously found that allelic polymorphisms in this region altered the
P. vivax
DBL domain antigenic character, which contrasts with changes in receptor specificity attributed to polymorphisms in some homologous ligands of
Plasmodium falciparum
. To further investigate the relative importance of conserved and polymorphic residues within this DBL central region, we identified residues critical for receptor recognition by site-directed mutagenesis. Seventy-seven surface-predicted residues of the Sal-1 DBL domain were substituted with alanine and assayed for erythrocyte binding activity by expression of the mutant proteins on the surface of transiently transfected COS cells. The functional effect of alanine substitution varied from nil to complete loss of DBL erythrocyte-binding activity. Mutations that caused loss of ligand function mostly occurred in discontinuous clusters of conserved residues, whereas nearly all mutations in polymorphic residues did not affect erythrocyte binding. These data delineate DBL domain residues essential for receptor recognition.