bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of pressure in rubber elasticity
Authors: Bower A. F. , Weiner J. H.
Published: June 2004

We describe a series of molecular dynamics computations that reveal an intimate connection at the atomic scale between difference stress (which resists stretches) and pressure (which resists volume changes) in an idealized elastomer, in contrast to the classical theory of rubber elasticity. Our simulations idealize the elastomer as a “pearl necklace,” in which the covalent bonds are stiff linear springs, while nonbonded atoms interact through a Lennard-Jones potential with energy εLJ and radius σLJ. We calculate the difference stress t11−(t22+t33)/2 and mean stress (t11+t22+t33)/3 induced by a constant volume extension in the x1 direction, as a function of temperature T and reduced density ρ*=NσIJ3/ν. Here, N is the number of atoms in the simulation cell and ν is the cell volume. Results show that for ρ*<1, the difference stress is purely entropic and is in good agreement with the classical affine network model of rubber elasticity, which neglects nonbonded interactions. However, data presented by van Krevelen [Properties of Polymers, 3rd ed. (Elsevier, Amsterdam, 1990), p. 79] indicate that rubber at standard conditions corresponds to ρ*=1.2. For ρ*>1, the system is entropic for kT/εLJ>2, but at lower temperatures the difference stress contains an additional energy component, which increases as ρ* increases and temperature decreases. Finally, the model exhibits a glass transition for ρ*=1.2 and kT/εLJ≈2. The atomic-scale processes responsible for generating stress are explored in detail. Simulations demonstrate that the repulsive portion of the Lennard-Jones potential provides a contribution σnbr>0 to the difference stress, the attractive portion provides σnba≈0, while the covalent bonds provide σb<0. In contrast, their respective contributions to the mean stress satisfy Πnbr<0, Πnba>0, and Πb<0. Analytical calculations, together with simulations, demonstrate that mean and difference stresses are related by σnbr=−AΠnbr〈P2(θb)〉, σb=BΠb〈P2(θb)〉, where 〈P2(θb)〉 is a measure of the anisotropy of the orientation of the covalent bonds, and A and B are coefficients that depend weakly on ρ* and temperature. For high values of ρ*, we find that |σnbr|≫|σb|, and in this regime our model predicts behavior that is in good agreement with experimental data of D.L. Quested et al. [J. Appl. Phys. 52, 5977 (1981)] for the influence of pressure on the difference stress induced by stretching solithane.
Concentration-dependent self-diffusion of liquids in nanopores: A nuclear magnetic resonance study
Authors: Valiullin Rustem , Kortunov Pavel , Kärger Jörg , Timoshenko Victor
Published: June 2004

Nuclear magnetic resonance has been applied to study the details of molecular motion of low-molecular-weight polar and nonpolar organic liquids in nanoporous silicon crystals of straight cylindrical pore morphology at different pore loadings. Effective self-diffusion coefficients as obtained using the pulsed field gradient nuclear magnetic resonance method were found to pass through a maximum with increasing concentration for all liquids under study. Taking account of a concentration-dependent coexistence of capillary condensed, adsorbed and gaseous phases a generalized model for the effective self-diffusion coefficient was developed and shown to satisfactorily explain the experimental results. An explicit use of the adsorption isotherm properties within the model extends its applicability to the mesoporous range and highlights the role of surface interaction for the transport of molecules in small pores. The problem of surface diffusion and diffusion of multilayered molecules is also addressed.
Thermoreversible crosslinking of polyelectrolyte chains
Authors: Ermoshkin A. V. , Kudlay A. N. , Olvera de la Cruz M.
Published: June 2004

Thermoreversible crosslinking of polyelectrolyte chains via short-range attractions such as hydrogen bonding induced by uncharged or charged particles is studied within the Flory model of ideal association. Electrostatic interactions between the charges at different linking fractions are taken into account by using a generalized random phase approximation approach which includes the network connectivity. We find that at certain concentration of linking agents an infinitely large polymer network is formed. We calculate the structural gelation lines for linkers of different charges and functionalities.
Self-consistent Ornstein–Zernike approximation for the Sogami–Ise fluid
Authors: Schöll-Paschinger Elisabeth
Published: June 2004

We generalize the self-consistent Ornstein–Zernike approximation (SCOZA) to a fluid of particles with a pair potential consisting of a hard-core repulsion and a linear combination of Sogami–Ise tails, w(r)=−εσ∑ν(Kν/r+Lνzν)e−zν(r−σ). The formulation and implementation of the SCOZA takes advantage of the availability of semianalytic results for such systems within the mean-spherical approximation. The predictions for the thermodynamics, the phase behavior and the critical point are compared with optimized random phase approximation results; further, the effect of thermodynamic consistency is investigated.
Transitions between disordered phases in supercooled liquid silicon
Authors: Miranda Caetano R. , Antonelli Alex
Published: June 2004

We have investigated the transitions between disordered phases in supercooled liquid silicon using computer simulations. The thermodynamic properties were directly obtained from the free energy, which was computed using the recently proposed reversible scaling method. The calculated free energies of the crystalline and liquid phases of silicon at zero pressure, obtained using the environment dependent interatomic potential, are in excellent agreement with the available experimental data. The results show that, at zero pressure, a weak first-order liquid–liquid transition occurs at 1135 K and a continuous liquid–amorphous transition takes place at 843 K. These results are consistent with the existence of a second critical point for the liquid–liquid transition at a negative pressure.
Nonequilibrium melting and crystallization of a model Lennard-Jones system
Authors: Luo Sheng-Nian , Strachan Alejandro , Swift Damian C.
Published: June 2004

Nonequilibrium melting and crystallization of a model Lennard-Jones system were investigated with molecular dynamics simulations to quantify the maximum superheating/supercooling at fixed pressure, and over-pressurization/over-depressurization at fixed temperature. The temperature and pressure hystereses were found to be equivalent with regard to the Gibbs free energy barrier for nucleation of liquid or solid. These results place upper bounds on hysteretic effects of solidification and melting in high heating- and strain-rate experiments such as shock wave loading and release. The authors also demonstrate that the equilibrium melting temperature at a given pressure can be obtained directly from temperatures at the maximum superheating and supercooling on the temperature hysteresis; this approach, called the hysteresis method, is a conceptually simple and computationally inexpensive alternative to solid–liquid coexistence simulation and thermodynamic integration methods, and should be regarded as a general method. We also found that the extent of maximum superheating/supercooling is weakly pressure dependent, and the solid–liquid interfacial energy increases with pressure. The Lindemann fractional root-mean-squared displacement of solid and liquid at equilibrium and extreme metastable states is quantified, and is predicted to remain constant (0.14) at high pressures for solid at the equilibrium melting temperature.
Confinement effect on the adsorption from a binary liquid system near liquid/liquid phase separation
Authors: Rother Gernot , Woywod Dirk , Schoen Martin , Findenegg Gerhard H.
Published: June 2004

The preferential adsorption of one component of a binary system at the inner surfaces of mesoporous silica glasses was studied in a wide composition range at temperatures close to liquid/liquid phase separation. Confinement effects on the adsorption were investigated by using three controlled-pore glass (CPG-10) materials of different mean pore size (10 to 50 nm). For the experimental system (2-butoxyethanol+water), which exhibits an upper miscibility gap, strong preferential adsorption of water occurs, as the coexistence curve is approached at bulk compositions, at which water is the minority component. In this strong adsorption regime the area-related surface excess amount of adsorbed water decreases with decreasing pore width, while the shift in the volume-related mean composition of the pore liquid shows an opposite trend, i.e., greatest deviation from bulk composition occurring in the most narrow pores. A simple mean-field lattice model of a liquid mixture confined by parallel walls is adopted to rationalize these experimental findings. This model reproduces the main findings of the confinement effect on the adsorption near liquid/liquid phase separation.
Phase diagram of subphtalocyanine ordering on Ag(111)
Authors: Petrauskas V. , Lapinskas S. , Tornau E. E.
Published: June 2004

A model of subphtalocyanine molecules ordering on Ag(111) is proposed. We have demonstrated that the driving force of the ordering into honeycomb and hexagonal close packed patterns is a balance of intermolecular and subphtalocyanine–Ag interactions which can be generally expressed by a potential with infinite exclusion in a sufficiently large number of nearest coordination spheres of Ag(111) lattice and oscillatingly decaying behavior outside the sphere of exclusion. To cope with computational problems due to large size of the molecules compared to the substrate lattice period, we introduce the rescaling of Ag(111) lattice, and took into account an infinite exclusion of first, second, and third neighbors, attraction—of fourth and fifth, and repulsion—of sixth and seventh. The phase diagram is obtained by the lattice gas model using Monte Carlo simulations. Very strong first order phase transitions, causing the two-phase coexistence, were found between disordered and honeycomb as well as between disordered and hexagonal closed packed phases.
Droplet behavior in the presence of insoluble surfactants
Authors: Kruijt-Stegeman Y. W. , van de Vosse F. N. , Meijer H. E. H.
Published: June 2004

The time-dependent behavior of droplets in the presence of insoluble surfactants, i.e., droplet elongation in supercritical flow (capillary number Ca=0.1) and droplet breakup in a quiescent matrix, is studied using a finite element method. The interfacial tension coefficient σ as a function of the surfactant concentration Γ is described using the Langmuir equation of state, σ=σ0+RTΓ∞ ln(1−Γ/Γ∞). For droplets in an equal viscosity system, the influence of parameters Γ, Γ∞, and the Péclet number (ratio between surfactant convection and diffusion rate) on the elongation behavior has been investigated, whereas droplet breakup is considered for various values of the Péclet number for trace concentrations Γ≪Γ∞ of an insoluble surfactant. Depending on the surfactant used, a surfactant covered droplet in supercritical flow may deform more than or less than a clean droplet, as is the case in subcritical flow. Two processes compete: surfactant accumulation near the tips due to convection and overall surfactant dilution due to an increase of interfacial area. Nevertheless, the main effect of surfactants on dispersive mixing is due to the fact that upon breakup, the daughter droplets have a different interfacial tension coefficient. Especially in time-dependent processes, this may have a huge impact on the final droplet distribution.
Existence and construction of the transmutation operator
Authors: Boumenir A. , Tuan Vu Kim
Published: June 2004

We prove the existence of a transmutation operator between two weighted Sturm–Liouville operators. We also provide an explicit formula for the transmutation operator and a construction algorithm. An example and an application to an inverse spectral problem are also considered.
Spherical harmonics and basic coupling coefficients for the group SO(5) in an SO(3) basis
Authors: Rowe D. J. , Turner P. S. , Repka J.
Published: June 2004

An easily programmable algorithm is given for the computation of SO(5) spherical harmonics needed to complement the radial (beta) wave functions to form an orthonormal basis of wave functions for the five-dimensional harmonic oscillator. It is shown how these functions can be used to compute the (Clebsch–Gordan a.k.a. Wigner) coupling coefficients for combining pairs of irreps in this space to other irreps. This is of particular value for the construction of the matrices of Hamiltonians and transition operators that arise in applications of nuclear collective models. Tables of the most useful coupling coefficients are given in the Appendix.
Mesoscopic chiral reshaping of the Ag(110) surface induced by the organic molecule PVBA
Authors: Pascual J. I. , Barth J. V. , Ceballos G. , Trimarchi G. , De Vita A. , Kern K. , Rust H.-P.
Published: June 2004

We report scanning tunneling microscopy observations on the restructuring of a Ag(110) surface induced by the molecule 4-[trans-2-(pyrid-4-yl-vinyl)]benzoic acid (PVBA). Our data reveal that the surface undergoes a mesoscopic step faceting following exposure to submonolayer coverages and thermal activation. A sawtooth arrangement evolves implying long-range mass transport of substrate atoms and forming a regular arrangement of kink sites. Its formation is associated with the molecules’ functional headgroups forming carboxylates with {100} Ag microfacets at step edges, and eventually operating to reshape the surface morphology. Interestingly, the resulting microfacets act as chiral templates for the growth of supramolecular PVBA structures. Theoretical modeling based on ab initio results indicates that chiral recognition processes discriminating between the two enantiomers of adsorbed PVBA molecules occur in this process.
Low-energy electron induced restructuring of water monolayers on NaCl(100)
Authors: Toennies J. P. , Traeger F. , Vogt J. , Weiss H.
Published: June 2004

The influence of electron irradiation on the controversially discussed monolayer structure of H2O on NaCl(100) is investigated with helium atom diffraction before and after a low-damage low-energy electron diffraction (LEED) experiment. The ordered (1×1) structure observed initially with He atoms is found to be transformed to a stable c(4×2) structure after a 90 eV electron dosage of only 1015 electrons cm−2 or about 2 incident electrons per adsorbate molecule. Based on previously reported structure models for the two phases, the transition is attributed to a reorientation, and a possible compression of the water film induced by the electrons.
Magic clusters MAu4 (M=Ti and Zr) and their dimers: How magic are they?
Authors: Ghanty Tapan K. , Chandrakumar K. R. S. , Ghosh Swapan K.
Published: June 2004

The stability of closed shell bimetallic magic clusters MAu4 (M=Ti and Zr) is investigated theoretically through ab initio molecular orbital calculations. Both these clusters have tetrahedral structures and are found to be associated with large values of the ionization potential, HOMO-LUMO gap as well as the binding energies, which are characteristic of the magic clusters. However, the cluster–cluster interaction energy corresponding to a dimer formation is found to be unusually high (∼5–7 eV) in contradiction to the usual properties of a magic cluster and is attributed to a 3-center–2-electron M–Au–M type bridge bonding as well as aurophilic attraction. Gross geometrical features of the individual clusters are, however, mostly retained in the dimer, thus satisfying the basic requirements for the cluster-assembled materials. This work would have important implications in the design of novel cluster-based nanomaterials for various nanoscale applications.
Vibronic states in single molecules: C60 and C70 on ultrathin Al2O3 films
Authors: Liu N. , Pradhan N. A. , Ho W.
Published: June 2004

Vibronic states are observed in single C60 and C70 molecules by scanning tunneling microscopy. When single fullerene molecules are adsorbed on a thin layer of Al2O3 grown on a NiAl(110) substrate, equally spaced features are observed in the differential conductance (dI/dV), which are clearly resolved in d2I/dV2 spectra. These features are attributed to the vibronic states of the molecule. The vibronic progressions are sensitive to the molecular orientations and can have different spacings in different electronic bands of the same molecule. For C60, these vibronic states are associated with the intramolecular Ag and Hg vibrational modes. Vibronic states are not resolved in molecules adsorbed on the metal surface. However, inelastic electron tunneling spectroscopy exhibits a vibrational mode at 64 meV for C60 and 61 meV for C70 adsorbed on NiAl(110).
No evidence for large-scale proton ordering in Antarctic ice from powder neutron diffraction
Authors: Fortes A. D. , Wood I. G. , Grigoriev D. , Alfredsson M. , Kipfstuhl S. , Knight K. S. , Smith R. I.
Published: June 2004

We have examined a sample of 3000 year old Antarctic ice, collected at the Kohnen Station, by time-of-flight powder neutron diffraction to test the hypothesis of Fukazawa et al. [e.g., Ann. Glaciol. 31, 247 (2000)] that such ice may be partially proton ordered. Great care was taken to keep our sample below the proposed ordering temperature (237 K) at all times, but we did not observe any evidence of proton ordering.
Over-expression of HMW glutenin subunit Glu-B1 7x in hexaploid wheat varieties (Triticum aestivum)
Authors: Vawser M-J. , Cornish G. B.
Published: June 2004

In Canada in 1993, a special market class of wheat, Canada Western Extra Strong (CWES), was established to segregate wheat varieties known to produce very strong and extensible doughs. These exceptional dough properties enable CWES cultivars to be blended with wheats of lesser quality as well as being suited to the manufacture of frozen dough products. The high molecular weight (HMW) glutenin allele (Glu-B1al) that confers these properties, particularly dough strength, has now been identified. Typically, the presence of the Glu-B1al (7+8*) allele is associated with the overexpression of HMW-GS 1Bx 7. RP-HPLC was used to quantify the proportion (% area) of individual HMW-GS relative to total HMW-GS in wheat varieties of different origin. The B genome contributed the highest percentage of HMW-GS, with the exception of Glu-B1d (6+8*) where the D genome contributed the most. Cultivars that possessed the Glu-B1al allele contained a significantly higher (P < 0.001) proportion of HMW-GS (56.80 ± 3.25%) encoded by the B genome. This suggests that the proportion of Glu-B1 subunits, relative to the total amount of HMW-GS expressed, has a major effect on dough strength. We also identified germplasm, of different origin, that contains the Glu-B1al allele and overexpresses subunit 7, including the most likely source of this allele in bread wheat cultivars. The Glu-B1al allele in the varieties identified in this paper could be traced, at least through one parent, to the Argentinean bread wheat cultivar Klein Universal II. RP-HPLC elution and expression profiles of various common HMW-GS are also discussed.
The Biological Collections in CSIRO: a National Heritage?
Authors: Day M. F. C. , Hewson H. , Fagg M. , Doran J. , Turnbull J. , J.Ilic  , Jeffrey S. , Last P. , Graham A. , Chesser T. , Bougher N.
Published: June 2004

From the organization's earliest days, several Divisions of CSIRO have assembled substantial collections of biological species. These include a wide variety of plants and animals. Some collections consist of live organisms, some of preserved material. The origins and the functions of the collections vary; most of them now contain material of considerable value. Their history is intriguing, and their future has continued to be a question of importance.
Spatiotemporal retinoid-X receptor activation detected in live vertebrate embryos
Authors: Luria Ayala , Furlow J. David
Published: June 2004

Most studies on the nuclear retinoid-X receptor (RXR) have focused on its role as a heterodimeric partner but less about its own activation pattern during development and the distribution of potential endogenous ligands. The aim of this study is to visualize the distribution of activated RXRα in live transgenic
Xenopus laevis
embryos across a wide range of developmental stages. We adopted a nuclear receptor–Gal4 fusion/upstream activation sequence-based reporter system for our assay. Strong activation of the RXRα ligand-binding domain was observed in a segment of the spinal cord just posterior to the hindbrain. This activation is first detected in neurula stage embryos and persists up to swimming tadpole stages, after which activation strongly declines. Addition of exogenous ligands, such as 9-
cis
retinoic acid or
all-trans
retinoic acid, expands the activation of RXR throughout the spinal cord but not in the brain, whereas the RXR-specific ligand LG268 expanded the Gal4–RXR activation into the brain and olfactory epithelia. Treatment with the RAR-specific ligand 4-(
E
-2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl)benzoic acid or thyroid hormone had no effect on Gal4–RXR activation, whereas these compounds significantly increased their corresponding Gal4/receptor fusion proteins under similar conditions. Embryos expressing a Gal4–RXR fusion protein with a deletion in the ligand-dependent activation domain (AF2) show no reporter gene activation. The results shown in this paper reveal a specific activation pattern for Gal4–RXRα specifically in the developing spinal cord and suggest the existence of RXR ligand “hot-spots” in this region.
Suppression of p160ROCK bypasses cell cycle arrest after Aurora-A/STK15 depletion
Authors: Du Jian , Hannon Gregory J.
Published: June 2004

Alterations in the expression and activity of the centrosomal kinase, Aurora-A/serine/threonine kinase 15 (STK15), affect genomic stability, disrupt the fidelity of centrosome duplication, and induce cellular transformation. Here, we provide evidence that p160ROCK, a Rho-associate serine/threonine kinase, associates with Aurora-A in a protein complex with other STK15-associated factors. Suppression of Aurora-A by small interfering RNA in HeLa cells blocks the ability of centrosomes to organize normal mitotic spindles, induces G
2
/M cell cycle arrest, and promotes accumulation of tetraploid cells. In many cases, one outcome of such abnormalities is apoptosis. Introduction of a second genetic lesion, suppression of p160ROCK by RNA interference, can rescue abnormal mitotic spindle formation, release the G
2
/M cell cycle arrest, and alleviate apoptosis, leading to a greater accumulation of aneuploid cells. These results suggest that Aurora-A and p160ROCK act in a common genetic pathway that promotes and monitors progression through G
2
/M.
Hypoxic inducible factor 1α, extracellular signal-regulated kinase, and p53 are regulated by distinct threshold concentrations of nitric oxide
Authors: Thomas Douglas D. , Espey Michael Graham , Ridnour Lisa A. , Hofseth Lorne J. , Mancardi Daniele , Harris Curtis C. , Wink David A.
Published: June 2004

NO produced in tumors can either positively or negatively regulate growth. To examine this dichotomy, effects of NO concentration and duration on the posttranslational regulation of several key proteins were examined in human breast MCF7 cells under aerobic conditions. We found that different concentration thresholds of NO appear to elicit a discrete set of signal transduction pathways. At low steady-state concentrations of NO (<50 nM), extracellular signal-regulated kinase (ERK) phosphorylation was induced via a guanylate cyclase-dependent mechanism. Hypoxic inducible factor 1α (HIF-1α) accumulation was associated with an intermediate amount of NO (>100 nM), whereas p53 serine 15 phosphorylation occurred at considerably higher levels (>300 nM). ERK phosphorylation was transient during NO exposure. HIF-1α stabilization paralleled the presence of NO, whereas p53 serine 15 phosphorylation was detected during, and persisted after, NO exposure. The dose-dependent effects of synthetic NO donors were mimicked by activated macrophages cocultured with MCF7 cells at varying ratios. ERK and HIF-1α activation was similar in breast cancer cell lines either mutant (MB231) or null (MB157) in p53. The stabilization of HIF-1α by NO was not observed with increased MCF7 cell density, demonstrating the interrelationship between NO and O2consumption. The findings show that concentration and duration of NO exposure are critical determinants in the regulation of tumor-related proteins.
RETRACTED: Structure of vaccinia complement protein in complex with heparin and potential implications for complement regulation
Authors: Ganesh Vannakambadi K. , Smith Scott A. , Kotwal Girish J. , Murthy Krishna H. M.
Published: June 2004

Vaccinia virus complement control protein (VCP), a homolog of the regulators of the complement activation family of proteins, inhibits complement activation through mechanisms similar to human fluid-phase complement regulators factor H and C4b-binding protein. VCP has a heparin-binding activity that assists vaccinia in host interactions. Interaction with cell-surface polyanions like heparin is centrally important in the functioning of fluid-phase complement regulators and is the basis of host-target discrimination by the alternative pathway. We report the structure of VCP in complex with a heparin decasaccharide, which reveals changes in VCP that might be pertinent to complement regulation. Properties that VCP shares with fluid-phase complement regulators suggest that such conformational changes may be of relevance in the functioning of other complement regulators. Additionally, comparison of VCP–heparin interactions with potentially similar interactions in factor H might enable understanding of the structural basis of familial hemolytic uremic syndrome, attributed to mutational disruption of heparin and C3b binding by factor H.
Kinetic isotope effects in Ras-catalyzed GTP hydrolysis: Evidence for a loose transition state
Authors: Du Xinlin , Black Gavin E. , Lecchi Paolo , Abramson Fred P. , Sprang Stephen R.
Published: June 2004

A remote labeling method has been developed to determine
18
O kinetic isotope effects (KIEs) in Ras-catalyzed GTP hydrolysis. Substrate mixtures consist of
13
C-depleted GTP and [
18
O,
13
C]GTP that contains
18
O at phosphoryl positions of mechanistic interest and
13
C at all carbon positions of the guanosine moiety. Isotope ratios of the nonvolatile substrates and products are measured by using a chemical reaction interface/isotope ratio mass spectrometer. The isotope effects are 1.0012 (0.0026) in the γ nonbridge oxygens, 1.0194 (0.0025) in the leaving group oxygens (the β–γ oxygen and the two β nonbridge oxygens), and 1.0105 (0.0016) in the two β nonbridge oxygens. The KIE in the β–γ bridge oxygen was computed to be 1.0116 or 1.0088 by two different methods. The significant KIE in the leaving group reveals that chemistry is largely rate-limiting whereas the KIEs in the γ nonbridge oxygens and the leaving group indicate a loose transition state that approaches a metaphosphate. The KIE in the two β nonbridge oxygens is roughly equal to that in the β–γ bridge oxygen. This indicates that, in the transition state, Ras shifts one-half of the negative charge that arises from P
γ
–O
β–γ
fission from the β–γ bridge oxygen to the two β nonbridge oxygens. The KIE effects, interpreted in light of structural and spectroscopic data, suggest that Ras promotes a loose transition state by stabilizing negative charge in the β–γ bridge and β nonbridge oxygens of GTP.
Identification of the xenosensors regulating human 5-aminolevulinate synthase
Authors: Podvinec Michael , Handschin Christoph , Looser Renate , Meyer Urs A.
Published: June 2004

Heme is an essential component of numerous hemoproteins with functions including oxygen transport, energy metabolism, and drug biotransformation. In nonerythropoietic cells, 5-aminolevulinate synthase (ALAS1) is the rate-limiting enzyme in heme biosynthesis. Upon exposure to drugs that induce cytochromes P450 and other drug-metabolizing enzymes, ALAS1 is transcriptionally up-regulated, increasing the rate of heme biosynthesis to provide heme for cytochrome P450 hemoproteins. We used a combinedin silico-in vitroapproach to identify sequences in theALAS1gene that mediate direct transcriptional response to xenobiotic challenge. We have characterized two enhancer elements, located 20 and 16 kb upstream of the transcriptional start site. Both elements respond to prototypic inducer drugs and interact with the human pregnane X receptor NR1I2 and the human constitutive androstane receptor NR1I3. Our results suggest that the fundamental mechanism of drug induction is the same for cytochromes P450 and ALAS1. Transcriptional activation of theALAS1gene is the first step in the coordinated up-regulation of apoprotein and heme synthesis in response to exogenous and endogenous signals controlling heme levels. Understanding the direct effects of drugs on heme synthesis is of clinical interest, particularly in patients with hepatic porphyrias.
Visualization of ribosome-recycling factor on the
Escherichia coli
70S ribosome: Functional implications
Authors: Agrawal Rajendra K. , Sharma Manjuli R. , Kiel Michael C. , Hirokawa Go , Booth Timothy M. , Spahn Christian M. T. , Grassucci Robert A. , Kaji Akira , Frank Joachim
Published: June 2004

After the termination step of protein synthesis, a deacylated tRNA and mRNA remain associated with the ribosome. The ribosome-recycling factor (RRF), together with elongation factor G (EF-G), disassembles this posttermination complex into mRNA, tRNA, and the ribosome. We have obtained a three-dimensional cryo-electron microscopic map of a complex of the
Escherichia coli
70S ribosome and RRF. We find that RRF interacts mainly with the segments of the large ribosomal subunit's (50S) rRNA helices that are involved in the formation of two central intersubunit bridges, B2a and B3. The binding of RRF induces considerable conformational changes in some of the functional domains of the ribosome. As compared to its binding position derived previously by hydroxyl radical probing study, we find that RRF binds further inside the intersubunit space of the ribosome such that the tip of its domain I is shifted (by ≈13 Å) toward protein L5 within the central protuberance of the 50S subunit, and domain II is oriented more toward the small ribosomal subunit (30S). Overlapping binding sites of RRF, EF-G, and the P-site tRNA suggest that the binding of EF-G would trigger the removal of deacylated tRNA from the P site by moving RRF toward the ribosomal E site, and subsequent removal of mRNA may be induced by a shift in the position of 16S rRNA helix 44, which harbors part of the mRNA.
A cardiac arrhythmia syndrome caused by loss of ankyrin-B function
Authors: Mohler Peter J. , Splawski Igor , Napolitano Carlo , Bottelli Georgia , Sharpe Leah , Timothy Katherine , Priori Silvia G. , Keating Mark T. , Bennett Vann
Published: June 2004

220-kDa ankyrin-B is required for coordinated assembly of Na/Ca exchanger, Na/K ATPase, and inositol trisphosphate (Ins
P
3
) receptor at transverse-tubule/sarcoplasmic reticulum sites in cardiomyocytes. A loss-of-function mutation of ankyrin-B identified in an extended kindred causes a dominantly inherited cardiac arrhythmia, initially described as type 4 long QT syndrome. Here we report the identification of eight unrelated probands harboring ankyrin-B loss-of-function mutations, including four previously undescribed mutations, whose clinical features distinguish the cardiac phenotype associated with loss of ankyrin-B activity from classic long QT syndromes. Humans with ankyrin-B mutations display varying degrees of cardiac dysfunction including bradycardia, sinus arrhythmia, idiopathic ventricular fibrillation, catecholaminergic polymorphic ventricular tachycardia, and risk of sudden death. However, a prolonged rate-corrected QT interval was not a consistent feature, indicating that ankyrin-B dysfunction represents a clinical entity distinct from classic long QT syndromes. The mutations are localized in the ankyrin-B regulatory domain, which distinguishes function of ankyrin-B from ankyrin-G in cardiomyocytes. All mutations abolish ability of ankyrin-B to restore abnormal Ca
2+
dynamics and abnormal localization and expression of Na/Ca exchanger, Na/K ATPase, and Ins
P
3
R in ankyrin-B
+/-
cardiomyocytes. This study, considered together with the first description of ankyrin-B mutation associated with cardiac dysfunction, supports a previously undescribed paradigm for human disease due to abnormal coordination of multiple functionally related ion channels and transporters, in this case the Na/K ATPase, Na/Ca exchanger, and Ins
P
3
receptor.
The topoisomerase IV ParC subunit colocalizes with the
Caulobacter
replisome and is required for polar localization of replication origins
Authors: Wang Sherry C. , Shapiro Lucy
Published: June 2004

The process of bacterial DNA replication generates chromosomal topological constraints that are further confounded by simultaneous transcription. Topoisomerases play a key role in ensuring orderly replication and partition of DNA in the face of a continuously changing DNA tertiary structure. In addition to topological constraints, the cellular position of the replication origin is strictly controlled during the cell cycle. In
Caulobacter crescentus
, the origin of DNA replication is located at the cell pole. Upon initiation of DNA replication, one copy of the duplicated origin sequence rapidly appears at the opposite cell pole. To determine whether the maintenance of DNA topology contributes to the dynamic positioning of a specific DNA region within the cell, we examined origin localization in cells that express temperature-sensitive forms of either the ParC or ParE subunit of topoisomerase (Topo) IV. We found that in the absence of active Topo IV, replication initiation can occur but a significant percent of replication origins are either no longer moved to or maintained at the cell poles. During the replication process, the ParC subunit colocalizes with the replisome, whereas the ParE subunit is dispersed throughout the cell. However, an active ParE subunit is required for ParC localization to the replisome as it moves from the cell pole to the division plane during chromosome replication. We propose that the maintenance of DNA topology throughout the cell cycle contributes to the dynamic positioning of the origin sequence within the cell.
Random sequencing of an induced
Taxus
cell cDNA library for identification of clones involved in Taxol biosynthesis
Authors: Jennewein Stefan , Wildung Mark R. , Chau MyDoanh , Walker Kevin , Croteau Rodney
Published: June 2004

Biosynthesis of the anticancer drug Taxol involves 19 enzymatic steps from the universal diterpenoid progenitor geranylgeranyl diphosphate derived by the plastidial methylerythritol phosphate pathway for isoprenoid precursor supply. To gain further insight about Taxol biosynthesis relevant to the improved production of this drug and to draw inferences about the organization, regulation, and origins of this complex natural product pathway, random sequencing of a cDNA library derived from
Taxus cuspidata
cells (induced for taxoid biosynthesis with methyl jasmonate) was undertaken. This effort revealed surprisingly high abundances for transcripts of several of the 12 defined genes of Taxol biosynthesis, yielded cDNAs encoding two previously uncharacterized cytochrome P450 taxoid hydroxylases, and provided candidate genes for all but one of the remaining seven steps of this extended sequence of reactions.
A neurokinin 1 receptor antagonist decreases postoperative peritoneal adhesion formation and increases peritoneal fibrinolytic activity
Authors: Reed Karen L. , Fruin A. Brent , Gower Adam C. , Stucchi Arthur F. , Leeman Susan E. , Becker James M.
Published: June 2004

Fibrous adhesions remain a major sequela of abdominal surgery. The proinflammatory peptide substance P (SP), known to participate in inflammatory events, may play a key role in adhesion formation. This hypothesis was tested by using an antagonist, CJ-12,255 (Pfizer), that blocks the binding of SP to the neurokinin 1 receptor (NK-1R). Adhesion formation was surgically induced in the peritoneum of rats receiving daily doses of the NK-1R antagonist (NK-1RA; 5.0 or 10.0 mg/kg per day) or saline. On postoperative day 7, both the low and high doses of NK-1RA significantly (P< 0.05) reduced adhesion formation by 45% and 53%, respectively, compared with controls. Subsequently, the effect of NK-1RA administration on peritoneal fibrinolytic activity was investigated to determine a potential mechanism for SP action in the peritoneum. Samples were collected from nonoperated controls and from animals 24 h postsurgery that were administered either NK-1RA or saline. Fibrinolytic activity in peritoneal fluid was assayed by zymography, and expression of tissue plasminogen activator (tPA) and plasminogen activator inhibitor 1, both regulators of fibrinolytic activity, was assessed in peritoneal tissue and fluid by RT-PCR and bioassay, respectively. NK-1RA administration led to a marked (P< 0.05) increase in tPA mRNA levels in peritoneal tissue compared with nonoperated and saline-administered animals. Likewise, NK-1RA administration significantly (P< 0.05) increased tPA in the peritoneal fluid. These data suggest that activation of the NK-1R promotes peritoneal adhesion formation by limiting fibrinolytic activity in the postoperative peritoneum, thus enabling fibrinous adhesions to persist.
The type of sugar moiety is a major determinant of the small intestinal uptake and subsequent biliary excretion of dietary quercetin glycosides
Authors: Arts Ilja C. W. , Sesink Aloys L. A. , Faassen-Peters Maria , Hollman Peter C. H.
Published: June 2004

Quercetin is an important dietary flavonoid with putative beneficial effects in the prevention of cancer and CVD. The in vivo bioactivity of quercetin depends on its bioavailability, which varies widely between foods. We used an in situ rat intestinal perfusion model to study whether differential small intestinal hydrolysis of the sugar moiety of five naturally occurring quercetin glycosides determines the small intestinal uptake and subsequent biliary excretion of quercetin. After 30 min perfusion, a decrease of intact quercetin glycoside in perfusate was observed for quercetin-3-O-ß-glucoside (20·9 (sem 1·4) μmol/l) and quercetin-4′-O-ß-glucoside (23·5 (sem 1·6) μmol/l), but not of quercetin-3-O-ß-galactoside, quercetin-3-O-ß-rhamnoside and quercetin-3-O-α-arabinopyranoside. Appearance of free quercetin in perfusate and conjugated quercetin metabolites (quercetin, isorhamnetin, and tamarixetin) in portal and peripheral plasma and bile were also significantly greater after treatment with quercetin-3-O-ß-glucoside or quercetin-4′-O-ß-glucoside compared with any of the other glycosides. Thus, the type of sugar moiety is a major determinant of the small intestinal absorption of quercetin glycosides, but the position (3 or 4′) of the glucose moiety does not further influence absorption. The poor bioavailability of important dietary quercetin glycosides has implications for their in vivo bioactivities.
Viscoelastic properties of the small intestinal and caecal contents of the chicken
Authors: Takahashi T. , Goto M. , Sakata T.
Published: June 2004

We measured the coefficients of viscosity, shear rates and shear stresses of chicken small intestinal and caecal contents, including solid particles, using a tube-flow viscometer. The coefficients of viscosity of chicken small intestinal and caecal contents were correlated negatively with their shear rates, a characteristic typical of non-Newtonian fluids. The coefficient of viscosity of the small intestinal contents was lower than that of the caecal contents at a shear rate of 1 s−1. Chicken caecal contents were more viscous than pig caecal contents. The exponential relationship between shear stress and shear rate showed that chicken small intestinal and caecal contents had an apparent Herschel–Bulkley fluid nature. These results indicate that solid particles, including uric acid crystals, are mainly responsible for the viscosity of the digesta in the chicken.
Dietary sources of vitamin C, vitamin E and specific carotenoids in Spain
Authors: García-Closas Reina , Berenguer Antonio , Tormo María José , Sánchez María José , Quirós José R. , Navarro Carmen , Arnaud Rosario , Dorronsoro Miren , Chirlaque María Dolores , Barricarte Aurelio , Ardanaz Eva , Amiano Pillar , Martinez Carmen , Agudo Antonio , González Carlos A.
Published: June 2004

A cross-sectional study was conducted within the Spanish cohort of the European Prospective Investigation in Cancer and Nutrition to assess the principal food sources of vitamin C, vitamin E, α-carotene, β-carotene, lycopene, lutein, β-cryptoxanthin and zeaxanthin in an adult Spanish population. The study included 41 446 healthy volunteers (25 812 women and 15 634 men), aged 29–69 years, from three Spanish regions in the north (Asturias, Navarra and Guipúzcoa) and two in the south (Murcia and Granada). Usual food intake was estimated by personal interview through a computerized version of a dietary history questionnaire. Foods that provided at least two-thirds of the studied nutrients were: fruits (mainly oranges) (51 %) and fruiting vegetables (mainly tomato and sweet pepper) (20 %) for vitamin C; vegetable oils (sunflower and olive) (40 %), non-citrus fruits (10 %), and nuts and seeds (8 %) for vitamin E; root vegetables (carrots) (82 %) for α-carotene; green leafy (28 %), root (24 %) and fruiting vegetables (22 %) for β-carotene; fruiting vegetables (fresh tomato) (72 %) for lycopene; green leafy vegetables (64 %) for lutein; citrus fruits (68 %) for β-cryptoxanthin; citrus fruits (43 %) and green leafy vegetables (20 %) for zeaxanthin. In conclusion, the main food sources of nutrients with redox properties have been identified in a Mediterranean country. This could provide an insight into the interpretation of epidemiological studies investigating the role of diet in health and disease.
Latroids and their representation by codes over modules
Authors: Vertigan Dirk
Published: June 2004

It has been known for some time that there is a connection between linear codes over fields and matroids represented over fields. In fact a generator matrix for a linear code over a field is also a representation of a matroid over that field. There are intimately related operations of deletion, contraction, minors and duality on both the code and the matroid. The weight enumerator of the code is an evaluation of the Tutte polynomial of the matroid, and a standard identity relating the Tutte polynomials of dual matroids gives rise to a MacWilliams identity relating the weight enumerators of dual codes. More recently, codes over rings and modules have been considered, and MacWilliams type identities have been found in certain cases. In this paper we consider codes over rings and modules with code duality based on a Morita duality of categories of modules. To these we associate latroids, defined here. We generalize notions of deletion, contraction, minors and duality, on both codes and latroids, and examine all natural relations among these. We define generating functions associated with codes and latroids, and prove identities relating them, generalizing above-mentioned generating functions and identities.
Quantum deformations of fundamental groups of oriented 3-manifolds
Authors: Kaiser Uwe
Published: June 2004

We compute two-term skein modules of framed oriented links in oriented

3
3

-manifolds. They contain the self-writhe and total linking number invariants of framed oriented links in a universal way. The relations in a natural presentation of the skein module are interpreted as monodromies in the space of immersions of circles into the

3
3

-manifold.
The Deligne complex for the four-strand braid group
Authors: Charney Ruth
Published: June 2004

This paper concerns the homotopy type of hyperplane arrangements associated to infinite Coxeter groups acting as reflection groups on

C

n

\mathbb C^n

. A long-standing conjecture states that the complement of such an arrangement should be aspherical. Some partial results on this conjecture were previously obtained by the author and M. Davis. In this paper, we extend those results to another class of Coxeter groups. The key technical result is that the spherical Deligne complex for the 4-strand braid group is CAT(1).
Identities of graded algebras and codimension growth
Authors: Bahturin Yu. , Zaicev M.
Published: June 2004

Let

A
=

⊕

g
∈
G

A
g

A=\oplus _{g\in G}A_g

be a

G
G

-graded associative algebra over a field of characteristic zero. In this paper we develop a conjecture that relates the exponent of the growth of polynomial identities of the identity component

A
e

A_e

to that of the whole of

A
A

, in the case where the support of the grading is finite. We prove the conjecture in several natural cases, one of them being the case where

A
A

is finite dimensional and

A
e

A_e

has polynomial growth.
When does the subadditivity theorem for multiplier ideals hold?
Authors: Takagi Shunsuke , Watanabe Kei-ichi
Published: June 2004

Demailly, Ein and Lazarsfeld proved the subadditivity theorem for multiplier ideals on nonsingular varieties, which states the multiplier ideal of the product of ideals is contained in the product of the individual multiplier ideals. We prove that, in the two-dimensional case, the subadditivity theorem holds on log terminal singularities. However, in the higher dimensional case, we have several counterexamples. We consider the subadditivity theorem for monomial ideals on toric rings and construct a counterexample on a three-dimensional toric ring.
On the asymptotic behavior of a complete bounded minimal surface in ℝ³
Authors: Martín Francisco , Morales Santiago
Published: June 2004

In this paper we construct an example of a complete minimal disk which is properly immersed in a ball of

R

3

\mathbb {R}^3

.
On the classification of full factors of type III
Authors: Shlyakhtenko Dimitri
Published: June 2004

We introduce a new invariant

S

(
M
)

\mathscr {S}(M)

for type III factors

M
M

with no almost-periodic weights. We compute this invariant for certain free Araki-Woods factors. We show that Connes’ invariant

τ
\tau

cannot distinguish all isomorphism classes of free Araki-Woods factors. We show that there exists a continuum of mutually non-isomorphic free Araki-Woods factors, each without almost-periodic weights.
Quadratic forms and Pfister neighbors in characteristic 2
Authors: Hoffmann Detlev , Laghribi Ahmed
Published: June 2004

We study Pfister neighbors and their characterization over fields of characteristic

2
2

, where we include the case of singular forms. We give a somewhat simplified proof of a theorem of Fitzgerald which provides a criterion for when a nonsingular quadratic form

q
q

is similar to a Pfister form in terms of the hyperbolicity of this form over the function field of a form

φ
\varphi

which is dominated by

q
q

. From this, we derive an analogue in characteristic

2
2

of a result by Knebusch saying that, in characteristic

≠
2

\neq 2

, a form is a Pfister neighbor if its anisotropic part over its own function field is defined over the base field. Our result includes certain cases of singular forms, but we also give examples which show that Knebusch’s result generally fails in characteristic

2
2

for singular forms. As an application, we characterize certain forms of height

1
1

in the sense of Knebusch whose quasi-linear parts are of small dimension. We also develop some of the basics of a theory of totally singular quadratic forms. This is used to give a new interpretation of the notion of the height of a standard splitting tower as introduced by the second author in an earlier paper.