bluuebunny/crossref_metadata_2025 huggingface dataset:
The Piezoelectric Resonator and the Effect of Electrode Spacing upon Frequency
Authors: Cady Walter G.
Published: January 2005

A new formulation of piezo-resonator theory, called for convenience the ``mechanical theory,'' is developed for a crystal resonator with gap between crystal and electrodes, involving the increase in effective stiffness caused by space or surface charge, and explaining the increase in resonance frequency with increasing gap. The cases treated are thickness vibrations (both compressional and shear) of a plate, and lengthwise compressional vibrations of a bar. Specialized values of the elastic, dielectric and piezoelectric constants are employed, depending upon the nature of the elastic reactions for each cut and for each mode of vibration. The mechanical theory is compared with the customary ``electrical theory,'' according to which the resonator maintains a constant stiffness, the increase in frequency with increasing gap being accounted for by the electrical reactance of the gap considered as a series capacitance. When the crystal surfaces are equipotential (thickness vibrations, or lengthwise vibrations of a bar whose surfaces have been covered with a metallic deposit), the two theories are in agreement. It is shown that the mechanical theory, unlike the electrical theory, describes correctly the performance of a vibrating crystal bar that is not metallically coated. The characteristics of the resonator and the contrast between the two theories are illustrated by resonance-circle and phase diagrams. The relative increase in frequency caused by the gap is shown to be Δf/f0=Uw/(e+kw), where f0 is the frequency at zero gap, f0+Δf the frequency with a gap of width w, e the thickness of the crystal in the direction of the applied electric field, k the dielectric constant and U=16ε2/πc, ε being the appropriate piezoelectric constant and c the effective elastic constant at zero gap. In the case of the uncoated bar, the function U has to be multiplied by π2/8. Observations were made with eight quartz crystals of the following cuts: Y-cut, X-cut, BT- and AC-cuts (notation of Lack, Willard and Fair) for thickness vibrations, and an X-cut bar for lengthwise vibrations. With small gaps, the experimental values of the function U are, except with the BT- and AC-cuts, from 13 to 60 percent smaller than the theoretical values. In most cases the discrepancy becomes still greater at large gap values. The probable reasons for these discrepancies are discussed, with the conclusion that a large increase in frequency with gap may be taken as a criterion of a good resonator (large piezoelectric constant, freedom from twinning and coupling). A Rochelle salt Y-cut 45° bar when tested for the gap effect showed a satisfactory agreement with theory, considering the uncertainty in the values of the dielectric and piezoelectric constants. It is shown that the effect of gap upon frequency can be utilized in determining approximately the piezoelectric constant of a crystal. The theory of the dependence of frequency upon gap for overtone vibrations is briefly discussed.
The Thermionic Amplification of Direct Currents
Authors: Macdonald P. A.
Published: January 2005

The principles and practical applications of thermionic tubes are discussed at some length in relation to the amplification of direct currents.
Plastic Properties of Shellac
Authors: Gardner Wm. Howlett
Published: January 2005

The plastic properties of shellac is a subject of international interest, but one which has received relatively little study. In this paper, those properties such as polymerization, aggregation, condensation in the presence of chemicals, and adsorption of water, which would affect rheological measurements are reviewed and discussed.
A Method of Analyzing Experimental Results Obtained from Elasto-Viscous Bodies
Authors: Gemant Andrew
Published: January 2005

An attempt is made to develop a general method of analyzing experimental results concerned with the behavior of elasto-viscous bodies. It is shown that the transient equation for relaxation processes can be deduced from the experimental impedance formula, and that relaxation experiments are in agreement with the deduced transient equation. A differential equation relating stress, strain and time is derived from the experimental impedance formula. The relation of this equation toithe well-known Maxwell equation is discussed.
The Flow of Gas-Liquid Mixtures Through Unconsolidated Sands
Authors: Wyckoff R. D. , Botset H. G.
Published: January 2005

A method is described for studying the flow of gas-liquid mixtures through unconsolidated sands. Results are given for experiments on four sands of widely different permeabilities using carbon dioxide and water as the fluids. A relation between permeability and liquid-saturation of the sand is found which permits the correlation of saturation and the steady state flow of the gas and liquid components. Generalization of these results for all unconsolidated sands seems permissible. The phenomena of equilibrium permeability and equilibrium liquid-saturation are described and their significance discussed. It is believed that the experimental attack and type of analysis is applicable to the general problem of the flow of gas-liquid mixtures through porous media.
A Hydrodynamical Theory of Piston Ring Lubrication
Authors: Castleman R. A.
Published: January 2005

It is shown that, making the assumption that oils as used in engine lubrication cannot stand absolute tension, and taking into account the observed tendency of the bearing faces of piston rings to wear into an uneven shape with the ``high'' point near the middle and a very gentle slope to each edge, Reynolds' theory of bearing lubrication can be extended to ring lubrication. A practical application of this extension is outlined and illustrated. Results of calculations, based on this extension, of ring clearance and wear under average working conditions are in substantial agreement with a number of observations.
The dissociation dynamics of He⋯I 35Cl(B,v′=2,3) complexes with varying amounts of internal energy
Authors: Darr Joshua P. , Loomis Richard A. , McCoy Anne B.
Published: January 2005

The He⋯I 35Cl intermolecular vibrational levels with n′=0–6 that are bound within the He+ICl(B,v′=3) potential [A. B. McCoy, J. P. Darr, D. S. Boucher, P. R. Winter, M. D. Bradke, and R. A. Loomis, J. Chem. Phys. 120, 2677 (2004)] are identified in laser-induced fluorescence experiments performed at very low temperatures within a supersonic expansion. Comparisons of the positions and intensities of these lines with the excitation spectra, calculated using potential surfaces to describe the interactions between the helium atom and ICl in its ground and excited state, assist in the assignments. Based on these comparisons the excited state potential was rescaled so that the experimental and calculated J′=0 energies agree to within the experimental uncertainties for all but the lowest, n′=0, intermolecular level. Two-laser, action, and pump-probe spectroscopy experiments indicate that the bound He⋯I 35Cl(B,v′=3) intermolecular vibrational levels undergo vibrational predissociation forming rotationally excited I 35Cl(B,v′=2,j′) products with distributions that depend upon the initial intermolecular vibrational level excited. Action spectra recorded in the ICl B-X, 2-0 region while monitoring the Δv=0, I 35Cl(B,v′=2) channel reveal two additional dissociation mechanisms for the He⋯I 35Cl(B,v′) excited state complexes: rotational predissociation of discrete metastable states lying slightly above the He+I 35Cl(B,v′=2) asymptote and direct dissociation that occurs when the linear conformer is excited to the continuum of states above the same asymptote. The rotational predissociation pathway forms I 35Cl(B,v′=2,j′) products in all of the rotational states energetically accessible. The direct dissociation mechanism yields very cold rotational product state distributions; for instance, the average rotational energy in the product state distribution measured when the linear complexes are prepared 20 cm−1 above the dissociation limit is only 1.51 cm−1, representing only 7.6% of the available energy.
A general formula for the rate of resonant transfer of energy between two electric multipole moments of arbitrary order using molecular quantum electrodynamics
Authors: Salam A.
Published: January 2005

A general expression is derived for the matrix element for the resonant transfer of energy between an initially excited donor species and an acceptor moiety in the ground state, with each entity possessing an electric multipole moment of arbitrary order. In the quantum electrodynamical framework employed, the coupling between the pair is mediated by the exchange of a single virtual photon. The probability amplitude found from second-order perturbation theory is a product of the electric moments located at each center and the resonant multipole-multipole interaction tensor. Using the Fermi golden rule, a general formula for the rate of energy transfer is obtained. As an illustration of the efficacy of the theory developed, rates of excitation energy exchange are calculated for systems interacting through dipole-quadrupole, dipole-octupole, quadrupole-quadrupole, and the familiar dipole-dipole coupling. For each of the cases examined, the near- and far-zone limits of the migration rate are calculated from the result valid for all donor-acceptor separations beyond wave function overlap. Expression of the octupole contribution to the transfer rate in terms of its irreducible components of weights 1 and 3 leads to new features. The octupole weight-1 term is found to contribute only when the interaction is retarded, while the dipole-octupole weight-1 contribution appears as a higher-order correction term to the dipole-dipole rate. Order of magnitude estimates are given for the contributions of dipole-quadrupole and dipole-octupole terms relative to the leading dipole-dipole rate for near-, intermediate-, and far-zone separations to further understand the role played by higher multipole moments in the transfer of excitation and the mechanism dominating the process.
Coarse-grained kinetic computations for rare events: Application to micelle formation
Authors: Kopelevich Dmitry I. , Panagiotopoulos Athanassios Z. , Kevrekidis Ioannis G.
Published: January 2005

We discuss a coarse-grained approach to the computation of rare events in the context of grand canonical Monte Carlo (GCMC) simulations of self-assembly of surfactant molecules into micelles. The basic assumption is that the computational system dynamics can be decomposed into two parts—fast (noise) and slow (reaction coordinates) dynamics, so that the system can be described by an effective, coarse-grained Fokker–Planck (FP) equation. While such an assumption may be valid in many circumstances, an explicit form of FP equation is not always available. In our computations we bypass the analytic derivation of such an effective FP equation. The effective free energy gradient and the state-dependent magnitude of the random noise, which are necessary to formulate the effective Fokker–Planck equation, are obtained from ensembles of short bursts of microscopic simulations with judiciously chosen initial conditions. The reaction coordinate in our micelle formation problem is taken to be the size of a cluster of surfactant molecules. We test the validity of the effective FP description in this system and reconstruct a coarse-grained free energy surface in good agreement with full-scale GCMC simulations. We also show that, for very small clusters, the cluster size ceases to be a good reaction coordinate for a one-dimensional effective description. We discuss possible ways to improve the current model and to take higher-dimensional coarse-grained dynamics into account.
Ultrafast molecular dynamics of liquid aromatic molecules and the mixtures with CCl4
Authors: Shirota Hideaki
Published: January 2005

The ultrafast molecular dynamics of liquid aromatic molecules, benzene, toluene, ethylbenzene, cumene, and 1,3-diphenylpropane, and the mixtures with CCl4 have been investigated by means of femtosecond optical heterodyne-detected Raman-induced Kerr effect spectroscopy. The picosecond Kerr transients of benzene, toluene, ethylbenzene, and cumene and the mixtures with CCl4 show a biexponential feature. 1,3-Diphenylpropane and the mixtures with CCl4 show triexponential picosecond Kerr transients. The slow relaxation time constants of the aromatic molecules and the mixtures with CCl4 are qualitatively described by the Stoke-Einstein-Debye hydrodynamic model. The ultrafast dynamics have been discussed based on the Kerr spectra in the frequency range of 0–800 cm−1 obtained by the Fourier transform analysis of the Kerr transients. The line shapes of the low-frequency intermolecular spectra located at 0–180 cm−1 frequency range have been analyzed by two Brownian oscillators (∼11 cm−1 and ∼45 cm−1 peaks) and an antisymmetric Gaussian function (∼65 cm−1 peak). The spectrum shape of 1,3-diphenylpropane is quite different from the spectrum shapes of the other aromatic molecules for the low magnitude of the low-frequency mode of 1,3-diphenylpropane and/or an intramolecular vibration. Although the concentration dependences of the low- and intermediate-frequency intermolecular modes (Brownian oscillators) do not show a significant trend, the width of high-frequency intermolecular mode (antisymmetric Gaussian) becomes narrower with the higher CCl4 concentration for all the aromatics mixtures with CCl4. The result indicates that the inhomogeneity of the intermolecular vibrational mode in aromatics/CCl4 mixtures is decreasing with the lower concentration of aromatics. The intramolecular vibrational modes of the aromatic molecules observed in the Kerr spectra are also shown with the calculation results based on the density functional theory.
Autocorrelator consisting of a solar-blind photomultiplier for use in the near-ultraviolet region
Authors: Ihara K. , Zaitsu S. , Imasaka T.
Published: January 2005

The development of an autocorrelator based on a two-photon absorption of a photomultiplier photocathode is described. A solar-blind photomultiplier, sensitive in the far-ultraviolet region, is used to detect a two-photon absorption in the near-ultraviolet region. Such an autocorrelator can be used to measure the pulsewidth of a laser (396nm, 110fs) produced by the second harmonic generation of a Ti:sapphire laser.
Split rheometer Couette attachment to enable sample extraction
Authors: Guthrie Sarah E. , Idziak Stefan H. J.
Published: January 2005

We report on the development of a Couette attachment insert for a rheometer, which is designed to split in half, enabling intact sample extraction of cocoa butter crystallized from the melt under known dynamic stress conditions. This cell is capable of producing a sample 1mm thick. At shear rates of 90–720s−1 and final temperatures of 18–20°C it was shown that the sample will completely separate from the cell surface intact.
Noncontact determination of elastic moduli by two-dimensional Fourier transformation and laser ultrasonic technique
Authors: Zhang Xinya , Jackson Ted , Lafond Emmanuel
Published: January 2005

A laboratory instrument that utilizes broadband laser ultrasonics and two-dimensional Fourier transformation for signal processing has been developed to characterize the properties of various foils and plates. Laser ultrasonics generation is achieved by using a pulsed laser which deposits pulsed laser energy on the surface of the specimen. The displacement of the resulting broadband ultrasonic modes is monitored using a two-wave mixing photorefractive interferometer. By means of the two-dimensional Fourier transformation of the detected spatial and temporal displacement wave forms, the image of density of state (DOS) for the excited ultrasound is obtained, and from it the materials properties are extracted. Results are presented for a 150μm thick paper sample, a 50μm stainless steel foil, and a 1.27mm thick aluminum plate. The DOS image demonstrates the ability to measure the properties of each generated ultrasonic modes and provides a direct, nondestructive, measure of elastic moduli of the tested specimens.
Omnidirectional plane beam generation by a hollow tube prism
Authors: Kong H. J. , Choi Jin , Park Y. H. , Shin J. S. , Lee S. K. , Lee D. W. , Yi S. W.
Published: January 2005

We report a new optical element which diffuses the one-dimensional laser beam into an omnidirectional plane beam. We name it as a hollow tube prism based on its tubular structure. By numerical simulation and experiment we have shown that the rays of the transmitted light propagate to all directions in the two-dimensional plane through infinite refractions and reflections at the inner and the outer surfaces of the hollow tube. With a proper dielectric multilayer coating on the outer surface, the transmitted light becomes uniform over all angles. The uniformity of the intensity distribution is evaluated by the contrast. We have obtained the contrast of 0.467 for the coated hollow tube prism while the uncoated one has the contrast of 0.953.
Electron paramagnetic resonance studies of the high-spin molecule Cr10(OMe)20(O2CCMe3)10
Authors: Sharmin Sonia , Ardavan Arzhang , Blundell Stephen J. , Coldea Amalia I. , McInnes Eric J. L. , Low David
Published: January 2005

We report millimeter-wave magneto-optical measurements on the high-spin molecule, Cr10(OMe)20(O2CCMe3)10. The dependence of the electron paramagnetic resonance as a function of orientation and temperature demonstrates that this compound behaves as a single molecule magnet, and exhibits one of the smallest zero-field splittings (D=−0.045±0.004K) yet reported for such a system.
Recording of cell action potentials with AlGaN∕GaN field-effect transistors
Authors: Steinhoff Georg , Baur Barbara , Wrobel Günter , Ingebrandt Sven , Offenhäusser Andreas , Dadgar Armin , Krost Alois , Stutzmann Martin , Eickhoff Martin
Published: January 2005

An AlGaN∕GaN electrolyte gate field-effect transistor array for the detection of electrical cell signals has been realized. The low-frequency noise power spectral density of these devices exhibits a 1∕f characteristic with a dimensionless Hooge parameter of 5×10−3. The equivalent gate-input noise under operation conditions has a peak-to-peak amplitude of 15μV, one order of magnitude smaller than for common silicon-based devices used for extracellular recordings. Extracellular action potentials from a confluent layer of rat heart muscle cells cultivated directly on the nonmetallized gate surface were recorded with a signal amplitude of 75μV and a signal-to-noise ratio of 5:1.
Magnetoelectric resonance-bandwidth broadening of Terfenol-D/epoxy-Pb(Zr,Ti)O3 bilayers in parallel and series connections
Authors: Yu H. , Zeng M. , Wang Y. , Wan J. G. , Liu J.-M.
Published: January 2005

The bandwidth of magnetoelectric (ME) resonance for a combined structure where several Terfenol-D/epoxy-Pb(Zr,Ti)O3 bilayers are connected in parallel and series was measured. A relationship between the bilayer length and resonance frequency was used to design the combined structure, in which the bilayered components of different lengths were connected in the parallel and series forms, respectively. The measured giant ME effect of the combined structure showed a much wider frequency response to external field than a single bilayered structure, and the ME effect far from the resonance ranges was enhanced significantly too. A qualitative analysis based on the equivalent circuit concept was presented to explain these effects.
Synthesis and optical properties of well-aligned ZnO nanorod array on an undoped ZnO film
Authors: Jie Jiansheng , Wang Guanzhong , Chen Yiming , Han Xinhai , Wang Qingtao , Xu Bo , Hou J. G.
Published: January 2005

High-density well-aligned ZnO nanorod array was successfully synthesized on a PLD prepared undoped ZnO film by a catalyst-free method. X-ray diffraction and scanning electron microscopy show that the nanorods are well-oriented perpendicular to the substrate. The photoluminescence from free excitons and Raman spectra of the ZnO nanorods reflect the high purity and nearly defect free structure of nanorods. The well-aligned feature of the nanorod array is attributed to the nanorods’ epitaxial growth from the ZnO film.
Elastic and electromechanical properties of polypropylene foam ferroelectrets
Authors: Dansachmüller M. , Schwödiauer R. , Bauer-Gogonea S. , Bauer S. , Paajanen M. , Raukola J.
Published: January 2005

Internally charged closed-cell polymer electrets exhibit ferroelectric-like behavior and have been called ferroelectrets. They are attractive for soft electroactive transducers, the high compressibility leads to d33 transducer coefficients exceeding those of ferroelectric polymers. A technique for the measurement of the elastic modulus and the transducer coefficient of ferroelectrets is reported. The elastic behavior of ferroelectretic polypropylene foams is correlated with the piezoelectric-like properties. Prestress treatments linearize the transducer properties.
Theoretical study of nitrogen vacancies in Ti4AlN3
Authors: Music Denis , Ahuja Rajeev , Schneider Jochen M.
Published: January 2005

We have investigated the energetics of the N vacancy formation in Ti4AlN3 by ab initio calculations. We identify N 2a sites (Wyckoff notation) in Ti4AlN2.75 as the most probable vacancy sites based on the energetics of vacancy formation. Furthermore, Ti4AlN3 does not exhibit any states at the Fermi level. Introducing N vacancies causes states to appear at the Fermi level, which may enable electron transport. Recently measured conductivity data [Finkel et al., Phys. Rev. B 67, 235108 (2003)] for Ti4AlN3 can be understood based on our calculations.
Capping layer effects in the structure and composition of Co nanoparticle ultrathin films
Authors: Arbiol J. , Peiró F. , Cornet A. , Clavero C. , Cebollada A. , Armelles G. , Huttel Y.
Published: January 2005

In this work, we present the correlation of the magnetic and structural properties of Co nanoparticles deposited by sputtering on Si3N4 substrates at different temperatures, and covered with different capping layers, two insulators, AlN and MgO, and a metal, Pt. High-resolution transmission electron microscopy shows the formation of CoPt3 and Co2N, for the Pt and AlN capping layers, respectively, giving to a significant change of the magnetic behavior. When using a cap of MgO, energy-filtered transmission electron microscopy shows an oxidized shell covering the Co nanoparticles with thickness decreasing as the deposition temperature increases, explaining the changes in the magnetic response induced by the MgO capping layer.
The effects of upstream DNA on open complex formation by
Escherichia coli
RNA polymerase
Authors: Davis Caroline A. , Capp Michael W. , Record M. Thomas , Saecker Ruth M.
Published: January 2005

Binding of activators to upstream DNA sequences regulates transcription initiation by affecting the stability of the initial RNA polymerase (RNAP)–promoter complex and/or the rate of subsequent conformational changes required to form the open complex (RP
O
). Here we observe that the presence of nonspecific upstream DNA profoundly affects an early step in formation of the transcription bubble. Kinetic studies with the λP
R
promoter and
Escherichia coli
RNAP reveal that the presence of DNA upstream of base pair -47 greatly increases the rate of forming RP
O
, without significantly affecting its rate of dissociation. We find that this increase is largely due to an acceleration of the rate-limiting step (isomerization) in RP
O
formation, a step that occurs after polymerase binds. Footprinting experiments reveal striking structural differences downstream of the transcription start site (+1) in the first kinetically significant intermediate when upstream DNA is present. On the template strand, the DNase I downstream boundary of this early intermediate is +20 when upstream DNA is present but is shortened by approximately two helical turns when upstream DNA beyond -47 is removed. KMnO
4
footprinting reveals an identical initiation bubble (-11 to +2), but unusual reactivity of template strand upstream cytosines (-12, -14, and -15) on the truncated promoter. Based on this work, we propose that early wrapping interactions between upstream DNA and the polymerase exterior strongly affect the events that control entry and subsequent unwinding of the DNA start site in the jaws of polymerase.
S-nitroso proteome ofMycobacterium tuberculosis: Enzymes of intermediary metabolism and antioxidant defense
Authors: Rhee Kyu Y. , Erdjument-Bromage Hediye , Tempst Paul , Nathan Carl F.
Published: January 2005

The immune response toMycobacterium tuberculosis(Mtb) includes expression of nitric oxide (NO) synthase (NOS)2, whose products can kill Mtbin vitrowith a molar potency greater than that of many conventional antitubercular agents. However, the targets of reactive nitrogen intermediates (RNIs) in Mtb are unknown. One major action of RNIs is protein S-nitrosylation. Here, we describe, to our knowledge, the first proteomic analysis of S-nitrosylation in a whole organism after treating Mtb with bactericidal concentrations of RNIs. The 29S-nitroso proteins identified are all enzymes, mostly serving intermediary metabolism, lipid metabolism, and/or antioxidant defense. Many are essential or implicated in virulence, including defense against RNIs. For each of two target enzymes tested, lipoamide dehydrogenase and mycobacterial proteasome ATPase, S-nitrosylation caused enzyme inhibition. Moreover, endogenously biotinylated proteins were driven into mixed disulfide complexes. Targeting of metabolic enzymes and antioxidant defenses by means of protein S-nitrosylation and mixed disulfide bonding may contribute to the antimycobacterial actions of RNIs.
Altered pharmacology and distinct coactivator usage for estrogen receptor-dependent transcription through activating protein-1
Authors: Cheung Edwin , Acevedo Mari Luz , Cole Philip A. , Kraus W. Lee
Published: January 2005

Estrogen signaling occurs through at least two distinct molecular pathways: (
i
) direct binding of liganded estrogen receptors (ERs) to estrogen-responsive DNA elements (EREs) (the “ER/ERE pathway”) and (
ii
) indirect recruitment of liganded ERs to activating protein-1 (AP-1)-responsive DNA elements via heterodimers of Fos and Jun (the “ER/AP-1 pathway”). We have developed a biochemical assay for examining ligand-regulated transcription by ERs in the ER/AP-1 pathway. This assay recapitulates the altered (i.e., agonistic) pharmacology of selective estrogen receptor modulator drugs in this pathway reported previously by using various cell-based assays. We used our biochemical assay to examine the detailed mechanisms of ER/AP-1-dependent transcription. Our studies indicate that (
i
) ERα/AP-1 complexes play a critical role in promoting the formation of stable RNA polymerase II preinitiation complexes leading to transcription initiation, (
ii
) chromatin is a key determinant of estrogen and selective estrogen receptor modulator signaling in the ERα/AP-1 pathway, (
iii
) distinct domains of ERα are required for recruitment to DNA-bound Fos/Jun heterodimers and transcriptional activation at AP-1 sites, and (
iv
) different enhancer/activator combinations in the ERα and AP-1 pathways use coactivators in distinct ways. These studies have increased our understanding of the molecular mechanisms underlying ligand-dependent signaling in the ER/AP-1 pathway and demonstrate the usefulness of this biochemical approach.
Combinatorial biosynthesis of antitumor indolocarbazole compounds
Authors: Sánchez César , Zhu Lili , Braña Alfredo F. , Salas Aaroa P. , Rohr Jürgen , Méndez Carmen , Salas José A.
Published: January 2005

Rebeccamycin and staurosporine are natural products with antitumor properties, which belong to the family of indolocarbazole alkaloids. An intense effort currently exists for the generation of indolocarbazole derivatives for the treatment of several diseases, including cancer and neurodegenerative disorders. Here, we report a biological process based on combinatorial biosynthesis for the production of indolocarbazole compounds (or their precursors) in engineered microorganisms as a complementary approach to chemical synthesis. We have dissected and reconstituted the entire biosynthetic pathway for rebeccamycin in a convenient actinomycete host,
Streptomyces albus.
This task was achieved by coexpressing different combinations of genes isolated from the rebeccamycin-producing microorganism. Also, a gene (
staC
) was identified in staurosporine-producing microbes and was shown to have a key role to differentiate the biosynthetic pathways for the two indolocarbazoles. Last, incorporation of the
pyrH
and
thal
genes, encoding halogenases from different microorganisms, resulted in production of derivatives with chlorine atoms at novel positions. We produced >30 different compounds by using the recombinant strains generated in this work.
The pattern of intron loss
Authors: Roy Scott W. , Gilbert Walter
Published: January 2005

We studied intron loss in 684 groups of orthologous genes from seven fully sequenced eukaryotic genomes. We found that introns closer to the 3′ ends of genes are preferentially lost, as predicted if introns are lost through gene conversion with a reverse transcriptase product of a spliced mRNA. Adjacent introns tend to be lost in concert, as expected if such events span multiple intron positions. Directly contrary to the expectations of some, introns that do not interrupt codons (phase zero) are more, not less, likely to be lost, an intriguing and previously unappreciated result. Adjacent introns with matching phases are not more likely to be retained, as would be expected if they enjoyed a relative selective advantage. The findings of 3′ and phase zero intron loss biases are in direct contradiction to an extremely recent study of fungi intron evolution. All patterns are less pronounced in the lineage leading to
Caenorhabditis elegans
, suggesting that the process of intron loss may be qualitatively different in nematodes. Our results support a reverse transcriptase-mediated model of intron loss.
An agent-based approach for modeling molecular self-organization
Authors: Troisi Alessandro , Wong Vance , Ratner Mark A.
Published: January 2005

Agent-based modeling is a technique currently used to simulate complex systems in computer science and social science. Here, we propose its application to the problem of molecular self-assembly. A system is allowed to evolve from a separated to an aggregated state following a combination of stochastic, deterministic, and adaptive rules. We consider the problem of packing rigid shapes on a lattice to verify that this algorithm produces more nearly optimal aggregates with less computational effort than comparable Monte Carlo simulations.
Advances in measuring lifespan in the yeast
Saccharomyces cerevisiae
Authors: Minois Nadège , Frajnt Magdalena , Wilson Chris , Vaupel James W.
Published: January 2005

Much research aimed at discovering the genetic bases of longevity focuses on the budding yeast
Saccharomyces cerevisiae.
Unfortunately, yeast researchers use a definition of longevity not applied to other species. We propose here a method that makes it possible to estimate for yeast the same measures of longevity calculated for other species. We also show that the conventional method (equating longevity with the number of offspring) is only an approximate measure of true chronological lifespan. Our method will allow results for yeast to be compared more correctly with those for other species.
Induction, differentiation, and remodeling of blood vessels after transplantation of Bcl-2-transduced endothelial cells
Authors: Enis David R. , Shepherd Benjamin R. , Wang Yinong , Qasim Asif , Shanahan Catherine M. , Weissberg Peter L. , Kashgarian Michael , Pober Jordan S. , Schechner Jeffrey S.
Published: January 2005

Implants of collagen-fibronectin gels containing Bcl-2-transduced human umbilical vein endothelial cells (Bcl-2-HUVECs) induce the formation of human endothelial cell (EC)/murine vascular smooth muscle cell (VSMC) chimeric vessels in immunodeficient mice. Microfil casting of the vasculature 60 d after implantation reveals highly branched microvascular networks within the implants that connect with and induce remodeling of conduit vessels arising from the abdominal wall circulation. Approximately 85% of vessels within the implants are lined by Bcl-2-positive human ECs expressing VEGFR1, VEGFR2, and Tie-2, but not integrin αvβ3. The human ECs are seated on a well formed human laminin/collagen IV-positive basement membrane, and are surrounded by mouse VSMCs expressing SM-α actin, SM myosin, SM22α, and calponin, all markers of contractile function. Transmission electron microscopy identified well formed EC–EC junctions, chimeric arterioles with concentric layers of contractile VSMC, chimeric capillaries surrounded by pericytes, and chimeric venules. Bcl-2-HUVEC-lined vessels retain 70-kDa FITC-dextran, but not 3-kDa dextran; local histamine rapidly induces leak of 70-kDa FITC-dextran or India ink. As in skin, TNF induces E-selectin and vascular cell adhesion molecule 1 only on venular ECs, whereas intercellular adhesion molecule-1 is up-regulated on all human ECs. Bcl-2-HUVEC implants are able to engraft within and increase perfusion of ischemic mouse gastrocnemius muscle after femoral artery ligation. These studies show that cultured Bcl-2-HUVECs can differentiate into arterial, venular, and capillary-like ECs when implantedin vivo, and induce arteriogenic remodeling of the local mouse vessels. Our results support the utility of differentiated EC transplantation to treat tissue ischemia.
Cell cycle-dependent translocation of PRC1 on the spindle by Kif4 is essential for midzone formation and cytokinesis
Authors: Zhu Changjun , Jiang Wei
Published: January 2005

The spindle midzone, a conspicuous network of antiparallel interdigitating nonkinetochore microtubules between separating chromosomes, plays a crucial role in regulating the initiation and completion of cytokinesis. In this study, we report the use of time-lapse microscopy and a human kinesin endoribonucleases RNase III-prepared short interfering RNA (esiRNA) library to identify Kif4 as a motor protein that translocates PRC1, a spindle midzone-associated cyclin-dependent kinase substrate protein, to the plus ends of interdigitating spindle microtubules during the metaphase-to-anaphase transition. We show that Kif4 binds to PRC1 through its “stalk plus tail” domains and Kif4 and PRC1 colocalize on the spindle midzone/midbody during anaphase and cytokinesis. Suppression of Kif4 expression by Kif4 esiRNA results in the inhibition of PRC1 translocation, a block of the midzone formation, and a failure of cytokinesis. PRC1 translocation and midzone formation can be restored, and the cytokinetic defects can be rescued in Kif4 esiRNA-treated cells by coexpression of Kif4 but not its motor dead mutant Kif4md. Furthermore, we show that cyclin-dependent kinase phosphorylation of PRC1 controls the timing of PRC1 translocation by Kif4. These results, in light of the crucial role of PRC1 in midzone formation, indicate that cell cycle-dependent translocation of PRC1 by Kif4 is essential for midzone formation and cytokinesis.
Selective up-regulation of PDE1B2 upon monocyte-to-macrophage differentiation
Authors: Bender Andrew T. , Ostenson Cari L. , Wang Edith H. , Beavo Joseph A.
Published: January 2005

Granulocyte–macrophage colony-stimulating factor (GM-CSF) is a major regulator of monocyte to macrophage differentiation. In both humans and mice, the main phenotype of decreased GM-CSF function is pulmonary proteinosis due to aberrant function of alveolar macrophages. Recently, this cytokine has been shown to up-regulate a cyclic nucleotide phosphodiesterase, PDE1B. Two PDE1B variants with unique N-terminal sequences, PDE1B1 and PDE1B2, have been identified. Here, we report that the previously uncharacterized PDE1B2 is selectively increased by GM-CSF by stimulation of transcription at a previously unknown transcriptional start site. Analysis of the exon and intron organization of the PDE1B gene reveals that PDE1B2 has a different N-terminal sequence because of a separate first exon that is located 11.5 kb downstream from the PDE1B1 first exon. By using 5′-RACE, alignment of EST sequences, and a luciferase-reporter system, we provide evidence that PDE1B2 has a separate transcriptional start site from PDE1B1 that can be activated by monocyte differentiation. Furthermore, IL-4 treatment in the presence of GM-CSF, which shifts the differentiation from a macrophage to a dendritic cell phenotype, suppresses the up-regulation of PDE1B2. Induction of PDE1B2 is also found in T cells upon activation by PHA. Therefore, PDE1B2 may have a regulatory role in multiple immune cell types. Last, characterization of the catalytic properties of recombinant PDE1B2 shows that it prefers cGMP over cAMP as a substrate and, thus, is likely to regulate cGMP in macrophages. Also, PDE1B2 has a nearly 3-fold lower EC
50
for activation by calmodulin than PDE1B1.
Hereditary persistence of α-fetoprotein and
H19
expression in liver of BALB/cJ mice is due to a retrovirus insertion in the
Zhx2
gene
Authors: Perincheri Sudhir , Dingle R. W. Cameron , Peterson Martha L. , Spear Brett T.
Published: January 2005

The α-fetoprotein (
AFP
) and
H19
genes are transcribed at high levels in the mammalian fetal liver but are rapidly repressed postnatally. This repression in the liver is controlled, at least in part, by the
Afr1
gene.
Afr1
was defined >25 years ago when BALB/cJ mice were found to have 5- to 20-fold higher adult serum AFP levels compared with all other mouse strains; subsequent studies showed that this elevation was due to higher
Afp
expression in the liver.
H19
, which has become a model for genomic imprinting, was identified initially in a screen for
Afr1
-regulated genes. The BALB/cJ allele (

Afr1
b

) is recessive to the wild-type allele (

Afr1
a

), consistent with the idea that
Afr1
functions as a repressor. By high-resolution mapping, we identified a gene that maps to the
Afr1
interval on chromosome 15 and encodes a putative zinc fingers and homeoboxes (ZHX) protein. In BALB/cJ mice, this gene contains a murine endogenous retrovirus within its first intron and produces predominantly an aberrant transcript that no longer encodes a functional protein. Liver-specific overexpression of a
Zhx2
transgene restores wild-type
H19
repression on a BALB/cJ background, confirming that this gene is responsible for hereditary persistence of
Afp
and
H19
in the livers of BALB/cJ mice. Thus we have identified a genetically defined transcription factor that is involved in developmental gene silencing in mammals. We present a model to explain the liver-specific phenotype in BALB/cJ mice, even though
Afr1
is a ubiquitously expressed gene.
Methods for strand-specific DNA detection with cationic conjugated polymers suitable for incorporation into DNA chips and microarrays
Authors: Liu Bin , Bazan Guillermo C.
Published: January 2005

A strand-specific DNA sensory method is described based on surface-bound peptide nucleic acids and water-soluble cationic conjugated polymers. The main transduction mechanism operates by taking advantage of the net increase in negative charge at the peptide nucleic acid surface that occurs upon single-stranded DNA hybridization. Electrostatic forces cause the oppositely charged cationic conjugated polymer to bind selectively to the “complementary” surfaces. This approach circumvents the current need to label the probe or target strands. The polymer used in these assays is poly[9,9′-bis(6′′-
N,N,N
-trimethylammonium)hexyl)fluorene-
co
-alt-4,7-(2,1,3-benzothiadiazole) dibromide], which was specifically designed and synthesized to be compatible with excitation sources used in commonly used DNA microarray readers. Furthermore, the utility of poly[9,9′-bis(6′′-
N,N,N
-trimethylammonium)-hexyl)fluorene-
co
-alt-4,7-(2,1,3-benzothiadiazole) dibromide] has been demonstrated in homogenous and solid-state assays that involve fluorescence resonance energy transfer to a reporter dye (Cy5) and that can benefit from the light harvesting properties observed in water-soluble conjugated polymers.
The fluorescence resonance energy transfer (FRET) gate: A time-resolved study
Authors: Xu Qing-Hua , Wang Shu , Korystov Dmitry , Mikhailovsky Alexander , Bazan Guillermo C. , Moses Daniel , Heeger Alan J.
Published: January 2005

The two-step energy-transfer process in a self-assembled complex comprising a cationic conjugated polymer (CCP) and a dsDNA is investigated by using pump-dump-emission spectroscopy and time-correlated single-photon counting; energy is transferred from the CCP to an ethidium bromide (EB) molecule intercalated into the dsDNA through a fluorescein molecule linked to one terminus of the DNA. Time-dependent anisotropy measurements indicate that the inefficient direct energy transfer from the CCP to the intercalated EB results from the near orthogonality of their transition moments. These measurements also show that the transition moment of the fluorescein spans a range of angular distributions and lies between that of the CCP and EB. Consequently, the fluorescein acts as a fluorescence resonance energy-transfer gate to relay the excitation energy from the CCP to the EB.
Inhibition of cardiac myofibroblast formation and collagen synthesis by activation and overexpression of adenylyl cyclase
Authors: Swaney James S. , Roth David M. , Olson Erik R. , Naugle Jennifer E. , Meszaros J. Gary , Insel Paul A.
Published: January 2005

Transformation of fibroblasts to myofibroblasts, characterized by expression of α-smooth muscle actin (α-SMA) and production of extracellular matrix (ECM) components, is a key event in connective tissue remodeling. Approaches to inhibit this transformation are needed in tissues, such as the heart, where excessive ECM production by cardiac fibroblasts (CFs) causes fibrosis, myocardial stiffening, and cardiac dysfunction. We tested whether adenylyl cyclase (AC) activation (increased cAMP levels) modulates the transformation of adult rat CF to myofibroblasts, as assessed by immunofluorescent microscopy, immunoblotting, and collagen synthesis. A 24-h incubation of CF with TGF-β or angiotensin II increased α-SMA expression, which was inhibited by the AC agonist forskolin and a cAMP analog that activates protein kinase A. Treatment with forskolin blunted serum-, TGF-β-, and angiotensin II-stimulated collagen synthesis. CFs engineered to overexpress type 6 AC had enhanced forskolin-promoted cAMP formation, greater inhibition by forskolin of TGF-β-stimulated α-SMA expression, and a decrease in the EC
50
of forskolin to reduce serum-stimulated collagen synthesis. The AC stimulatory agonist adrenomedullin inhibited collagen synthesis in CF that overexpressed AC6 but not in controls. Thus, AC stimulation blunts collagen synthesis and, in parallel, the transformation of adult rat CF to myofibroblasts. AC overexpression enhances these effects, “uncovering” an inhibition by adrenomedullin. These findings implicate cAMP as an inhibitor of ECM formation by means of blockade of the transformation of CF to myofibroblasts and suggest that increasing AC expression, thereby enhancing cAMP generation through stimulation of receptors expressed on CF, could provide a means to attenuate and prevent cardiac fibrosis and its sequelae.
Rapid hyperosmotic coinduction of two tilapia (
Oreochromis mossambicus
) transcription factors in gill cells
Authors: Fiol Diego F. , Kültz Dietmar
Published: January 2005

Gills of euryhaline teleosts are excellent models for studying osmotic-stress adaptation because they directly contact the aquatic environment and are an important effector tissue during osmotic stress. We acclimated tilapia (
Oreochromis mossambicus
) from fresh water (FW) to seawater (SW); performed suppression subtractive hybridization of gill mRNAs; and identified two transcription factors, osmotic stress transcription factor 1 (OSTF1) and the tilapia homolog of transcription factor II B (TFIIB), that are rapidly and transiently induced during hyperosmotic stress. mRNA levels increase 6-fold for OSTF1 and 4-fold for TFIIB, and they reach maxima 2 h after SW transfer. Protein levels increase 7.5-fold for OSTF1 and 9-fold for TFIIB, and they reach maxima 4 h after SW transfer. Induction of OSTF1 and TFIIB increases gradually with increasing salinity. Induction of OSTF1 and TFIIB is specific for osmotic stress and absent during oxidative stress (1 mM H
2
O
2
) or heat shock (+10°C). Bioinformatic analysis of OSTF1 reveals that it is a transcription factor of the TGF-β-stimulated clone 22/GILZ family. Because some mammalian homologs are strongly induced by glucocorticoids, OSTF1 may represent the molecular link between the SW hormone cortisol and transcriptional regulation of ion transport and cell differentiation in teleost gills. Coinduction of OSTF1 and TFIIB may serve to recruit TFIIB preferentially to OSTF1 target genes during hyperosmotic stress and compensate for reduced rates of transcription resulting from salt-induced chromatin compaction. We conclude that OSTF1 and TFIIB are critical elements of osmosensory signal transduction in euryhaline teleosts that mediate osmotic adaptation by means of transcriptional regulation.
Evasion of antibody neutralization in emerging severe acute respiratory syndrome coronaviruses
Authors: Yang Zhi-yong , Werner Heidi C. , Kong Wing-pui , Leung Kwanyee , Traggiai Elisabetta , Lanzavecchia Antonio , Nabel Gary J.
Published: January 2005

Molecular characterization of the severe acute respiratory syndrome coronavirus has revealed genetic diversity among isolates. The spike (S) glycoprotein, the major target for vaccine and immune therapy, shows up to 17 substitutions in its 1,255-aa sequence; however, the biologic significance of these changes is unknown. Here, the functional effects of S mutations have been determined by analyzing their affinity for a viral receptor, human angiotensin-converting enzyme 2 (hACE-2), and their sensitivity to Ab neutralization with viral pseudotypes. Although minor differences among eight strains transmitted during human outbreaks in early 2003 were found, substantial functional changes were detected in S derived from a case in late 2003 from Guangdong province [S(GD03T0013)] and from two palm civets, S(SZ3) and S(SZ16). S(GD03T0013) depended less on the hACE-2 receptor and was markedly resistant to Ab inhibition. Unexpectedly, Abs that neutralized most human S glycoproteins enhanced entry mediated by the civet virus S glycoproteins. The mechanism of enhancement involved the interaction of Abs with conformational epitopes in the hACE-2-binding domain. Finally, improved immunogens and mAbs that minimize this complication have been defined. These data show that the entry of severe acute respiratory syndrome coronaviruses can be enhanced by Abs, and they underscore the need to address the evolving diversity of this newly emerged virus for vaccines and immune therapies.