bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Varying Media, Temperature, and Growth Rates on the Intracellular Concentrations of Yeast Amino Acids
Authors: Martínez‐Force Enrique , Benítez Tahía
Published: March 2005

Variations of the yeast free amino acid pool under different culture conditions were studied in two Saccharomyces strains, the laboratory haploid strain S288C and the industrial fermentative yeast IFI256. The internal amino acid pool of both strains was measured when grown in laboratory (minimal and complete) versus semiindustrial (molasses with or without added biotin and/or diammonium phosphate) media, in fermentable (glucose, fructose, sucrose) versus respirable (glycerol) carbon sources, in different temperatures (22, 30, and 37 °C), pHs (2. 0–4.75), and growth rates (0. 018–0.24 h−1) in continuous culture, and at different phases of the growth curve in batch culture (lag, exponential, early and late stationary). Results indicated that environmental conditions, particularly the presence of amino acids in the media, enormously influenced the intracellular amino acid concentration. Higher values were detected in molasses than in laboratory media and in fermentable carbon sources (glucose, fructose, sucrose) than in glycerol. Variations in the amino acid pool along the growth curve were greater at 37 °C than at other temperatures; in all cases, the highest values were measured at the begining of the exponential phase. In continuous culture and at different growth rates, intracellular free amino acid concentrations increased by 3–10‐fold when the growth rate was lower than 0.05 h−1, representing 20–35% of the total (free plus protein) amino acid content and indicating that amino acid yield was a partly growth‐linked parameter.
RNA Transcription from Immobilized DNA Templates
Authors: Marble H. Anthony , Davis Robert H.
Published: March 2005

We describe an RNA transcription protocol based on the multiple reuse of solid‐phase synthetic DNA templates. The templates are assembled onto streptavidin‐coated agarose beads via a single 5′‐terminal biotin located on the noncoding template strand. Transcription occurs in an aqueous buffered suspension containing solid‐phase DNA, dissolved enzyme (T7 RNA polymerase), and nucleoside triphosphate substrates (NTPs). A direct comparison of solution and solid‐phase templates under standard transcription conditions reveals similar initial reaction rates and overall yields. Immobilized templates store stably for periods of several months and are easily recovered by mild centrifugation. We demonstrate the successive reuse of these templates throughout 15 rounds of transcription. The templates remained active, although an incremental decay in transcription was observed beyond five rounds. Template activity was partially restored by supplementing the support‐bound oligonucleotide with fresh coding‐strand DNA. These findings indicate that multiple reuse of template is a viable strategy for reducing the amount of DNA template required in RNA transcription.
Eucalyptus Kraft Black Liquor Enhances Growth and Productivity of Spirulina in Outdoor Cultures
Authors: Chauhan Vikas S. , Singh Gurbaksh , Ramamurthy V.
Published: March 2005

Mass cultivation of microalgae for commercial applications suffers from poor productivities when measured against laboratory results or theoretical projections. In an effort to reduce this gap it was discovered that addition of eucalyptus kraft black liquor (BL) enhanced biomass productivity in outdoor cultures of Spirulina by increasing growth rate by 38% and biomass yield by 43%. BL treatment resulted in elevation of nitrogen assimilating enzyme activities and efficiency of phosphate utilization. Analyses of forenoon and afternoon oxygen production rates (OPRs) indicated higher photosynthetic and respiratory activity in BL‐treated cultures compared to untreated cultures.
Optimization of Rice α‐Amylase Production Using Temperature‐Sensitive Mutants of Saccharomyces cerevisiae for the PHO Regulatory System
Authors: Uchiyama Keiji , Ohtani Tomoko , Morimoto Masaaki , Shioya Suteaki , Suga Ken‐Ichi , Harashima Satoshi , Oshima Yasuji
Published: March 2005

A typical example of rational system synthesis for bioproduction by the cultivation of microorganisms harboring a recombinant plasmid was studied. First, two temperature‐controllable expression systems for a foreign gene in Saccharomyces cerevisiae were constructed. The promoter of the PHO84 gene, which encodes an inorganic phosphate (Pi) transporter of S. cerevisiae and is controlled by Pi concentration through the PHO regulatory system, was used. And two temperature‐sensitive mutants of S. cerevisiae for the PHO regulatory system were used as the host with rice α‐amylase expression vector. One was temperature‐sensitive pho81 mutant, SH3337, and the other was temperature‐sensitive pho80 mutant, YKU107. When the strain SH3337 is cultivated at a lower temperature, the rice α‐amylase gene connected downstream of the PHO84 promoter is expressed, but at a higher temperature, it is not. Conversely, with the strain YKU107, the transcription of the rice α‐amylase gene is induced at a higher temperature and repressed at a lower one. The optimal cultivation temperature strategies for maximum production of rice α‐amylase in batch cultures of these two recombinant strains were then determined by the Maximum Principle using the relationships of the specific growth and specific production rates to the cultivation temperature. The optimal strategies were easy to realize and were shown to be effective for maximum product. Finally, under these maximum α‐amylase production strategies, the α‐amylase activities and α‐amylase yields in terms of glucose consumption for these recombinant strains were calculated on the basis of experimental data and compared for various operation times. The study demonstrates how a foreign gene expression system can be synthesized using a temperature‐sensitive mutant with a given objective and under given constraints.
Fluctuating Shear Stress Effects on Stress Fiber Architecture and Energy Metabolism of Cultured Renal Cells
Authors: Bhat Vinayak D. , Windridge Paula A. , Cherry Robert S. , Mandel Lazaro J.
Published: March 2005

The project investigates the relationship between the external shear force and the actin cytoskeleton along with the metabolic changes occurring inside the cells due to this force. Anchorage‐dependent Madin Darby canine kidney (MDCK) cells were placed in spinner flasks with paddle‐type stirrers agitated at 20 rpm, where they experienced shear stress fluctuations from 0.02 to 0.27 dyn/cm2 in magnitude. Following fixation, permeabilization, and staining with rhodamine—phalloidin, the relative amounts and distribution of F‐actin stress fibers in the 1 μm basal layer of the cells were visualized by confocal microscopy. These structures disappeared after 12–15 h of exposure to shear stress. Previous results showed that the stress fibers disappear, leading to loss of epithelial attachment, after only 1 h of starvation‐induced energy depletion. Therefore, in this study, the energy metabolism of the cells was established by measuring adenosine triphosphate (ATP) levels at different time intervals. No statistical difference in ATP content was found between the shear‐stressed cells and the controls, showing that shear stresses cause cytoskeletal reorganization by a mechanism other than ATP depletion.
Derivation of Kinetic Equations for Growth on Single Substrates Based on General Properties of a Simple Metabolic Network
Authors: Heijnen J. J. , Romein B.
Published: March 2005

Research on microbial growth has resulted in a large number of different equations to describe growth kinetics, the most famous of which is that of Monod. In the present work, the case of single substrate limitation in the absence of substrate inhibition is studied. Metabolism can then be regarded as a simple network consisting of a single reaction for anabolism and another for catabolism. These reactions are interconnected by cofactors of rather constant concentration. Growth is described as a combination of substrate uptake kinetics and growth kinetics. The notion that enzymatic activities of anabolism and catabolism depend on growth rate leads to a number of substrate uptake models, which fall into a few families. Each of them can be described by a general and flexible three‐parameter equation. Well‐known equations like that of Monod and Blackman turn out to be special cases. It could be concluded that the presented equations show more or less the same behavior in a scaled uptake rate versus substrate concentration plot, although the (powered) Monod equation might in general be preferred because its overall shape seems to resemble experimental observations most.
Volatile and N isotope chemistry of the Molucca Sea collision zone: Tracing source components along the Sangihe Arc, Indonesia
Authors: Clor Laura E. , Fischer Tobias P. , Hilton David R. , Sharp Zachary D. , Hartono Udi
Published: March 2005

Volcanic gases are sensitive indicators of subduction processes and are used to evaluate the contributions from various source components. Nitrogen isotope systematics in particular are a valuable tool for determining the fate of organic matter in subduction zones. We present the first arc‐wide survey of trace gas chemistry and nitrogen isotope variations from the Sangihe Arc of northeastern Indonesia, where the narrow Molucca Sea Plate subducts beneath the Sangihe Arc to the west and the Halmahera Arc to the east. Relative volatile abundances and N isotopic compositions of volcanic gases show systematic along‐arc variations. Northern volcanoes exhibit low N2/He ratios and δ15N values (northern minima 542 and −7.3‰, respectively), indicating minimal addition of sediment to source magmas. In contrast, the southern part of the arc is characterized by high N2/He and δ15N values (southern maxima 2000 and +2.1‰, respectively), consistent with greater sediment contributions in the formation of the magmas. These observations can be correlated with the complex tectonic setting of the region whereby oblique collision between the two arcs has caused sediment obduction, decoupling the accretionary wedges from the underlying oceanic plate. In the north, where the collision is more developed, the lack of trace gas and N isotope evidence of sedimentary inputs to the source of arc magmas is consistent with enhanced sediment decoupling. In the south, where collision and accretionary wedge decoupling are not yet taking place, sediments would presumably subduct normally, in agreement with higher N2/He and δ15N values. Awu volcano, at the northernmost extension of the arc, is anomalous and exhibits high N2/He (2852) coupled with low δ15N (−3.3‰). These values are suggestive of increased slab contribution in the northernmost arc, possibly by slab melting as collision stalls the progress of the subducting plate and allows it to become superheated.
Sensitivity of ozone to bromine in the lower stratosphere
Authors: Salawitch R. J. , Weisenstein D. K. , Kovalenko L. J. , Sioris C. E. , Wennberg P. O. , Chance K. , Ko M. K. W. , McLinden C. A.
Published: March 2005

Measurements of BrO suggest that inorganic bromine (Bry) at and above the tropopause is 4 to 8 ppt greater than assumed in models used in past ozone trend assessment studies. This additional bromine is likely carried to the stratosphere by short‐lived biogenic compounds and their decomposition products, including tropospheric BrO. Including this additional bromine in an ozone trend simulation increases the computed ozone depletion over the past ∼25 years, leading to better agreement between measured and modeled ozone trends. This additional Bry (assumed constant over time) causes more ozone depletion because associated BrO provides a reaction partner for ClO, which increases due to anthropogenic sources. Enhanced Bry causes photochemical loss of ozone below ∼14 km to change from being controlled by HOx catalytic cycles (primarily HO2+O3) to a situation where loss by the BrO+HO2 cycle is also important.
Positive co-operative activity and dimerization of the isolated ABC ATPase domain of HlyB from Escherichia coli
Authors: BENABDELHAK Houssain , SCHMITT Lutz , HORN Carsten , JUMEL Kornelia , BLIGHT Mark A. , HOLLAND I. Barry
Published: March 2005

The ATPase activity of the ABC (ATP-binding cassette) ATPase domain of the HlyB (haemolysin B) transporter is required for secretion of Escherichia coli haemolysin via the type I pathway. Although ABC transporters are generally presumed to function as dimers, the precise role of dimerization remains unclear. In the present study, we have analysed the HlyB ABC domain, purified separately from the membrane domain, with respect to its activity and capacity to form physically detectable dimers. The ATPase activity of the isolated ABC domain clearly demonstrated positive co-operativity, with a Hill coefficient of 1.7. Furthermore, the activity is (reversibly) inhibited by salt concentrations in the physiological range accompanied by proportionately decreased binding of 8-azido-ATP. Inhibition of activity with increasing salt concentration resulted in a change in flexibility as detected by intrinsic tryptophan fluorescence. Finally, ATPase activity was sensitive towards orthovanadate, with an IC50 of 16 μM, consistent with the presence of transient dimers during ATP hydrolysis. Nevertheless, over a wide range of protein or of NaCl or KCl concentrations, the ABC ATPase was only detected as a monomer, as measured by ultracentrifugation or gel filtration. In contrast, in the absence of salt, the sedimentation velocity determined by analytical ultracentrifugation suggested a rapid equilibrium between monomers and dimers. Small amounts of dimers, but apparently only when stabilized by 8-azido-ATP, were also detected by gel filtration, even in the presence of salt. These data are consistent with the fact that monomers can interact at least transiently and are the important species during ATP hydrolysis.
NAADP binding to its target protein in sea urchin eggs requires phospholipids
Authors: CHURAMANI Dev , DICKINSON George D. , PATEL Sandip
Published: March 2005

Mobilization of intracellular Ca2+ pools by NAADP (nicotinic acid–adenine dinucleotide phosphate) is becoming increasingly recognized as an important determinant of complex Ca2+ signals. However, the properties of the putative Ca2+ channel activated by NAADP are poorly defined. In the present study, we provide evidence that binding of NAADP to its target protein in sea urchin eggs requires phospholipids. Decreasing the level of protein-bound lipid in detergent extracts by either dilution of the preparation at a fixed detergent concentration or increasing the detergent concentration at a fixed protein concentration inhibited [32P]NAADP binding. These effects were prevented by the addition of phospholipids, but not other related molecules, were reversible and were associated with a marked decrease in the apparent affinity of the target protein for its ligand. Additionally, we show that the extent of dissociation of NAADP–receptor ligand complexes during gel filtration in the presence of detergent correlates well with the extent of delipidation. Our data highlight the importance of the lipid environment for interaction of NAADP with its target protein.
Molecular cloning of the mouse IMINO system: an Na+- and Cl−-dependent proline transporter
Authors: KOWALCZUK Sonja , BRÖER Angelika , MUNZINGER Michael , TIETZE Nadine , KLINGEL Karin , BRÖER Stefan
Published: March 2005

Neurotransmitter transporters of the SLC6 family play an important role in the removal of neurotransmitters in brain tissue and in amino acid transport in epithelial cells. Here we demonstrate that the mouse homologue of slc6a20 has all properties of the long-sought IMINO system. The mouse has two homologues corresponding to the single human SLC6A20 gene: these have been named XT3 and XT3s1. Expression of mouse XT3s1, but not XT3, in Xenopus laevis oocytes induced an electrogenic Na+-and-Cl−-dependent transporter for proline, hydroxyproline, betaine, N-methylaminoisobutyric acid and pipecolic acid. Expression of XT3s1 was found in brain, kidney, small intestine, thymus, spleen and lung, whereas XT3 prevailed in kidney and lung. Accordingly we suggest that the two homologues be termed ‘XT3s1 IMINOB’ and ‘XT3 IMINOK’ to indicate the tissue expression of the two genes.
Correlation between perpendicular exchange bias and magnetic anisotropy in IrMn∕[Co∕Pt]n and [Pt∕Co]n∕IrMn multilayers
Authors: van Dijken Sebastiaan , Moritz Jerome , Coey J. M. D.
Published: March 2005

Perpendicular exchange bias has been observed for IrMn∕[Co∕Pt]n and [Pt∕Co]n∕IrMn multilayers in the as-deposited state. The exchange bias field is largest when the IrMn film is grown on magnetically saturated Co∕Pt multilayers (8.12mT for n=3), whereas it is considerably smaller when domain formation in the IrMn film occurs before Co∕Pt deposition (3.30mT for n=3). After annealing at 220°C in an out-of-plane magnetic field the perpendicular exchange bias field and magnetic anisotropy are considerably larger for the Co∕Pt multilayers with an IrMn film at the bottom. The apparent correlation between bias and anisotropy is explained by the dependence of the perpendicular exchange bias field on the orientation of the Co spins near the Co∕IrMn interface.
Investigation of Ge nanocrytals in a metal-insulator-semiconductor structure with a HfO2∕SiO2 stack as the tunnel dielectric
Authors: Wang Shiye , Liu Weili , Wan Qing , Dai J. Y. , Lee P. F. , Suhua Luo , Shen Qinwo , Zhang Miao , Song Zhitang , Lin Chenglu
Published: March 2005

A metal-insulator-semiconductor (MIS) structure containing a HfO2 control gate, a Ge nanocrystal-embedded HfO2 dielectric and a HfO2∕SiO2 stack layer as tunnel oxide, was fabricated by an electron-beam evaporation method. High-resolution transmission electron microscopy study revealed that the HfO2∕SiO2 stack layer minimized Ge penetration, leading to the formation of Ge nanocrystals that are self-aligned between the tunnel oxide and the capping HfO2 layer. Influence of different annealing conditions on the formation and distribution of Ge nanocrystals was studied. Current–voltage (I–V) and capacitance–voltage (C–V) measurements revealed promising electrical characteristics of the MIS structure, and relatively high stored charge density of 1012cm−2 was achieved.
A theoretical and experimental investigation of light extraction from polymer light-emitting diodes
Authors: Ziebarth Jonathan M. , McGehee Michael D.
Published: March 2005

Using numerical modeling techniques we predict the emission into air, substrate, polymer/indium tin oxide (ITO), and surface-plasmon modes of a polymer light-emitting diode. The results give good insight into the possible efficiency increases that can be expected for various light extraction techniques. In addition, the effects of various optical properties and layer thicknesses on the optical performance of the device are reported. We show how modification of the substrate can be used to concentrate light into mode types from which light can be easily extracted. We then report experimental results for two very different light extraction techniques. First, we demonstrate how Bragg gratings can be used to extract light from waveguide modes in the polymer/ITO layers. With an optimized Bragg grating, we have increased the external power efficiency by 25% at high brightness levels. In addition, we have used substrate-shaping techniques to extract light from waveguide modes in the glass substrate. In this case, we were able to increase the efficiency by over 60%. Finally, we compare our numerical and experimental results to summarize the possible benefits of various light extraction strategies.
p
H
measurements with single ZnO nanorods integrated with a microchannel
Authors: Kang B. S. , Ren F. , Heo Y. W. , Tien L. C. , Norton D. P. , Pearton S. J.
Published: March 2005

Single ZnO nanorods with Ohmic contacts at either end exhibit large changes in current upon exposing the surface region to polar liquids introduced through an integrated microchannel. The polar nature of the electrolyte introduced led to a change of surface charges on the nanorod, producing a change in surface potential at the semiconductor∕liquid interface. The nanorods exhibit a linear change in conductance between pH 2 and 12 of 8.5nS∕pH in the dark and 20nS∕pH when illuminated with ultraviolet (365nm) light. The nanorods show stable operation with a resolution of ∼0.1pH over the entire pH range. The results indicate that ZnO nanorods may have applications in integrated chemical, gas, and fluid monitoring sensors.
Mechanical strain and defect distributions in GaAs-based diode lasers monitored during operation
Authors: Tien Tran Quoc , Tomm Jens W. , Oudart Myriam , Nagle Julien
Published: March 2005

We monitor the mechanical strain and the defect concentration in AlGaAs–GaAs-based high-power diode laser arrays. This allows studying the interplay between these extrinsic parameters in dependence on device operation. There are two parameters, which contribute to the spread of the mechanical strain, the local position at the device, and, the device operation time that substantially enhances the strain. For midgap levels as well as shallower defect levels, which are due to physically different defects, very different creation scenarios are observed. The concentration of shallow defects and band-tail states is strongly correlated with compressive strain in their vicinity, no matter how the strain is created. For midgap levels, there is no direct correlation; however, an increase by a factor of 3 after 1500h of operation time is observed. The knowledge on defect creation scenarios is extensible to other GaAs-based devices.
Influence of trapping on the exciton dynamics of AlxGa1−xAs films
Authors: Amo A. , Martin M. D. , Kłopotowski Ł. , Viña L. , Toropov A. I. , Zhuravlev K. S.
Published: March 2005

We present a systematic study on the exciton relaxation in high-purity AlGaAs epilayers. The time for the excitonic photoluminescence to reach its maximum intensity, defined as tmax, shows a nonmonotonic dependence on excitation density which is attributed to a competition between exciton localization and carrier–carrier scattering. A phenomenological four level model fully describes the influence of exciton localization on tmax. This localization effect is enhanced by the increase of the Al content in the alloy and disappears when localization is hindered by rising the lattice temperature above the exciton trapping energy.
Coherent vortical structures in numerical simulations of buoyant plumes from wildland fires
Authors: Cunningham Philip , Goodrick Scott L. , Hussaini M. Yousuff , Linn Rodman R.
Published: March 2005

The structure and dynamics of buoyant plumes arising from surface-based heat sources in a vertically sheared ambient atmospheric flow are examined via simulations of a three-dimensional, compressible numerical model. Simple circular heat sources and asymmetric elliptical ring heat sources that are representative of wildland fires of moderate intensity are considered. Several different coherent vortical structures that dominate the plume structure and evolution are evident in the simulations, and these structures correspond well with those observed in plumes from wildland fires. For the circular source, these structures include: (i) a counter-rotating vortex pair aligned with the plume trajectory that is associated with a bifurcation of the plume, (ii) transverse shear-layer vortices on the upstream face of the plume, and (iii) vertically oriented wake vortices that form periodically with alternating sign on either side of the downstream edge of the plume base. For the elliptical ring source, a streamwise counter-rotating vortex pair is apparent on each flank, and a transverse horizontal vortex is observed above the head of the source. In all simulations the plume cross section is represented poorly by a self-similar Gaussian distribution.
TheAnopheles gambiaedetoxification chip: A highly specific microarray to study metabolic-based insecticide resistance in malaria vectors
Authors: David Jean-Philippe , Strode Clare , Vontas John , Nikou Dimitra , Vaughan Ashley , Pignatelli Patricia M. , Louis Christos , Hemingway Janet , Ranson Hilary
Published: March 2005

Metabolic pathways play an important role in insecticide resistance, but the full spectra of the genes involved in resistance has not been established. We constructed a microarray containing unique fragments from 230Anopheles gambiaegenes putatively involved in insecticide metabolism [cytochrome P450s (P450s), GSTs, and carboxylesterases and redox genes, partners of the P450 oxidative metabolic complex, and various controls]. We used this detox chip to monitor the expression of the detoxifying genes in insecticide resistant and susceptibleAn. gambiaelaboratory strains. Five genes were strongly up-regulated in the dichlorodiphenyltrichloroethane-resistant strainZAN/U. These genes included the GSTGSTE2, which has previously been implicated in dichlorodiphenyltrichloroethane resistance, two P450s, and two peroxidase genes.GSTE2was also elevated in the pyrethroid-resistantRSPstrain. In addition, the P450CYP325A3, belonging to a class not previously associated with insecticide resistance, was expressed at statistically higher levels in this strain. The applications of this detox chip and its potential contribution to malaria vector insecticide resistance management programs are discussed.
Mechanism of phagolysosome biogenesis block by viable
Mycobacterium tuberculosis
Authors: Vergne Isabelle , Chua Jennifer , Lee Hwang-Ho , Lucas Megan , Belisle John , Deretic Vojo
Published: March 2005

Live
Mycobacterium tuberculosis
persists in macrophage phagosomes by interfering with phagolysosome biogenesis. Here, using four-dimensional microscopy and
in vitro
assays, we report the principal difference between phagosomes containing live and dead mycobacteria. Phosphatidylinositol 3-phosphate (PI3P), a membrane trafficking regulatory lipid essential for phagosomal acquisition of lysosomal constituents, is retained on phagosomes harboring dead mycobacteria but is continuously eliminated from phagosomes with live bacilli. We show that the exclusion of PI3P from live mycobacterial phagosomes can be only transiently reversed by Ca
2+
fluxes, and that live
M. tuberculosis
secretes a lipid phosphatase, SapM, that hydrolyzes PI3P, inhibits phagosome–late endosome fusion
in vitro
, and contributes to inhibition of phagosomal maturation.
Cytosolic abscisic acid activates guard cell anion channels without preceding Ca
2+
signals
Authors: Levchenko Victor , Konrad Kai R. , Dietrich Petra , Roelfsema M. Rob G. , Hedrich Rainer
Published: March 2005

The phytohormone abscisic acid (ABA) reports on the water status of the plant and induces stomatal closure. Guard cell anion channels play a central role in this response, because they mediate anion efflux, and in turn, cause a depolarization-induced K
+
release. We recorded early steps in ABA signaling, introducing multibarreled microelectrodes in guard cells of intact plants. Upon external ABA treatment, anion channels transiently activated after a lag phase of ≈2 min. As expected for a cytosolic ABA receptor, iontophoretic ABA loading into the cytoplasm initiated a rise in anion current without delay. These ABA responses could be elicited repetitively at resting and at largely depolarized potentials (e.g., 0 mV), ruling out signal transduction by means of hyperpolarization-activated calcium channels. Likewise, ABA stimulation did not induce a rise in the cytosolic free-calcium concentration. However, the presence of ≈100 nM background Ca
2+
was required for anion channel function, because the action of ABA on anion channels was repressed after loading of the Ca
2+
chelator 1,2-bis(2-aminophenoxy)ethane-
N
,
N
,
N
′,
N
′-tetraacetate. The chain of events appears very direct, because none of the tested putative ABA-signaling intermediates (inositol 1,4,5 trisphosphate, inositol hexakisphosphate, nicotinic acid adenine dinucleotide phosphate, and cyclic ADP-ribose), could mimic ABA as anion channel activator. In patch-clamp experiments, cytosolic ABA also evoked anion current transients carried by R- and S-type anion channels. The response was dose-dependent with half-maximum activation at 2.6 μM ABA. Our studies point to an ABA pathway initiated by ABA binding to a cytosolic receptor that within seconds activates anion channels, and in turn, leads to depolarization of the plasma membrane.
Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers
Authors: Ibrahim El Chérif , Schaal Thomas D. , Hertel Klemens J. , Reed Robin , Maniatis Tom
Published: March 2005

The 5′ and 3′ splice sites within an intron can, in principle, be joined to those within any other intron during pre-mRNA splicing. However, exons are joined in a strict 5′ to 3′ linear order in constitutively spliced pre-mRNAs. Thus, specific mechanisms must exist to prevent the random joining of exons. Here we report that insertion of exon sequences into an intron can inhibit splicing to the downstream 3′ splice site and that this inhibition is independent of intron size. The exon sequences required for splicing inhibition were found to be exonic enhancer elements, and their inhibitory activity requires the binding of serine/arginine-rich splicing factors. We conclude that exonic enhancers can act as barriers to prevent exon skipping and thereby may play a key role in ensuring the correct 5′ to 3′ linear order of exons in spliced mRNA.
Magnetic self-assembly of three-dimensional surfaces from planar sheets
Authors: Boncheva Mila , Andreev Stefan A. , Mahadevan L. , Winkleman Adam , Reichman David R. , Prentiss Mara G. , Whitesides Sue , Whitesides George M.
Published: March 2005

This report describes the spontaneous folding of flat elastomeric sheets, patterned with magnetic dipoles, into free-standing, 3D objects that are the topological equivalents of spherical shells. The path of the self-assembly is determined by a competition between mechanical and magnetic interactions. The potential of this strategy for the fabrication of 3D electronic devices is demonstrated by generating a simple electrical circuit surrounding a spherical cavity.
Making Space for Culture(s) in Boomtown. Some Alternative Futures for Development, Ownership and Participation in Leeds City Centre
Authors: Chatterton Paul , Unsworth Rachael
Published: March 2005

This paper looks at what kinds of spaces are emerging for cultures in Leeds, a city dubbed ‘boomtown’, due to an strong external appearance of a prosperous city on the move. What we suggest is that, while there is commitment to broad definitions of ‘culture’ as a way of life, on the ground, culture often equates to promoting property development and attracting mobile investment. We ask what are the barriers to doing cultures differently, and offer practical alternatives, in terms of development, ownership and participation, that could make space for different ideas and practices of cultures in boomtown Leeds.
Chromatin decondensation in S-phase involves recruitment of Cdk2 by Cdc45 and histone H1 phosphorylation
Authors: Alexandrow Mark G. , Hamlin Joyce L.
Published: March 2005

Cdc45 is required for initiation of DNA replication and fork progression, but its function in these processes remains unknown. We show that targeting Cdc45 to specific chromosomal sites in mammalian cells results in large-scale chromatin decondensation that strongly correlates with histone H1 phosphorylation. Cdk2 is recruited to sites of Cdc45 decondensation, and Cdk2 inhibitors reduce the level of decondensation. Targeting wild-type Cdk2, but not kinase-defective Cdk2, to chromatin is also effective at inducing decondensation involving phospho-H1. Cdc45, Cdk2, Cyclin A, and phospho-H1 associate with chromatin during S-phase, and Cdc45, Cdk2, and an active H1 kinase physically interact. Replicating DNA and phospho-H1 foci colocalize in vivo, and S-phase progression and H1 phosphorylation are directly related and Cdk2 dependent. Because Cdk2 colocalizes with replication foci and H1 regulates higher-order chromatin, we suggest a model in which Cdc45 recruits Cdk2 to replication foci, resulting in H1 phosphorylation, chromatin decondensation, and facilitation of fork progression.
ROCK-I regulates closure of the eyelids and ventral body wall by inducing assembly of actomyosin bundles
Authors: Shimizu Yoshihiko , Thumkeo Dean , Keel Jeongsin , Ishizaki Toshimasa , Oshima Hiroko , Oshima Masanobu , Noda Yoichi , Matsumura Fumio , Taketo Makoto M. , Narumiya Shuh
Published: March 2005

Rho-associated kinase (ROCK) I mediates signaling from Rho to the actin cytoskeleton. To investigate the in vivo functions of ROCK-I, we generated ROCK-I–deficient mice. Loss of ROCK-I resulted in failure of eyelid closure and closure of the ventral body wall, which gave rise to the eyes open at birth and omphalocele phenotypes in neonates. Most ROCK-I−/− mice died soon after birth as a result of cannibalization of the omphalocele by the mother. Actin cables that encircle the eye in the epithelial cells of the eyelid were disorganized and accumulation of filamentous actin at the umbilical ring was impaired, with loss of phosphorylation of the myosin regulatory light chain (MLC) at both sites, in ROCK-I−/− embryos. Stress fiber formation and MLC phosphorylation induced by EGF were also attenuated in primary keratinocytes from ROCK-I−/− mice. These results suggest that ROCK-I regulates closure of the eyelids and ventral body wall through organization of actomyosin bundles.
Self‐Similarity and the Evaluation of Long‐Time Nonhydrostatic Effects in Compositionally Driven Gravity Flows in Deep Surroundings
Authors: Antar N. , Moodie T. B.
Published: March 2005

In the study of compositionally driven gravity currents involving one or more homogeneous fluid layers, it has been customary to adopt the hydrostatic assumption for the pressure field in each layer which, in turn, leads to a depth‐independent horizontal velocity field in each of these layers and significant simplifications to the governing equations. Under this hydrostatic paradigm, each layer will then have its motion governed by the well‐known reduced dimension shallow‐water equations. For the so‐called ‐layer or reduced gravity shallow‐water equations, similarity solutions for fixed volume gravity currents released in rectangular geometry have been found. Very few attempts have been made to evaluate contributions arising from the possible loss of hydrostatic balance in the context of the problems treated using the classic shallow‐water approach. Where such attempts have been pursued, they have usually been carried out in a time‐independent context or using layer‐averaged equations and very small amplitude disturbances. The vast majority of these studies into nonhydrostatic effects do not include any relevant numerical work to assess these effects. In this paper, we develop an approach for evaluating nonhydrostatic contributions to the flow field for bottom gravity currents in deep surroundings and rectangular geometry. Our approach makes no assumptions on the amplitudes of the disturbances and does not depend on layer‐averaging in the governing equations. We seek asymptotic expansions of the solutions to the Euler equations for a shallow fluid by using the small parameter δ2, where δ is the aspect ratio of the flow regime. At leading order the equations enforce hydrostatic balance while those obtained at first order retain certain nonhydrostatic effects which we evaluate. Our method for evaluation of these first‐order contributions employs the self‐similar nature of the solution to the leading‐order equations in the new first‐order equations without any vertical averaging procedures being employed.
Probability of Winning at Tennis I. Theory and Data
Authors: Newton Paul K. , Keller Joseph B.
Published: March 2005

The probability of winning a game, a set, and a match in tennis are computed, based on each player's probability of winning a point on serve, which we assume are independent identically distributed (iid) random variables. Both two out of three and three out of five set matches are considered, allowing a 13‐point tiebreaker in each set, if necessary. As a by‐product of these formulas, we give an explicit proof that the probability of winning a set, and hence a match, is independent of which player serves first. Then, the probability of each player winning a 128‐player tournament is calculated. Data from the 2002 U.S. Open and Wimbledon tournaments are used both to validate the theory as well as to show how predictions can be made regarding the ultimate tournament champion. We finish with a brief discussion of evidence for non‐iid effects in tennis, and indicate how one could extend the current theory to incorporate such features.
On Tzitzéica Vortex Streets and Their Reciprocals in Subsonic Gas Dynamics
Authors: Rogers C. , Schief W. K. , Chow K. W. , Mak C. C.
Published: March 2005

Hydrodynamic vortex street solutions are generated based on an elliptic Tzitzéica model. A multiparameter class of reciprocal transformations is coupled with the action of a Bäcklund transformation to construct compressible vortex solutions of breather type valid in subsonic flow régimes of a generalized Kármán–Tsien gas.
Light‐chain‐restricted plasmacellular infiltrates in necrobiosis lipoidica – a clue to an underlying monoclonal gammopathy
Authors: Cioc Adina M. , Frambach Gwyn E. , Magro Cynthia M.
Published: March 2005

Background:  Necrobiosis lipoidica (NL) is a member of the palisading granulomatous dermatitides that is associated, in most cases, with diabetes mellitus. However, there are an increasing number of cases of NL associated with other forms of systemic disease. We describe a novel case of NL associated with a light‐chain‐restricted plasmacellular infiltrate; subsequent investigations established an underlying monoclonal gammopathy.

Methods:  Skin biopsy material was obtained and was processed in the usual fashion for hematoxylin and eosin (H&E) examination. Immunohistochemical staining was performed by utilizing kappa and lambda monoclonal antibodies (Dako Corporation, Carpentiera, CA, USA). Kappa and lambda in situ hybridization was also performed (Ventana Medical Systems, Tucson, AZ, USA).

Results:  A 55‐year‐old woman with a 5‐year history of bilateral thigh subcutaneous nodules underwent a skin biopsy, showing typical changes of NL; there was a concomitant prominent perivascular plasmacellular infiltrate. Kappa light chain restriction was observed amid the plasmacellular infiltrate. Bone marrow biopsy and immunophenotyping studies revealed a clonal plasmacytosis with kappa light chain restriction.

Conclusions:  Granulomatous inflammation, including NL, may be a cutaneous paraneoplastic expression of low‐grade B‐cell lymphoproliferative disease in the context of an underlying plasma cell dyscrasia.
The importance of mitotic rate as a prognostic factor for localized cutaneous melanoma
Authors: Barnhill Raymond L. , Katzen Jason , Spatz Alain , Fine Judith , Berwick Marianne
Published: March 2005

Background:  Tumor ulceration (TU) is considered the second most important prognostic factor after Breslow thickness for localized cutaneous malignant melanoma (CMM). However, many studies have not included mitotic rate (MR) with TU in these analyses. When both TU and MR are included in the same analysis, MR appears to be the more important than TU and TU loses its significance as an independent prognostic factor.

Methods:  The relative importance of TU and MR as prognostic factors in localized CMM were compared in a population‐based series of 650 consecutive invasive CMM cases ascertained from the Connecticut tumor registry and reviewed by a single dermatopathologist (RLB), during the period between January 15, 1987 and May 15, 1989. Seventeen clinical and histopathological variables including tumor thickness measured in mm, TU recorded as present or absent, and MR recorded as number per mm2 were included in an unconditional logistic regression model and selected for inclusion using a backward stepwise algorithm with death as an endpoint or at least five‐years follow‐up.

Results:  In the multivariate regression, the independent prognostic factors included: 1. tumor thickness in millimeters (OR = 1.5, 95% CI = 1.3−1.9) 2. moderate mitotic index (between 1 and 6): (OR = 8.3, 95% CI 2.4–28.7), 3. mitotic index (>6): (OR = 11.6, 95% CI = 3.0−44.6), 4. solar elastosis: (inversely associated with mortality)(OR = 0.4, 95% CI = 0.2−8). After adjustment for MR, TU lost its significance. When MR was left out of the analysis, ulceration then became an independent prognostic factor. The model with ulceration only (excluding MR) showed a relative risk (RR) of 2.4 (95%CI: 1.1–5.1). In the model with MR only, MR had a RR of 14.5 (95% CI3.9–53.7). Finally, regression analysis including both TU and MR yielded an RR of 11.6 for MR and 1.7 for TU.

Conclusions:  Our results suggest that MR as a proxy for tumor proliferation is a more important prognostic factor than TU.
Cutaneous lipomatous neurofibroma: characterization and frequency
Authors: Val‐Bernal J. Fernando , González‐Vela M. Carmen
Published: March 2005

Background:  There are numerous variants of cutaneous neurofibroma reflecting its manner of growth and histologic composition. Lipomatous neurofibroma is the latest described variant with only eight cases reported.

Methods:  A systematic study based on 320 consecutive specimens diagnosed of cutaneous neurofibroma was carried out. Conventional microscopy, immunohistochemistry, and statistical methods were used to determine the presence of fat cells, their amount, distribution, and frequency.

Results:  Intratumoral fat was observed in 22 (6.9%) neurofibromas. All these were dermal neurofibromas. Intraneoplastic fat was divided into two groups: focal and diffuse (regularly interspersed). Eighteen tumors (5.6%) presented adipocytes focally intermingled with the spindle cells. There were four (1.3%) neurofibromas showing spindle cell proliferation with regularly scattered adipocytes. Lipomatous neurofibroma was more frequent located on head and neck than non‐lipomatous neurofibroma ( p = 0.04). Neurofibromas without mature adipocytes were more frequently immunoreactive for CD34 compared with tumors showing intratumoral fat ( p = 0.02).

Conclusions:  We suggest that both metaplasia and aberrant adipose differentiation from multipotential cells may result in lipomatous neurofibroma. Focal presence of adipose cells may be attributable to metaplasia as the pathogenic mechanism. The fatty tissue being intrinsic to the tumor structure in its diffuse form, the lesion represents a distinctive tumor of the peripheral nerve sheath.
Rhabdomyomatous mesenchymal hamartoma associated with nasofrontal meningocele and dermoid cyst
Authors: Takeyama Junji , Hayashi Toshiaki , Sanada Takehiko , Shimanuki Yoshihisa , Saito Mioko , Shirane Reizo
Published: March 2005

A 1‐year‐6‐month‐old girl presented with a subcutaneous tumor of the forehead, which had developed since birth. The preoperative examinations showed nasofrontal bone defect with meningocele and subcutaneous tumor with cyst. The patient underwent excision of the tumor and reconstruction of the bone defect. Histologically, the skin tumor exhibited disordered arrangement of striated muscle fibers among normal dermal components, and the cyst was lined by cornified epithelium with a few hair adnexa and contained lamellated keratin. These findings were consistent with rhabdomyomatous mesenchymal hamartoma (RMH) and dermoid cyst. This is an interesting case of RMH co‐existing with nasofrontal meningocele and dermoid cyst in the same area. We suggest embryologic errors as a possible etiology, which is incomplete dysjunction of the neural ectoderm from the cutaneous ectoderm. Failure of insertion of mesoderm between the ectoderms caused the bone defect and the disordered proliferation and differentiation of mesoderm‐derived tissue, leading to formation of hamartoma.
Solid Solutions in the System LaMgAl11O19‐ LaMgGa11O19‐LaMgFe11O19
Authors: SCHöNWELSKI W. , HABEREY F. , LECKEBUSCH R. , ROSENBERG M. , SAHL K.
Published: March 2005

Solid Solutions with the magnetoplumbite structure in the System LaMgAl11O19‐LaMgGa11O19‐LaMgFe11O19 were studied by X‐ray diffractometry of sintered samples. Complete miscibility exists in the subsystem LaMgAl11O19‐LaMgGa11O19 and in a narrow adjacent ternary area with low iron content. In the other subsystems and in the major part of the ternary field, a magnetoplumbite phase occurs together with other compounds.
Structural Mechanisms of Anomalous Thermal Expansion of Cordierite‐Beryl and Other Framework Silicates
Authors: HOCHELLA M. F. , BROWN G. E.
Published: March 2005

The structural mechanisms controlling the anomalous thermal expansion behavior of the cordierite‐beryl type structure and other framework silicates are discussed. The expansion of a particular silicate framework depends on the temperature response of the framework itself involving T–O–T and O–T–O angular changes, the expansion coefficient(s) of the nontetrahedral bonds, if present, and the interplay between these two factors. For cordierite, beryl, andβ‐eucryptite, expanding nontetrahedral bonds play a critical role in driving the anomalous thermal expansion observed. Forβ‐spodumene and the feldspars, the thermal response of the framework dominates the expansion mechanism. The effects of channel constituents on the thermal expansion of the cordierite‐beryl framework are also discussed.
Experimental Evidence for the Existence of the Ti3B4 Phase
Authors: Spear Karl E. , Mcdowell Penny , Mcmahon Francis
Published: March 2005

Experimental evidence for the formation of Ti3B4 with an orthorhombic Ta3B4‐type structure is presented. This phase forms by a peritectic reaction between TiB2 and liquid at ∼2200°C and is stable to temperatures at least as low as 1690°C, the lowest temperature at which samples were annealed. No evidence was found to indicate the presence of a second high‐temperature form of this phase, as has been reported in the literature.
Universal Method of Stress Analysis of Viscoelastic‐Elastic Composites
Authors: BOROVINSII SERGEI V. , MAZURIN OLEG V.
Published: March 2005

The stresses which are caused by differing thermal expansion values of materials and depend on the processes of structural and mechanical relaxation in glass are considered. The analysis of stresses in cylindrical coaxial seals may be reduced to computation of stresses in equivalent sandwich seals; this calculation can be accomplished by using a well‐known algorithm. The results of the calculations agree well with existing experimental data.
Transmission Electron Microscopy and Microanalytical Studies of Ion‐Beam‐Thinned Sections of Tricalcium Silicate Paste
Authors: GROVES G. W. , Le SUEUR P. J. , SINCLAIR W.
Published: March 2005

Mature tricalcium silicate cement pastes were examined in ion‐beam‐thinned sections. The microstructure consisted of very homogeneous amorphous hydrate gel surrounding residual unhydrated cores of tricalcium silicate, these regions being linked by a fibrillar outer hydration product. Carbonation had produced microcrystals of calcite within the outer product only. X‐ray microanalysis gave Ca: Si ratios for the hydrate regions which showed considerable deviations but were‐on average in fairly good agreement with indirectly determined Ca: Si ratios of pastes of the same material. There was no significant difference in composition between inner and outer hydration products.
Modeling Density Contributions in Preceramic Polymer/Ceramic Powder Systems
Authors: Schwartz K. B. , Rowcliffe D.J.
Published: March 2005

A model is presented that examines the mixing of ceramic powders with preceramic polymer binders that are converted to ceramic material on pyrolysis. Such polymer/powder systems, which have applications in the compaction of both SiC and Si3N4 powders, can be effective in increasing the green density of die‐pressed bodies. This model examines the relative importance of various physical parameters of the components of the system in maximizing the green density of the resulting pyrolyzed body.