bluuebunny/crossref_metadata_2025 huggingface dataset:
Electromagnetic models of the lightning return stroke
Authors: Baba Yoshihiro , Rakov Vladimir A.
Published: February 2007

Lightning return‐stroke models are needed for specifying the source in studying the production of transient optical emission (elves) in the lower ionosphere, the energetic radiation from lightning, and characterization of the Earth's electromagnetic environment, as well as studying lightning interaction with various objects and systems. Reviewed here are models based on Maxwell's equations and referred to as electromagnetic models. These models are relatively new and most rigorous of all models suitable for computing lightning electromagnetic fields. Maxwell's equations are numerically solved to yield the distribution of current along the lightning channel. Different numerical techniques, including the method of moments (MoM) and the finite difference time domain (FDTD) method, are employed. In order to achieve a desirable current‐wave propagation speed (lower than the speed of light in air), the channel‐representing wire is embedded in a dielectric (other than air) or loaded by additional distributed series inductance. Capacitive loading has been also suggested. The artificial dielectric medium is used only for finding the distribution of current along the lightning channel, after which the channel is allowed to radiate in air. Resistive loading is used to control current attenuation with height. In contrast with distributed circuit and so‐called engineering models, electromagnetic return‐stroke models allow a self‐consistent full‐wave solution for both lightning‐current distribution and resultant electromagnetic fields. In this review, we discuss advantages and disadvantages of four return‐stroke channel representations: a perfectly conducting/resistive wire in air, a wire embedded in a dielectric (other than air), a wire in air loaded by additional distributed series inductance, and a wire in air having additional distributed shunt capacitance. Further, we describe and compare different methods of excitation used in electromagnetic return‐stroke models: closing a charged vertical wire at its bottom with a specified grounded circuit, a delta‐gap electric field source, and a lumped current source. Finally, we review and compare representative numerical techniques used in electromagnetic modeling of the lightning return stroke: MoMs in the time and frequency domains and the FDTD method. We additionally consider the so‐called hybrid model of the lightning return stroke that employs a combination of electromagnetic and circuit theories and compare this model to electromagnetic models.
Simulations of cumulus clouds using a spectral microphysics cloud‐resolving model
Authors: Fan Jiwen , Zhang Renyi , Li Guohui , Tao Wei‐Kuo , Li Xiaowen
Published: February 2007

We have investigated the effects of aerosols on the development of cumulus clouds using a two‐dimensional spectral‐bin cloud‐resolving model. A convective cloud event occurring on 24 August 2000 in Houston, Texas, was simulated and the model results were compared with available radar and rain gauge measurements. Simulations assuming different aerosol chemical compositions were conducted to examine the impacts on cumulus development. The cloud microphysical and macrophysical properties changed considerably with the aerosol chemical properties. With varying the aerosol composition from only (NH4)2SO4, (NH4)2SO4 with soluble organics, to (NH4)2SO4 with slightly soluble organics, the number of activated aerosols in cloud decreased accordingly, leading to a decrease in the cloud droplet number concentration and an increase in the droplet size. Increasing activated aerosols resulted in the increase of ice crystal formation by homogeneous freezing, more extensive riming, lower supersaturation (Sw and Sice), less efficient growth of graupel, and more melting precipitation. Ice microphysical processes were more sensitive to the changes of aerosol chemical properties than the warm rain processes. The changes in macrophysical properties were more evident: The increase of activated aerosols resulted in longer cell lifetime, larger cell size, stronger secondary convective cell, and more accumulated precipitation. The simulation with the aerosol composition of (NH4)2SO4 with slightly soluble organics and an activation scheme of a reformulation of the Köhler theory to include the effect of slightly soluble organics and soluble HNO3 agreed well with the observations. The simulation captured the major convective cell observed from the field measurements. The predicted convective cell intensity, cell size, cell lifetime, and accumulated rain were in agreement with the observations.
Geochemistry of Martian soil and bedrock in mantled and less mantled terrains with gamma ray data from Mars Odyssey
Authors: Newsom Horton E. , Crumpler Larry S. , Reedy Robert C. , Petersen Michael T. , Newsom Gary C. , Evans Larry G. , Taylor G. Jeffrey , Keller John M. , Janes Daniel M. , Boynton William V. , Kerry Kris. E. , Karunatillake Suniti
Published: February 2007

Surficial materials, including soil and dust, are abundant in the upper tens of centimeters of the Martian surface sensed by the Mars Odyssey Gamma Ray Spectrometer (GRS). Seven large areas (14% of the Martian surface) that represent possible compositional end‐members were selected, including three regions heavily mantled with surficial materials. The selection process included mapping the ratio of exposed rocky terrain to surficial materials using high‐resolution imagery. GRS data for H, Cl, Fe, Si, K, and Th were obtained for each area. The areas are chemically homogeneous within each area, given the spatial resolution and analytical uncertainty of the GRS data. However, substantial chemical differences exist among the areas, including the different mantled terrains, contrary to earlier assumptions that surficial materials are globally homogeneous due to aeolian mixing. The observed chemical differences among the areas may be due to variations in the protolith compositions, extent of alteration of the protolith regions, or post soil formation processes. The abundances of Cl, K, and Th in rockier (but still soil‐rich) areas such as Syrtis Major Planum can be explained by mixing between a soil with higher concentrations of Cl, K, and Th, similar to the abundances in the mantled terrains (and some of the landing sites), and crustal rocks containing lower abundances of these elements, similar to Martian meteorites.
Apollo sample 70051 and high‐ and low‐Ti lunar soil simulants MLS‐1A and JSC‐1A: Implications for future lunar exploration
Authors: Hill Eddy , Mellin Michael J. , Deane Bill , Liu Yang , Taylor Lawrence A.
Published: February 2007

Plans for establishment of a manned lunar base make it imperative that considerable research be performed on the use of lunar rocks and soil for in situ resource utilization (ISRU). Samples and simulants of lunar soil must be established for these studies. We present here the bulk and mineral chemistries of unusual Apollo 17 sample 70051, the <45‐μm fraction of 70051, and the bulk and mineral chemistries of lunar soil simulants MLS‐1A, JSC‐1A, and JSC‐1Af. Comparison to lunar soils collected during the Apollo missions shows that 70051 has bulk chemistry similar to that of soils from the North Massif bounding the Valley of Taurus‐Littrow. Particle‐size distribution reveals 70051 to differ significantly from bona fide lunar soils. It is a coarse, immature sample with >80 % of particles >50 μm, and a constrained range of particle sizes (∼50% of particles are 50–100 μm in size) when compared to typical Apollo 17 soils (e.g., 71501,1 has ∼20% of particles in the 50–100 μm range). Plagioclase, present in rock fragments and as mineral fragments (up to sizes ∼1 mm), is the main phase present (50.5 vol%). Simulant JSC‐1A has a chemistry that is atypical for most of the Moon and contains 49.3 vol% glass. Simulant MLS‐1A resembles the FeO, TiO2 and Al2O3 contents of mare basalt soils. Both lunar soil simulants have specific properties for certain in situ resource utilization studies, however, neither fully matches both the physical and chemical characteristics of lunar soil. Sample 70051, as a 1.4‐kg haphazard mixture of lunar soil particles, is probably the best of the Apollo “soil” samples to be allocated for various ISRU investigations, where the uniqueness of lunar soils is deemed a necessity for study.
Habitat of early life: Solar X‐ray and UV radiation at Earth's surface 4–3.5 billion years ago
Authors: Cnossen Ingrid , Sanz‐Forcada Jorge , Favata Fabio , Witasse Olivier , Zegers Tanja , Arnold Neil F.
Published: February 2007

Solar X‐ray and UV radiation (0.1–320 nm) received at Earth's surface is an important aspect of the circumstances under which life formed on Earth. The quantity that is received depends on two main variables: the emission of radiation by the young Sun and its extinction through absorption and scattering by the Earth's early atmosphere. The spectrum emitted by the Sun when life formed, between 4 and 3.5 Ga, was modeled here, including the effects of flares and activity cycles, using a solar‐like star that has the same age now as the Sun had 4–3.5 Ga. Atmospheric extinction was calculated using the Beer‐Lambert law, assuming several density profiles for the atmosphere of the Archean Earth. We found that almost all radiation with a wavelength shorter than 200 nm is attenuated effectively, even by very tenuous atmospheres. Longer‐wavelength radiation is progressively less well attenuated, and its extinction is more sensitive to atmospheric composition. Minor atmospheric components, such as methane, ozone, water vapor, etc., have only negligible effects, but changes in CO2 concentration can cause large differences in surface flux. Differences due to variability in solar emission are small compared to this. In all cases surface radiation levels on the Archean Earth were several orders of magnitude higher in the 200–300 nm wavelength range than current levels in this range. That means that any form of life that might have been present at Earth's surface 4–3.5 Ga must have been exposed to much higher quantities of damaging radiation than at present.
Schizosaccharomyces pombe minimum genome factory
Authors: Giga‐Hama Yuko , Tohda Hideki , Takegawa Kaoru , Kumagai Hiromichi
Published: February 2007

Various systems for the production of useful proteins have been developed using the fission yeast Schizosaccharomyces pombe as a host, and some are now being used commercially. It is necessary, however, to improve the system further for the production of low‐cost chemicals and commodities, so that the host becomes more economical and productive and can be widely used for the production of different molecules. We hypothesized that many S. pombe genes are not necessary under nutrient‐rich growth conditions; or rather, they serve only to waste energy when seen from the viewpoint of protein production, because their products are necessary only for adaptation to different environments. Thus we have tried to create S. pombe mutants that are dedicated to heterologous protein production by deleting as many non‐essential genes as possible. Putative essential genes were mapped using the genome information of S. pombe. The transcriptome of gene disruptants was analysed using microarrays and, using this system, a new promoter was identified. The method (called the Latour method) has been developed to delete efficiently a large region from the chromosome, resulting in the establishment of mutant strains lacking approx. 500 kb of genetic material. New experimental strains auxotrophic for six nutrients were established that were conveniently used for co‐expression of proteins using multiple plasmids. An efficient transformation method has also been developed that is useful for investigating heterologous protein production in a variety of strains. Incidentally, in heterologous protein production systems, products are often degraded, leading to a decline in production efficiency. Thus, to examine heterologous protein production, we created 52 S. pombe mutant strains in each of which a single protease gene was destroyed. We also successfully constructed strains in which multiple protease genes were disrupted. As a result, it was shown that the production of a model protein, human growth hormone, was increased in this strain. Furthermore, we obtained many strains that lacked genes related to glucose metabolism, intracellular transport or biosynthesis of sugar chains. The present minireview covers the results of functional analysis of these strains. By preparing strains in which large chromosomal regions have been deleted and then combining strains defective in various functional genes, the establishment of effective hosts will become possible.
Kinetic properties of mutant deoxyguanosine kinase in a case of reversible hepatic mtDNA depletion
Authors: Mousson de camaret Bénédicte , Taanman Jan-Willem , Padet Sylvie , Chassagne Maïté , Mayençon Martine , Clerc-Renaud Pascale , Mandon Ginette , Zabot Marie-Thérèse , Lachaux Alain , Bozon Dominique
Published: February 2007

DGUOK [dG (deoxyguanosine) kinase] is one of the two mitochondrial deoxynucleoside salvage pathway enzymes involved in precursor synthesis for mtDNA (mitochondrial DNA) replication. DGUOK is responsible for the initial rate-limiting phosphorylation of the purine deoxynucleosides, using a nucleoside triphosphate as phosphate donor. Mutations in the DGUOK gene are associated with the hepato-specific and hepatocerebral forms of MDS (mtDNA depletion syndrome). We identified two missense mutations (N46S and L266R) in the DGUOK gene of a previously reported child, now 10 years old, who presented with an unusual revertant phenotype of liver MDS. The kinetic properties of normal and mutant DGUOK were studied in mitochondrial preparations from cultured skin fibroblasts, using an optimized methodology. The N46S/L266R DGUOK showed 14 and 10% residual activity as compared with controls with dG and deoxyadenosine as phosphate acceptors respectively. Similar apparent negative co-operativity in the binding of the phosphate acceptors to the wild-type enzyme was found for the mutant. In contrast, abnormal bimodal kinetics were shown with ATP as the phosphate donor, suggesting an impairment of the ATP binding mode at the phosphate donor site. No kinetic behaviours were found for two other patients with splicing defects or premature stop codon. The present study represents the first characterization of the enzymatic kinetic properties of normal and mutant DGUOK in organello and our optimized protocol allowed us to demonstrate a residual activity in skin fibroblast mitochondria from a patient with a revertant phenotype of MDS. The residual DGUOK activity may play a crucial role in the phenotype reversal.
NAADP induces pH changes in the lumen of acidic Ca2+ stores
Authors: Morgan Anthony J. , Galione Antony
Published: February 2007

NAADP (nicotinic acid–adenine dinucleotide phosphate)-induced Ca2+ release has been proposed to occur selectively from acidic stores in several cell types, including sea urchin eggs. Using fluorescence measurements, we have investigated whether NAADP-induced Ca2+ release alters the pHL (luminal pH) within these acidic stores in egg homogenates and observed their prompt, concentration-dependent alkalinization by NAADP (but not β-NAD+ or NADP). Like Ca2+ release, the pHL change was desensitized by low concentrations of NAADP suggesting it was secondary to NAADP receptor activation. Moreover, this was a direct effect of NAADP upon the acidic stores and not secondary to increases in cytosolic Ca2+ as it was not mimicked by IP3 (inositol 1,4,5-trisphosphate), cADPR (cyclic adenine diphosphoribose), ionomycin, thapsigargin or by direct addition of Ca2+, and was not blocked by EGTA. The results of the present study further support acidic stores as targets for NAADP and for the first time reveal an adjunct role for NAADP in regulating the pHL of intracellular organelles.
Insulin-stimulated exocytosis of GLUT4 is enhanced by IRAP and its partner tankyrase
Authors: Yeh Tsung-Yin J. , Sbodio Juan I. , Tsun Zhi-Yang , Luo Biao , Chi Nai-Wen
Published: February 2007

The glucose transporter GLUT4 and the aminopeptidase IRAP (insulin-responsive aminopeptidase) are the major cargo proteins of GSVs (GLUT4 storage vesicles) in adipocytes and myocytes. In the basal state, most GSVs are sequestered in perinuclear and other cytosolic compartments. Following insulin stimulation, GSVs undergo exocytic translocation to insert GLUT4 and IRAP into the plasma membrane. The mechanisms regulating GSV trafficking are not fully defined. In the present study, using 3T3-L1 adipocytes transfected with siRNAs (small interfering RNAs), we show that insulin-stimulated IRAP translocation remained intact despite substantial GLUT4 knockdown. By contrast, insulin-stimulated GLUT4 translocation was impaired upon IRAP knockdown, indicating that IRAP plays a role in GSV trafficking. We also show that knockdown of tankyrase, a Golgi-associated IRAP-binding protein that co-localizes with perinuclear GSVs, attenuated insulin-stimulated GSV translocation and glucose uptake without disrupting insulin-induced phosphorylation cascades. Moreover, iodixanol density gradient analyses revealed that tankyrase knockdown altered the basal-state partitioning of GLUT4 and IRAP within endosomal compartments, apparently by shifting both proteins toward less buoyant compartments. Importantly, the afore-mentioned effects of tankyrase knockdown were reproduced by treating adipocytes with PJ34, a general PARP (poly-ADP-ribose polymerase) inhibitor that abrogated tankyrase-mediated protein modification known as poly-ADP-ribosylation. Collectively, these findings suggest that physiological GSV trafficking depends in part on the presence of IRAP in these vesicles, and that this process is regulated by tankyrase and probably its PARP activity.
Mechanism for the degradation of origin recognition complex containing Orc5p with a defective Walker A motif and its suppression by over-production of Orc4p in yeast cells
Authors: Makise Masaki , Takahashi Naoko , Matsuda Kazuya , Yamairi Fumiko , Suzuki Keitarou , Tsuchiya Tomofusa , Mizushima Tohru
Published: February 2007

Orc5p is one of six subunits constituting the ORC (origin recognition complex), a possible initiator of chromosomal DNA replication in eukaryotes. Orc5p contains a Walker A motif. We recently reported that a strain of Saccharomyces cerevisiae having a mutation in Orc5p's Walker A motif (orc5-A), showed cell-cycle arrest at G2/M and degradation of ORC at high temperatures (37 °C). Over-production of Orc4p, another subunit of ORC, specifically suppressed these phenotypes [Takahashi, Yamaguchi, Yamairi, Makise, Takenaka, Tsuchiya and Mizushima (2004) J. Biol. Chem. 279, 8469–8477]. In the present study, we examined the mechanisms of ORC degradation and of its suppression by Orc4p over-production. In orc5-A, at high temperatures, ORC is degraded by proteasomes; either addition of a proteasome inhibitor, or introduction of a mutation of either tan1-1 or nob1-4 that inhibits proteasomes, prevented ORC degradation. Introduction of the tan1-1 mutation restored cell cycle progression, suggesting that the defect was due to ORC degradation by proteasomes. Yeast two-hybrid and co-immunoprecipitation analyses suggested that Orc5p interacts preferentially with Orc4p and that the orc5-A mutation diminishes this interaction. We suggest that this interaction is mediated by the C-terminal region of Orc4p, and the N-terminal region of Orc5p. Based on these observations, we consider that ATP binding to Orc5p is required for efficient interaction with Orc4p and that, in orc5-A, loss of this interaction at higher temperatures allows proteasomes to degrade ORC, causing growth defects. This model could also explain why over-production of Orc4p suppresses the orc5-A strain's phenotype.
Ubc9 interacts with Lu/BCAM adhesion glycoproteins and regulates their stability at the membrane of polarized MDCK cells
Authors: Collec Emmanuel , El nemer Wassim , Gauthier Emilie , Gane Pierre , Lecomte Marie-Christine , Dhermy Didier , Cartron Jean Pierre , Colin Yves , Le van kim Caroline , Rahuel Cécile
Published: February 2007

Lu (Lutheran) blood group and BCAM (basal cell adhesion molecule) antigens both reside on two gp (glycoprotein) isoforms, Lu and Lu(v13), that differ by the size of their cytoplasmic tail. They are receptors of laminin-10/11 and are expressed in RBCs (red blood cells), epithelial cells of multiple tissues and vascular endothelial cells. To gain more insights into the biological function of Lu/BCAM gps, we looked for potential partners of their cytoplasmic tail. We isolated Ubc9 (ubiquitin-conjugating enzyme 9) protein by screening a human kidney library using the yeast two-hybrid system. Lu/Ubc9 interaction was validated by GST (glutathione S-transferase) pull-down and co-immunoprecipitation experiments. Endogenous Ubc9 formed a complex with endogenous or recombinant Lu gp in A498 and MDCK (Madin–Darby canine kidney) epithelial cells respectively. Replacement of Lys585 by alanine in the Lu gp abolished in vitro and ex vivo interactions of Lu gp with Ubc9 protein. Lu K585A mutant transfected in MDCK cells exhibited a normal basolateral membrane expression but was overexpressed at the surface of polarized MDCK cells as compared with wild-type Lu. Pulse–chase experiments showed extended half-life of Lu K585A gp at the plasma membrane, suggesting an impaired endocytosis of this mutant leading to protein accumulation at the membrane. Furthermore, we showed that the ability of MDCK-Lu K585A cells to spread on immobilized laminin was dramatically decreased. Our results support a physiological role for the direct interaction between Lu gp and Ubc9 protein and reveal a role for this enzyme in regulating the stability of Lu gp at the cell membrane.
Accessory proteins assist exonuclease-deficient bacteriophage T4 DNA polymerase in replicating past an abasic site
Authors: Blanca Giuseppina , Delagoutte Emmanuelle , Tanguy le gac Nicolas , Johnson Neil P. , Baldacci Giuseppe , Villani Giuseppe
Published: February 2007

Replicative DNA polymerases, such as T4 polymerase, possess both elongation and 3′–5′ exonuclease proofreading catalytic activities. They arrest at the base preceding DNA damage on the coding DNA strand and specialized DNA polymerases have evolved to replicate across the lesion by a process known as TLS (translesion DNA synthesis). TLS is considered to take place in two steps that often require different enzymes, insertion of a nucleotide opposite the damaged template base followed by extension from the inserted nucleotide. We and others have observed that inactivation of the 3′–5′ exonuclease function of T4 polymerase enables TLS across a single site-specific abasic [AP (apurinic/apyrimidinic)] lesion. In the present study we report a role for auxiliary replicative factors in this reaction. When replication is performed with a large excess of DNA template over DNA polymerase in the absence of auxiliary factors, the exo− polymerase (T4 DNA polymerase deficient in the 3′–5′ exonuclease activity) inserts one nucleotide opposite the AP site but does not extend past the lesion. Addition of the clamp processivity factor and the clamp loader complex restores primer extension across an AP lesion on a circular AP-containing DNA substrate by the exo− polymerase, but has no effect on the wild-type enzyme. Hence T4 DNA polymerase exhibits a variety of responses to DNA damage. It can behave as a replicative polymerase or (in the absence of proofreading activity) as a specialized DNA polymerase and carry out TLS. As a specialized polymerase it can function either as an inserter or (with the help of accessory proteins) as an extender. The capacity to separate these distinct functions in a single DNA polymerase provides insight into the biochemical requirements for translesion DNA synthesis.
Rab27a is a key component of the secretory machinery of azurophilic granules in granulocytes
Authors: Munafó Daniela B. , Johnson Jennifer L. , Ellis Beverly A. , Rutschmann Sophie , Beutler Bruce , Catz Sergio D.
Published: February 2007

Neutrophils kill micro-organisms using microbicidal products that they release into the phagosome or into the extracellular space. The secretory machinery utilized by neutrophils is poorly characterized. We show that the small GTPase Rab27a is an essential component of the secretory machinery of azurophilic granules in granulocytes. Rab27a-deficient mice have impaired secretion of MPO (myeloperoxidase) into the plasma in response to lipopolysaccharide. Cell fractionation analysis revealed that Rab27a and the Rab27a effector protein JFC1/Slp1 (synaptotagmin-like protein 1) are distributed principally in the low-density fraction containing a minor population of MPO-containing granules. By immunofluorescence microscopy, we detected Rab27a and JFC1/Slp1 in a minor subpopulation of MPO-containing granules. Interference with the JFC1/Slp1–Rab27a secretory machinery impaired secretion of MPO in permeabilized neutrophils. The expression of Rab27a was dramatically increased when promyelocytic HL-60 cells were differentiated into granulocytes but not when they were differentiated into monocytes. Down-regulation of Rab27a in HL-60 cells by RNA interference did not affect JFC1/Slp1 expression but significantly decreased the secretion of MPO. Neither Rab27a nor JFC1/Slp1 was integrated into the phagolysosome membrane during phagocytosis. Neutrophils from Rab27a-deficient mice efficiently phagocytose zymosan opsonized particles and deliver MPO to the phagosome. We conclude that Rab27a and JFC1/Slp1 permit MPO release into the surrounding milieu and constitute key components of the secretory machinery of azurophilic granules in granulocytes. Our results suggest that the granules implicated in cargo release towards the surrounding milieu are molecularly and mechanistically different from those involved in their release towards the phagolysosome.
Slow-onset inhibition of fumarylacetoacetate hydrolase by phosphinate mimics of the tetrahedral intermediate: kinetics, crystal structure and pharmacokinetics
Authors: Bateman Raynard L. , Ashworth Justin , Witte John F. , Baker L.-J. , Bhanumoorthy Pullooru , Timm David E. , Hurley Thomas D. , Grompe Markus , Mcclard Ronald W.
Published: February 2007

FAH (fumarylacetoacetate hydrolase) catalyses the final step of tyrosine catabolism to produce fumarate and acetoacetate. HT1 (hereditary tyrosinaemia type 1) results from deficiency of this enzyme. Previously, we prepared a partial mimic of the putative tetrahedral intermediate in the reaction catalysed by FAH co-crystallized with the enzyme to reveal details of the mechanism [Bateman, Bhanumoorthy, Witte, McClard, Grompe and Timm (2001) J. Biol. Chem. 276, 15284–15291]. We have now successfully synthesized complete mimics CEHPOBA {4-[(2-carboxyethyl)-hydroxyphosphinyl]-3-oxobutyrate} and COPHPAA {3-[(3-carboxy-2-oxopropyl)hydroxyphosphinyl]acrylate}, which inhibit FAH in slow-onset tight-binding mode with Ki values of 41 and 12 nM respectively. A high-resolution (1.35 Å; 1 Å=0.1 nm) crystal structure of the FAH·CEHPOBA complex was solved to reveal the affinity determinants for these compounds and to provide further insight into the mechanism of FAH catalysis. These compounds are active in vivo, and CEHPOBA demonstrated a notable dose-dependent increase in SA (succinylacetone; a metabolite seen in patients with HT1) in mouse serum after repeated injections, and, following a single injection (1 μmol/g; intraperitoneal), only a modest regain of FAH enzyme activity was detected in liver protein isolates after 24 h. These potent inhibitors provide a means to chemically phenocopy the metabolic defects of either HT1 or FAH knockout mice and promise future pharmacological utility for hepatocyte transplantation.
Postulated role of interdomain interaction between regions 1 and 2 within type 1 ryanodine receptor in the pathogenesis of porcine malignant hyperthermia
Authors: Murayama Takashi , Oba Toshiharu , Hara Hiroshi , Wakebe Kikuo , Ikemoto Noriaki , Ogawa Yasuo
Published: February 2007

We have demonstrated recently that CICR (Ca2+-induced Ca2+ release) activity of RyR1 (ryanodine receptor 1) is held to a low level in mammalian skeletal muscle (‘suppression’ of the channel) and that this is largely caused by the interdomain interaction within RyR1 [Murayama, Oba, Kobayashi, Ikemoto and Ogawa (2005) Am. J. Physiol. Cell Physiol. 288, C1222–C1230]. To test the hypothesis that aberration of this suppression mechanism is involved in the development of channel dysfunctions in MH (malignant hyperthermia), we investigated properties of the RyR1 channels from normal and MHS (MH-susceptible) pig skeletal muscles with an Arg615→Cys mutation using [3H]ryanodine binding, single-channel recordings and SR (sarcoplasmic reticulum) Ca2+ release. The RyR1 channels from MHS muscle (RyR1MHS) showed enhanced CICR activity compared with those from the normal muscle (RyR1N), although there was little or no difference in the sensitivity to several ligands tested (Ca2+, Mg2+ and adenine nucleotide), nor in the FKBP12 (FK506-binding protein 12) regulation. DP4, a domain peptide matching the Leu2442–Pro2477 region of RyR1 which was reported to activate the Ca2+ channel by weakening the interdomain interaction, activated the RyR1N channel in a concentration-dependent manner, and the highest activity of the affected channel reached a level comparable with that of the RyR1MHS channel with no added peptide. The addition of DP4 to the RyR1MHS channel produced virtually no further effect on the channel activity. These results suggest that stimulation of the RyR1MHS channel caused by affected inter-domain interaction between regions 1 and 2 is an underlying mechanism for dysfunction of Ca2+ homoeostasis seen in the MH phenotype.
Hormonal regulation of the Menkes and Wilson copper-transporting ATPases in human placental Jeg-3 cells
Authors: Hardman Belinda , Michalczyk Agnes , Greenough Mark , Camakaris James , Mercer Julian F. B. , Ackland M. Leigh
Published: February 2007

Copper deficiency during pregnancy results in early embryonic death and foetal structural abnormalities including skeletal, pulmonary and cardiovascular defects. During pregnancy, copper is transported from the maternal circulation to the foetus by mechanisms which have not been clearly elucidated. Two copper-transporting ATPases, Menkes (ATP7A; MNK) and Wilson (ATP7B; WND), are expressed in the placenta and both are involved in placental copper transport, as copper accumulates in the placenta in both Menkes and Wilson disease. The regulatory mechanisms of MNK and WND and their exact role in the placenta are unknown. Using a differentiated polarized Jeg-3 cell culture model of placental trophoblasts, MNK and WND were shown to be expressed within these cells. Distinct roles for MNK and WND are suggested on the basis of their opposing responses to insulin. Insulin and oestrogen increased both MNK mRNA and protein levels, altered the localization of MNK towards the basolateral membrane in a copper-independent manner, and increased the transport of copper across this membrane. In contrast, levels of WND were decreased in response to insulin, and the protein was located in a tight perinuclear region, with a corresponding decrease in copper efflux across the apical membrane. These results are consistent with a model of copper transport in the placenta in which MNK delivers copper to the foetus and WND returns excess copper to the maternal circulation. Insulin and oestrogen stimulate copper transport to the foetus by increasing the expression of MNK and reducing the expression of WND. These data show for the first time that MNK and WND are differentially regulated by the hormones insulin and oestrogen in human placental cells.
The dependence of enzyme activity on temperature: determination and validation of parameters
Authors: Peterson Michelle E. , Daniel Roy M. , Danson Michael J. , Eisenthal Robert
Published: February 2007

Traditionally, the dependence of enzyme activity on temperature has been described by a model consisting of two processes: the catalytic reaction defined by ΔGDaggercat, and irreversible inactivation defined by ΔGDaggerinact. However, such a model does not account for the observed temperature-dependent behaviour of enzymes, and a new model has been developed and validated. This model (the Equilibrium Model) describes a new mechanism by which enzymes lose activity at high temperatures, by including an inactive form of the enzyme (Einact) that is in reversible equilibrium with the active form (Eact); it is the inactive form that undergoes irreversible thermal inactivation to the thermally denatured state. This equilibrium is described by an equilibrium constant whose temperature-dependence is characterized in terms of the enthalpy of the equilibrium, ΔHeq, and a new thermal parameter, Teq, which is the temperature at which the concentrations of Eact and Einact are equal; Teq may therefore be regarded as the thermal equivalent of Km. Characterization of an enzyme with respect to its temperature-dependent behaviour must therefore include a determination of these intrinsic properties. The Equilibrium Model has major implications for enzymology, biotechnology and understanding the evolution of enzymes. The present study presents a new direct data-fitting method based on fitting progress curves directly to the Equilibrium Model, and assesses the robustness of this procedure and the effect of assay data on the accurate determination of Teq and its associated parameters. It also describes simpler experimental methods for their determination than have been previously available, including those required for the application of the Equilibrium Model to non-ideal enzyme reactions.
Elevated oxidative stress in erythrocytes due to a SOD1 deficiency causes anaemia and triggers autoantibody production
Authors: Iuchi Yoshihito , Okada Futoshi , Onuma Kunishige , Onoda Tadashi , Asao Hironobu , Kobayashi Masanobu , Fujii Junichi
Published: February 2007

Reactive oxygen species are involved in the aging process and diseases. Despite the important role of Cu/Zn SOD (superoxide dismutase) encoded by SOD1, SOD1−/− mice appear to grow normally under conventional breeding conditions. In the present paper we report on a novel finding showing a distinct connection between oxidative stress in erythrocytes and the production of autoantibodies against erythrocytes in SOD1−/− mice. Evidence is presented to show that SOD1 is primarily required for maintaining erythrocyte lifespan by suppressing oxidative stress. A SOD1 deficiency led to an increased erythrocyte vulnerability by the oxidative modification of proteins and lipids, resulting in anaemia and compensatory activation of erythropoiesis. The continuous destruction of oxidized erythrocytes appears to induce the formation of autoantibodies against certain erythrocyte components, e.g. carbonic anhydrase II, and the immune complex is deposited in the glomeruli. The administration of an antioxidant, N-acetylcysteine, suppressed erythrocyte oxidation, ameliorated the anaemia, and inhibited the production of autoantibodies. These data imply that a high level of oxidative stress in erythrocytes increases the production of autoantibodies, possibly leading to an autoimmune response, and that the intake of antioxidants would prevent certain autoimmune responses by maintaining an appropriate redox balance in erythrocytes.
Cr(VI)-stimulated STAT3 tyrosine phosphorylation and nuclear translocation in human airway epithelial cells requires Lck
Authors: O'hara Kimberley A. , Vaghjiani Rasilaben J. , Nemec Antonia A. , Klei Linda R. , Barchowsky Aaron
Published: February 2007

Chronic inhalation of low amounts of Cr(VI) promotes pulmonary diseases and cancers through poorly defined mechanisms. SFKs (Src family kinases) in pulmonary airway cells may mediate Cr(VI) signalling for lung injury, although the downstream effectors of Cr(VI)-stimulated SFKs and how they relate to pathogenic gene induction are unknown. Therefore SFK-dependent activation of transcription factors by non-cytotoxic exposure of human bronchial epithelial cells to Cr(VI) was determined. Protein–DNA binding arrays demonstrated that exposing BEAS 2B cells to 5 μM Cr(VI) for 4 and 24 h resulted in increased protein binding to 25 and 43 cis-elements respectively, while binding to 12 and 16 cis-elements decreased. Of note, Cr(VI) increased protein binding to several STAT (signal transducer and activator of transcription) cis-elements. Cr(VI) stimulated acute tyrosine phosphorylation and nuclear translocation of STAT1 over a 4 h period and a prolonged activation of STAT3 that reached a peak between 48 and 72 h. This prolonged activation was observed for both STAT3α and STAT3β. Immunofluorescent confocal microscopy confirmed that Cr(VI) increased nuclear localization of phosphorylated STAT3 for more than 72 h in both primary and BEAS 2B human airway cells. Cr(VI) induced transactivation of both a STAT3-driven luciferase reporter construct and the endogenous inflammatory gene IL-6 (interleukin-6). Inhibition with siRNA (small interfering RNA) targeting the SFK Lck, but not dominant-negative JAK (Janus kinase), prevented Cr(VI)-stimulated phosphorylation of both STAT3 isoforms and induction of IL-6. The results suggest that Cr(VI) activates epithelial cell Lck to signal for prolonged STAT3 activation and transactivation of IL-6, an important immunomodulator of lung disease progression.
The power to reduce: pyridine nucleotides – small molecules with a multitude of functions
Authors: Pollak Nadine , Dölle Christian , Ziegler Mathias
Published: February 2007

The pyridine nucleotides NAD and NADP play vital roles in metabolic conversions as signal transducers and in cellular defence systems. Both coenzymes participate as electron carriers in energy transduction and biosynthetic processes. Their oxidized forms, NAD+ and NADP+, have been identified as important elements of regulatory pathways. In particular, NAD+ serves as a substrate for ADP-ribosylation reactions and for the Sir2 family of NAD+-dependent protein deacetylases as well as a precursor of the calcium mobilizing molecule cADPr (cyclic ADP-ribose). The conversions of NADP+ into the 2′-phosphorylated form of cADPr or to its nicotinic acid derivative, NAADP, also result in the formation of potent intracellular calcium-signalling agents. Perhaps, the most critical function of NADP is in the maintenance of a pool of reducing equivalents which is essential to counteract oxidative damage and for other detoxifying reactions. It is well known that the NADPH/NADP+ ratio is usually kept high, in favour of the reduced form. Research within the past few years has revealed important insights into how the NADPH pool is generated and maintained in different subcellular compartments. Moreover, tremendous progress in the molecular characterization of NAD kinases has established these enzymes as vital factors for cell survival. In the present review, we summarize recent advances in the understanding of the biosynthesis and signalling functions of NAD(P) and highlight the new insights into the molecular mechanisms of NADPH generation and their roles in cell physiology.
Differential regulation of the Menkes and Wilson disease copper transporters by hormones: an integrated model of metal transport in the placenta
Authors: Richardson Des R. , Suryo rahmanto Yohan
Published: February 2007

Copper (Cu) plays a critical role in the developing foetus, but virtually nothing is known concerning the regulation of its uptake and metabolism in the placenta. In this issue of the Biochemical Journal, Hardman and colleagues, using a model of placental trophoblasts in culture, identify differential hormonal regulation of two copper-transporting ATPases; namely, those responsible for Menkes disease (ATP7A; MNK) and Wilson disease (ATP7B; WND). Insulin and oestrogen, which are essential during gestation, up-regulate MNK and this leads to trafficking of the MNK protein from the Golgi to the basolateral membrane, resulting in increased Cu efflux. At the same time, insulin decreased WND levels, and this leads to intracellular sequestration of the protein to a perinuclear region that reduces apical Cu release. As such, this results in a concerted flux of Cu from the basolateral surface of the trophoblast that would potentially be used by the developing foetus. An integrated model of vectorized Cu transport is proposed, which involves co-ordinated expression of transporters, organelle interactions and probable protein–protein interactions. The findings have wider implications for considering general models of intracellular metal transport.
Vibrational fingerprint of the structural tuning in push-pull organic chromophores with quinoid or proaromatic spacers
Authors: Casado Juan , Moreno Oliva María , Ruiz Delgado M. Carmen , López Navarrete Juan T. , Sánchez Luis , Martín Nazario , Andreu Raquel , Carrasquer Laura , Garín Javier , Orduna Jesús
Published: February 2007

The Raman spectra of a series of push-pull molecules containing probenzenoid or quinoid spacers which are substituted with 1,3-dithiol-2-ylidene as donor and dicyano-methylene or barbituric acid as acceptors have been analyzed. The experimental spectra have been assigned and interpreted according to density functional theory calculations. Correlations between the Raman spectra of the isolated spacers and of the substituted molecules have been done. Raman bands in the 1620–1560cm−1 interval provide vibrational markers of the quinoid↔aromatic structural evolution. This finding is supported by a careful inspection of geometrical parameters, namely, bond length alteration data and particular bond distances. As a result, the peak positions and relative intensities of these Raman features can be used to evaluate the benzenoid character of the spacer as a function of the donor/acceptor substitution pattern. This paper shows that Raman spectroscopy is a powerful spectroscopic tool for the analysis of the conjugational properties (i.e., intramolecular donor→acceptor charge transfer) of new organic materials.
K
-shell and extreme ultraviolet spectroscopic signatures of structured Ar puff Z-pinch loads with high K-shell x-ray yield
Authors: Failor B. H. , Sze H. M. , Banister J. W. , Levine J. S. , Qi N. , Apruzese J. P. , Lojewski D. Y.
Published: February 2007

Structured 12-cm-diam Ar gas-puff loads have recently produced Z-pinch implosions with reduced Rayleigh-Taylor instability growth and increased K-shell x-ray yield [H. Sze, J. Banister, B. H. Failor, J. S. Levine, N. Qi, A. L. Velikovich, J. Davis, D. Lojewski, and P. Sincerny, Phys. Rev. Lett. 95, 105001 (2005)]. To better understand the dynamics of these loads, we have measured the extreme ultraviolet (XUV) emission resolved radially, spectrally, and axially. Radial measurements indicated a compressed diameter of ≈3mm, consistent with the observed load inductance change and an imploded-mass consisting of a ≈1.5-mm-diam, hot, K-shell-emitting core and a cooler surrounding blanket. Spectral measurements indicate that, if the load is insufficiently heated, then radiation from the core will rapidly photoheat the outer blanket, producing a strong increase in XUV emission. Also, adding a massive center jet (⩾20% of load mass) increases the rise and fall times of the XUV emission to ⩾40ns, consistent with a more adiabatic compression and heating of the load. Axial measurements show that, despite differences in the XUV and K-shell emission time histories, the K-shell x-ray yield is insensitive to axial variations in load mass.
Monte Carlo simulations of stress relaxation of entanglement-free Fraenkel chains. II. Nonlinear polymer viscoelasticity
Authors: Lin Y.-H. , Das A. K.
Published: February 2007

The nonlinear viscoelastic behavior of the Fraenkel-chain model is studied with respect to the constitutive equation of the Rouse model. Distinctly different from the results of the Rouse model, the Fraenkel-chain model gives the following characteristic nonlinear behavior: (a) The two distinct dynamic modes in the relaxation modulus GS(t,λ)—as observed in the linear region reported in Paper I [Y.-H. Lin and A. K. Das, J. Chem. Phys. 126, 074902 (2007), preceding paper]—or in the first normal-stress difference function GΨ1(t,λ) are shown to have different strain dependences: strain hardening for the fast mode and strain softening for the slow mode. (b) The Lodge–Meissner relation GS(t,λ)=GΨ1(t,λ) holds over the whole time range, which has been shown both analytically and by simulation. (c) The second normal-stress difference is nonzero, being positive in the fast-mode region and negative in the slow-mode region. The comparisons between orientation and stress for all tensor components consistently confirm the strong correlation of the slow mode as well as its entropic nature with the segmental-orientation anisotropy as shown in the linear region studied in Paper I. A consequence of this correlation is the applicability of the stress-optical rule in the slow-mode region. This also leads to the expectation that the damping function h(λ)=GS(t,λ)∕GS(t,λ→0) and the ratio between the first and second normal-stress differences, N2(t,λ)∕N1(t,λ), are described by the orientation tensor which has the same form as that given by Doi and Edwards [J. Chem. Soc. Faraday Trans. 2 74, 1789 (1978); 74, 1802 (1978)] with independent-alignment approximation for an entangled system. The similarity between the slow mode of an entanglement-free Fraenkel-chain system and the terminal mode of an entangled polymer system as observed in the comparison of theory, simulation, and experiment suggests that the close correlation of the entropic nature of the mode with the orientation anisotropy—as of the Fraenkel segment or the primitive step in the Doi–Edwards theory—is a generally valid physical concept in polymer viscoelasticity.
Thermally stimulated glow peaks in Ge-doped cultured quartz crystals and their radiation response
Authors: Bahadur Harish
Published: February 2007

Ge-doped crystalline quartz has been examined for its thermally stimulated luminescence and has been found to exhibit TL-glow peaks at 100, 200, and 310 °C. While the peaks at 100 and 310 °C have already been noticed in conventionally grown quartz, the new peak at 200 °C, observed in the present studies, appears to be due to the presence of Ge in quartz lattice. The radiation dependence of this peak upon irradiation at 300 K by high energy electrons (1.75 MeV) has been presented and the results have been compared and discussed in terms of the hydroxyl defects in natural, cultured, and Ge-doped cultured quartz.
Single-order-parameter description of glass-forming liquids: A one-frequency test
Authors: Ellegaard Niels L. , Christensen Tage , Christiansen Peder Voetmann , Olsen Niels Boye , Pedersen Ulf R. , Schrøder Thomas B. , Dyre Jeppe C.
Published: February 2007

Thermoviscoelastic linear-response functions are calculated from the master equation describing viscous liquid inherent dynamics. From the imaginary parts of the frequency-dependent isobaric specific heat, isothermal compressibility, and isobaric thermal expansion coefficient, we define a “linear dynamic Prigogine-Defay ratio” ΛTp(ω) with the property that if ΛTp(ω)=1 at one frequency, then ΛTp(ω) is unity at all frequencies. This happens if and only if there is a single-order-parameter description of the thermoviscoelastic linear responses via an order parameter (which may be nonexponential in time). Generalizations to other cases of thermodynamic control parameters than temperature and pressure are also presented.